set dir = $cwd
-set VER = 3.1
+set VER = 3.2
set MANDIR = online
set HTML = $cwd/html
set HTMLOL = $HTML/$MANDIR
<td ALIGN=LEFT VALIGN=TOP WIDTH=280>
<br><br>
<h2>
-GROMACS 3.1<br>
+GROMACS 3.2<br>
Online Reference</h2>
</td>
</TABLE></TD>
<td ALIGN=RIGHT VALIGN=BOTTOM WIDTH="*" NOSAVE>
-<B>VERSION 3.1<br>
-Wed 27 Feb 2002</B></td>
+<B>VERSION 3.2<br>
+Sun 25 Jan 2004</B></td>
</tr>
</table>
# Don't edit - this file is generated automatically from Makefile.am
#
-man_MANS = g_dih.1 g_msd.1 g_tcaf.1 nmrun.1 \
- do_dssp.1 g_dipoles.1 g_nmeig.1 g_traj.1 \
- pdb2gmx.1 editconf.1 g_disre.1 g_nmens.1 \
- g_velacc.1 protonate.1 eneconv.1 g_dist.1 \
- g_order.1 genbox.1 tpbconv.1 g_anaeig.1 \
- g_dyndom.1 g_potential.1 genconf.1 trjcat.1 \
- g_analyze.1 g_enemat.1 g_rama.1 genion.1 \
- trjconv.1 g_angle.1 g_energy.1 g_rdf.1 \
- genpr.1 trjorder.1 g_bond.1 g_gyrate.1 \
- g_rms.1 gmxcheck.1 wheel.1 g_bundle.1 \
- g_h2order.1 g_rmsdist.1 gmxdump.1 x2top.1 \
- g_chi.1 g_hbond.1 g_rmsf.1 grompp.1 \
- xpm2ps.1 g_cluster.1 g_helix.1 g_rotacf.1 \
- highway.1 xrama.1 g_confrms.1 g_lie.1 \
- g_saltbr.1 make_ndx.1 g_covar.1 g_mdmat.1 \
- g_sas.1 mdrun.1 g_density.1 g_mindist.1 \
- g_sgangle.1 mk_angndx.1 g_morph.1 g_sorient.1 \
- ngmx.1 g_dielectric.1
+man_MANS = \
+ anadock.1 g_cluster.1 g_filter.1 g_potential.1 \
+ g_velacc.1 ngmx.1 cdist.1 g_clustsize.1 \
+ g_gyrate.1 g_rama.1 g_wham.1 pdb2gmx.1 \
+ disco.1 g_confrms.1 g_h2order.1 g_rdf.1 \
+ genbox.1 protonate.1 do_dssp.1 g_covar.1 \
+ g_hbond.1 g_rms.1 genconf.1 tpbconv.1 \
+ editconf.1 g_density.1 g_helix.1 g_rmsdist.1 \
+ genion.1 trjcat.1 eneconv.1 g_dielectric.1 \
+ g_lie.1 g_rmsf.1 genpr.1 trjconv.1 \
+ ffscan.1 g_dih.1 g_mdmat.1 g_rotacf.1 \
+ gmxcheck.1 trjorder.1 g_anaeig.1 g_dipoles.1 \
+ g_mindist.1 g_saltbr.1 gmxdump.1 wheel.1 \
+ g_analyze.1 g_disre.1 g_morph.1 g_sas.1 \
+ grompp.1 x2top.1 g_angle.1 g_dist.1 \
+ g_msd.1 g_sgangle.1 highway.1 xpm2ps.1 \
+ g_bond.1 g_dyndom.1 g_nmeig.1 g_sorient.1 \
+ make_ndx.1 xrama.1 g_bundle.1 g_enemat.1 \
+ g_nmens.1 g_tcaf.1 mdrun.1 g_chi.1 \
+ g_energy.1 g_order.1 g_traj.1 mk_angndx.1
EXTRA_DIST = ${man_MANS}
\ No newline at end of file
-.TH do_dssp 1 "Thu 28 Feb 2002"
+.TH do_dssp 1 "Sun 25 Jan 2004"
.SH NAME
do_dssp
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3do_dssp\fP
.BI "-f" " traj.xtc "
.BI "-ta" " totarea.xvg "
.BI "-aa" " averarea.xvg "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb
+ Structure+mass(db): tpr tpb tpa gro g96 pdb xml
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
-.TH editconf 1 "Thu 28 Feb 2002"
+.TH editconf 1 "Sun 25 Jan 2004"
.SH NAME
editconf
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3editconf\fP
.BI "-f" " conf.gro "
.BI "-o" " out.gro "
.BI "-bf" " bfact.dat "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-[no]w" ""
.BI "-[no]ndef" ""
.BI "-d" " real "
.BI "-[no]c" ""
.BI "-center" " vector "
+.BI "-translate" " vector "
.BI "-rotate" " vector "
.BI "-[no]princ" ""
.BI "-scale" " vector "
.BI "-density" " real "
+.BI "-[no]vol" ""
.BI "-[no]pbc" ""
.BI "-[no]mead" ""
.BI "-[no]grasp" ""
.SH FILES
.BI "-f" " conf.gro"
.B Input
- Generic structure: gro g96 pdb tpr tpb tpa
+ Generic structure: gro g96 pdb tpr tpb tpa xml
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-o" " out.gro"
.B Output
- Generic structure: gro g96 pdb
+ Generic structure: gro g96 pdb xml
.BI "-bf" " bfact.dat"
.B Input, Opt.
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 0"
Set the nicelevel
.BI "-center" " vector" " 0 0 0"
Coordinates of geometrical center
+.BI "-translate" " vector" " 0 0 0"
+ Translation
+
.BI "-rotate" " vector" " 0 0 0"
Rotation around the X, Y and Z axes in degrees
.BI "-density" " real" " 1000"
Density (g/l) of the output box achieved by scaling
+.BI "-[no]vol" " yes"
+ Compute and print volume of the box
+
.BI "-[no]pbc" " no"
Remove the periodicity (make molecule whole again)
-.TH eneconv 1 "Thu 28 Feb 2002"
+.TH eneconv 1 "Sun 25 Jan 2004"
.SH NAME
eneconv
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3eneconv\fP
.BI "-f" " ener.edr "
.BI "-o" " fixed.edr "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " real "
.BI "-e" " real "
.BI "-scalefac" " real "
.BI "-[no]error" ""
.SH DESCRIPTION
-When
+With
+.I multiple files
+specified for the
.B -f
-is
-.I not
-specified:
+option:
Concatenates several energy files in sorted order.
In case of double time frames the one
With
+.I one file
+specified for
.B -f
-specified:
+:
Reads one energy file and writes another, applying the
.B -dt
to select which frames to write.
.SH FILES
.BI "-f" " ener.edr"
-.B Input
+.B Input, Mult.
Generic energy: edr ene
.BI "-o" " fixed.edr"
-.B Output, Opt.
+.B Output
Generic energy: edr ene
.SH OTHER OPTIONS
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
-.TH g_anaeig 1 "Thu 28 Feb 2002"
+.TH g_anaeig 1 "Sun 25 Jan 2004"
.SH NAME
g_anaeig
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_anaeig\fP
.BI "-v" " eigenvec.trr "
.BI "-f" " traj.xtc "
.BI "-s" " topol.tpr "
.BI "-n" " index.ndx "
-.BI "-eig1" " eigenval1.xvg "
+.BI "-eig" " eigenval.xvg "
.BI "-eig2" " eigenval2.xvg "
-.BI "-disp" " eigdisp.xvg "
+.BI "-comp" " eigcomp.xvg "
+.BI "-rmsf" " eigrmsf.xvg "
.BI "-proj" " proj.xvg "
.BI "-2d" " 2dproj.xvg "
.BI "-3d" " 3dproj.pdb "
.BI "-over" " overlap.xvg "
.BI "-inpr" " inprod.xpm "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
-.B -disp
-: plot all atom displacements of eigenvectors
+.B -comp
+: plot the vector components per atom of eigenvectors
.B -first
to
+.B -rmsf
+: plot the RMS fluctuation per atom of eigenvectors
+
+.B -first
+to
+.B -last
+(requires
+.B -eig
+).
+
+
+
.B -proj
: calculate projections of a trajectory on eigenvectors
When
.B -v
,
-.B -eig1
+.B -eig
,
.B -v2
and
.BI "-s" " topol.tpr"
.B Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb
+ Structure+mass(db): tpr tpb tpa gro g96 pdb xml
.BI "-n" " index.ndx"
.B Input, Opt.
Index file
-.BI "-eig1" " eigenval1.xvg"
+.BI "-eig" " eigenval.xvg"
.B Input, Opt.
xvgr/xmgr file
.B Input, Opt.
xvgr/xmgr file
-.BI "-disp" " eigdisp.xvg"
+.BI "-comp" " eigcomp.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-rmsf" " eigrmsf.xvg"
.B Output, Opt.
xvgr/xmgr file
.BI "-3d" " 3dproj.pdb"
.B Output, Opt.
- Generic structure: gro g96 pdb
+ Generic structure: gro g96 pdb xml
.BI "-filt" " filtered.xtc"
.B Output, Opt.
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
-.TH g_analyze 1 "Thu 28 Feb 2002"
+.TH g_analyze 1 "Sun 25 Jan 2004"
.SH NAME
g_analyze
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_analyze\fP
.BI "-f" " graph.xvg "
.BI "-ee" " errest.xvg "
.BI "-g" " fitlog.log "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-[no]w" ""
.BI "-[no]time" ""
.BI "-[no]d" ""
.BI "-bw" " real "
.BI "-errbar" " enum "
+.BI "-filter" " real "
.BI "-[no]power" ""
.BI "-[no]subav" ""
.BI "-[no]oneacf" ""
the error is sigma*sqrt(2/T (a tau1 + (1-a) tau2)).
+Option
+.B -filter
+prints the RMS high-frequency fluctuation
+of each set and over all sets with respect to a filtered average.
+The filter is proportional to cos(pi t/len) where t goes from -len/2
+to len/2. len is supplied with the option
+.B -filter
+.
+This filter reduces oscillations with period len/2 and len by a factor
+of 0.79 and 0.33 respectively.
+
+
Option
.B -power
fits the data to b ta, which is accomplished
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
.B 90
+.BI "-filter" " real" " 0"
+ Print the high-frequency fluctuation after filtering with a cosine filter of length
+
.BI "-[no]power" " no"
Fit data to: b ta
.B vac
,
.B exp5
-or
+,
.B exp7
+or
+.B exp9
.BI "-ncskip" " int" " 0"
-.TH g_angle 1 "Thu 28 Feb 2002"
+.TH g_angle 1 "Sun 25 Jan 2004"
.SH NAME
g_angle
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_angle\fP
.BI "-f" " traj.xtc "
.BI "-oh" " trhisto.xvg "
.BI "-oc" " dihcorr.xvg "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa
+ Generic run input: tpr tpb tpa xml
.BI "-n" " angle.ndx"
.B Input
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
.B vac
,
.B exp5
-or
+,
.B exp7
+or
+.B exp9
.BI "-ncskip" " int" " 0"
-.TH g_bond 1 "Thu 28 Feb 2002"
+.TH g_bond 1 "Sun 25 Jan 2004"
.SH NAME
g_bond
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_bond\fP
.BI "-f" " traj.xtc "
.BI "-l" " bonds.log "
.BI "-d" " distance.xvg "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-blen" " real "
.BI "-tol" " real "
.BI "-[no]aver" ""
+.BI "-[no]averdist" ""
.SH DESCRIPTION
g_bond makes a distribution of bond lengths. If all is well a
gaussian distribution should be made when using a harmonic potential.
.B -d
plots all the distances as a function of time.
This requires a structure file for the atom and residue names in
-the output.
+the output. If however the option
+.B -averdist
+is given (as well
+or separately) the average bond length is plotted instead.
.SH FILES
.BI "-f" " traj.xtc"
.B Input
.BI "-s" " topol.tpr"
.B Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb
+ Structure+mass(db): tpr tpb tpa gro g96 pdb xml
.BI "-o" " bonds.xvg"
.B Output
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
Half width of distribution as fraction of blen
.BI "-[no]aver" " yes"
- Sum up distributions
+ Average bond length distributions
+
+.BI "-[no]averdist" " yes"
+ Average distances (turns on -d)
\- It should be possible to get bond information from the topology.
-.TH g_bundle 1 "Thu 28 Feb 2002"
+.TH g_bundle 1 "Sun 25 Jan 2004"
.SH NAME
g_bundle
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_bundle\fP
.BI "-f" " traj.xtc "
.BI "-okl" " bun_kinkl.xvg "
.BI "-oa" " axes.pdb "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb
+ Structure+mass(db): tpr tpb tpa gro g96 pdb xml
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
-.TH g_chi 1 "Thu 28 Feb 2002"
+.TH g_chi 1 "Sun 25 Jan 2004"
.SH NAME
g_chi
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_chi\fP
-.BI "-c" " conf.gro "
+.BI "-s" " conf.gro "
.BI "-f" " traj.xtc "
.BI "-o" " order.xvg "
.BI "-p" " order.pdb "
.BI "-jc" " Jcoupling.xvg "
.BI "-corr" " dihcorr.xvg "
.BI "-g" " chi.log "
+.BI "-ot" " dihtrans.xvg "
+.BI "-oh" " trhisto.xvg "
+.BI "-rt" " restrans.xvg "
+.BI "-cp" " chiprodhisto.xvg "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-[no]rama" ""
.BI "-[no]viol" ""
.BI "-[no]all" ""
+.BI "-[no]rad" ""
.BI "-[no]shift" ""
-.BI "-run" " int "
+.BI "-binwidth" " int "
+.BI "-core_rotamer" " real "
.BI "-maxchi" " enum "
.BI "-[no]normhisto" ""
.BI "-[no]ramomega" ""
.BI "-bfact" " real "
+.BI "-[no]chi_prod" ""
+.BI "-[no]HChi" ""
.BI "-bmax" " real "
.BI "-acflen" " int "
.BI "-[no]normalize" ""
amino acid backbone and sidechains.
It can compute dihedral angle as a function of time, and as
histogram distributions.
-Output is in form of xvgr files, as well as a LaTeX table of the
-number of transitions per nanosecond.
-
-
-Order parameters S2 for each of the dihedrals are calculated and
-output as xvgr file and optionally as a pdb file with the S2
-values as B-factor.
+The distributions (histo-(dihedral)(RESIDUE).xvg) are cumulative over all residues of each type.
If option
-.B -c
+.B -corr
is given, the program will
calculate dihedral autocorrelation functions. The function used
is C(t) = cos(chi(tau)) cos(chi(tau+t)) . The use of cosines
(Van der Spoel & Berendsen (1997),
.B Biophys. J. 72
, 2032-2041).
+Separate files for each dihedral of each residue
+(corr(dihedral)(RESIDUE)(nresnr).xvg) are output, as well as a
+file containing the information for all residues (argument of
+.B -corr
+).
+
+
+With option
+.B -all
+, the angles themselves as a function of time for
+each residue are printed to separate files (dihedral)(RESIDUE)(nresnr).xvg.
+These can be in radians or degrees.
+
+
+A log file (argument
+.B -g
+) is also written. This contains
+
+(a) information about the number of residues of each type.
+
+(b) The NMR 3J coupling constants from the Karplus equation.
+
+(c) a table for each residue of the number of transitions between
+rotamers per nanosecond, and the order parameter S2 of each dihedral.
+
+(d) a table for each residue of the rotamer occupancy.
+
+All rotamers are taken as 3-fold, except for omegas and chi-dihedrals
+to planar groups (i.e. chi2 of aromatics asp and asn, chi3 of glu
+and gln, and chi4 of arg), which are 2-fold. "rotamer 0" means
+that the dihedral was not in the core region of each rotamer.
+The width of the core region can be set with
+.B -core_rotamer
+
+
+
+The S2 order parameters are also output to an xvg file
+(argument
+.B -o
+) and optionally as a pdb file with
+the S2 values as B-factor (argument
+.B -p
+).
+The total number of rotamer transitions per timestep
+(argument
+.B -ot
+), the number of transitions per rotamer
+(argument
+.B -rt
+), and the 3J couplings (argument
+.B -jc
+),
+can also be written to .xvg files.
+
+
+If
+.B -chi_prod
+is set (and maxchi 0), cumulative rotamers, e.g.
+1+9(chi1-1)+3(chi2-1)+(chi3-1) (if the residue has three 3-fold
+dihedrals and maxchi = 3)
+are calculated. As before, if any dihedral is not in the core region,
+the rotamer is taken to be 0. The occupancies of these cumulative
+rotamers (starting with rotamer 0) are written to the file
+that is the argument of
+.B -cp
+, and if the
+.B -all
+flag
+is given, the rotamers as functions of time
+are written to chiproduct(RESIDUE)(nresnr).xvg
+and their occupancies to histo-chiproduct(RESIDUE)(nresnr).xvg.
The option
as a function of the phi and psi angles, that is, in a Ramachandran plot
the average omega angle is plotted using color coding.
.SH FILES
-.BI "-c" " conf.gro"
+.BI "-s" " conf.gro"
.B Input
- Generic structure: gro g96 pdb tpr tpb tpa
+ Generic structure: gro g96 pdb tpr tpb tpa xml
.BI "-f" " traj.xtc"
.B Input
.B Output
Log file
+.BI "-ot" " dihtrans.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-oh" " trhisto.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-rt" " restrans.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-cp" " chiprodhisto.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
.SH OTHER OPTIONS
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
.BI "-[no]all" " no"
Output separate files for every dihedral.
+.BI "-[no]rad" " no"
+ in angle vs time files, use radians rather than degrees.
+
.BI "-[no]shift" " no"
Compute chemical shifts from Phi/Psi angles
-.BI "-run" " int" " 1"
- perform running average over ndeg degrees for histograms
+.BI "-binwidth" " int" " 1"
+ bin width for histograms (degrees)
+
+.BI "-core_rotamer" " real" " 0.5"
+ only the central -core_rotamer*(360/multiplicity) belongs to each rotamer (the rest is assigned to rotamer 0)
.BI "-maxchi" " enum" " 0"
calculate first ndih Chi dihedrals:
.BI "-bfact" " real" " -1"
B-factor value for pdb file for atoms with no calculated dihedral order parameter
+.BI "-[no]chi_prod" " no"
+ compute a single cumulative rotamer for each residue
+
+.BI "-[no]HChi" " no"
+ Include dihedrals to sidechain hydrogens
+
.BI "-bmax" " real" " 0"
Maximum B-factor on any of the atoms that make up a dihedral, for the dihedral angle to be considere in the statistics. Applies to database work where a number of X-Ray structures is analyzed. -bmax = 0 means no limit.
.B vac
,
.B exp5
-or
+,
.B exp7
+or
+.B exp9
.BI "-ncskip" " int" " 0"
\- Produces MANY output files (up to about 4 times the number of residues in the protein, twice that if autocorrelation functions are calculated). Typically several hundred files are output.
+\- Phi and psi dihedrals are calculated in a non-standard way, using H-N-CA-C for phi instead of C(-)-N-CA-C, and N-CA-C-O for psi instead of N-CA-C-N(+). This causes (usually small) discrepancies with the output of other tools like g_rama.
+
+\- -r0 option does not work properly
+
+\- Rotamers with multiplicity 2 are printed in chi.log as if they had multiplicity 3, with the 3rd (g(+)) always having probability 0
+
-.TH g_cluster 1 "Thu 28 Feb 2002"
+.TH g_cluster 1 "Sun 25 Jan 2004"
.SH NAME
g_cluster
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_cluster\fP
.BI "-f" " traj.xtc "
.BI "-clid" " clust-id.xvg "
.BI "-cl" " clusters.pdb "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-nst" " int "
.BI "-rmsmin" " real "
.BI "-method" " enum "
+.BI "-minstruct" " int "
.BI "-[no]binary" ""
.BI "-M" " int "
.BI "-P" " int "
.BI "-s" " topol.tpr"
.B Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb
+ Structure+mass(db): tpr tpb tpa gro g96 pdb xml
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
.B gromos
+.BI "-minstruct" " int" " 1"
+ Minimum number of structures in cluster for coloring in the xpm file
+
.BI "-[no]binary" " no"
Treat the RMSD matrix as consisting of 0 and 1, where the cut-off is given by -cutoff
-.TH g_confrms 1 "Thu 28 Feb 2002"
+.TH g_confrms 1 "Sun 25 Jan 2004"
.SH NAME
g_confrms
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_confrms\fP
.BI "-f1" " conf1.gro "
.BI "-o" " fit.pdb "
.BI "-n1" " fit1.ndx "
.BI "-n2" " fit2.ndx "
+.BI "-no" " match.ndx "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
+.BI "-[no]w" ""
.BI "-[no]one" ""
.BI "-[no]pbc" ""
+.BI "-[no]fit" ""
+.BI "-[no]name" ""
+.BI "-[no]bfac" ""
.SH DESCRIPTION
g_confrms computes the root mean square deviation (RMSD) of two
structures after LSQ fitting the second structure on the first one.
The two structures do NOT need to have the same number of atoms,
only the two index groups used for the fit need to be identical.
-
+With
+.B -name
+only matching atom names from the selected groups
+will be used for the fit and RMSD calculation. This can be useful
+when comparing mutants of a protein.
The superimposed structures are written to file. In a
the two structures will be written as separate models
(use
.B rasmol -nmrpdb
-).
+). Also in a
+.B .pdb
+file, B-factors
+calculated from the atomic MSD values can be written with
+.B -bfac
+.
.SH FILES
.BI "-f1" " conf1.gro"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb
+ Structure+mass(db): tpr tpb tpa gro g96 pdb xml
.BI "-f2" " conf2.gro"
.B Input
- Generic structure: gro g96 pdb tpr tpb tpa
+ Generic structure: gro g96 pdb tpr tpb tpa xml
.BI "-o" " fit.pdb"
.B Output
- Generic structure: gro g96 pdb
+ Generic structure: gro g96 pdb xml
.BI "-n1" " fit1.ndx"
.B Input, Opt.
.B Input, Opt.
Index file
+.BI "-no" " match.ndx"
+.B Output, Opt.
+ Index file
+
.SH OTHER OPTIONS
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
.BI "-[no]one" " no"
Only write the fitted structure to file
.BI "-[no]pbc" " no"
Try to make molecules whole again
+.BI "-[no]fit" " yes"
+ Do least squares superposition of the target structure to the reference
+
+.BI "-[no]name" " no"
+ Only compare matching atom names
+
+.BI "-[no]bfac" " no"
+ Output B-factors from atomic MSD values
+
-.TH g_covar 1 "Thu 28 Feb 2002"
+.TH g_covar 1 "Sun 25 Jan 2004"
.SH NAME
g_covar
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_covar\fP
.BI "-f" " traj.xtc "
.BI "-v" " eigenvec.trr "
.BI "-av" " average.pdb "
.BI "-l" " covar.log "
+.BI "-ascii" " covar.dat "
.BI "-xpm" " covar.xpm "
.BI "-xpma" " covara.xpm "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
is non mass-weighted, the fit will also be non mass-weighted.
+
The eigenvectors are written to a trajectory file (
.B -v
).
+Option
+.B -ascii
+writes the whole covariance matrix to
+an ASCII file. The order of the elements is: x1x1, x1y1, x1z1, x1x2, ...
+
+
+
Option
.B -xpm
writes the whole covariance matrix to an xpm file.
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb
+ Structure+mass(db): tpr tpb tpa gro g96 pdb xml
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-av" " average.pdb"
.B Output
- Generic structure: gro g96 pdb
+ Generic structure: gro g96 pdb xml
.BI "-l" " covar.log"
.B Output
Log file
+.BI "-ascii" " covar.dat"
+.B Output, Opt.
+ Generic data file
+
.BI "-xpm" " covar.xpm"
.B Output, Opt.
X PixMap compatible matrix file
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
-.TH g_density 1 "Thu 28 Feb 2002"
+.TH g_density 1 "Sun 25 Jan 2004"
.SH NAME
g_density
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_density\fP
.BI "-f" " traj.xtc "
.BI "-ei" " electrons.dat "
.BI "-o" " density.xvg "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa
+ Generic run input: tpr tpb tpa xml
.BI "-ei" " electrons.dat"
.B Input, Opt.
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
-.TH g_dielectric 1 "Thu 28 Feb 2002"
+.TH g_dielectric 1 "Sun 25 Jan 2004"
.SH NAME
g_dielectric
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_dielectric\fP
.BI "-f" " Mtot.xvg "
.BI "-o" " epsw.xvg "
.BI "-c" " cole.xvg "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
.B vac
,
.B exp5
-or
+,
.B exp7
+or
+.B exp9
.BI "-nsmooth" " int" " 3"
-.TH g_dih 1 "Thu 28 Feb 2002"
+.TH g_dih 1 "Sun 25 Jan 2004"
.SH NAME
g_dih
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_dih\fP
.BI "-f" " traj.xtc "
.BI "-s" " topol.tpr "
.BI "-o" " hello.out "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa
+ Generic run input: tpr tpb tpa xml
.BI "-o" " hello.out"
.B Output
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
-.TH g_dipoles 1 "Thu 28 Feb 2002"
+.TH g_dipoles 1 "Sun 25 Jan 2004"
.SH NAME
g_dipoles
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_dipoles\fP
.BI "-enx" " ener.edr "
.BI "-s" " topol.tpr "
.BI "-n" " index.ndx "
.BI "-o" " Mtot.xvg "
-.BI "-e" " epsilon.xvg "
+.BI "-eps" " epsilon.xvg "
.BI "-a" " aver.xvg "
.BI "-d" " dipdist.xvg "
.BI "-c" " dipcorr.xvg "
.BI "-g" " gkr.xvg "
.BI "-q" " quadrupole.xvg "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
low dielectric media
-The file dip.xvg contains the total dipole moment of a frame, the
+The file Mtot.xvg contains the total dipole moment of a frame, the
components as well as the norm of the vector.
The file aver.xvg contains |Mu|2 and |Mu| 2 during the
simulation.
-The file dip.xvg contains the distribution of dipole moments during
+The file dipdist.xvg contains the distribution of dipole moments during
the simulation
The mu_max is used as the highest value in the distribution graph.
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa
+ Generic run input: tpr tpb tpa xml
.BI "-n" " index.ndx"
.B Input, Opt.
.B Output
xvgr/xmgr file
-.BI "-e" " epsilon.xvg"
+.BI "-eps" " epsilon.xvg"
.B Output
xvgr/xmgr file
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
.B vac
,
.B exp5
-or
+,
.B exp7
+or
+.B exp9
.BI "-ncskip" " int" " 0"
-.TH g_disre 1 "Thu 28 Feb 2002"
+.TH g_disre 1 "Sun 25 Jan 2004"
.SH NAME
g_disre
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_disre\fP
.BI "-s" " topol.tpr "
.BI "-dr" " restr.xvg "
.BI "-l" " disres.log "
.BI "-n" " viol.ndx "
+.BI "-q" " viol.pdb "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-[no]w" ""
.BI "-ntop" " int "
.SH DESCRIPTION
-g_disre computes violations of distance restraints. If necessary
-all protons can be added to a protein molecule. The program allways
+g_disre computes violations of distance restraints.
+If necessary all protons can be added to a protein molecule
+using the protonate program.
+
+
+The program allways
computes the instantaneous violations rather than time-averaged,
because this analysis is done from a trajectory file afterwards
-it does not make sense to use time averaging.
+it does not make sense to use time averaging. However,
+the time averaged values per restraint are given in the log file.
An index file may be used to select specific restraints for
printing.
+
+
+When the optional
+.B -q
+flag is given a pdb file coloured by the
+amount of average violations.
.SH FILES
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa
+ Generic run input: tpr tpb tpa xml
.BI "-f" " traj.xtc"
.B Input
.B Input, Opt.
Index file
+.BI "-q" " viol.pdb"
+.B Output, Opt.
+ Protein data bank file
+
.SH OTHER OPTIONS
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
-.BI "-ntop" " int" " 6"
+.BI "-ntop" " int" " 0"
Number of large violations that are stored in the log file every step
-.TH g_dist 1 "Thu 28 Feb 2002"
+.TH g_dist 1 "Sun 25 Jan 2004"
.SH NAME
g_dist
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_dist\fP
.BI "-f" " traj.xtc "
.BI "-n" " index.ndx "
.BI "-o" " dist.xvg "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa
+ Generic run input: tpr tpb tpa xml
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
-.TH g_dyndom 1 "Thu 28 Feb 2002"
+.TH g_dyndom 1 "Sun 25 Jan 2004"
.SH NAME
g_dyndom
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_dyndom\fP
.BI "-f" " dyndom.pdb "
.BI "-o" " rotated.xtc "
.BI "-n" " domains.ndx "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-firstangle" " real "
.BI "-lastangle" " real "
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 0"
Set the nicelevel
-.TH g_enemat 1 "Thu 28 Feb 2002"
+.TH g_enemat 1 "Sun 25 Jan 2004"
.SH NAME
g_enemat
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_enemat\fP
.BI "-f" " ener.edr "
.BI "-emat" " emat.xpm "
.BI "-etot" " energy.xvg "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-[no]free" ""
.BI "-temp" " real "
.SH DESCRIPTION
-g_enemat extracts an energy matrix from an energy file.
+g_enemat extracts an energy matrix from the energy file (
+.B -f
+).
With
.B -groups
a file must be supplied with on each
-line a group to be used. For these groups a matrices of
-interaction energies will be calculated. Also the total
-interaction energy energy per group is calculated.
+line a group of atoms to be used. For these groups matrix of
+interaction energies will be extracted from the energy file
+by looking for energy groups with names corresponding to pairs
+of groups of atoms. E.g. if your
+.B -groups
+file contains:
+
+
+.B 2
+
+
+
+.B Protein
+
+
+.B SOL
-An approximation of the free energy is calculated using:
+
+then energy groups with names like 'Coul-SR:Protein-SOL' and
+'LJ:Protein-SOL' are expected in the energy file (although
+
+.B g_enemat
+is most useful if many groups are analyzed
+simultaneously). Matrices for different energy types are written
+out separately, as controlled by the
+
+.B -[no]coul
+,
+.B -[no]coulr
+,
+.B -[no]coul14
+,
+
+.B -[no]lj
+,
+.B -[no]lj14
+,
+
+.B -[no]bham
+and
+.B -[no]free
+options.
+Finally, the total interaction energy energy per group can be
+calculated (
+.B -etot
+).
+
+
+An approximation of the free energy can be calculated using:
E(free) = E0 + kT log( exp((E-E0)/kT) ), where ''
stands for time-average. A file with reference free energies
can be supplied to calculate the free energy difference
-with some reference state. Group names (e.g. residue names
+with some reference state. Group names (e.g. residue names)
in the reference file should correspond to the group names
as used in the
.B -groups
file, but a appended number
-(e.g. residue number)in the
+(e.g. residue number) in the
.B -groups
will be ignored
in the comparison.
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
Skip number of frames between data points
.BI "-[no]mean" " yes"
- with -groups calculates matrix of mean energies in stead of matrix for each timestep
+ with -groups extracts matrix of mean energies in stead of matrix for each timestep
.BI "-nlevels" " int" " 20"
number of levels for matrix colors
min value for energies
.BI "-[no]coul" " yes"
- calculate Coulomb SR energies
+ extract Coulomb SR energies
.BI "-[no]coulr" " no"
- calculate Coulomb LR energies
+ extract Coulomb LR energies
.BI "-[no]coul14" " no"
- calculate Coulomb 1-4 energies
+ extract Coulomb 1-4 energies
.BI "-[no]lj" " yes"
- calculate Lennard-Jones SR energies
+ extract Lennard-Jones SR energies
.BI "-[no]lj14" " no"
- calculate Lennard-Jones 1-4 energies
+ extract Lennard-Jones 1-4 energies
.BI "-[no]bham" " no"
- calculate Buckingham energies
+ extract Buckingham energies
.BI "-[no]free" " yes"
calculate free energy
-.TH g_energy 1 "Thu 28 Feb 2002"
+.TH g_energy 1 "Sun 25 Jan 2004"
.SH NAME
g_energy
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_energy\fP
.BI "-f" " ener.edr "
.BI "-vis" " visco.xvg "
.BI "-ravg" " runavgdf.xvg "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
With
.B -fee
-a free energy estimate is calculated using
-the formula: G = -ln e (E/kT) * kT, where k is Boltzmann's
-constant, T is set by
+an estimate is calculated for the free-energy
+difference with an ideal gas state:
+
+ Delta A = A(N,V,T) - A_idgas(N,V,T) = kT ln e(Upot/kT)
+
+ Delta G = G(N,p,T) - G_idgas(N,p,T) = kT ln e(Upot/kT)
+
+where k is Boltzmann's constant, T is set by
.B -fetemp
-and the average is over the
-ensemble (or time in a trajectory). Note that this is in principle
+andthe average is over the ensemble (or time in a trajectory).
+Note that this is in principle
only correct when averaging over the whole (Boltzmann) ensemble
and using the potential energy. This also allows for an entropy
-estimate using G = H - T S, where H is the enthalpy (H = U + p V)
-and S entropy.
+estimate using:
+
+ Delta S(N,V,T) = S(N,V,T) - S_idgas(N,V,T) = (Upot - Delta A)/T
+
+ Delta S(N,p,T) = S(N,p,T) - S_idgas(N,p,T) = (Upot + pV - Delta G)/T
+
When a second energy file is specified (
.BI "-s" " topol.tpr"
.B Input, Opt.
- Generic run input: tpr tpb tpa
+ Generic run input: tpr tpb tpa xml
.BI "-o" " energy.xvg"
.B Output
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
.B vac
,
.B exp5
-or
+,
.B exp7
+or
+.B exp9
.BI "-ncskip" " int" " 0"
-.TH g_gyrate 1 "Thu 28 Feb 2002"
+.TH g_gyrate 1 "Sun 25 Jan 2004"
.SH NAME
g_gyrate
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_gyrate\fP
.BI "-f" " traj.xtc "
.BI "-s" " topol.tpr "
.BI "-o" " gyrate.xvg "
+.BI "-acf" " moi-acf.xvg "
.BI "-n" " index.ndx "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-[no]w" ""
.BI "-[no]q" ""
.BI "-[no]p" ""
+.BI "-[no]moi" ""
+.BI "-acflen" " int "
+.BI "-[no]normalize" ""
+.BI "-P" " enum "
+.BI "-fitfn" " enum "
+.BI "-ncskip" " int "
+.BI "-beginfit" " real "
+.BI "-endfit" " real "
.SH DESCRIPTION
g_gyrate computes the radius of gyration of a group of atoms
and the radii of gyration about the x, y and z axes,as a function of time. The atoms are explicitly mass weighted.
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb
+ Structure+mass(db): tpr tpb tpa gro g96 pdb xml
.BI "-o" " gyrate.xvg"
.B Output
xvgr/xmgr file
+.BI "-acf" " moi-acf.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
.BI "-n" " index.ndx"
.B Input, Opt.
Index file
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
.BI "-[no]p" " no"
Calculate the radii of gyration about the principal axes.
+.BI "-[no]moi" " no"
+ Calculate the moments of inertia (defined by the principal axes).
+
+.BI "-acflen" " int" " -1"
+ Length of the ACF, default is half the number of frames
+
+.BI "-[no]normalize" " yes"
+ Normalize ACF
+
+.BI "-P" " enum" " 0"
+ Order of Legendre polynomial for ACF (0 indicates none):
+.B 0
+,
+.B 1
+,
+.B 2
+or
+.B 3
+
+
+.BI "-fitfn" " enum" " none"
+ Fit function:
+.B none
+,
+.B exp
+,
+.B aexp
+,
+.B exp_exp
+,
+.B vac
+,
+.B exp5
+,
+.B exp7
+or
+.B exp9
+
+
+.BI "-ncskip" " int" " 0"
+ Skip N points in the output file of correlation functions
+
+.BI "-beginfit" " real" " 0"
+ Time where to begin the exponential fit of the correlation function
+
+.BI "-endfit" " real" " -1"
+ Time where to end the exponential fit of the correlation function, -1 is till the end
+
-.TH g_h2order 1 "Thu 28 Feb 2002"
+.TH g_h2order 1 "Sun 25 Jan 2004"
.SH NAME
g_h2order
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_h2order\fP
.BI "-f" " traj.xtc "
.BI "-s" " topol.tpr "
.BI "-o" " order.xvg "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa
+ Generic run input: tpr tpb tpa xml
.BI "-o" " order.xvg"
.B Output
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
-.TH g_hbond 1 "Thu 28 Feb 2002"
+.TH g_hbond 1 "Sun 25 Jan 2004"
.SH NAME
g_hbond
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_hbond\fP
.BI "-f" " traj.xtc "
.BI "-hx" " hbhelix.xvg "
.BI "-hbn" " hbond.ndx "
.BI "-hbm" " hbmap.xpm "
-.BI "-da" " danum.xvg "
+.BI "-dan" " danum.xvg "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-[no]ins" ""
.BI "-a" " real "
.BI "-r" " real "
+.BI "-[no]da" ""
.BI "-abin" " real "
.BI "-rbin" " real "
.BI "-[no]nitacc" ""
+.BI "-[no]contact" ""
.BI "-shell" " real "
+.BI "-[no]dump" ""
+.BI "-max_hb" " real "
+.BI "-[no]merge" ""
.SH DESCRIPTION
g_hbond computes and analyzes hydrogen bonds. Hydrogen bonds are
determined based on cutoffs for the angle Donor - Hydrogen - Acceptor
index file.
-.B -da
+.B -dan
: write out the number of donors and acceptors analyzed for
each timeframe. This is especially usefull when using
.B -shell
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa
+ Generic run input: tpr tpb tpa xml
.BI "-n" " index.ndx"
.B Input, Opt.
.B Output, Opt.
X PixMap compatible matrix file
-.BI "-da" " danum.xvg"
+.BI "-dan" " danum.xvg"
.B Output, Opt.
xvgr/xmgr file
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
.BI "-[no]ins" " no"
Analyze solvent insertion
-.BI "-a" " real" " 60"
+.BI "-a" " real" " 30"
Cutoff angle (degrees, Donor - Hydrogen - Acceptor)
-.BI "-r" " real" " 0.25"
- Cutoff radius (nm, Hydrogen - Acceptor)
+.BI "-r" " real" " 0.35"
+ Cutoff radius (nm, X - Acceptor, see next option)
+
+.BI "-[no]da" " yes"
+ Use distance Donor-Acceptor (if TRUE) or Hydrogen-Acceptor (FALSE)
.BI "-abin" " real" " 1"
Binwidth angle distribution (degrees)
.BI "-[no]nitacc" " yes"
Regard nitrogen atoms as acceptors
+.BI "-[no]contact" " no"
+ Do not look for hydrogen bonds, but merely for contacts within the cut-off distance
+
.BI "-shell" " real" " -1"
when 0, only calculate hydrogen bonds within nm shell around one particle
+.BI "-[no]dump" " no"
+ Dump all hydrogen bond ACFs (maximum 1000) in a single xvg file for debugging
+
+.BI "-max_hb" " real" " 0"
+ Theoretical maximum number of hydrogen bonds used for normalizing HB autocorrelation function. Can be useful in case the program estimates it wrongly
+
+.BI "-[no]merge" " yes"
+ H-bonds between the same donor and accepter, but with different hydrogen are treated as a single H-bond. Mainly important for the ACF.
+
-.TH g_helix 1 "Thu 28 Feb 2002"
+.TH g_helix 1 "Sun 25 Jan 2004"
.SH NAME
g_helix
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_helix\fP
.BI "-s" " topol.tpr "
.BI "-cz" " zconf.gro "
.BI "-co" " waver.gro "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.SH FILES
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa
+ Generic run input: tpr tpb tpa xml
.BI "-n" " index.ndx"
.B Input
.BI "-cz" " zconf.gro"
.B Output
- Generic structure: gro g96 pdb
+ Generic structure: gro g96 pdb xml
.BI "-co" " waver.gro"
.B Output
- Generic structure: gro g96 pdb
+ Generic structure: gro g96 pdb xml
.SH OTHER OPTIONS
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
-.TH g_lie 1 "Thu 28 Feb 2002"
+.TH g_lie 1 "Sun 25 Jan 2004"
.SH NAME
g_lie
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_lie\fP
.BI "-f" " ener.edr "
.BI "-o" " lie.xvg "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
.BI "-Clj" " real" " 0.181"
Factor in the LIE equation for Lennard-Jones component of energy
-.BI "-Cqq" " real" " 0"
+.BI "-Cqq" " real" " 0.5"
Factor in the LIE equation for Coulomb component of energy
.BI "-ligand" " string" " none"
-.TH g_mdmat 1 "Thu 28 Feb 2002"
+.TH g_mdmat 1 "Sun 25 Jan 2004"
.SH NAME
g_mdmat
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_mdmat\fP
.BI "-f" " traj.xtc "
.BI "-frames" " dmf.xpm "
.BI "-no" " num.xvg "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb
+ Structure+mass(db): tpr tpb tpa gro g96 pdb xml
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
-.TH g_mindist 1 "Thu 28 Feb 2002"
+.TH g_mindist 1 "Sun 25 Jan 2004"
.SH NAME
g_mindist
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_mindist\fP
.BI "-f" " traj.xtc "
.BI "-od" " mindist.xvg "
.BI "-on" " numcont.xvg "
.BI "-o" " atm-pair.out "
+.BI "-ox" " mindist.xtc "
+.BI "-or" " mindistres.xvg "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-dt" " time "
+.BI "-tu" " enum "
.BI "-[no]w" ""
.BI "-[no]matrix" ""
+.BI "-[no]max" ""
.BI "-d" " real "
.BI "-[no]pi" ""
+.BI "-[no]split" ""
.SH DESCRIPTION
g_mindist computes the distance between one group and a number of
other groups.
Both the minimum distance and the number of contacts within a given
distance are written to two separate output files.
+With
+.B -or
+, minimum distances to each residue in the first
+group are determined and plotted as a function of reisdue number.
With option
has seen its periodic image during a simulation. Only one shift in
each direction is considered, giving a total of 26 shifts.
It also plots the maximum distance within the group and the lengths
-of the three box vectors. This option is very slow.
+of the three box vectors.
Other programs that calculate distances are
.BI "-s" " topol.tpr"
.B Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb
+ Structure+mass(db): tpr tpb tpa gro g96 pdb xml
.BI "-n" " index.ndx"
.B Input, Opt.
xvgr/xmgr file
.BI "-on" " numcont.xvg"
-.B Output
+.B Output, Opt.
xvgr/xmgr file
.BI "-o" " atm-pair.out"
-.B Output
+.B Output, Opt.
Generic output file
+.BI "-ox" " mindist.xtc"
+.B Output, Opt.
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-or" " mindistres.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
.SH OTHER OPTIONS
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
.BI "-dt" " time" " -1"
Only use frame when t MOD dt = first time (ps)
+.BI "-tu" " enum" " ps"
+ Time unit:
+.B ps
+,
+.B fs
+,
+.B ns
+,
+.B us
+,
+.B ms
+,
+.B s
+,
+.B m
+or
+.B h
+
+
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
.BI "-[no]matrix" " no"
Calculate half a matrix of group-group distances
+.BI "-[no]max" " no"
+ Calculate *maximum* distance instead of minimum
+
.BI "-d" " real" " 0.6"
Distance for contacts
.BI "-[no]pi" " no"
Calculate minimum distance with periodic images
+.BI "-[no]split" " no"
+ Split graph where time is zero
+
-.TH g_morph 1 "Thu 28 Feb 2002"
+.TH g_morph 1 "Sun 25 Jan 2004"
.SH NAME
g_morph
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_morph\fP
.BI "-f1" " conf1.gro "
.BI "-or" " rms-interm.xvg "
.BI "-n" " index.ndx "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-[no]w" ""
.BI "-ninterm" " int "
.SH FILES
.BI "-f1" " conf1.gro"
.B Input
- Generic structure: gro g96 pdb tpr tpb tpa
+ Generic structure: gro g96 pdb tpr tpb tpa xml
.BI "-f2" " conf2.gro"
.B Input
- Generic structure: gro g96 pdb tpr tpb tpa
+ Generic structure: gro g96 pdb tpr tpb tpa xml
.BI "-o" " interm.xtc"
.B Output
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 0"
Set the nicelevel
-.TH g_msd 1 "Thu 28 Feb 2002"
+.TH g_msd 1 "Sun 25 Jan 2004"
.SH NAME
g_msd
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_msd\fP
.BI "-f" " traj.xtc "
.BI "-o" " msd.xvg "
.BI "-mol" " diff_mol.xvg "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb
+ Structure+mass(db): tpr tpb tpa gro g96 pdb xml
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
-.TH g_nmeig 1 "Thu 28 Feb 2002"
+.TH g_nmeig 1 "Sun 25 Jan 2004"
.SH NAME
g_nmeig
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_nmeig\fP
.BI "-f" " hessian.mtx "
.BI "-o" " eigenval.xvg "
.BI "-v" " eigenvec.trr "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-[no]m" ""
.BI "-first" " int "
.SH DESCRIPTION
g_nmeig calculates the eigenvectors/values of a (Hessian) matrix,
which can be calculated with
-.B nmrun
+.B mdrun
.
The eigenvectors are written to a trajectory file (
.B -v
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb
+ Structure+mass(db): tpr tpb tpa gro g96 pdb xml
.BI "-o" " eigenval.xvg"
.B Output
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
-.TH g_nmens 1 "Thu 28 Feb 2002"
+.TH g_nmens 1 "Sun 25 Jan 2004"
.SH NAME
g_nmens
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_nmens\fP
.BI "-v" " eigenvec.trr "
.BI "-n" " index.ndx "
.BI "-o" " ensemble.xtc "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-temp" " real "
.BI "-seed" " int "
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb
+ Structure+mass(db): tpr tpb tpa gro g96 pdb xml
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
-.TH g_order 1 "Thu 28 Feb 2002"
+.TH g_order 1 "Sun 25 Jan 2004"
.SH NAME
g_order
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_order\fP
.BI "-f" " traj.xtc "
.BI "-od" " deuter.xvg "
.BI "-os" " sliced.xvg "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa
+ Generic run input: tpr tpb tpa xml
.BI "-o" " order.xvg"
.B Output
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
-.TH g_potential 1 "Thu 28 Feb 2002"
+.TH g_potential 1 "Sun 25 Jan 2004"
.SH NAME
g_potential
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_potential\fP
.BI "-f" " traj.xtc "
.BI "-oc" " charge.xvg "
.BI "-of" " field.xvg "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa
+ Generic run input: tpr tpb tpa xml
.BI "-o" " potential.xvg"
.B Output
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
-.TH g_rama 1 "Thu 28 Feb 2002"
+.TH g_rama 1 "Sun 25 Jan 2004"
.SH NAME
g_rama
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_rama\fP
.BI "-f" " traj.xtc "
.BI "-s" " topol.tpr "
.BI "-o" " rama.xvg "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa
+ Generic run input: tpr tpb tpa xml
.BI "-o" " rama.xvg"
.B Output
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
-.TH g_rdf 1 "Thu 28 Feb 2002"
+.TH g_rdf 1 "Sun 25 Jan 2004"
.SH NAME
g_rdf
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_rdf\fP
.BI "-f" " traj.xtc "
.BI "-sq" " sq.xvg "
.BI "-cn" " rdf_cn.xvg "
.BI "-hq" " hq.xvg "
-.BI "-image" " sq.xpm "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-[no]com" ""
.BI "-cut" " real "
.BI "-fade" " real "
-.BI "-grid" " real "
.BI "-nlevel" " int "
-.BI "-wave" " real "
+.BI "-startq" " real "
+.BI "-endq" " real "
+.BI "-energy" " real "
.SH DESCRIPTION
The structure of liquids can be studied by either neutron or X-ray
scattering. The most common way to describe liquid structure is by a
.BI "-s" " topol.tpr"
.B Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb
+ Structure+mass(db): tpr tpb tpa gro g96 pdb xml
.BI "-n" " index.ndx"
.B Input, Opt.
.B Output, Opt.
xvgr/xmgr file
-.BI "-image" " sq.xpm"
-.B Output, Opt.
- X PixMap compatible matrix file
-
.SH OTHER OPTIONS
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
.BI "-fade" " real" " 0"
From this distance onwards the RDF is tranformed by g'(r) = 1 + [g(r)-1] exp(-(r/fade-1)2 to make it go to 1 smoothly. If fade is 0.0 nothing is done.
-.BI "-grid" " real" " 0.05"
- Grid spacing (in nm) for FFTs when computing structure factors
-
.BI "-nlevel" " int" " 20"
Number of different colors in the diffraction image
-.BI "-wave" " real" " 0.1"
- Wavelength for X-rays/Neutrons for scattering. 0.1 nm corresponds to roughly 12 keV
+.BI "-startq" " real" " 0"
+ Starting q (1/nm)
+
+.BI "-endq" " real" " 60"
+ Ending q (1/nm)
+
+.BI "-energy" " real" " 12"
+ Energy of the incoming X-ray (keV)
-.TH g_rms 1 "Thu 28 Feb 2002"
+.TH g_rms 1 "Sun 25 Jan 2004"
.SH NAME
g_rms
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_rms\fP
.BI "-s" " topol.tpr "
.BI "-bin" " rmsd.dat "
.BI "-bm" " bond.xpm "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-[no]w" ""
.BI "-what" " enum "
.BI "-[no]pbc" ""
-.BI "-[no]fit" ""
+.BI "-fit" " enum "
.BI "-prev" " int "
.BI "-[no]split" ""
.BI "-skip" " int "
g_rms compares two structures by computing the root mean square
deviation (RMSD), the size-independent 'rho' similarity parameter
(rho) or the scaled rho (rhosc),
-reference Maiorov & Crippen, PROTEINS 22, 273 (1995).
+see Maiorov & Crippen, PROTEINS
+.B 22
+, 273 (1995).
This is selected by
.B -what
.
Each structure from a trajectory (
.B -f
) is compared to a
-reference structure from a run input file by least-squares fitting
-the structures on top of each other. The reference structure is taken
-from the structure file (
+reference structure. The reference structure
+is taken from the structure file (
.B -s
).
.B -mir
also a comparison with the mirror image of
the reference structure is calculated.
+This is useful as a reference for 'significant' values, see
+Maiorov & Crippen, PROTEINS
+.B 22
+, 273 (1995).
Option
.B -prev
-produces the comparison with a previous frame.
+produces the comparison with a previous frame
+the specified number of frames ago.
Option
.
-All the structures are fitted pairwise.
+Option
+.B -fit
+controls the least-squares fitting of
+the structures on top of each other: complete fit (rotation and
+translation), translation only, or no fitting at all.
With
.B -f2
, the 'other structures' are taken from a second
-trajectory.
+trajectory, this generates a comparison matrix of one trajectory
+versus the other.
Option
.SH FILES
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb
+ Structure+mass(db): tpr tpb tpa gro g96 pdb xml
.BI "-f" " traj.xtc"
.B Input
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
.BI "-[no]pbc" " yes"
PBC check
-.BI "-[no]fit" " yes"
- Fit to reference structure
+.BI "-fit" " enum" " rot+trans"
+ Fit to reference structure:
+.B rot+trans
+,
+.B translation
+or
+.B none
+
.BI "-prev" " int" " 0"
Compare with previous frame
-.TH g_rmsdist 1 "Thu 28 Feb 2002"
+.TH g_rmsdist 1 "Sun 25 Jan 2004"
.SH NAME
g_rmsdist
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_rmsdist\fP
.BI "-f" " traj.xtc "
.BI "-nmr6" " nmr6.xpm "
.BI "-noe" " noe.dat "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb
+ Structure+mass(db): tpr tpb tpa gro g96 pdb xml
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
-.TH g_rmsf 1 "Thu 28 Feb 2002"
+.TH g_rmsf 1 "Sun 25 Jan 2004"
.SH NAME
g_rmsf
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_rmsf\fP
.BI "-f" " traj.xtc "
.BI "-oc" " correl.xvg "
.BI "-dir" " rmsf.log "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb
+ Structure+mass(db): tpr tpb tpa gro g96 pdb xml
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
-.TH g_rotacf 1 "Thu 28 Feb 2002"
+.TH g_rotacf 1 "Sun 25 Jan 2004"
.SH NAME
g_rotacf
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_rotacf\fP
.BI "-f" " traj.xtc "
.BI "-n" " index.ndx "
.BI "-o" " rotacf.xvg "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa
+ Generic run input: tpr tpb tpa xml
.BI "-n" " index.ndx"
.B Input
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
.B vac
,
.B exp5
-or
+,
.B exp7
+or
+.B exp9
.BI "-ncskip" " int" " 0"
-.TH g_saltbr 1 "Thu 28 Feb 2002"
+.TH g_saltbr 1 "Sun 25 Jan 2004"
.SH NAME
g_saltbr
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_saltbr\fP
.BI "-f" " traj.xtc "
.BI "-s" " topol.tpr "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa
+ Generic run input: tpr tpb tpa xml
.SH OTHER OPTIONS
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
-.TH g_sas 1 "Thu 28 Feb 2002"
+.TH g_sas 1 "Sun 25 Jan 2004"
.SH NAME
g_sas
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_sas\fP
.BI "-f" " traj.xtc "
.BI "-s" " topol.tpr "
.BI "-o" " area.xvg "
-.BI "-r" " resarea.xvg "
+.BI "-or" " resarea.xvg "
+.BI "-oa" " atomarea.xvg "
.BI "-q" " connelly.pdb "
-.BI "-ao" " atomarea.xvg "
.BI "-n" " index.ndx "
.BI "-i" " surfat.itp "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-solsize" " real "
.BI "-ndots" " int "
.BI "-qmax" " real "
+.BI "-[no]f_index" ""
.BI "-minarea" " real "
-.BI "-skip" " int "
.BI "-[no]pbc" ""
.BI "-[no]prot" ""
.BI "-dgs" " real "
As a side effect the Connolly surface can be generated as well in
a pdb file where the nodes are represented as atoms and the vertices
connecting the nearest nodes as CONECT records. The area can be plotted
-per atom and per residue as well (option -ao). In combination with
-the latter option an
+per residue and atom as well (options
+.B -or
+and
+.B -oa
+).
+In combination with the latter option an
.B itp
-file can be generated (option -i)
+file can be
+generated (option
+.B -i
+)
which can be used to restrain surface atoms.
By default, periodic boundary conditions are taken into account,
-this can be turned off using the -pbc option.
+this can be turned off using the
+.B -pbc
+option.
.SH FILES
.BI "-f" " traj.xtc"
.B Input
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa
+ Generic run input: tpr tpb tpa xml
.BI "-o" " area.xvg"
.B Output
xvgr/xmgr file
-.BI "-r" " resarea.xvg"
-.B Output
+.BI "-or" " resarea.xvg"
+.B Output, Opt.
xvgr/xmgr file
-.BI "-q" " connelly.pdb"
+.BI "-oa" " atomarea.xvg"
.B Output, Opt.
- Protein data bank file
+ xvgr/xmgr file
-.BI "-ao" " atomarea.xvg"
+.BI "-q" " connelly.pdb"
.B Output, Opt.
- xvgr/xmgr file
+ Protein data bank file
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
.BI "-qmax" " real" " 0.2"
The maximum charge (e, absolute value) of a hydrophobic atom
+.BI "-[no]f_index" " no"
+ Determine from a group in the index file what are the hydrophobic atoms rather than from the charge
+
.BI "-minarea" " real" " 0.5"
The minimum area (nm2) to count an atom as a surface atom when writing a position restraint file (see help)
-.BI "-skip" " int" " 1"
- Do only every nth frame
-
.BI "-[no]pbc" " yes"
Take periodicity into account
-.TH g_sgangle 1 "Thu 28 Feb 2002"
+.TH g_sgangle 1 "Sun 25 Jan 2004"
.SH NAME
g_sgangle
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_sgangle\fP
.BI "-f" " traj.xtc "
.BI "-od1" " sg_dist1.xvg "
.BI "-od2" " sg_dist2.xvg "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa
+ Generic run input: tpr tpb tpa xml
.BI "-oa" " sg_angle.xvg"
.B Output
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
-.TH g_sorient 1 "Thu 28 Feb 2002"
+.TH g_sorient 1 "Sun 25 Jan 2004"
.SH NAME
g_sorient
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_sorient\fP
.BI "-f" " traj.xtc "
.BI "-ro" " sord.xvg "
.BI "-co" " scum.xvg "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-rmin" " real "
.BI "-rmax" " real "
.BI "-nbin" " int "
+.BI "-[no]pbc" ""
.SH DESCRIPTION
g_sorient analyzes solvent orientation around solutes.
It calculates two angles between the vector from one or more
and
.B -rmax
are
-considered each frame.
+considered for
+.B -o
+and
+.B -no
+each frame.
-.B -ro
+.B -co
: the sum over all solvent molecules within distance r
of cos(theta1) and 3cos2(theta2)-1 as a function of r.
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb
+ Structure+mass(db): tpr tpb tpa gro g96 pdb xml
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
.BI "-nbin" " int" " 20"
Number of bins
+.BI "-[no]pbc" " no"
+ Check PBC for the center of mass calculation. Only necessary when your reference group consists of several molecules.
+
-.TH g_tcaf 1 "Thu 28 Feb 2002"
+.TH g_tcaf 1 "Sun 25 Jan 2004"
.SH NAME
g_tcaf
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_tcaf\fP
.BI "-f" " traj.trr "
.BI "-oc" " tcaf_cub.xvg "
.BI "-ov" " visc_k.xvg "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-s" " topol.tpr"
.B Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb
+ Structure+mass(db): tpr tpb tpa gro g96 pdb xml
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
-.TH g_traj 1 "Thu 28 Feb 2002"
+.TH g_traj 1 "Sun 25 Jan 2004"
.SH NAME
g_traj
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_traj\fP
.BI "-f" " traj.xtc "
.BI "-cv" " veloc.pdb "
.BI "-cf" " force.pdb "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-[no]y" ""
.BI "-[no]z" ""
.BI "-[no]len" ""
+.BI "-scale" " real "
.SH DESCRIPTION
g_traj plots coordinates, velocities, forces and/or the box.
With
write the average velocities
and average forces as temperature factors to a pdb file with
the average coordinates. The temperature factors are scaled such
-that the maximum is 10. To get the velocities or forces of one
+that the maximum is 10. The scaling can be changed with the option
+
+.B -scale
+. To get the velocities or forces of one
frame set both
.B -b
and
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb
+ Structure+mass(db): tpr tpb tpa gro g96 pdb xml
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
.BI "-[no]len" " no"
Plot vector length
+.BI "-scale" " real" " 0"
+ Scale factor for pdb output, 0 is autoscale
+
-.TH g_velacc 1 "Thu 28 Feb 2002"
+.TH g_velacc 1 "Sun 25 Jan 2004"
.SH NAME
g_velacc
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3g_velacc\fP
.BI "-f" " traj.trr "
.BI "-n" " index.ndx "
.BI "-o" " vac.xvg "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-s" " topol.tpr"
.B Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb
+ Structure+mass(db): tpr tpb tpa gro g96 pdb xml
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
.B vac
,
.B exp5
-or
+,
.B exp7
+or
+.B exp9
.BI "-ncskip" " int" " 0"
-.TH genbox 1 "Thu 28 Feb 2002"
+.TH genbox 1 "Sun 25 Jan 2004"
.SH NAME
genbox
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3genbox\fP
.BI "-cp" " protein.gro "
.BI "-o" " out.gro "
.BI "-p" " topol.top "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-box" " vector "
.BI "-nmol" " int "
.SH FILES
.BI "-cp" " protein.gro"
.B Input, Opt.
- Generic structure: gro g96 pdb tpr tpb tpa
+ Generic structure: gro g96 pdb tpr tpb tpa xml
.BI "-cs" " spc216.gro"
.B Input, Opt., Lib.
- Generic structure: gro g96 pdb tpr tpb tpa
+ Generic structure: gro g96 pdb tpr tpb tpa xml
.BI "-ci" " insert.gro"
.B Input, Opt.
- Generic structure: gro g96 pdb tpr tpb tpa
+ Generic structure: gro g96 pdb tpr tpb tpa xml
.BI "-o" " out.gro"
.B Output
- Generic structure: gro g96 pdb
+ Generic structure: gro g96 pdb xml
.BI "-p" " topol.top"
.B In/Out, Opt.
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
-.TH genconf 1 "Thu 28 Feb 2002"
+.TH genconf 1 "Sun 25 Jan 2004"
.SH NAME
genconf
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3genconf\fP
.BI "-f" " conf.gro "
.BI "-o" " out.gro "
.BI "-trj" " traj.xtc "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-nbox" " vector "
.BI "-dist" " vector "
.SH FILES
.BI "-f" " conf.gro"
.B Input
- Generic structure: gro g96 pdb tpr tpb tpa
+ Generic structure: gro g96 pdb tpr tpb tpa xml
.BI "-o" " out.gro"
.B Output
- Generic structure: gro g96 pdb
+ Generic structure: gro g96 pdb xml
.BI "-trj" " traj.xtc"
.B Input, Opt.
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 0"
Set the nicelevel
-.TH genion 1 "Thu 28 Feb 2002"
+.TH genion 1 "Sun 25 Jan 2004"
.SH NAME
genion
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3genion\fP
.BI "-s" " topol.tpr "
+.BI "-table" " table.xvg "
.BI "-n" " index.ndx "
.BI "-o" " out.gro "
.BI "-g" " genion.log "
.BI "-pot" " pot.pdb "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-np" " int "
.BI "-pname" " string "
.BI "-rmin" " real "
.BI "-[no]random" ""
.BI "-seed" " int "
+.BI "-scale" " real "
.SH DESCRIPTION
genion replaces solvent molecules by monoatomic ions at
the position of the first atoms with the most favorable electrostatic
normal GROMACS particle based methods (in contrast to other methods
based on solving the Poisson-Boltzmann equation).
The potential is recalculated after every ion insertion.
-If specified in the run input file, a reaction field or shift function
-can be used.
+If specified in the run input file, a reaction field, shift function
+or user function can be used. For the user function a table file
+can be specified with the option
+.B -table
+.
The group of solvent molecules should be continuous and all molecules
should have the same number of atoms.
The user should add the ion molecules to the topology file and include
Ion names for Gromos96 should include the charge.
-The potential can be written as B-factors
+With the option
+.B -pot
+the potential can be written as B-factors
in a pdb file (for visualisation using e.g. rasmol).
-The unit of the potential is 0.001 kJ/(mol e).
+The unit of the potential is 1000 kJ/(mol e), the scaling be changed
+with the
+.B -scale
+option.
For larger ions, e.g. sulfate we recommended to use genbox.
.SH FILES
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa
+ Generic run input: tpr tpb tpa xml
+
+.BI "-table" " table.xvg"
+.B Input, Opt.
+ xvgr/xmgr file
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-o" " out.gro"
.B Output
- Generic structure: gro g96 pdb
+ Generic structure: gro g96 pdb xml
.BI "-g" " genion.log"
.B Output
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
.BI "-seed" " int" " 1993"
Seed for random number generator
+.BI "-scale" " real" " 0.001"
+ Scaling factor for the potential for -pot
+
-.TH genpr 1 "Thu 28 Feb 2002"
+.TH genpr 1 "Sun 25 Jan 2004"
.SH NAME
genpr
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3genpr\fP
.BI "-f" " conf.gro "
.BI "-n" " index.ndx "
.BI "-o" " posre.itp "
+.BI "-of" " freeze.ndx "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-fc" " vector "
+.BI "-freeze" " real "
.SH DESCRIPTION
genpr produces an include file for a topology containing
a list of atom numbers and three force constants for the
in the topology start at 1 and the numbers in the input file for
genpr number consecutively from 1, genpr will only produce a useful
file for the first molecule.
+
+
+The -of option produces an index file that can be used for
+freezing atoms. In this case the input file must be a pdb file.
.SH FILES
.BI "-f" " conf.gro"
.B Input
- Generic structure: gro g96 pdb tpr tpb tpa
+ Generic structure: gro g96 pdb tpr tpb tpa xml
.BI "-n" " index.ndx"
.B Input, Opt.
.B Output
Include file for topology
+.BI "-of" " freeze.ndx"
+.B Output, Opt.
+ Index file
+
.SH OTHER OPTIONS
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 0"
Set the nicelevel
.BI "-fc" " vector" " 1000 1000 1000"
force constants (kJ mol-1 nm-2)
+.BI "-freeze" " real" " 0"
+ if the -of option or this one is given an index file will be written containing atom numbers of all atoms that have a B-factor less than the level given here
+
-.TH gmxcheck 1 "Thu 28 Feb 2002"
+.TH gmxcheck 1 "Sun 25 Jan 2004"
.SH NAME
gmxcheck
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3gmxcheck\fP
.BI "-f" " traj.xtc "
.BI "-e" " ener.edr "
.BI "-e2" " ener2.edr "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-vdwfac" " real "
.BI "-bonlo" " real "
and
.B -s2
are supplied.
+Similarly a pair of trajectory files can be compared (using the
+.B -f2
+
+option), or a pair of energy files (using the
+.B -e2
+option).
.SH FILES
.BI "-f" " traj.xtc"
.B Input, Opt.
.BI "-s1" " top1.tpr"
.B Input, Opt.
- Generic run input: tpr tpb tpa
+ Generic run input: tpr tpb tpa xml
.BI "-s2" " top2.tpr"
.B Input, Opt.
- Generic run input: tpr tpb tpa
+ Generic run input: tpr tpb tpa xml
.BI "-c" " topol.tpr"
.B Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb
+ Structure+mass(db): tpr tpb tpa gro g96 pdb xml
.BI "-e" " ener.edr"
.B Input, Opt.
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 0"
Set the nicelevel
-.TH gmxdump 1 "Thu 28 Feb 2002"
+.TH gmxdump 1 "Sun 25 Jan 2004"
.SH NAME
gmxdump
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3gmxdump\fP
.BI "-s" " topol.tpr "
.BI "-f" " traj.xtc "
.BI "-e" " ener.edr "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-[no]nr" ""
.SH DESCRIPTION
.SH FILES
.BI "-s" " topol.tpr"
.B Input, Opt.
- Generic run input: tpr tpb tpa
+ Generic run input: tpr tpb tpa xml
.BI "-f" " traj.xtc"
.B Input, Opt.
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 0"
Set the nicelevel
-.TH grompp 1 "Thu 28 Feb 2002"
+.TH grompp 1 "Sun 25 Jan 2004"
.SH NAME
grompp
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3grompp\fP
.BI "-f" " grompp.mdp "
.BI "-po" " mdout.mdp "
.BI "-c" " conf.gro "
.BI "-r" " conf.gro "
+.BI "-rb" " conf.gro "
.BI "-n" " index.ndx "
.BI "-deshuf" " deshuf.ndx "
.BI "-p" " topol.top "
.BI "-pp" " processed.top "
.BI "-o" " topol.tpr "
.BI "-t" " traj.trr "
+.BI "-e" " ener.edr "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-[no]v" ""
.BI "-time" " real "
.BI "-load" " string "
.BI "-maxwarn" " int "
.BI "-[no]check14" ""
+.BI "-[no]renum" ""
.SH DESCRIPTION
The gromacs preprocessor
reads a molecular topology file, checks the validity of the
When using position restraints a file with restraint coordinates
can be supplied with
.B -r
-, otherwise constraining will be done
-relative to the conformation from the
+, otherwise restraining will be done
+with respect to the conformation from the
.B -c
option.
+For free energy calculation the the coordinates for the B topology
+can be supplied with
+.B -rb
+, otherwise they will be equal to
+those of the A topology.
Starting coordinates can be read from trajectory with
in your
.B .mdp
-file. If you want to continue a crashed run, it is
+file. An energy file can be supplied with
+
+.B -e
+to have exact restarts when using pressure and/or
+temperature coupling. For an exact restart do not forget to turn off
+velocity generation and turn on unconstrained starting when constraints
+are present in the system.
+If you want to continue a crashed run, it is
easier to use
.B tpbconv
.
in water this does not make a difference, however for a system where
you have many copies of different molecules (e.g. liquid mixture
or membrane/water system) the option is definitely a must.
+The output trajectories will also be shuffled.
+.B grompp
+writes
+an index file (option
+.B -deshuf
+) which can be used with
+
+.B trjconv
+to deshuffle the trajectories.
A further optimization for parallel systems is the
.BI "-c" " conf.gro"
.B Input
- Generic structure: gro g96 pdb tpr tpb tpa
+ Generic structure: gro g96 pdb tpr tpb tpa xml
.BI "-r" " conf.gro"
.B Input, Opt.
- Generic structure: gro g96 pdb tpr tpb tpa
+ Generic structure: gro g96 pdb tpr tpb tpa xml
+
+.BI "-rb" " conf.gro"
+.B Input, Opt.
+ Generic structure: gro g96 pdb tpr tpb tpa xml
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-o" " topol.tpr"
.B Output
- Generic run input: tpr tpb tpa
+ Generic run input: tpr tpb tpa xml
.BI "-t" " traj.trr"
.B Input, Opt.
Full precision trajectory: trr trj
+.BI "-e" " ener.edr"
+.B Input, Opt.
+ Generic energy: edr ene
+
.SH OTHER OPTIONS
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 0"
Set the nicelevel
.BI "-[no]check14" " no"
Remove 1-4 interactions without Van der Waals
+.BI "-[no]renum" " yes"
+ Renumber atomtypes and minimize number of atomtypes
+
-.TH highway 1 "Thu 28 Feb 2002"
+.TH highway 1 "Sun 25 Jan 2004"
.SH NAME
highway
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3highway\fP
.BI "-f" " highway.dat "
.BI "-a" " auto.dat "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 0"
Set the nicelevel
-.TH make_ndx 1 "Thu 28 Feb 2002"
+.TH make_ndx 1 "Sun 25 Jan 2004"
.SH NAME
make_ndx
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3make_ndx\fP
.BI "-f" " conf.gro "
.BI "-n" " index.ndx "
.BI "-o" " index.ndx "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
+.BI "-natoms" " int "
+.BI "-[no]verbose" ""
.SH DESCRIPTION
Index groups are necessary for almost every gromacs program.
All these programs can generate default index groups. You ONLY
When no index file is supplied, also make_ndx will generate the
default groups.
With the index editor you can select on atom, residue and chain names
-and numbers, you can use NOT, AND and OR, you can split groups
+and numbers.
+When a run input file is supplied you can also select on atom type.
+You can use NOT, AND and OR, you can split groups
into chains, residues or atoms. You can delete and rename groups.
The atom numbering in the editor and the index file starts at 1.
.SH FILES
.BI "-f" " conf.gro"
-.B Input
- Generic structure: gro g96 pdb tpr tpb tpa
+.B Input, Opt.
+ Generic structure: gro g96 pdb tpr tpb tpa xml
.BI "-n" " index.ndx"
-.B Input, Opt.
+.B Input, Opt., Mult.
Index file
.BI "-o" " index.ndx"
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 0"
Set the nicelevel
+.BI "-natoms" " int" " 0"
+ set number of atoms (default: read from coordinate or index file)
+
+.BI "-[no]verbose" " no"
+ Verbose output
+
-.TH mdrun 1 "Thu 28 Feb 2002"
+.TH mdrun 1 "Sun 25 Jan 2004"
.SH NAME
mdrun
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3mdrun\fP
.BI "-s" " topol.tpr "
.BI "-e" " ener.edr "
.BI "-g" " md.log "
.BI "-dgdl" " dgdl.xvg "
+.BI "-field" " field.xvg "
.BI "-table" " table.xvg "
.BI "-rerun" " rerun.xtc "
.BI "-ei" " sam.edi "
.BI "-pd" " pull.pdo "
.BI "-pn" " pull.ndx "
.BI "-mtx" " nm.mtx "
+.BI "-dn" " dipole.ndx "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-deffnm" " string "
.BI "-np" " int "
+.BI "-nt" " int "
.BI "-[no]v" ""
.BI "-[no]compact" ""
.BI "-[no]multi" ""
See manual.
+Finally some experimental algorithms can be tested when the
+appropriate options have been given. Currently under
+investigation are: polarizibility, glass simulations,
+Free energy perturbation, X-Ray bombardments
+and parallel independent simulations.
+
+
When mdrun receives a TERM signal, it will set nsteps to the current
step plus one. When mdrun receives a USR1 signal, it will set nsteps
to the next multiple of nstxout after the current step.
When running with MPI, a signal to one of the mdrun processes
is sufficient, this signal should not be sent to mpirun or
the mdrun process that is the parent of the others.
-Finally some experimental algorithms can be tested when the
-appropriate options have been given. Currently under
-investigation are: polarizibility, glass simulations,
-Free energy perturbation, X-Ray bombardments
-and parallel independent simulations.
.SH FILES
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa
+ Generic run input: tpr tpb tpa xml
.BI "-o" " traj.trr"
.B Output
.BI "-c" " confout.gro"
.B Output
- Generic structure: gro g96 pdb
+ Generic structure: gro g96 pdb xml
.BI "-e" " ener.edr"
.B Output
.B Output, Opt.
xvgr/xmgr file
+.BI "-field" " field.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
.BI "-table" " table.xvg"
.B Input, Opt.
xvgr/xmgr file
.B Output, Opt.
Hessian matrix
+.BI "-dn" " dipole.ndx"
+.B Output, Opt.
+ Index file
+
.SH OTHER OPTIONS
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
.BI "-np" " int" " 1"
Number of nodes, must be the same as used for grompp
+.BI "-nt" " int" " 1"
+ Number of threads to start on each node
+
.BI "-[no]v" " no"
Be loud and noisy
-.TH mk_angndx 1 "Thu 28 Feb 2002"
+.TH mk_angndx 1 "Sun 25 Jan 2004"
.SH NAME
mk_angndx
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3mk_angndx\fP
.BI "-s" " topol.tpr "
.BI "-n" " angle.ndx "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-type" " enum "
.SH DESCRIPTION
.SH FILES
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa
+ Generic run input: tpr tpb tpa xml
.BI "-n" " angle.ndx"
.B Output
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 0"
Set the nicelevel
-.TH ngmx 1 "Thu 28 Feb 2002"
+.TH ngmx 1 "Sun 25 Jan 2004"
.SH NAME
ngmx
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3ngmx\fP
.BI "-f" " traj.xtc "
.BI "-s" " topol.tpr "
.BI "-n" " index.ndx "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa
+ Generic run input: tpr tpb tpa xml
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 0"
Set the nicelevel
-.TH pdb2gmx 1 "Thu 28 Feb 2002"
+.TH pdb2gmx 1 "Sun 25 Jan 2004"
.SH NAME
pdb2gmx
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3pdb2gmx\fP
.BI "-f" " eiwit.pdb "
.BI "-n" " clean.ndx "
.BI "-q" " clean.pdb "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-[no]merge" ""
+.BI "-ff" " string "
+.BI "-water" " enum "
.BI "-[no]inter" ""
.BI "-[no]ss" ""
.BI "-[no]ter" ""
.BI "-[no]his" ""
.BI "-angle" " real "
.BI "-dist" " real "
-.BI "-posrefc" " real "
.BI "-[no]una" ""
-.BI "-[no]sort" ""
-.BI "-[no]H14" ""
.BI "-[no]ignh" ""
-.BI "-[no]alldih" ""
+.BI "-[no]missing" ""
+.BI "-posrefc" " real "
.BI "-dummy" " enum "
.BI "-[no]heavyh" ""
.BI "-[no]deuterate" ""
.SH DESCRIPTION
-This program reads a pdb file, lets you choose a forcefield, reads
+This program reads a pdb file, reads
some database files, adds hydrogens to the molecules and generates
coordinates in Gromacs (Gromos) format and a topology in Gromacs format.
These files can subsequently be processed to generate a run input file.
+The force fields supported currently are:
+
+
+G43a1 GROMOS96 43a1 Forcefield (official distribution)
+
+
+oplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
+
+
+G43b1 GROMOS96 43b1 Vacuum Forcefield (official distribution)
+
+
+gmx Gromacs Forcefield (a modified GROMOS87, see manual)
+
+
+G43a2 GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)
+
+
+The corresponding data files can be found in the library directory
+with names like ffXXXX.YYY. Check chapter 5 of the manual for more
+information about file formats.
+
+
Note that a pdb file is nothing more than a file format, and it
need not necessarily contain a protein structure. Every kind of
molecule for which there is support in the database can be converted.
-
-.B -sort
-will sort all residues according to the order in the
-database, sometimes this is necessary to get charge groups
-together.
-
-
-
-.B -alldih
-will generate all proper dihedrals instead of only
-those with as few hydrogens as possible, this is useful for use with
-the Charmm forcefield.
-
-
The option
.B -dummy
removes hydrogen and fast improper dihedral
done for water hydrogens to slow down the rotational motion of water.
The increase in mass of the hydrogens is subtracted from the bonded
(heavy) atom so that the total mass of the system remains the same.
-Reference Feenstra et al., J. Comput. Chem. 20, 786 (1999).
.SH FILES
.BI "-f" " eiwit.pdb"
.B Input
- Generic structure: gro g96 pdb tpr tpb tpa
+ Generic structure: gro g96 pdb tpr tpb tpa xml
.BI "-o" " conf.gro"
.B Output
- Generic structure: gro g96 pdb
+ Generic structure: gro g96 pdb xml
.BI "-p" " topol.top"
.B Output
.BI "-q" " clean.pdb"
.B Output, Opt.
- Generic structure: gro g96 pdb
+ Generic structure: gro g96 pdb xml
.SH OTHER OPTIONS
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 0"
Set the nicelevel
.BI "-[no]merge" " no"
Merge multiple chains into one molecule
+.BI "-ff" " string" " G43a1"
+ Select the force field, supported are: G43a1, oplsaa, gmx, G43a2, G43b1. Run pdb2gmx -h for more information.
+
+.BI "-water" " enum" " spc"
+ Water model to use: with GROMOS we recommend SPC, with OPLS, TIP4P:
+.B spc
+,
+.B spce
+,
+.B tip3p
+,
+.B tip4p
+or
+.B tip5p
+
+
.BI "-[no]inter" " no"
Set the next 6 options to interactive
.BI "-dist" " real" " 0.3"
Maximum donor-acceptor distance for a H-bond (nm)
-.BI "-posrefc" " real" " 1000"
- Force constant for position restraints
-
.BI "-[no]una" " no"
Select aromatic rings with united CH atoms on Phenylalanine, Tryptophane and Tyrosine
-.BI "-[no]sort" " yes"
- Sort the residues according to database
-
-.BI "-[no]H14" " no"
- Use 1-4 interactions between hydrogen atoms
-
.BI "-[no]ignh" " no"
Ignore hydrogen atoms that are in the pdb file
-.BI "-[no]alldih" " no"
- Generate all proper dihedrals
+.BI "-[no]missing" " no"
+ Continue when atoms are missing, dangerous
+
+.BI "-posrefc" " real" " 1000"
+ Force constant for position restraints
.BI "-dummy" " enum" " none"
Convert atoms to dummy atoms:
-.TH protonate 1 "Thu 28 Feb 2002"
+.TH protonate 1 "Sun 25 Jan 2004"
.SH NAME
protonate
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3protonate\fP
.BI "-s" " topol.tpr "
.BI "-n" " index.ndx "
.BI "-o" " protonated.xtc "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.SH FILES
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb
+ Structure+mass(db): tpr tpb tpa gro g96 pdb xml
.BI "-f" " traj.xtc"
.B Input, Opt.
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 0"
Set the nicelevel
-.TH tpbconv 1 "Thu 28 Feb 2002"
+.TH tpbconv 1 "Sun 25 Jan 2004"
.SH NAME
tpbconv
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3tpbconv\fP
.BI "-s" " topol.tpr "
.BI "-f" " traj.trr "
+.BI "-e" " ener.edr "
.BI "-n" " index.ndx "
.BI "-o" " tpxout.tpr "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-time" " real "
.BI "-extend" " real "
Note that a frame with coordinates and velocities is needed,
which means that when you never write velocities, you can not use
tpbconv and you have to start the run again from the beginning.
+When pressure and/or temperature coupling is used an energy file
+can be supplied to get an exact continuation of the original run.
.SH FILES
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa
+ Generic run input: tpr tpb tpa xml
.BI "-f" " traj.trr"
.B Input, Opt.
Full precision trajectory: trr trj
+.BI "-e" " ener.edr"
+.B Input, Opt.
+ Generic energy: edr ene
+
.BI "-n" " index.ndx"
.B Input, Opt.
Index file
.BI "-o" " tpxout.tpr"
.B Output
- Generic run input: tpr tpb tpa
+ Generic run input: tpr tpb tpa xml
.SH OTHER OPTIONS
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 0"
Set the nicelevel
-.TH trjcat 1 "Thu 28 Feb 2002"
+.TH trjcat 1 "Sun 25 Jan 2004"
.SH NAME
trjcat
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3trjcat\fP
+.BI "-f" " traj.xtc "
.BI "-o" " trajout.xtc "
.BI "-n" " index.ndx "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-tu" " enum "
.BI "-b" " time "
.BI "-[no]vel" ""
.BI "-[no]settime" ""
.BI "-[no]sort" ""
+.BI "-[no]keeplast" ""
.BI "-[no]cat" ""
.SH DESCRIPTION
trjcat concatenates several input trajectory files in sorted order.
.B -cat
you can simply paste several files
together without removal of frames with identical time stamps.
+
+
+One important option is inferred when the output file is amongst the
+input files. In that case that particular file will be appended to
+which implies you do not need to store double the amount of data.
+Obviously the file to append to has to be the one with lowest starting
+time since one can only append at the end of a file.
.SH FILES
+.BI "-f" " traj.xtc"
+.B Input, Mult.
+ Generic trajectory: xtc trr trj gro g96 pdb
+
.BI "-o" " trajout.xtc"
.B Output
Generic trajectory: xtc trr trj gro g96 pdb
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
.BI "-[no]sort" " yes"
Sort trajectory files (not frames)
+.BI "-[no]keeplast" " no"
+ keep overlapping frames at end of trajectory
+
.BI "-[no]cat" " no"
do not discard double time frames
-.TH trjconv 1 "Thu 28 Feb 2002"
+.TH trjconv 1 "Sun 25 Jan 2004"
.SH NAME
trjconv
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3trjconv\fP
.BI "-f" " traj.xtc "
.BI "-n" " index.ndx "
.BI "-fr" " frames.ndx "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-[no]center" ""
.BI "-box" " vector "
.BI "-shift" " vector "
-.BI "-[no]fit" ""
-.BI "-[no]pfit" ""
+.BI "-fit" " enum "
.BI "-ndec" " int "
.BI "-[no]vel" ""
.BI "-[no]force" ""
.BI "-[no]app" ""
.BI "-split" " time "
.BI "-[no]sep" ""
+.BI "-[no]ter" ""
.SH DESCRIPTION
trjconv can convert trajectory files in many ways:
Option
.B -pbc
sets the type of periodic boundary condition
-treatment.
+treatment:
+
+*
.B whole
puts the atoms in the box and then makes
broken molecules whole (a run input file is required).
+Atom number 1 of each molecule will be inside the box.
+
+*
+.B com
+puts the center of mass of all
+.I residues
+
+in the box. Not that this can break molecules that consist of
+more than one residue (e.g. proteins).
+*
.B inbox
puts all the atoms in the box.
+*
.B nojump
checks if atoms jump across the box and then puts
them back. This has the effect that all molecules
for this procedure is taken from the structure file, if one is
supplied, otherwise it is the first frame.
+*
+.B cluster
+clusters all the atoms in the selected index
+such that they are all closest to the center of mass of the cluster
+which is iteratively updated. Note that this will only give meaningful
+results if you in fact have a cluster. Luckily that can be checked
+afterwards using a trajectory viewer.
+
+
.B -pbc
is ignored when
.B -fit
-of
+or
.B -pfit
is set,
in that case molecules will be made whole.
in your input trajectory, so if these are inaccurate use the
.B -timestep
+option to modify the time (this can be done
+simultaneously). For making smooth movies the program
+.B g_filter
-option to modify the time (this can be done simultaneously).
+can reduce the number of frames while using low-pass frequency
+filtering, this reduces aliasing of high frequency motions.
Using
.BI "-s" " topol.tpr"
.B Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb
+ Structure+mass(db): tpr tpb tpa gro g96 pdb xml
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
Change time step between input frames (ps)
.BI "-pbc" " enum" " none"
- PBC treatment:
+ PBC treatment (see help text for full description):
.B none
,
.B whole
,
.B inbox
-or
+,
.B nojump
+,
+.B cluster
+or
+.B com
.BI "-ur" " enum" " rect"
.BI "-shift" " vector" " 0 0 0"
All coordinates will be shifted by framenr*shift
-.BI "-[no]fit" " no"
- Fit molecule to ref structure in the structure file
+.BI "-fit" " enum" " none"
+ Fit molecule to ref structure in the structure file:
+.B none
+,
+.B rot+trans
+,
+.B translation
+or
+.B progressive
-.BI "-[no]pfit" " no"
- Progressive fit, to the previous fitted structure
.BI "-ndec" " int" " 3"
Precision for .xtc and .gro writing in number of decimal places
.BI "-[no]sep" " no"
Write each frame to a separate .gro, .g96 or .pdb file
+.BI "-[no]ter" " no"
+ Use 'TER' in pdb file as end of frame in stead of default 'ENDMDL'
+
-.TH trjorder 1 "Thu 28 Feb 2002"
+.TH trjorder 1 "Sun 25 Jan 2004"
.SH NAME
trjorder
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3trjorder\fP
.BI "-f" " traj.xtc "
.BI "-n" " index.ndx "
.BI "-o" " ordered.xtc "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
of molecules would consist of all the water atoms. When an index group
of the first n waters is made, the ordered trajectory can be used
with any Gromacs program to analyze the n closest waters.
+
+
+If the output file is a pdb file, the distance to the reference target
+will be stored in the B-factor field in order to color with e.g. rasmol.
.SH FILES
.BI "-f" " traj.xtc"
.B Input
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb
+ Structure+mass(db): tpr tpb tpa gro g96 pdb xml
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
-.TH wheel 1 "Thu 28 Feb 2002"
+.TH wheel 1 "Sun 25 Jan 2004"
.SH NAME
wheel
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3wheel\fP
.BI "-f" " nnnice.dat "
.BI "-o" " plot.eps "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-r0" " int "
.BI "-rot0" " real "
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 19"
Set the nicelevel
-.TH x2top 1 "Thu 28 Feb 2002"
+.TH x2top 1 "Sun 25 Jan 2004"
.SH NAME
x2top
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3x2top\fP
.BI "-f" " conf.gro "
.BI "-o" " out.top "
.BI "-r" " out.rtp "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-scale" " real "
+.BI "-ff" " enum "
.BI "-nexcl" " int "
.BI "-[no]H14" ""
.BI "-[no]alldih" ""
+.BI "-[no]remdih" ""
.BI "-[no]pairs" ""
.BI "-name" " string "
.BI "-[no]pbc" ""
.SH FILES
.BI "-f" " conf.gro"
.B Input
- Generic structure: gro g96 pdb tpr tpb tpa
+ Generic structure: gro g96 pdb tpr tpb tpa xml
.BI "-o" " out.top"
.B Output, Opt.
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 0"
Set the nicelevel
.BI "-scale" " real" " 1.1"
Scaling factor for bonds with unknown atom types relative to atom type O
+.BI "-ff" " enum" " G43a1"
+ Select the force field for your simulation:
+.B G43a1
+,
+.B oplsaa
+,
+.B gmx
+,
+.B G43a2
+or
+.B G43b1
+
+
.BI "-nexcl" " int" " 3"
Number of exclusions
-.BI "-[no]H14" " no"
+.BI "-[no]H14" " yes"
Use 3rd neighbour interactions for hydrogen atoms
.BI "-[no]alldih" " no"
Generate all proper dihedrals
+.BI "-[no]remdih" " no"
+ Remove dihedrals on the same bond as an improper
+
.BI "-[no]pairs" " yes"
Output 1-4 interactions (pairs) in topology file
Name of your molecule
.BI "-[no]pbc" " yes"
- Use periodic boundary conditions. Please set the GMXFULLPBC environment variable as well.
+ Use periodic boundary conditions.
.BI "-[no]param" " no"
Print parameters in the output
-.TH xpm2ps 1 "Thu 28 Feb 2002"
+.TH xpm2ps 1 "Sun 25 Jan 2004"
.SH NAME
xpm2ps
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3xpm2ps\fP
.BI "-f" " root.xpm "
.BI "-o" " plot.eps "
.BI "-xpm" " root.xpm "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-[no]w" ""
.BI "-[no]frame" ""
.BI "-gradient" " vector "
.BI "-skip" " int "
.BI "-[no]zeroline" ""
+.BI "-legoffset" " int "
.SH DESCRIPTION
xpm2ps makes a beautiful color plot of an XPixelMap file.
Labels and axis can be displayed, when they are supplied
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 0"
Set the nicelevel
.BI "-[no]zeroline" " no"
insert line in xpm matrix where axis label is zero
+.BI "-legoffset" " int" " 0"
+ Skip first N colors from xpm file for the legend
+
-.TH xrama 1 "Thu 28 Feb 2002"
+.TH xrama 1 "Sun 25 Jan 2004"
.SH NAME
xrama
-.B VERSION 3.1
+.B VERSION 3.2.0
.SH SYNOPSIS
\f3xrama\fP
.BI "-f" " traj.xtc "
.BI "-s" " topol.tpr "
.BI "-[no]h" ""
-.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-e" " time "
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa
+ Generic run input: tpr tpb tpa xml
.SH OTHER OPTIONS
.BI "-[no]h" " no"
Print help info and quit
-.BI "-[no]X" " no"
- Use dialog box GUI to edit command line options
-
.BI "-nice" " int" " 0"
Set the nicelevel
shopt -s extglob
+_anadock_compl() {
+local p c
+COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -ox -od -of -g -h -nice -free -norms -cutoff' -- $c)); return 0; fi
+case "$p" in
+-f) COMPREPLY=( $(compgen -X '!*.pdb*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-ox) COMPREPLY=( $(compgen -X '!*.pdb*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-od) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-of) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-g) COMPREPLY=( $(compgen -X '!*.log*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac }
+complete -F _anadock_compl anadock
+shopt -s extglob
+_cdist_compl() {
+local p c
+COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -s -g -q -d -o -n -dom -h -nice -noengh -bm -am -pm -rr -ar -er -vm -lm -il -dm -im -nm -hm -hb -nobon -nonb -measure -maxdist -add -vir -sm' -- $c)); return 0; fi
+case "$p" in
+-sm) COMPREPLY=( $(compgen -W ' none tri tetra ' -- $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-g) COMPREPLY=( $(compgen -X '!*.log*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-q) COMPREPLY=( $(compgen -X '!*.pdb*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-d) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-o) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-dom) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac }
+complete -F _cdist_compl cdist
+shopt -s extglob
+_disco_compl() {
+local p c
+COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -g -f -d -do -c -center -n -o -keep -viol -h -nice -nf -nit -nov -nochiral -nopep -lower -weighted -dump -cubic -explicit -fit -nbcheck -nstprint -ranlist -noranlistfirst -lowdev -seed -box -grow' -- $c)); return 0; fi
+case "$p" in
+-g) COMPREPLY=( $(compgen -X '!*.log*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-f) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-d) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-do) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-c) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|xml|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-center) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|xml|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-o) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-keep) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-viol) COMPREPLY=( $(compgen -X '!*.pdb*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac }
+complete -F _disco_compl disco
+shopt -s extglob
_do_dssp_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -ssdump -map -o -sc -a -ta -aa -h -X -nice -b -e -dt -tu -w -sss' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -ssdump -map -o -sc -a -ta -aa -h -nice -b -e -dt -tu -w -sss' -- $c)); return 0; fi
case "$p" in
-tu) COMPREPLY=( $(compgen -W ' ps fs ns us ms s m h ' -- $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-ssdump) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-map) COMPREPLY=( $(compgen -X '!*.map*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-a) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-ta) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-aa) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _do_dssp_compl do_dssp
shopt -s extglob
_editconf_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -n -o -bf -h -X -nice -w -ndef -bt -box -angles -d -c -center -rotate -princ -scale -density -pbc -mead -grasp -rvdw -atom -legend -label' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -n -o -bf -h -nice -w -ndef -bt -box -angles -d -c -center -translate -rotate -princ -scale -density -novol -pbc -mead -grasp -rvdw -atom -legend -label' -- $c)); return 0; fi
case "$p" in
-bt) COMPREPLY=( $(compgen -W ' tric cubic dodecahedron octahedron ' -- $c ));;
--f) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-f) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--o) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-o) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|xml|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-bf) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _editconf_compl editconf
shopt -s extglob
_eneconv_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -o -h -X -nice -b -e -dt -offset -settime -nosort -scalefac -noerror' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -o -h -nice -b -e -dt -offset -settime -nosort -scalefac -noerror' -- $c)); return 0; fi
case "$p" in
-f) COMPREPLY=( $(compgen -X '!*.+(edr|ene)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.+(edr|ene)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _eneconv_compl eneconv
shopt -s extglob
_ffscan_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -s -g -table -parm -ga -h -X -nice -tol -fmax -epot -nocomb -npow -ratio -logeps -nov' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -s -g -table -parm -ga -c -e -o -h -nice -tol -fmax -nocomb -npow -logeps -v -epot -fepot -pres -fpres -fmsf -molsize -nmol' -- $c)); return 0; fi
case "$p" in
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-g) COMPREPLY=( $(compgen -X '!*.log*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-table) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-parm) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-ga) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+-c) COMPREPLY=( $(compgen -X '!*.gro*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-e) COMPREPLY=( $(compgen -X '!*.+(edr|ene)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-o) COMPREPLY=( $(compgen -X '!*.+(trr|trj)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac }
complete -F _ffscan_compl ffscan
shopt -s extglob
_g_anaeig_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -v -v2 -f -s -n -eig1 -eig2 -disp -proj -2d -3d -filt -extr -over -inpr -h -X -nice -b -e -dt -tu -w -first -last -skip -max -nframes -split' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -v -v2 -f -s -n -eig -eig2 -comp -rmsf -proj -2d -3d -filt -extr -over -inpr -h -nice -b -e -dt -tu -w -first -last -skip -max -nframes -split' -- $c)); return 0; fi
case "$p" in
-tu) COMPREPLY=( $(compgen -W ' ps fs ns us ms s m h ' -- $c ));;
-v) COMPREPLY=( $(compgen -X '!*.+(trr|trj)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-v2) COMPREPLY=( $(compgen -X '!*.+(trr|trj)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--eig1) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-eig) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-eig2) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--disp) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-comp) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-rmsf) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-proj) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-2d) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--3d) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-3d) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|xml|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-filt) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-extr) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-over) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-inpr) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_anaeig_compl g_anaeig
shopt -s extglob
_g_analyze_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -ac -msd -cc -dist -av -ee -g -h -X -nice -w -notime -b -e -n -d -bw -errbar -power -nosubav -oneacf -acflen -nonormalize -P -fitfn -ncskip -beginfit -endfit' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -ac -msd -cc -dist -av -ee -g -h -nice -w -notime -b -e -n -d -bw -errbar -filter -power -nosubav -oneacf -acflen -nonormalize -P -fitfn -ncskip -beginfit -endfit' -- $c)); return 0; fi
case "$p" in
-errbar) COMPREPLY=( $(compgen -W ' none stddev error 90 ' -- $c ));;
-P) COMPREPLY=( $(compgen -W ' 0 1 2 3 ' -- $c ));;
--fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 ' -- $c ));;
+-fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 exp9 ' -- $c ));;
-f) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-ac) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-msd) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-av) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-ee) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-g) COMPREPLY=( $(compgen -X '!*.log*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_analyze_compl g_analyze
shopt -s extglob
_g_angle_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -od -ov -of -ot -oh -oc -h -X -nice -b -e -dt -w -type -all -binwidth -chandler -avercorr -acflen -nonormalize -P -fitfn -ncskip -beginfit -endfit' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -od -ov -of -ot -oh -oc -h -nice -b -e -dt -w -type -all -binwidth -chandler -avercorr -acflen -nonormalize -P -fitfn -ncskip -beginfit -endfit' -- $c)); return 0; fi
case "$p" in
-type) COMPREPLY=( $(compgen -W ' angle dihedral improper ryckaert-bellemans ' -- $c ));;
-P) COMPREPLY=( $(compgen -W ' 0 1 2 3 ' -- $c ));;
--fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 ' -- $c ));;
+-fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 exp9 ' -- $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-od) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-ov) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-ot) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-oh) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-oc) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_angle_compl g_angle
shopt -s extglob
_g_bond_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -n -s -o -l -d -h -X -nice -b -e -dt -w -blen -tol -noaver' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -n -s -o -l -d -h -nice -b -e -dt -w -blen -tol -noaver -noaverdist' -- $c)); return 0; fi
case "$p" in
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-l) COMPREPLY=( $(compgen -X '!*.log*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-d) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_bond_compl g_bond
shopt -s extglob
_g_bundle_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -ol -od -oz -ot -otr -otl -ok -okr -okl -oa -h -X -nice -b -e -dt -tu -na -z' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -ol -od -oz -ot -otr -otl -ok -okr -okl -oa -h -nice -b -e -dt -tu -na -z' -- $c)); return 0; fi
case "$p" in
-tu) COMPREPLY=( $(compgen -W ' ps fs ns us ms s m h ' -- $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-ol) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-od) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-okr) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-okl) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-oa) COMPREPLY=( $(compgen -X '!*.pdb*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_bundle_compl g_bundle
shopt -s extglob
_g_chi_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -c -f -o -p -ss -jc -corr -g -h -X -nice -b -e -dt -w -r0 -phi -psi -omega -rama -viol -all -shift -run -maxchi -nonormhisto -ramomega -bfact -bmax -acflen -nonormalize -P -fitfn -ncskip -beginfit -endfit' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -s -f -o -p -ss -jc -corr -g -ot -oh -rt -cp -h -nice -b -e -dt -w -r0 -phi -psi -omega -rama -viol -all -rad -shift -binwidth -core_rotamer -maxchi -nonormhisto -ramomega -bfact -chi_prod -HChi -bmax -acflen -nonormalize -P -fitfn -ncskip -beginfit -endfit' -- $c)); return 0; fi
case "$p" in
-maxchi) COMPREPLY=( $(compgen -W ' 0 1 2 3 4 5 6 ' -- $c ));;
-P) COMPREPLY=( $(compgen -W ' 0 1 2 3 ' -- $c ));;
--fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 ' -- $c ));;
--c) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 exp9 ' -- $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-p) COMPREPLY=( $(compgen -X '!*.pdb*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-jc) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-corr) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-g) COMPREPLY=( $(compgen -X '!*.log*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+-ot) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-oh) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-rt) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-cp) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac }
complete -F _g_chi_compl g_chi
shopt -s extglob
_g_cluster_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -dm -o -g -dist -ev -sz -tr -ntr -clid -cl -h -X -nice -b -e -dt -tu -w -dista -nlevels -keepfree -cutoff -nofit -max -skip -av -wcl -nst -rmsmin -method -binary -M -P -seed -niter -kT' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -dm -o -g -dist -ev -sz -tr -ntr -clid -cl -h -nice -b -e -dt -tu -w -dista -nlevels -keepfree -cutoff -nofit -max -skip -av -wcl -nst -rmsmin -method -minstruct -binary -M -P -seed -niter -kT' -- $c)); return 0; fi
case "$p" in
-tu) COMPREPLY=( $(compgen -W ' ps fs ns us ms s m h ' -- $c ));;
-method) COMPREPLY=( $(compgen -W ' linkage jarvis-patrick monte-carlo diagonalization gromos ' -- $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-dm) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-ntr) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-clid) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-cl) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_cluster_compl g_cluster
shopt -s extglob
_g_clustsize_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -n -o -nc -mc -ac -h -X -nice -b -e -dt -w -cut -nskip -nlevels -rgblo -rgbhi' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -o -ow -nc -mc -ac -hc -h -nice -b -e -dt -tu -w -cut -mol -nskip -nlevels -rgblo -rgbhi' -- $c)); return 0; fi
case "$p" in
+-tu) COMPREPLY=( $(compgen -W ' ps fs ns us ms s m h ' -- $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.tpr*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-ow) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-nc) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-mc) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-ac) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+-hc) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac }
complete -F _g_clustsize_compl g_clustsize
shopt -s extglob
_g_confrms_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f1 -f2 -o -n1 -n2 -h -X -nice -one -pbc' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f1 -f2 -o -n1 -n2 -no -h -nice -w -one -pbc -nofit -name -bfac' -- $c)); return 0; fi
case "$p" in
--f1) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--f2) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--o) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-f1) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-f2) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-o) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|xml|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n1) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n2) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+-no) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac }
complete -F _g_confrms_compl g_confrms
shopt -s extglob
_g_covar_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -o -v -av -l -xpm -xpma -h -X -nice -b -e -dt -tu -nofit -ref -mwa -last' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -o -v -av -l -ascii -xpm -xpma -h -nice -b -e -dt -tu -nofit -ref -mwa -last' -- $c)); return 0; fi
case "$p" in
-tu) COMPREPLY=( $(compgen -W ' ps fs ns us ms s m h ' -- $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-v) COMPREPLY=( $(compgen -X '!*.+(trr|trj)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--av) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-av) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|xml|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-l) COMPREPLY=( $(compgen -X '!*.log*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-ascii) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-xpm) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-xpma) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_covar_compl g_covar
shopt -s extglob
_g_density_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -n -s -ei -o -h -X -nice -b -e -dt -w -d -sl -number -ed -count' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -n -s -ei -o -h -nice -b -e -dt -w -d -sl -number -ed -count' -- $c)); return 0; fi
case "$p" in
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-ei) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_density_compl g_density
shopt -s extglob
_g_dielectric_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -d -o -c -h -X -nice -b -e -dt -w -fft -nox1 -eint -bfit -efit -tail -A -tau1 -tau2 -eps0 -epsRF -fix -ffn -nsmooth' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -d -o -c -h -nice -b -e -dt -w -fft -nox1 -eint -bfit -efit -tail -A -tau1 -tau2 -eps0 -epsRF -fix -ffn -nsmooth' -- $c)); return 0; fi
case "$p" in
--ffn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 ' -- $c ));;
+-ffn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 exp9 ' -- $c ));;
-f) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-d) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-c) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_dielectric_compl g_dielectric
shopt -s extglob
_g_dih_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -o -h -X -nice -b -e -dt -w -sa -mult' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -o -h -nice -b -e -dt -w -sa -mult' -- $c)); return 0; fi
case "$p" in
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.out*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_dih_compl g_dih
shopt -s extglob
_g_dipoles_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -enx -f -s -n -o -e -a -d -c -g -q -h -X -nice -b -e -dt -w -mu -mumax -epsilonRF -skip -temp -avercorr -gkratom -acflen -nonormalize -P -fitfn -ncskip -beginfit -endfit' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -enx -f -s -n -o -eps -a -d -c -g -q -h -nice -b -e -dt -w -mu -mumax -epsilonRF -skip -temp -avercorr -gkratom -acflen -nonormalize -P -fitfn -ncskip -beginfit -endfit' -- $c)); return 0; fi
case "$p" in
-P) COMPREPLY=( $(compgen -W ' 0 1 2 3 ' -- $c ));;
--fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 ' -- $c ));;
+-fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 exp9 ' -- $c ));;
-enx) COMPREPLY=( $(compgen -X '!*.+(edr|ene)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--e) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-eps) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-a) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-d) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-c) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-g) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-q) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_dipoles_compl g_dipoles
shopt -s extglob
_g_disre_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -s -f -ds -da -dn -dm -dr -l -n -h -X -nice -b -e -dt -w -ntop' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -s -f -ds -da -dn -dm -dr -l -n -q -h -nice -b -e -dt -w -ntop' -- $c)); return 0; fi
case "$p" in
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-ds) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-da) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-dr) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-l) COMPREPLY=( $(compgen -X '!*.log*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+-q) COMPREPLY=( $(compgen -X '!*.pdb*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac }
complete -F _g_disre_compl g_disre
shopt -s extglob
_g_dist_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -o -h -X -nice -b -e -dt -dist' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -o -h -nice -b -e -dt -dist' -- $c)); return 0; fi
case "$p" in
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_dist_compl g_dist
shopt -s extglob
_g_dyndom_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -o -n -h -X -nice -firstangle -lastangle -nframe -maxangle -trans -head -tail' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -o -n -h -nice -firstangle -lastangle -nframe -maxangle -trans -head -tail' -- $c)); return 0; fi
case "$p" in
-f) COMPREPLY=( $(compgen -X '!*.pdb*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_dyndom_compl g_dyndom
shopt -s extglob
-_genbox_compl() {
-local p c
-COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -cp -cs -ci -o -p -h -X -nice -box -nmol -try -seed -vdwd -shell' -- $c)); return 0; fi
-case "$p" in
--cp) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--cs) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--ci) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--o) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--p) COMPREPLY=( $(compgen -X '!*.top*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
-complete -F _genbox_compl genbox
-shopt -s extglob
-_genconf_compl() {
-local p c
-COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -o -trj -h -X -nice -nbox -dist -seed -rot -shuffle -sort -block -nmolat -maxrot -renumber' -- $c)); return 0; fi
-case "$p" in
--f) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--o) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--trj) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
-complete -F _genconf_compl genconf
-shopt -s extglob
_g_enemat_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -groups -eref -emat -etot -h -X -nice -b -e -dt -w -sum -skip -nomean -nlevels -max -min -nocoul -coulr -coul14 -nolj -lj14 -bham -nofree -temp' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -groups -eref -emat -etot -h -nice -b -e -dt -w -sum -skip -nomean -nlevels -max -min -nocoul -coulr -coul14 -nolj -lj14 -bham -nofree -temp' -- $c)); return 0; fi
case "$p" in
-f) COMPREPLY=( $(compgen -X '!*.+(edr|ene)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-groups) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-eref) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-emat) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-etot) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_enemat_compl g_enemat
shopt -s extglob
_g_energy_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -f2 -s -o -viol -pairs -ora -ort -oda -odr -odt -corr -vis -ravg -h -X -nice -b -e -w -fee -fetemp -zero -sum -dp -mutot -skip -aver -nmol -ndf -fluc -orinst -acflen -nonormalize -P -fitfn -ncskip -beginfit -endfit' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -f2 -s -o -viol -pairs -ora -ort -oda -odr -odt -corr -vis -ravg -h -nice -b -e -w -fee -fetemp -zero -sum -dp -mutot -skip -aver -nmol -ndf -fluc -orinst -acflen -nonormalize -P -fitfn -ncskip -beginfit -endfit' -- $c)); return 0; fi
case "$p" in
-P) COMPREPLY=( $(compgen -W ' 0 1 2 3 ' -- $c ));;
--fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 ' -- $c ));;
+-fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 exp9 ' -- $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(edr|ene)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-f2) COMPREPLY=( $(compgen -X '!*.+(edr|ene)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-viol) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-pairs) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-corr) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-vis) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-ravg) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_energy_compl g_energy
shopt -s extglob
-_genion_compl() {
+_g_filter_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -s -n -o -g -pot -h -X -nice -np -pname -pq -nn -nname -nq -rmin -random -seed' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -ol -oh -h -nice -b -e -dt -w -nf -all -nonojump -fit' -- $c)); return 0; fi
case "$p" in
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--o) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--g) COMPREPLY=( $(compgen -X '!*.log*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--pot) COMPREPLY=( $(compgen -X '!*.pdb*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
-complete -F _genion_compl genion
-shopt -s extglob
-_genpr_compl() {
-local p c
-COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -n -o -h -X -nice -fc' -- $c)); return 0; fi
-case "$p" in
--f) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--o) COMPREPLY=( $(compgen -X '!*.itp*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
-complete -F _genpr_compl genpr
+-ol) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-oh) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac }
+complete -F _g_filter_compl g_filter
shopt -s extglob
_g_gyrate_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -o -n -h -X -nice -b -e -dt -w -q -p' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -o -acf -n -h -nice -b -e -dt -w -q -p -moi -acflen -nonormalize -P -fitfn -ncskip -beginfit -endfit' -- $c)); return 0; fi
case "$p" in
+-P) COMPREPLY=( $(compgen -W ' 0 1 2 3 ' -- $c ));;
+-fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 exp9 ' -- $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-acf) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_gyrate_compl g_gyrate
shopt -s extglob
_g_h2order_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -n -nm -s -o -h -X -nice -b -e -dt -w -d -sl' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -n -nm -s -o -h -nice -b -e -dt -w -d -sl' -- $c)); return 0; fi
case "$p" in
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-nm) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_h2order_compl g_h2order
shopt -s extglob
_g_hbond_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -g -sel -num -ac -dist -ang -hx -hbn -hbm -da -h -X -nice -b -e -dt -ins -a -r -abin -rbin -nonitacc -shell' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -g -sel -num -ac -dist -ang -hx -hbn -hbm -dan -h -nice -b -e -dt -ins -a -r -noda -abin -rbin -nonitacc -contact -shell -dump -max_hb -nomerge' -- $c)); return 0; fi
case "$p" in
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-g) COMPREPLY=( $(compgen -X '!*.log*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-sel) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-hx) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-hbn) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-hbm) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--da) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+-dan) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac }
complete -F _g_hbond_compl g_hbond
shopt -s extglob
_g_helix_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -s -n -f -to -cz -co -h -X -nice -b -e -dt -w -r0 -q -noF -db -ev -ahxstart -ahxend' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -s -n -f -to -cz -co -h -nice -b -e -dt -w -r0 -q -noF -db -ev -ahxstart -ahxend' -- $c)); return 0; fi
case "$p" in
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-to) COMPREPLY=( $(compgen -X '!*.g87*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--cz) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--co) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+-cz) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|xml|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-co) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|xml|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac }
complete -F _g_helix_compl g_helix
shopt -s extglob
_g_lie_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -o -h -X -nice -b -e -dt -w -Elj -Eqq -Clj -Cqq -ligand' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -o -h -nice -b -e -dt -w -Elj -Eqq -Clj -Cqq -ligand' -- $c)); return 0; fi
case "$p" in
-f) COMPREPLY=( $(compgen -X '!*.+(edr|ene)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_lie_compl g_lie
shopt -s extglob
_g_mdmat_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -mean -frames -no -h -X -nice -b -e -dt -t -nlevels' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -mean -frames -no -h -nice -b -e -dt -t -nlevels' -- $c)); return 0; fi
case "$p" in
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-mean) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-frames) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-no) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_mdmat_compl g_mdmat
shopt -s extglob
_g_mindist_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -od -on -o -h -X -nice -b -e -dt -w -matrix -d -pi' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -od -on -o -ox -or -h -nice -b -e -dt -tu -w -matrix -max -d -pi -split' -- $c)); return 0; fi
case "$p" in
+-tu) COMPREPLY=( $(compgen -W ' ps fs ns us ms s m h ' -- $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-od) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-on) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.out*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+-ox) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-or) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac }
complete -F _g_mindist_compl g_mindist
shopt -s extglob
_g_morph_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f1 -f2 -o -or -n -h -X -nice -w -ninterm -first -last -nofit' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f1 -f2 -o -or -n -h -nice -w -ninterm -first -last -nofit' -- $c)); return 0; fi
case "$p" in
--f1) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--f2) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-f1) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-f2) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-or) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_morph_compl g_morph
shopt -s extglob
_g_msd_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -o -mol -h -X -nice -b -e -dt -tu -w -type -lateral -ngroup -nomw -trestart -beginfit -endfit' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -o -mol -h -nice -b -e -dt -tu -w -type -lateral -ngroup -nomw -trestart -beginfit -endfit' -- $c)); return 0; fi
case "$p" in
-tu) COMPREPLY=( $(compgen -W ' ps fs ns us ms s m h ' -- $c ));;
-type) COMPREPLY=( $(compgen -W ' no x y z ' -- $c ));;
-lateral) COMPREPLY=( $(compgen -W ' no x y z ' -- $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-mol) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_msd_compl g_msd
shopt -s extglob
-_gmxcheck_compl() {
-local p c
-COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -f2 -s1 -s2 -c -e -e2 -h -X -nice -vdwfac -bonlo -bonhi -tol -lastener' -- $c)); return 0; fi
-case "$p" in
--f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--f2) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s1) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s2) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--c) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--e) COMPREPLY=( $(compgen -X '!*.+(edr|ene)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--e2) COMPREPLY=( $(compgen -X '!*.+(edr|ene)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
-complete -F _gmxcheck_compl gmxcheck
-shopt -s extglob
-_gmxdump_compl() {
-local p c
-COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -s -f -e -h -X -nice -nonr' -- $c)); return 0; fi
-case "$p" in
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--e) COMPREPLY=( $(compgen -X '!*.+(edr|ene)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
-complete -F _gmxdump_compl gmxdump
-shopt -s extglob
_g_nmeig_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -o -v -h -X -nice -nom -first -last' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -o -v -h -nice -nom -first -last' -- $c)); return 0; fi
case "$p" in
-f) COMPREPLY=( $(compgen -X '!*.mtx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-v) COMPREPLY=( $(compgen -X '!*.+(trr|trj)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_nmeig_compl g_nmeig
shopt -s extglob
_g_nmens_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -v -e -s -n -o -h -X -nice -temp -seed -num -first -last' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -v -e -s -n -o -h -nice -temp -seed -num -first -last' -- $c)); return 0; fi
case "$p" in
-v) COMPREPLY=( $(compgen -X '!*.+(trr|trj)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-e) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_nmens_compl g_nmens
shopt -s extglob
_g_order_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -n -s -o -od -os -h -X -nice -b -e -dt -w -d -sl -szonly -unsat' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -n -s -o -od -os -h -nice -b -e -dt -w -d -sl -szonly -unsat' -- $c)); return 0; fi
case "$p" in
-d) COMPREPLY=( $(compgen -W ' z x y ' -- $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-od) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-os) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_order_compl g_order
shopt -s extglob
_g_potential_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -n -s -o -oc -of -h -X -nice -b -e -dt -w -d -sl -cb -ce -tz -spherical' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -n -s -o -oc -of -h -nice -b -e -dt -w -d -sl -cb -ce -tz -spherical' -- $c)); return 0; fi
case "$p" in
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-oc) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-of) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_potential_compl g_potential
shopt -s extglob
_g_rama_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -o -h -X -nice -b -e -dt -w' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -o -h -nice -b -e -dt -w' -- $c)); return 0; fi
case "$p" in
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_rama_compl g_rama
shopt -s extglob
_g_rdf_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -o -sq -cn -hq -image -h -X -nice -b -e -dt -w -bin -com -cut -fade -grid -nlevel -wave' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -o -sq -cn -hq -h -nice -b -e -dt -w -bin -com -cut -fade -nlevel -startq -endq -energy' -- $c)); return 0; fi
case "$p" in
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-sq) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-cn) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-hq) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--image) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_rdf_compl g_rdf
shopt -s extglob
_g_rms_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -s -f -f2 -n -o -mir -a -dist -m -bin -bm -h -X -nice -b -e -dt -tu -w -what -nopbc -nofit -prev -split -skip -skip2 -max -min -bmax -bmin -nlevels' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -s -f -f2 -n -o -mir -a -dist -m -bin -bm -h -nice -b -e -dt -tu -w -what -nopbc -fit -prev -split -skip -skip2 -max -min -bmax -bmin -nlevels' -- $c)); return 0; fi
case "$p" in
-tu) COMPREPLY=( $(compgen -W ' ps fs ns us ms s m h ' -- $c ));;
-what) COMPREPLY=( $(compgen -W ' rmsd rho rhosc ' -- $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-fit) COMPREPLY=( $(compgen -W ' rot+trans translation none ' -- $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-f2) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-m) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-bin) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-bm) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_rms_compl g_rms
shopt -s extglob
_g_rmsdist_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -equiv -o -rms -scl -mean -nmr3 -nmr6 -noe -h -X -nice -b -e -dt -w -nlevels -max -nosumh' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -equiv -o -rms -scl -mean -nmr3 -nmr6 -noe -h -nice -b -e -dt -w -nlevels -max -nosumh' -- $c)); return 0; fi
case "$p" in
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-equiv) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-nmr3) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-nmr6) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-noe) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_rmsdist_compl g_rmsdist
shopt -s extglob
_g_rmsf_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -q -oq -ox -o -od -oc -dir -h -X -nice -b -e -dt -w -res -aniso' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -q -oq -ox -o -od -oc -dir -h -nice -b -e -dt -w -res -aniso' -- $c)); return 0; fi
case "$p" in
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-q) COMPREPLY=( $(compgen -X '!*.pdb*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-oq) COMPREPLY=( $(compgen -X '!*.pdb*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-od) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-oc) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-dir) COMPREPLY=( $(compgen -X '!*.log*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_rmsf_compl g_rmsf
shopt -s extglob
-_grompp_compl() {
-local p c
-COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -po -c -r -n -deshuf -p -pp -o -t -h -X -nice -nov -time -np -shuffle -sort -normdumbds -load -maxwarn -check14' -- $c)); return 0; fi
-case "$p" in
--f) COMPREPLY=( $(compgen -X '!*.mdp*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--po) COMPREPLY=( $(compgen -X '!*.mdp*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--c) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--r) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--deshuf) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--p) COMPREPLY=( $(compgen -X '!*.top*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--pp) COMPREPLY=( $(compgen -X '!*.top*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--o) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--t) COMPREPLY=( $(compgen -X '!*.+(trr|trj)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
-complete -F _grompp_compl grompp
-shopt -s extglob
_g_rotacf_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -o -h -X -nice -b -e -dt -w -d -noaver -acflen -nonormalize -P -fitfn -ncskip -beginfit -endfit' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -o -h -nice -b -e -dt -w -d -noaver -acflen -nonormalize -P -fitfn -ncskip -beginfit -endfit' -- $c)); return 0; fi
case "$p" in
-P) COMPREPLY=( $(compgen -W ' 0 1 2 3 ' -- $c ));;
--fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 ' -- $c ));;
+-fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 exp9 ' -- $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_rotacf_compl g_rotacf
shopt -s extglob
_g_saltbr_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -h -X -nice -b -e -dt -t -sep' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -h -nice -b -e -dt -t -sep' -- $c)); return 0; fi
case "$p" in
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac }
complete -F _g_saltbr_compl g_saltbr
shopt -s extglob
_g_sas_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -o -r -q -ao -n -i -h -X -nice -b -e -dt -w -solsize -ndots -qmax -minarea -skip -nopbc -noprot -dgs' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -o -or -oa -q -n -i -h -nice -b -e -dt -w -solsize -ndots -qmax -f_index -minarea -nopbc -noprot -dgs' -- $c)); return 0; fi
case "$p" in
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--r) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-or) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-oa) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-q) COMPREPLY=( $(compgen -X '!*.pdb*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--ao) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-i) COMPREPLY=( $(compgen -X '!*.itp*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_sas_compl g_sas
shopt -s extglob
_g_sgangle_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -n -s -oa -od -od1 -od2 -h -X -nice -b -e -dt -w' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -n -s -oa -od -od1 -od2 -h -nice -b -e -dt -w' -- $c)); return 0; fi
case "$p" in
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-oa) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-od) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-od1) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-od2) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_sgangle_compl g_sgangle
shopt -s extglob
_g_sorient_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -o -no -ro -co -h -X -nice -b -e -dt -w -com -rmin -rmax -nbin' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -o -no -ro -co -h -nice -b -e -dt -w -com -rmin -rmax -nbin -pbc' -- $c)); return 0; fi
case "$p" in
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-no) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-ro) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-co) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_sorient_compl g_sorient
shopt -s extglob
_g_tcaf_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -ot -oa -o -of -oc -ov -h -X -nice -b -e -dt -w -mol -k34 -wt' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -ot -oa -o -of -oc -ov -h -nice -b -e -dt -w -mol -k34 -wt' -- $c)); return 0; fi
case "$p" in
-f) COMPREPLY=( $(compgen -X '!*.+(trr|trj)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-ot) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-oa) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-of) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-oc) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-ov) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_tcaf_compl g_tcaf
shopt -s extglob
_g_traj_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -ox -ov -of -ob -ot -ekt -ekr -cv -cf -h -X -nice -b -e -dt -tu -w -com -mol -nojump -nox -noy -noz -len' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -ox -ov -of -ob -ot -ekt -ekr -cv -cf -h -nice -b -e -dt -tu -w -com -mol -nojump -nox -noy -noz -len -scale' -- $c)); return 0; fi
case "$p" in
-tu) COMPREPLY=( $(compgen -W ' ps fs ns us ms s m h ' -- $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-ox) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-ov) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-ekr) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-cv) COMPREPLY=( $(compgen -X '!*.pdb*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-cf) COMPREPLY=( $(compgen -X '!*.pdb*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_traj_compl g_traj
shopt -s extglob
_g_velacc_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -o -h -X -nice -b -e -dt -w -mol -acflen -nonormalize -P -fitfn -ncskip -beginfit -endfit' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -o -h -nice -b -e -dt -w -mol -acflen -nonormalize -P -fitfn -ncskip -beginfit -endfit' -- $c)); return 0; fi
case "$p" in
-P) COMPREPLY=( $(compgen -W ' 0 1 2 3 ' -- $c ));;
--fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 ' -- $c ));;
+-fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 exp9 ' -- $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(trr|trj)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _g_velacc_compl g_velacc
shopt -s extglob
+_g_wham_compl() {
+local p c
+COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -o -hist -h -nice -w -min -max -bins -noprof -temp -flip -tol' -- $c)); return 0; fi
+case "$p" in
+-o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-hist) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac }
+complete -F _g_wham_compl g_wham
+shopt -s extglob
+_genbox_compl() {
+local p c
+COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -cp -cs -ci -o -p -h -nice -box -nmol -try -seed -vdwd -shell' -- $c)); return 0; fi
+case "$p" in
+-cp) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-cs) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-ci) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-o) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|xml|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-p) COMPREPLY=( $(compgen -X '!*.top*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac }
+complete -F _genbox_compl genbox
+shopt -s extglob
+_genconf_compl() {
+local p c
+COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -o -trj -h -nice -nbox -dist -seed -rot -shuffle -sort -block -nmolat -maxrot -renumber' -- $c)); return 0; fi
+case "$p" in
+-f) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-o) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|xml|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-trj) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac }
+complete -F _genconf_compl genconf
+shopt -s extglob
+_genion_compl() {
+local p c
+COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -s -table -n -o -g -pot -h -nice -np -pname -pq -nn -nname -nq -rmin -random -seed -scale' -- $c)); return 0; fi
+case "$p" in
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-table) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-o) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|xml|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-g) COMPREPLY=( $(compgen -X '!*.log*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-pot) COMPREPLY=( $(compgen -X '!*.pdb*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac }
+complete -F _genion_compl genion
+shopt -s extglob
+_genpr_compl() {
+local p c
+COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -n -o -of -h -nice -fc -freeze' -- $c)); return 0; fi
+case "$p" in
+-f) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-o) COMPREPLY=( $(compgen -X '!*.itp*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-of) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac }
+complete -F _genpr_compl genpr
+shopt -s extglob
+_gmxcheck_compl() {
+local p c
+COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -f2 -s1 -s2 -c -e -e2 -h -nice -vdwfac -bonlo -bonhi -tol -lastener' -- $c)); return 0; fi
+case "$p" in
+-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-f2) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s1) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s2) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-c) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-e) COMPREPLY=( $(compgen -X '!*.+(edr|ene)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-e2) COMPREPLY=( $(compgen -X '!*.+(edr|ene)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac }
+complete -F _gmxcheck_compl gmxcheck
+shopt -s extglob
+_gmxdump_compl() {
+local p c
+COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -s -f -e -h -nice -nonr' -- $c)); return 0; fi
+case "$p" in
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-e) COMPREPLY=( $(compgen -X '!*.+(edr|ene)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac }
+complete -F _gmxdump_compl gmxdump
+shopt -s extglob
+_grompp_compl() {
+local p c
+COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -po -c -r -rb -n -deshuf -p -pp -o -t -e -h -nice -nov -time -np -shuffle -sort -normdumbds -load -maxwarn -check14 -norenum' -- $c)); return 0; fi
+case "$p" in
+-f) COMPREPLY=( $(compgen -X '!*.mdp*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-po) COMPREPLY=( $(compgen -X '!*.mdp*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-c) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-r) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-rb) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-deshuf) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-p) COMPREPLY=( $(compgen -X '!*.top*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-pp) COMPREPLY=( $(compgen -X '!*.top*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-o) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-t) COMPREPLY=( $(compgen -X '!*.+(trr|trj)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-e) COMPREPLY=( $(compgen -X '!*.+(edr|ene)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac }
+complete -F _grompp_compl grompp
+shopt -s extglob
_highway_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -a -h -X -nice -b -e -dt' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -a -h -nice -b -e -dt' -- $c)); return 0; fi
case "$p" in
-f) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-a) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _highway_compl highway
shopt -s extglob
_make_ndx_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -n -o -h -X -nice' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -n -o -h -nice -natoms -verbose' -- $c)); return 0; fi
case "$p" in
--f) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-f) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _make_ndx_compl make_ndx
shopt -s extglob
_mdrun_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -s -o -x -c -e -g -dgdl -table -rerun -ei -eo -j -jo -ffout -devout -runav -pi -po -pd -pn -mtx -h -X -nice -deffnm -np -v -nocompact -multi -glas -ionize' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -s -o -x -c -e -g -dgdl -field -table -rerun -ei -eo -j -jo -ffout -devout -runav -pi -po -pd -pn -mtx -dn -h -nice -deffnm -np -nt -v -nocompact -multi -glas -ionize' -- $c)); return 0; fi
case "$p" in
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.+(trr|trj)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-x) COMPREPLY=( $(compgen -X '!*.xtc*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--c) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-c) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|xml|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-e) COMPREPLY=( $(compgen -X '!*.+(edr|ene)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-g) COMPREPLY=( $(compgen -X '!*.log*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-dgdl) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-field) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-table) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-rerun) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-ei) COMPREPLY=( $(compgen -X '!*.edi*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-pd) COMPREPLY=( $(compgen -X '!*.pdo*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-pn) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-mtx) COMPREPLY=( $(compgen -X '!*.mtx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+-dn) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac }
complete -F _mdrun_compl mdrun
shopt -s extglob
_mk_angndx_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -s -n -h -X -nice -type' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -s -n -h -nice -type' -- $c)); return 0; fi
case "$p" in
-type) COMPREPLY=( $(compgen -W ' angle g96-angle dihedral improper ryckaert-bellemans phi-psi ' -- $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _mk_angndx_compl mk_angndx
shopt -s extglob
_ngmx_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -h -X -nice -b -e -dt' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -h -nice -b -e -dt' -- $c)); return 0; fi
case "$p" in
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _ngmx_compl ngmx
shopt -s extglob
_pdb2gmx_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -o -p -i -n -q -h -X -nice -merge -inter -ss -ter -lys -asp -glu -his -angle -dist -posrefc -una -nosort -H14 -ignh -alldih -dummy -heavyh -deuterate' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -o -p -i -n -q -h -nice -merge -ff -water -inter -ss -ter -lys -asp -glu -his -angle -dist -una -ignh -missing -posrefc -dummy -heavyh -deuterate' -- $c)); return 0; fi
case "$p" in
+-water) COMPREPLY=( $(compgen -W ' spc spce tip3p tip4p tip5p ' -- $c ));;
-dummy) COMPREPLY=( $(compgen -W ' none hydrogens aromatics ' -- $c ));;
--f) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--o) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-f) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-o) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|xml|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-p) COMPREPLY=( $(compgen -X '!*.top*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-i) COMPREPLY=( $(compgen -X '!*.itp*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--q) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+-q) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|xml|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac }
complete -F _pdb2gmx_compl pdb2gmx
shopt -s extglob
_protonate_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -s -f -n -o -h -X -nice -b -e -dt' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -s -f -n -o -h -nice -b -e -dt' -- $c)); return 0; fi
case "$p" in
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _protonate_compl protonate
shopt -s extglob
_tpbconv_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -s -f -n -o -h -X -nice -time -extend -until -zeroq -nounconstrained' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -s -f -e -n -o -h -nice -time -extend -until -zeroq -nounconstrained' -- $c)); return 0; fi
case "$p" in
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(trr|trj)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-e) COMPREPLY=( $(compgen -X '!*.+(edr|ene)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--o) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+-o) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac }
complete -F _tpbconv_compl tpbconv
shopt -s extglob
_trjcat_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -o -n -h -X -nice -tu -b -e -dt -prec -novel -settime -nosort -cat' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -o -n -h -nice -tu -b -e -dt -prec -novel -settime -nosort -keeplast -cat' -- $c)); return 0; fi
case "$p" in
-tu) COMPREPLY=( $(compgen -W ' ps fs ns us ms s m h ' -- $c ));;
+-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _trjcat_compl trjcat
shopt -s extglob
_trjconv_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -o -s -n -fr -h -X -nice -b -e -tu -w -skip -dt -dump -t0 -timestep -pbc -ur -center -box -shift -fit -pfit -ndec -novel -force -trunc -exec -app -split -sep' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -o -s -n -fr -h -nice -b -e -tu -w -skip -dt -dump -t0 -timestep -pbc -ur -center -box -shift -fit -ndec -novel -force -trunc -exec -app -split -sep -ter' -- $c)); return 0; fi
case "$p" in
-tu) COMPREPLY=( $(compgen -W ' ps fs ns us ms s m h ' -- $c ));;
--pbc) COMPREPLY=( $(compgen -W ' none whole inbox nojump ' -- $c ));;
+-pbc) COMPREPLY=( $(compgen -W ' none whole inbox nojump cluster com ' -- $c ));;
-ur) COMPREPLY=( $(compgen -W ' rect tric compact ' -- $c ));;
+-fit) COMPREPLY=( $(compgen -W ' none rot+trans translation progressive ' -- $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-fr) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _trjconv_compl trjconv
shopt -s extglob
_trjorder_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -o -h -X -nice -b -e -dt -na -da' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -o -h -nice -b -e -dt -na -da' -- $c)); return 0; fi
case "$p" in
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _trjorder_compl trjorder
shopt -s extglob
_wheel_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -o -h -X -nice -r0 -rot0 -T -nonn' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -o -h -nice -r0 -rot0 -T -nonn' -- $c)); return 0; fi
case "$p" in
-f) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.eps*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _wheel_compl wheel
shopt -s extglob
_x2top_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -o -r -h -X -nice -scale -nexcl -H14 -alldih -nopairs -name -nopbc -param -noround -kb -kt -kp' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -o -r -h -nice -scale -ff -nexcl -noH14 -alldih -remdih -nopairs -name -nopbc -param -noround -kb -kt -kp' -- $c)); return 0; fi
case "$p" in
--f) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-ff) COMPREPLY=( $(compgen -W ' G43a1 oplsaa gmx G43a2 G43b1 ' -- $c ));;
+-f) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.top*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-r) COMPREPLY=( $(compgen -X '!*.rtp*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _x2top_compl x2top
shopt -s extglob
_xpm2ps_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -f2 -di -do -o -xpm -h -X -nice -w -noframe -title -yonce -legend -diag -combine -bx -by -rainbow -gradient -skip -zeroline' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -f2 -di -do -o -xpm -h -nice -w -noframe -title -yonce -legend -diag -combine -bx -by -rainbow -gradient -skip -zeroline -legoffset' -- $c)); return 0; fi
case "$p" in
-title) COMPREPLY=( $(compgen -W ' top once ylabel none ' -- $c ));;
-legend) COMPREPLY=( $(compgen -W ' both first second none ' -- $c ));;
-do) COMPREPLY=( $(compgen -X '!*.m2p*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.eps*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-xpm) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+esac }
complete -F _xpm2ps_compl xpm2ps
shopt -s extglob
_xrama_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -h -X -nice -b -e -dt' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -h -nice -b -e -dt' -- $c)); return 0; fi
case "$p" in
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac; };
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|xml)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac }
complete -F _xrama_compl xrama
-complete do_dssp "n/-tu/( ps fs ns us ms s m h)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-ssdump/f:*.dat{,.gz,.Z}/" "n/-map/f:*.map{,.gz,.Z}/" "n/-o/f:*.xpm{,.gz,.Z}/" "n/-sc/f:*.xvg{,.gz,.Z}/" "n/-a/f:*.xpm{,.gz,.Z}/" "n/-ta/f:*.xvg{,.gz,.Z}/" "n/-aa/f:*.xvg{,.gz,.Z}/" "c/-/( f s n ssdump map o sc a ta aa h X nice b e dt tu w sss)/"
-complete editconf "n/-bt/( tric cubic dodecahedron octahedron)/" "n/-f/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-bf/f:*.dat{,.gz,.Z}/" "c/-/( f n o bf h X nice w ndef bt box angles d c center rotate princ scale density pbc mead grasp rvdw atom legend label)/"
-complete eneconv "n/-f/f:*.{edr,ene}{,.gz,.Z}/" "n/-o/f:*.{edr,ene}{,.gz,.Z}/" "c/-/( f o h X nice b e dt offset settime nosort scalefac noerror)/"
-complete ffscan "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "n/-table/f:*.xvg{,.gz,.Z}/" "n/-parm/f:*.dat{,.gz,.Z}/" "n/-ga/f:*.dat{,.gz,.Z}/" "c/-/( s g table parm ga h X nice tol fmax epot nocomb npow ratio logeps nov)/"
-complete g_anaeig "n/-tu/( ps fs ns us ms s m h)/" "n/-v/f:*.{trr,trj}{,.gz,.Z}/" "n/-v2/f:*.{trr,trj}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-eig1/f:*.xvg{,.gz,.Z}/" "n/-eig2/f:*.xvg{,.gz,.Z}/" "n/-disp/f:*.xvg{,.gz,.Z}/" "n/-proj/f:*.xvg{,.gz,.Z}/" "n/-2d/f:*.xvg{,.gz,.Z}/" "n/-3d/f:*.{gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-filt/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-extr/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-over/f:*.xvg{,.gz,.Z}/" "n/-inpr/f:*.xpm{,.gz,.Z}/" "c/-/( v v2 f s n eig1 eig2 disp proj 2d 3d filt extr over inpr h X nice b e dt tu w first last skip max nframes split)/"
-complete g_analyze "n/-errbar/( none stddev error 90)/" "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7)/" "n/-f/f:*.xvg{,.gz,.Z}/" "n/-ac/f:*.xvg{,.gz,.Z}/" "n/-msd/f:*.xvg{,.gz,.Z}/" "n/-cc/f:*.xvg{,.gz,.Z}/" "n/-dist/f:*.xvg{,.gz,.Z}/" "n/-av/f:*.xvg{,.gz,.Z}/" "n/-ee/f:*.xvg{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "c/-/( f ac msd cc dist av ee g h X nice w notime b e n d bw errbar power nosubav oneacf acflen nonormalize P fitfn ncskip beginfit endfit)/"
-complete g_angle "n/-type/( angle dihedral improper ryckaert-bellemans)/" "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-od/f:*.xvg{,.gz,.Z}/" "n/-ov/f:*.xvg{,.gz,.Z}/" "n/-of/f:*.xvg{,.gz,.Z}/" "n/-ot/f:*.xvg{,.gz,.Z}/" "n/-oh/f:*.xvg{,.gz,.Z}/" "n/-oc/f:*.xvg{,.gz,.Z}/" "c/-/( f s n od ov of ot oh oc h X nice b e dt w type all binwidth chandler avercorr acflen nonormalize P fitfn ncskip beginfit endfit)/"
-complete g_bond "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-l/f:*.log{,.gz,.Z}/" "n/-d/f:*.xvg{,.gz,.Z}/" "c/-/( f n s o l d h X nice b e dt w blen tol noaver)/"
-complete g_bundle "n/-tu/( ps fs ns us ms s m h)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-ol/f:*.xvg{,.gz,.Z}/" "n/-od/f:*.xvg{,.gz,.Z}/" "n/-oz/f:*.xvg{,.gz,.Z}/" "n/-ot/f:*.xvg{,.gz,.Z}/" "n/-otr/f:*.xvg{,.gz,.Z}/" "n/-otl/f:*.xvg{,.gz,.Z}/" "n/-ok/f:*.xvg{,.gz,.Z}/" "n/-okr/f:*.xvg{,.gz,.Z}/" "n/-okl/f:*.xvg{,.gz,.Z}/" "n/-oa/f:*.pdb{,.gz,.Z}/" "c/-/( f s n ol od oz ot otr otl ok okr okl oa h X nice b e dt tu na z)/"
-complete g_chi "n/-maxchi/( 0 1 2 3 4 5 6)/" "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7)/" "n/-c/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-p/f:*.pdb{,.gz,.Z}/" "n/-ss/f:*.dat{,.gz,.Z}/" "n/-jc/f:*.xvg{,.gz,.Z}/" "n/-corr/f:*.xvg{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "c/-/( c f o p ss jc corr g h X nice b e dt w r0 phi psi omega rama viol all shift run maxchi nonormhisto ramomega bfact bmax acflen nonormalize P fitfn ncskip beginfit endfit)/"
-complete g_cluster "n/-tu/( ps fs ns us ms s m h)/" "n/-method/( linkage jarvis-patrick monte-carlo diagonalization gromos)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-dm/f:*.xpm{,.gz,.Z}/" "n/-o/f:*.xpm{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "n/-dist/f:*.xvg{,.gz,.Z}/" "n/-ev/f:*.xvg{,.gz,.Z}/" "n/-sz/f:*.xvg{,.gz,.Z}/" "n/-tr/f:*.xpm{,.gz,.Z}/" "n/-ntr/f:*.xvg{,.gz,.Z}/" "n/-clid/f:*.xvg{,.gz,.Z}/" "n/-cl/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "c/-/( f s n dm o g dist ev sz tr ntr clid cl h X nice b e dt tu w dista nlevels keepfree cutoff nofit max skip av wcl nst rmsmin method binary M P seed niter kT)/"
-complete g_clustsize "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xpm{,.gz,.Z}/" "n/-nc/f:*.xvg{,.gz,.Z}/" "n/-mc/f:*.xvg{,.gz,.Z}/" "n/-ac/f:*.xvg{,.gz,.Z}/" "c/-/( f n o nc mc ac h X nice b e dt w cut nskip nlevels rgblo rgbhi)/"
-complete g_confrms "n/-f1/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-f2/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n1/f:*.ndx{,.gz,.Z}/" "n/-n2/f:*.ndx{,.gz,.Z}/" "c/-/( f1 f2 o n1 n2 h X nice one pbc)/"
-complete g_covar "n/-tu/( ps fs ns us ms s m h)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-v/f:*.{trr,trj}{,.gz,.Z}/" "n/-av/f:*.{gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-l/f:*.log{,.gz,.Z}/" "n/-xpm/f:*.xpm{,.gz,.Z}/" "n/-xpma/f:*.xpm{,.gz,.Z}/" "c/-/( f s n o v av l xpm xpma h X nice b e dt tu nofit ref mwa last)/"
-complete g_density "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-ei/f:*.dat{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "c/-/( f n s ei o h X nice b e dt w d sl number ed count)/"
-complete g_dielectric "n/-ffn/( none exp aexp exp_exp vac exp5 exp7)/" "n/-f/f:*.xvg{,.gz,.Z}/" "n/-d/f:*.xvg{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-c/f:*.xvg{,.gz,.Z}/" "c/-/( f d o c h X nice b e dt w fft nox1 eint bfit efit tail A tau1 tau2 eps0 epsRF fix ffn nsmooth)/"
-complete g_dih "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.out{,.gz,.Z}/" "c/-/( f s o h X nice b e dt w sa mult)/"
-complete g_dipoles "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7)/" "n/-enx/f:*.{edr,ene}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-e/f:*.xvg{,.gz,.Z}/" "n/-a/f:*.xvg{,.gz,.Z}/" "n/-d/f:*.xvg{,.gz,.Z}/" "n/-c/f:*.xvg{,.gz,.Z}/" "n/-g/f:*.xvg{,.gz,.Z}/" "n/-q/f:*.xvg{,.gz,.Z}/" "c/-/( enx f s n o e a d c g q h X nice b e dt w mu mumax epsilonRF skip temp avercorr gkratom acflen nonormalize P fitfn ncskip beginfit endfit)/"
-complete g_disre "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-ds/f:*.xvg{,.gz,.Z}/" "n/-da/f:*.xvg{,.gz,.Z}/" "n/-dn/f:*.xvg{,.gz,.Z}/" "n/-dm/f:*.xvg{,.gz,.Z}/" "n/-dr/f:*.xvg{,.gz,.Z}/" "n/-l/f:*.log{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "c/-/( s f ds da dn dm dr l n h X nice b e dt w ntop)/"
-complete g_dist "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "c/-/( f s n o h X nice b e dt dist)/"
-complete g_dyndom "n/-f/f:*.pdb{,.gz,.Z}/" "n/-o/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "c/-/( f o n h X nice firstangle lastangle nframe maxangle trans head tail)/"
-complete genbox "n/-cp/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-cs/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-ci/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-p/f:*.top{,.gz,.Z}/" "c/-/( cp cs ci o p h X nice box nmol try seed vdwd shell)/"
-complete genconf "n/-f/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-trj/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "c/-/( f o trj h X nice nbox dist seed rot shuffle sort block nmolat maxrot renumber)/"
-complete g_enemat "n/-f/f:*.{edr,ene}{,.gz,.Z}/" "n/-groups/f:*.dat{,.gz,.Z}/" "n/-eref/f:*.dat{,.gz,.Z}/" "n/-emat/f:*.xpm{,.gz,.Z}/" "n/-etot/f:*.xvg{,.gz,.Z}/" "c/-/( f groups eref emat etot h X nice b e dt w sum skip nomean nlevels max min nocoul coulr coul14 nolj lj14 bham nofree temp)/"
-complete g_energy "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7)/" "n/-f/f:*.{edr,ene}{,.gz,.Z}/" "n/-f2/f:*.{edr,ene}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-viol/f:*.xvg{,.gz,.Z}/" "n/-pairs/f:*.xvg{,.gz,.Z}/" "n/-ora/f:*.xvg{,.gz,.Z}/" "n/-ort/f:*.xvg{,.gz,.Z}/" "n/-oda/f:*.xvg{,.gz,.Z}/" "n/-odr/f:*.xvg{,.gz,.Z}/" "n/-odt/f:*.xvg{,.gz,.Z}/" "n/-corr/f:*.xvg{,.gz,.Z}/" "n/-vis/f:*.xvg{,.gz,.Z}/" "n/-ravg/f:*.xvg{,.gz,.Z}/" "c/-/( f f2 s o viol pairs ora ort oda odr odt corr vis ravg h X nice b e w fee fetemp zero sum dp mutot skip aver nmol ndf fluc orinst acflen nonormalize P fitfn ncskip beginfit endfit)/"
-complete genion "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "n/-pot/f:*.pdb{,.gz,.Z}/" "c/-/( s n o g pot h X nice np pname pq nn nname nq rmin random seed)/"
-complete genpr "n/-f/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.itp{,.gz,.Z}/" "c/-/( f n o h X nice fc)/"
-complete g_gyrate "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "c/-/( f s o n h X nice b e dt w q p)/"
-complete g_h2order "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-nm/f:*.ndx{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "c/-/( f n nm s o h X nice b e dt w d sl)/"
-complete g_hbond "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "n/-sel/f:*.ndx{,.gz,.Z}/" "n/-num/f:*.xvg{,.gz,.Z}/" "n/-ac/f:*.xvg{,.gz,.Z}/" "n/-dist/f:*.xvg{,.gz,.Z}/" "n/-ang/f:*.xvg{,.gz,.Z}/" "n/-hx/f:*.xvg{,.gz,.Z}/" "n/-hbn/f:*.ndx{,.gz,.Z}/" "n/-hbm/f:*.xpm{,.gz,.Z}/" "n/-da/f:*.xvg{,.gz,.Z}/" "c/-/( f s n g sel num ac dist ang hx hbn hbm da h X nice b e dt ins a r abin rbin nonitacc shell)/"
-complete g_helix "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-to/f:*.g87{,.gz,.Z}/" "n/-cz/f:*.{gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-co/f:*.{gro,g96,pdb,brk,ent}{,.gz,.Z}/" "c/-/( s n f to cz co h X nice b e dt w r0 q noF db ev ahxstart ahxend)/"
-complete g_lie "n/-f/f:*.{edr,ene}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "c/-/( f o h X nice b e dt w Elj Eqq Clj Cqq ligand)/"
-complete g_mdmat "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-mean/f:*.xpm{,.gz,.Z}/" "n/-frames/f:*.xpm{,.gz,.Z}/" "n/-no/f:*.xvg{,.gz,.Z}/" "c/-/( f s n mean frames no h X nice b e dt t nlevels)/"
-complete g_mindist "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-od/f:*.xvg{,.gz,.Z}/" "n/-on/f:*.xvg{,.gz,.Z}/" "n/-o/f:*.out{,.gz,.Z}/" "c/-/( f s n od on o h X nice b e dt w matrix d pi)/"
-complete g_morph "n/-f1/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-f2/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-or/f:*.xvg{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "c/-/( f1 f2 o or n h X nice w ninterm first last nofit)/"
-complete g_msd "n/-tu/( ps fs ns us ms s m h)/" "n/-type/( no x y z)/" "n/-lateral/( no x y z)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-mol/f:*.xvg{,.gz,.Z}/" "c/-/( f s n o mol h X nice b e dt tu w type lateral ngroup nomw trestart beginfit endfit)/"
-complete gmxcheck "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-f2/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s1/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-s2/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-c/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-e/f:*.{edr,ene}{,.gz,.Z}/" "n/-e2/f:*.{edr,ene}{,.gz,.Z}/" "c/-/( f f2 s1 s2 c e e2 h X nice vdwfac bonlo bonhi tol lastener)/"
-complete gmxdump "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-e/f:*.{edr,ene}{,.gz,.Z}/" "c/-/( s f e h X nice nonr)/"
-complete g_nmeig "n/-f/f:*.mtx{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-v/f:*.{trr,trj}{,.gz,.Z}/" "c/-/( f s o v h X nice nom first last)/"
-complete g_nmens "n/-v/f:*.{trr,trj}{,.gz,.Z}/" "n/-e/f:*.xvg{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "c/-/( v e s n o h X nice temp seed num first last)/"
-complete g_order "n/-d/( z x y)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-od/f:*.xvg{,.gz,.Z}/" "n/-os/f:*.xvg{,.gz,.Z}/" "c/-/( f n s o od os h X nice b e dt w d sl szonly unsat)/"
-complete g_potential "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-oc/f:*.xvg{,.gz,.Z}/" "n/-of/f:*.xvg{,.gz,.Z}/" "c/-/( f n s o oc of h X nice b e dt w d sl cb ce tz spherical)/"
-complete g_rama "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "c/-/( f s o h X nice b e dt w)/"
-complete g_rdf "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-sq/f:*.xvg{,.gz,.Z}/" "n/-cn/f:*.xvg{,.gz,.Z}/" "n/-hq/f:*.xvg{,.gz,.Z}/" "n/-image/f:*.xpm{,.gz,.Z}/" "c/-/( f s n o sq cn hq image h X nice b e dt w bin com cut fade grid nlevel wave)/"
-complete g_rms "n/-tu/( ps fs ns us ms s m h)/" "n/-what/( rmsd rho rhosc)/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-f2/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-mir/f:*.xvg{,.gz,.Z}/" "n/-a/f:*.xvg{,.gz,.Z}/" "n/-dist/f:*.xvg{,.gz,.Z}/" "n/-m/f:*.xpm{,.gz,.Z}/" "n/-bin/f:*.dat{,.gz,.Z}/" "n/-bm/f:*.xpm{,.gz,.Z}/" "c/-/( s f f2 n o mir a dist m bin bm h X nice b e dt tu w what nopbc nofit prev split skip skip2 max min bmax bmin nlevels)/"
-complete g_rmsdist "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-equiv/f:*.dat{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-rms/f:*.xpm{,.gz,.Z}/" "n/-scl/f:*.xpm{,.gz,.Z}/" "n/-mean/f:*.xpm{,.gz,.Z}/" "n/-nmr3/f:*.xpm{,.gz,.Z}/" "n/-nmr6/f:*.xpm{,.gz,.Z}/" "n/-noe/f:*.dat{,.gz,.Z}/" "c/-/( f s n equiv o rms scl mean nmr3 nmr6 noe h X nice b e dt w nlevels max nosumh)/"
-complete g_rmsf "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-q/f:*.pdb{,.gz,.Z}/" "n/-oq/f:*.pdb{,.gz,.Z}/" "n/-ox/f:*.pdb{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-od/f:*.xvg{,.gz,.Z}/" "n/-oc/f:*.xvg{,.gz,.Z}/" "n/-dir/f:*.log{,.gz,.Z}/" "c/-/( f s n q oq ox o od oc dir h X nice b e dt w res aniso)/"
-complete grompp "n/-f/f:*.mdp{,.gz,.Z}/" "n/-po/f:*.mdp{,.gz,.Z}/" "n/-c/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-r/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-deshuf/f:*.ndx{,.gz,.Z}/" "n/-p/f:*.top{,.gz,.Z}/" "n/-pp/f:*.top{,.gz,.Z}/" "n/-o/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-t/f:*.{trr,trj}{,.gz,.Z}/" "c/-/( f po c r n deshuf p pp o t h X nice nov time np shuffle sort normdumbds load maxwarn check14)/"
-complete g_rotacf "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "c/-/( f s n o h X nice b e dt w d noaver acflen nonormalize P fitfn ncskip beginfit endfit)/"
-complete g_saltbr "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "c/-/( f s h X nice b e dt t sep)/"
-complete g_sas "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-r/f:*.xvg{,.gz,.Z}/" "n/-q/f:*.pdb{,.gz,.Z}/" "n/-ao/f:*.xvg{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-i/f:*.itp{,.gz,.Z}/" "c/-/( f s o r q ao n i h X nice b e dt w solsize ndots qmax minarea skip nopbc noprot dgs)/"
-complete g_sgangle "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-oa/f:*.xvg{,.gz,.Z}/" "n/-od/f:*.xvg{,.gz,.Z}/" "n/-od1/f:*.xvg{,.gz,.Z}/" "n/-od2/f:*.xvg{,.gz,.Z}/" "c/-/( f n s oa od od1 od2 h X nice b e dt w)/"
-complete g_sorient "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-no/f:*.xvg{,.gz,.Z}/" "n/-ro/f:*.xvg{,.gz,.Z}/" "n/-co/f:*.xvg{,.gz,.Z}/" "c/-/( f s n o no ro co h X nice b e dt w com rmin rmax nbin)/"
-complete g_tcaf "n/-f/f:*.{trr,trj}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-ot/f:*.xvg{,.gz,.Z}/" "n/-oa/f:*.xvg{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-of/f:*.xvg{,.gz,.Z}/" "n/-oc/f:*.xvg{,.gz,.Z}/" "n/-ov/f:*.xvg{,.gz,.Z}/" "c/-/( f s n ot oa o of oc ov h X nice b e dt w mol k34 wt)/"
-complete g_traj "n/-tu/( ps fs ns us ms s m h)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-ox/f:*.xvg{,.gz,.Z}/" "n/-ov/f:*.xvg{,.gz,.Z}/" "n/-of/f:*.xvg{,.gz,.Z}/" "n/-ob/f:*.xvg{,.gz,.Z}/" "n/-ot/f:*.xvg{,.gz,.Z}/" "n/-ekt/f:*.xvg{,.gz,.Z}/" "n/-ekr/f:*.xvg{,.gz,.Z}/" "n/-cv/f:*.pdb{,.gz,.Z}/" "n/-cf/f:*.pdb{,.gz,.Z}/" "c/-/( f s n ox ov of ob ot ekt ekr cv cf h X nice b e dt tu w com mol nojump nox noy noz len)/"
-complete g_velacc "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7)/" "n/-f/f:*.{trr,trj}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "c/-/( f s n o h X nice b e dt w mol acflen nonormalize P fitfn ncskip beginfit endfit)/"
-complete highway "n/-f/f:*.dat{,.gz,.Z}/" "n/-a/f:*.dat{,.gz,.Z}/" "c/-/( f a h X nice b e dt)/"
-complete make_ndx "n/-f/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.ndx{,.gz,.Z}/" "c/-/( f n o h X nice)/"
-complete mdrun "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.{trr,trj}{,.gz,.Z}/" "n/-x/f:*.xtc{,.gz,.Z}/" "n/-c/f:*.{gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-e/f:*.{edr,ene}{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "n/-dgdl/f:*.xvg{,.gz,.Z}/" "n/-table/f:*.xvg{,.gz,.Z}/" "n/-rerun/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-ei/f:*.edi{,.gz,.Z}/" "n/-eo/f:*.edo{,.gz,.Z}/" "n/-j/f:*.gct{,.gz,.Z}/" "n/-jo/f:*.gct{,.gz,.Z}/" "n/-ffout/f:*.xvg{,.gz,.Z}/" "n/-devout/f:*.xvg{,.gz,.Z}/" "n/-runav/f:*.xvg{,.gz,.Z}/" "n/-pi/f:*.ppa{,.gz,.Z}/" "n/-po/f:*.ppa{,.gz,.Z}/" "n/-pd/f:*.pdo{,.gz,.Z}/" "n/-pn/f:*.ndx{,.gz,.Z}/" "n/-mtx/f:*.mtx{,.gz,.Z}/" "c/-/( s o x c e g dgdl table rerun ei eo j jo ffout devout runav pi po pd pn mtx h X nice deffnm np v nocompact multi glas ionize)/"
-complete mk_angndx "n/-type/( angle g96-angle dihedral improper ryckaert-bellemans phi-psi)/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "c/-/( s n h X nice type)/"
-complete ngmx "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "c/-/( f s n h X nice b e dt)/"
-complete pdb2gmx "n/-dummy/( none hydrogens aromatics)/" "n/-f/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-p/f:*.top{,.gz,.Z}/" "n/-i/f:*.itp{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-q/f:*.{gro,g96,pdb,brk,ent}{,.gz,.Z}/" "c/-/( f o p i n q h X nice merge inter ss ter lys asp glu his angle dist posrefc una nosort H14 ignh alldih dummy heavyh deuterate)/"
-complete protonate "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "c/-/( s f n o h X nice b e dt)/"
-complete tpbconv "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-f/f:*.{trr,trj}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "c/-/( s f n o h X nice time extend until zeroq nounconstrained)/"
-complete trjcat "n/-tu/( ps fs ns us ms s m h)/" "n/-o/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "c/-/( o n h X nice tu b e dt prec novel settime nosort cat)/"
-complete trjconv "n/-tu/( ps fs ns us ms s m h)/" "n/-pbc/( none whole inbox nojump)/" "n/-ur/( rect tric compact)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-o/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-fr/f:*.ndx{,.gz,.Z}/" "c/-/( f o s n fr h X nice b e tu w skip dt dump t0 timestep pbc ur center box shift fit pfit ndec novel force trunc exec app split sep)/"
-complete trjorder "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "c/-/( f s n o h X nice b e dt na da)/"
-complete wheel "n/-f/f:*.dat{,.gz,.Z}/" "n/-o/f:*.eps{,.gz,.Z}/" "c/-/( f o h X nice r0 rot0 T nonn)/"
-complete x2top "n/-f/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.top{,.gz,.Z}/" "n/-r/f:*.rtp{,.gz,.Z}/" "c/-/( f o r h X nice scale nexcl H14 alldih nopairs name nopbc param noround kb kt kp)/"
-complete xpm2ps "n/-title/( top once ylabel none)/" "n/-legend/( both first second none)/" "n/-diag/( first second none)/" "n/-combine/( halves add sub mult div)/" "n/-rainbow/( no blue red)/" "n/-f/f:*.xpm{,.gz,.Z}/" "n/-f2/f:*.xpm{,.gz,.Z}/" "n/-di/f:*.m2p{,.gz,.Z}/" "n/-do/f:*.m2p{,.gz,.Z}/" "n/-o/f:*.eps{,.gz,.Z}/" "n/-xpm/f:*.xpm{,.gz,.Z}/" "c/-/( f f2 di do o xpm h X nice w noframe title yonce legend diag combine bx by rainbow gradient skip zeroline)/"
-complete xrama "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "c/-/( f s h X nice b e dt)/"
+complete anadock "n/-f/f:*.pdb{,.gz,.Z}/" "n/-ox/f:*.pdb{,.gz,.Z}/" "n/-od/f:*.xvg{,.gz,.Z}/" "n/-of/f:*.xvg{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "c/-/( f ox od of g h nice free norms cutoff)/"
+complete cdist "n/-sm/( none tri tetra)/" "n/-s/f:*.{tpr,tpb,tpa,xml,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "n/-q/f:*.pdb{,.gz,.Z}/" "n/-d/f:*.dat{,.gz,.Z}/" "n/-o/f:*.dat{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-dom/f:*.ndx{,.gz,.Z}/" "c/-/( s g q d o n dom h nice noengh bm am pm rr ar er vm lm il dm im nm hm hb nobon nonb measure maxdist add vir sm)/"
+complete disco "n/-g/f:*.log{,.gz,.Z}/" "n/-f/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-d/f:*.dat{,.gz,.Z}/" "n/-do/f:*.dat{,.gz,.Z}/" "n/-c/f:*.{gro,g96,pdb,brk,xml,ent}{,.gz,.Z}/" "n/-center/f:*.{gro,g96,pdb,brk,xml,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-keep/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-viol/f:*.pdb{,.gz,.Z}/" "c/-/( g f d do c center n o keep viol h nice nf nit nov nochiral nopep lower weighted dump cubic explicit fit nbcheck nstprint ranlist noranlistfirst lowdev seed box grow)/"
+complete do_dssp "n/-tu/( ps fs ns us ms s m h)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-ssdump/f:*.dat{,.gz,.Z}/" "n/-map/f:*.map{,.gz,.Z}/" "n/-o/f:*.xpm{,.gz,.Z}/" "n/-sc/f:*.xvg{,.gz,.Z}/" "n/-a/f:*.xpm{,.gz,.Z}/" "n/-ta/f:*.xvg{,.gz,.Z}/" "n/-aa/f:*.xvg{,.gz,.Z}/" "c/-/( f s n ssdump map o sc a ta aa h nice b e dt tu w sss)/"
+complete editconf "n/-bt/( tric cubic dodecahedron octahedron)/" "n/-f/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,xml,ent}{,.gz,.Z}/" "n/-bf/f:*.dat{,.gz,.Z}/" "c/-/( f n o bf h nice w ndef bt box angles d c center translate rotate princ scale density novol pbc mead grasp rvdw atom legend label)/"
+complete eneconv "n/-f/f:*.{edr,ene}{,.gz,.Z}/" "n/-o/f:*.{edr,ene}{,.gz,.Z}/" "c/-/( f o h nice b e dt offset settime nosort scalefac noerror)/"
+complete ffscan "n/-s/f:*.{tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "n/-table/f:*.xvg{,.gz,.Z}/" "n/-parm/f:*.dat{,.gz,.Z}/" "n/-ga/f:*.dat{,.gz,.Z}/" "n/-c/f:*.gro{,.gz,.Z}/" "n/-e/f:*.{edr,ene}{,.gz,.Z}/" "n/-o/f:*.{trr,trj}{,.gz,.Z}/" "c/-/( s g table parm ga c e o h nice tol fmax nocomb npow logeps v epot fepot pres fpres fmsf molsize nmol)/"
+complete g_anaeig "n/-tu/( ps fs ns us ms s m h)/" "n/-v/f:*.{trr,trj}{,.gz,.Z}/" "n/-v2/f:*.{trr,trj}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-eig/f:*.xvg{,.gz,.Z}/" "n/-eig2/f:*.xvg{,.gz,.Z}/" "n/-comp/f:*.xvg{,.gz,.Z}/" "n/-rmsf/f:*.xvg{,.gz,.Z}/" "n/-proj/f:*.xvg{,.gz,.Z}/" "n/-2d/f:*.xvg{,.gz,.Z}/" "n/-3d/f:*.{gro,g96,pdb,brk,xml,ent}{,.gz,.Z}/" "n/-filt/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-extr/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-over/f:*.xvg{,.gz,.Z}/" "n/-inpr/f:*.xpm{,.gz,.Z}/" "c/-/( v v2 f s n eig eig2 comp rmsf proj 2d 3d filt extr over inpr h nice b e dt tu w first last skip max nframes split)/"
+complete g_analyze "n/-errbar/( none stddev error 90)/" "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7 exp9)/" "n/-f/f:*.xvg{,.gz,.Z}/" "n/-ac/f:*.xvg{,.gz,.Z}/" "n/-msd/f:*.xvg{,.gz,.Z}/" "n/-cc/f:*.xvg{,.gz,.Z}/" "n/-dist/f:*.xvg{,.gz,.Z}/" "n/-av/f:*.xvg{,.gz,.Z}/" "n/-ee/f:*.xvg{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "c/-/( f ac msd cc dist av ee g h nice w notime b e n d bw errbar filter power nosubav oneacf acflen nonormalize P fitfn ncskip beginfit endfit)/"
+complete g_angle "n/-type/( angle dihedral improper ryckaert-bellemans)/" "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7 exp9)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-od/f:*.xvg{,.gz,.Z}/" "n/-ov/f:*.xvg{,.gz,.Z}/" "n/-of/f:*.xvg{,.gz,.Z}/" "n/-ot/f:*.xvg{,.gz,.Z}/" "n/-oh/f:*.xvg{,.gz,.Z}/" "n/-oc/f:*.xvg{,.gz,.Z}/" "c/-/( f s n od ov of ot oh oc h nice b e dt w type all binwidth chandler avercorr acflen nonormalize P fitfn ncskip beginfit endfit)/"
+complete g_bond "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-l/f:*.log{,.gz,.Z}/" "n/-d/f:*.xvg{,.gz,.Z}/" "c/-/( f n s o l d h nice b e dt w blen tol noaver noaverdist)/"
+complete g_bundle "n/-tu/( ps fs ns us ms s m h)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-ol/f:*.xvg{,.gz,.Z}/" "n/-od/f:*.xvg{,.gz,.Z}/" "n/-oz/f:*.xvg{,.gz,.Z}/" "n/-ot/f:*.xvg{,.gz,.Z}/" "n/-otr/f:*.xvg{,.gz,.Z}/" "n/-otl/f:*.xvg{,.gz,.Z}/" "n/-ok/f:*.xvg{,.gz,.Z}/" "n/-okr/f:*.xvg{,.gz,.Z}/" "n/-okl/f:*.xvg{,.gz,.Z}/" "n/-oa/f:*.pdb{,.gz,.Z}/" "c/-/( f s n ol od oz ot otr otl ok okr okl oa h nice b e dt tu na z)/"
+complete g_chi "n/-maxchi/( 0 1 2 3 4 5 6)/" "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7 exp9)/" "n/-s/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-p/f:*.pdb{,.gz,.Z}/" "n/-ss/f:*.dat{,.gz,.Z}/" "n/-jc/f:*.xvg{,.gz,.Z}/" "n/-corr/f:*.xvg{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "n/-ot/f:*.xvg{,.gz,.Z}/" "n/-oh/f:*.xvg{,.gz,.Z}/" "n/-rt/f:*.xvg{,.gz,.Z}/" "n/-cp/f:*.xvg{,.gz,.Z}/" "c/-/( s f o p ss jc corr g ot oh rt cp h nice b e dt w r0 phi psi omega rama viol all rad shift binwidth core_rotamer maxchi nonormhisto ramomega bfact chi_prod HChi bmax acflen nonormalize P fitfn ncskip beginfit endfit)/"
+complete g_cluster "n/-tu/( ps fs ns us ms s m h)/" "n/-method/( linkage jarvis-patrick monte-carlo diagonalization gromos)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-dm/f:*.xpm{,.gz,.Z}/" "n/-o/f:*.xpm{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "n/-dist/f:*.xvg{,.gz,.Z}/" "n/-ev/f:*.xvg{,.gz,.Z}/" "n/-sz/f:*.xvg{,.gz,.Z}/" "n/-tr/f:*.xpm{,.gz,.Z}/" "n/-ntr/f:*.xvg{,.gz,.Z}/" "n/-clid/f:*.xvg{,.gz,.Z}/" "n/-cl/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "c/-/( f s n dm o g dist ev sz tr ntr clid cl h nice b e dt tu w dista nlevels keepfree cutoff nofit max skip av wcl nst rmsmin method minstruct binary M P seed niter kT)/"
+complete g_clustsize "n/-tu/( ps fs ns us ms s m h)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.tpr{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xpm{,.gz,.Z}/" "n/-ow/f:*.xpm{,.gz,.Z}/" "n/-nc/f:*.xvg{,.gz,.Z}/" "n/-mc/f:*.xvg{,.gz,.Z}/" "n/-ac/f:*.xvg{,.gz,.Z}/" "n/-hc/f:*.xvg{,.gz,.Z}/" "c/-/( f s n o ow nc mc ac hc h nice b e dt tu w cut mol nskip nlevels rgblo rgbhi)/"
+complete g_confrms "n/-f1/f:*.{tpr,tpb,tpa,xml,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-f2/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,xml,ent}{,.gz,.Z}/" "n/-n1/f:*.ndx{,.gz,.Z}/" "n/-n2/f:*.ndx{,.gz,.Z}/" "n/-no/f:*.ndx{,.gz,.Z}/" "c/-/( f1 f2 o n1 n2 no h nice w one pbc nofit name bfac)/"
+complete g_covar "n/-tu/( ps fs ns us ms s m h)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-v/f:*.{trr,trj}{,.gz,.Z}/" "n/-av/f:*.{gro,g96,pdb,brk,xml,ent}{,.gz,.Z}/" "n/-l/f:*.log{,.gz,.Z}/" "n/-ascii/f:*.dat{,.gz,.Z}/" "n/-xpm/f:*.xpm{,.gz,.Z}/" "n/-xpma/f:*.xpm{,.gz,.Z}/" "c/-/( f s n o v av l ascii xpm xpma h nice b e dt tu nofit ref mwa last)/"
+complete g_density "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-ei/f:*.dat{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "c/-/( f n s ei o h nice b e dt w d sl number ed count)/"
+complete g_dielectric "n/-ffn/( none exp aexp exp_exp vac exp5 exp7 exp9)/" "n/-f/f:*.xvg{,.gz,.Z}/" "n/-d/f:*.xvg{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-c/f:*.xvg{,.gz,.Z}/" "c/-/( f d o c h nice b e dt w fft nox1 eint bfit efit tail A tau1 tau2 eps0 epsRF fix ffn nsmooth)/"
+complete g_dih "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-o/f:*.out{,.gz,.Z}/" "c/-/( f s o h nice b e dt w sa mult)/"
+complete g_dipoles "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7 exp9)/" "n/-enx/f:*.{edr,ene}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-eps/f:*.xvg{,.gz,.Z}/" "n/-a/f:*.xvg{,.gz,.Z}/" "n/-d/f:*.xvg{,.gz,.Z}/" "n/-c/f:*.xvg{,.gz,.Z}/" "n/-g/f:*.xvg{,.gz,.Z}/" "n/-q/f:*.xvg{,.gz,.Z}/" "c/-/( enx f s n o eps a d c g q h nice b e dt w mu mumax epsilonRF skip temp avercorr gkratom acflen nonormalize P fitfn ncskip beginfit endfit)/"
+complete g_disre "n/-s/f:*.{tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-ds/f:*.xvg{,.gz,.Z}/" "n/-da/f:*.xvg{,.gz,.Z}/" "n/-dn/f:*.xvg{,.gz,.Z}/" "n/-dm/f:*.xvg{,.gz,.Z}/" "n/-dr/f:*.xvg{,.gz,.Z}/" "n/-l/f:*.log{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-q/f:*.pdb{,.gz,.Z}/" "c/-/( s f ds da dn dm dr l n q h nice b e dt w ntop)/"
+complete g_dist "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "c/-/( f s n o h nice b e dt dist)/"
+complete g_dyndom "n/-f/f:*.pdb{,.gz,.Z}/" "n/-o/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "c/-/( f o n h nice firstangle lastangle nframe maxangle trans head tail)/"
+complete g_enemat "n/-f/f:*.{edr,ene}{,.gz,.Z}/" "n/-groups/f:*.dat{,.gz,.Z}/" "n/-eref/f:*.dat{,.gz,.Z}/" "n/-emat/f:*.xpm{,.gz,.Z}/" "n/-etot/f:*.xvg{,.gz,.Z}/" "c/-/( f groups eref emat etot h nice b e dt w sum skip nomean nlevels max min nocoul coulr coul14 nolj lj14 bham nofree temp)/"
+complete g_energy "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7 exp9)/" "n/-f/f:*.{edr,ene}{,.gz,.Z}/" "n/-f2/f:*.{edr,ene}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-viol/f:*.xvg{,.gz,.Z}/" "n/-pairs/f:*.xvg{,.gz,.Z}/" "n/-ora/f:*.xvg{,.gz,.Z}/" "n/-ort/f:*.xvg{,.gz,.Z}/" "n/-oda/f:*.xvg{,.gz,.Z}/" "n/-odr/f:*.xvg{,.gz,.Z}/" "n/-odt/f:*.xvg{,.gz,.Z}/" "n/-corr/f:*.xvg{,.gz,.Z}/" "n/-vis/f:*.xvg{,.gz,.Z}/" "n/-ravg/f:*.xvg{,.gz,.Z}/" "c/-/( f f2 s o viol pairs ora ort oda odr odt corr vis ravg h nice b e w fee fetemp zero sum dp mutot skip aver nmol ndf fluc orinst acflen nonormalize P fitfn ncskip beginfit endfit)/"
+complete g_filter "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-ol/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-oh/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "c/-/( f s n ol oh h nice b e dt w nf all nonojump fit)/"
+complete g_gyrate "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7 exp9)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-acf/f:*.xvg{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "c/-/( f s o acf n h nice b e dt w q p moi acflen nonormalize P fitfn ncskip beginfit endfit)/"
+complete g_h2order "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-nm/f:*.ndx{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "c/-/( f n nm s o h nice b e dt w d sl)/"
+complete g_hbond "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "n/-sel/f:*.ndx{,.gz,.Z}/" "n/-num/f:*.xvg{,.gz,.Z}/" "n/-ac/f:*.xvg{,.gz,.Z}/" "n/-dist/f:*.xvg{,.gz,.Z}/" "n/-ang/f:*.xvg{,.gz,.Z}/" "n/-hx/f:*.xvg{,.gz,.Z}/" "n/-hbn/f:*.ndx{,.gz,.Z}/" "n/-hbm/f:*.xpm{,.gz,.Z}/" "n/-dan/f:*.xvg{,.gz,.Z}/" "c/-/( f s n g sel num ac dist ang hx hbn hbm dan h nice b e dt ins a r noda abin rbin nonitacc contact shell dump max_hb nomerge)/"
+complete g_helix "n/-s/f:*.{tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-to/f:*.g87{,.gz,.Z}/" "n/-cz/f:*.{gro,g96,pdb,brk,xml,ent}{,.gz,.Z}/" "n/-co/f:*.{gro,g96,pdb,brk,xml,ent}{,.gz,.Z}/" "c/-/( s n f to cz co h nice b e dt w r0 q noF db ev ahxstart ahxend)/"
+complete g_lie "n/-f/f:*.{edr,ene}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "c/-/( f o h nice b e dt w Elj Eqq Clj Cqq ligand)/"
+complete g_mdmat "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-mean/f:*.xpm{,.gz,.Z}/" "n/-frames/f:*.xpm{,.gz,.Z}/" "n/-no/f:*.xvg{,.gz,.Z}/" "c/-/( f s n mean frames no h nice b e dt t nlevels)/"
+complete g_mindist "n/-tu/( ps fs ns us ms s m h)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-od/f:*.xvg{,.gz,.Z}/" "n/-on/f:*.xvg{,.gz,.Z}/" "n/-o/f:*.out{,.gz,.Z}/" "n/-ox/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-or/f:*.xvg{,.gz,.Z}/" "c/-/( f s n od on o ox or h nice b e dt tu w matrix max d pi split)/"
+complete g_morph "n/-f1/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-f2/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-o/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-or/f:*.xvg{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "c/-/( f1 f2 o or n h nice w ninterm first last nofit)/"
+complete g_msd "n/-tu/( ps fs ns us ms s m h)/" "n/-type/( no x y z)/" "n/-lateral/( no x y z)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-mol/f:*.xvg{,.gz,.Z}/" "c/-/( f s n o mol h nice b e dt tu w type lateral ngroup nomw trestart beginfit endfit)/"
+complete g_nmeig "n/-f/f:*.mtx{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-v/f:*.{trr,trj}{,.gz,.Z}/" "c/-/( f s o v h nice nom first last)/"
+complete g_nmens "n/-v/f:*.{trr,trj}{,.gz,.Z}/" "n/-e/f:*.xvg{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "c/-/( v e s n o h nice temp seed num first last)/"
+complete g_order "n/-d/( z x y)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-od/f:*.xvg{,.gz,.Z}/" "n/-os/f:*.xvg{,.gz,.Z}/" "c/-/( f n s o od os h nice b e dt w d sl szonly unsat)/"
+complete g_potential "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-oc/f:*.xvg{,.gz,.Z}/" "n/-of/f:*.xvg{,.gz,.Z}/" "c/-/( f n s o oc of h nice b e dt w d sl cb ce tz spherical)/"
+complete g_rama "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "c/-/( f s o h nice b e dt w)/"
+complete g_rdf "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-sq/f:*.xvg{,.gz,.Z}/" "n/-cn/f:*.xvg{,.gz,.Z}/" "n/-hq/f:*.xvg{,.gz,.Z}/" "c/-/( f s n o sq cn hq h nice b e dt w bin com cut fade nlevel startq endq energy)/"
+complete g_rms "n/-tu/( ps fs ns us ms s m h)/" "n/-what/( rmsd rho rhosc)/" "n/-fit/( rot+trans translation none)/" "n/-s/f:*.{tpr,tpb,tpa,xml,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-f2/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-mir/f:*.xvg{,.gz,.Z}/" "n/-a/f:*.xvg{,.gz,.Z}/" "n/-dist/f:*.xvg{,.gz,.Z}/" "n/-m/f:*.xpm{,.gz,.Z}/" "n/-bin/f:*.dat{,.gz,.Z}/" "n/-bm/f:*.xpm{,.gz,.Z}/" "c/-/( s f f2 n o mir a dist m bin bm h nice b e dt tu w what nopbc fit prev split skip skip2 max min bmax bmin nlevels)/"
+complete g_rmsdist "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-equiv/f:*.dat{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-rms/f:*.xpm{,.gz,.Z}/" "n/-scl/f:*.xpm{,.gz,.Z}/" "n/-mean/f:*.xpm{,.gz,.Z}/" "n/-nmr3/f:*.xpm{,.gz,.Z}/" "n/-nmr6/f:*.xpm{,.gz,.Z}/" "n/-noe/f:*.dat{,.gz,.Z}/" "c/-/( f s n equiv o rms scl mean nmr3 nmr6 noe h nice b e dt w nlevels max nosumh)/"
+complete g_rmsf "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-q/f:*.pdb{,.gz,.Z}/" "n/-oq/f:*.pdb{,.gz,.Z}/" "n/-ox/f:*.pdb{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-od/f:*.xvg{,.gz,.Z}/" "n/-oc/f:*.xvg{,.gz,.Z}/" "n/-dir/f:*.log{,.gz,.Z}/" "c/-/( f s n q oq ox o od oc dir h nice b e dt w res aniso)/"
+complete g_rotacf "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7 exp9)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "c/-/( f s n o h nice b e dt w d noaver acflen nonormalize P fitfn ncskip beginfit endfit)/"
+complete g_saltbr "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml}{,.gz,.Z}/" "c/-/( f s h nice b e dt t sep)/"
+complete g_sas "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-or/f:*.xvg{,.gz,.Z}/" "n/-oa/f:*.xvg{,.gz,.Z}/" "n/-q/f:*.pdb{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-i/f:*.itp{,.gz,.Z}/" "c/-/( f s o or oa q n i h nice b e dt w solsize ndots qmax f_index minarea nopbc noprot dgs)/"
+complete g_sgangle "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-oa/f:*.xvg{,.gz,.Z}/" "n/-od/f:*.xvg{,.gz,.Z}/" "n/-od1/f:*.xvg{,.gz,.Z}/" "n/-od2/f:*.xvg{,.gz,.Z}/" "c/-/( f n s oa od od1 od2 h nice b e dt w)/"
+complete g_sorient "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-no/f:*.xvg{,.gz,.Z}/" "n/-ro/f:*.xvg{,.gz,.Z}/" "n/-co/f:*.xvg{,.gz,.Z}/" "c/-/( f s n o no ro co h nice b e dt w com rmin rmax nbin pbc)/"
+complete g_tcaf "n/-f/f:*.{trr,trj}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-ot/f:*.xvg{,.gz,.Z}/" "n/-oa/f:*.xvg{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-of/f:*.xvg{,.gz,.Z}/" "n/-oc/f:*.xvg{,.gz,.Z}/" "n/-ov/f:*.xvg{,.gz,.Z}/" "c/-/( f s n ot oa o of oc ov h nice b e dt w mol k34 wt)/"
+complete g_traj "n/-tu/( ps fs ns us ms s m h)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-ox/f:*.xvg{,.gz,.Z}/" "n/-ov/f:*.xvg{,.gz,.Z}/" "n/-of/f:*.xvg{,.gz,.Z}/" "n/-ob/f:*.xvg{,.gz,.Z}/" "n/-ot/f:*.xvg{,.gz,.Z}/" "n/-ekt/f:*.xvg{,.gz,.Z}/" "n/-ekr/f:*.xvg{,.gz,.Z}/" "n/-cv/f:*.pdb{,.gz,.Z}/" "n/-cf/f:*.pdb{,.gz,.Z}/" "c/-/( f s n ox ov of ob ot ekt ekr cv cf h nice b e dt tu w com mol nojump nox noy noz len scale)/"
+complete g_velacc "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7 exp9)/" "n/-f/f:*.{trr,trj}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "c/-/( f s n o h nice b e dt w mol acflen nonormalize P fitfn ncskip beginfit endfit)/"
+complete g_wham "n/-o/f:*.xvg{,.gz,.Z}/" "n/-hist/f:*.xvg{,.gz,.Z}/" "c/-/( o hist h nice w min max bins noprof temp flip tol)/"
+complete genbox "n/-cp/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-cs/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-ci/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,xml,ent}{,.gz,.Z}/" "n/-p/f:*.top{,.gz,.Z}/" "c/-/( cp cs ci o p h nice box nmol try seed vdwd shell)/"
+complete genconf "n/-f/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,xml,ent}{,.gz,.Z}/" "n/-trj/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "c/-/( f o trj h nice nbox dist seed rot shuffle sort block nmolat maxrot renumber)/"
+complete genion "n/-s/f:*.{tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-table/f:*.xvg{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,xml,ent}{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "n/-pot/f:*.pdb{,.gz,.Z}/" "c/-/( s table n o g pot h nice np pname pq nn nname nq rmin random seed scale)/"
+complete genpr "n/-f/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.itp{,.gz,.Z}/" "n/-of/f:*.ndx{,.gz,.Z}/" "c/-/( f n o of h nice fc freeze)/"
+complete gmxcheck "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-f2/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s1/f:*.{tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-s2/f:*.{tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-c/f:*.{tpr,tpb,tpa,xml,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-e/f:*.{edr,ene}{,.gz,.Z}/" "n/-e2/f:*.{edr,ene}{,.gz,.Z}/" "c/-/( f f2 s1 s2 c e e2 h nice vdwfac bonlo bonhi tol lastener)/"
+complete gmxdump "n/-s/f:*.{tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-e/f:*.{edr,ene}{,.gz,.Z}/" "c/-/( s f e h nice nonr)/"
+complete grompp "n/-f/f:*.mdp{,.gz,.Z}/" "n/-po/f:*.mdp{,.gz,.Z}/" "n/-c/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-r/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-rb/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-deshuf/f:*.ndx{,.gz,.Z}/" "n/-p/f:*.top{,.gz,.Z}/" "n/-pp/f:*.top{,.gz,.Z}/" "n/-o/f:*.{tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-t/f:*.{trr,trj}{,.gz,.Z}/" "n/-e/f:*.{edr,ene}{,.gz,.Z}/" "c/-/( f po c r rb n deshuf p pp o t e h nice nov time np shuffle sort normdumbds load maxwarn check14 norenum)/"
+complete highway "n/-f/f:*.dat{,.gz,.Z}/" "n/-a/f:*.dat{,.gz,.Z}/" "c/-/( f a h nice b e dt)/"
+complete make_ndx "n/-f/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.ndx{,.gz,.Z}/" "c/-/( f n o h nice natoms verbose)/"
+complete mdrun "n/-s/f:*.{tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-o/f:*.{trr,trj}{,.gz,.Z}/" "n/-x/f:*.xtc{,.gz,.Z}/" "n/-c/f:*.{gro,g96,pdb,brk,xml,ent}{,.gz,.Z}/" "n/-e/f:*.{edr,ene}{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "n/-dgdl/f:*.xvg{,.gz,.Z}/" "n/-field/f:*.xvg{,.gz,.Z}/" "n/-table/f:*.xvg{,.gz,.Z}/" "n/-rerun/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-ei/f:*.edi{,.gz,.Z}/" "n/-eo/f:*.edo{,.gz,.Z}/" "n/-j/f:*.gct{,.gz,.Z}/" "n/-jo/f:*.gct{,.gz,.Z}/" "n/-ffout/f:*.xvg{,.gz,.Z}/" "n/-devout/f:*.xvg{,.gz,.Z}/" "n/-runav/f:*.xvg{,.gz,.Z}/" "n/-pi/f:*.ppa{,.gz,.Z}/" "n/-po/f:*.ppa{,.gz,.Z}/" "n/-pd/f:*.pdo{,.gz,.Z}/" "n/-pn/f:*.ndx{,.gz,.Z}/" "n/-mtx/f:*.mtx{,.gz,.Z}/" "n/-dn/f:*.ndx{,.gz,.Z}/" "c/-/( s o x c e g dgdl field table rerun ei eo j jo ffout devout runav pi po pd pn mtx dn h nice deffnm np nt v nocompact multi glas ionize)/"
+complete mk_angndx "n/-type/( angle g96-angle dihedral improper ryckaert-bellemans phi-psi)/" "n/-s/f:*.{tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "c/-/( s n h nice type)/"
+complete ngmx "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "c/-/( f s n h nice b e dt)/"
+complete pdb2gmx "n/-water/( spc spce tip3p tip4p tip5p)/" "n/-dummy/( none hydrogens aromatics)/" "n/-f/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,xml,ent}{,.gz,.Z}/" "n/-p/f:*.top{,.gz,.Z}/" "n/-i/f:*.itp{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-q/f:*.{gro,g96,pdb,brk,xml,ent}{,.gz,.Z}/" "c/-/( f o p i n q h nice merge ff water inter ss ter lys asp glu his angle dist una ignh missing posrefc dummy heavyh deuterate)/"
+complete protonate "n/-s/f:*.{tpr,tpb,tpa,xml,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "c/-/( s f n o h nice b e dt)/"
+complete tpbconv "n/-s/f:*.{tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-f/f:*.{trr,trj}{,.gz,.Z}/" "n/-e/f:*.{edr,ene}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.{tpr,tpb,tpa,xml}{,.gz,.Z}/" "c/-/( s f e n o h nice time extend until zeroq nounconstrained)/"
+complete trjcat "n/-tu/( ps fs ns us ms s m h)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-o/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "c/-/( f o n h nice tu b e dt prec novel settime nosort keeplast cat)/"
+complete trjconv "n/-tu/( ps fs ns us ms s m h)/" "n/-pbc/( none whole inbox nojump cluster com)/" "n/-ur/( rect tric compact)/" "n/-fit/( none rot+trans translation progressive)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-o/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-fr/f:*.ndx{,.gz,.Z}/" "c/-/( f o s n fr h nice b e tu w skip dt dump t0 timestep pbc ur center box shift fit ndec novel force trunc exec app split sep ter)/"
+complete trjorder "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "c/-/( f s n o h nice b e dt na da)/"
+complete wheel "n/-f/f:*.dat{,.gz,.Z}/" "n/-o/f:*.eps{,.gz,.Z}/" "c/-/( f o h nice r0 rot0 T nonn)/"
+complete x2top "n/-ff/( G43a1 oplsaa gmx G43a2 G43b1)/" "n/-f/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa,xml}{,.gz,.Z}/" "n/-o/f:*.top{,.gz,.Z}/" "n/-r/f:*.rtp{,.gz,.Z}/" "c/-/( f o r h nice scale ff nexcl noH14 alldih remdih nopairs name nopbc param noround kb kt kp)/"
+complete xpm2ps "n/-title/( top once ylabel none)/" "n/-legend/( both first second none)/" "n/-diag/( first second none)/" "n/-combine/( halves add sub mult div)/" "n/-rainbow/( no blue red)/" "n/-f/f:*.xpm{,.gz,.Z}/" "n/-f2/f:*.xpm{,.gz,.Z}/" "n/-di/f:*.m2p{,.gz,.Z}/" "n/-do/f:*.m2p{,.gz,.Z}/" "n/-o/f:*.eps{,.gz,.Z}/" "n/-xpm/f:*.xpm{,.gz,.Z}/" "c/-/( f f2 di do o xpm h nice w noframe title yonce legend diag combine bx by rainbow gradient skip zeroline legoffset)/"
+complete xrama "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,xml}{,.gz,.Z}/" "c/-/( f s h nice b e dt)/"
-compctl -x 's[-]' -s " f s n ssdump map o sc a ta aa h X nice b e dt tu w sss" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-ssdump]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-map]' -g '*.map(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-sc]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-a]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-ta]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-aa]' -g '*.xvg(|.gz|.Z) *(/)' -- do_dssp
-compctl -x 's[-]' -s " f n o bf h X nice w ndef bt box angles d c center rotate princ scale density pbc mead grasp rvdw atom legend label" - 'c[-1,-bt]' -s " tric cubic dodecahedron octahedron" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-bf]' -g '*.dat(|.gz|.Z) *(/)' -- editconf
-compctl -x 's[-]' -s " f o h X nice b e dt offset settime nosort scalefac noerror" - 'c[-1,-f]' -g '*.(edr|ene)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(edr|ene)(|.gz|.Z) *(/)' -- eneconv
-compctl -x 's[-]' -s " s g table parm ga h X nice tol fmax epot nocomb npow ratio logeps nov" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-table]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-parm]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-ga]' -g '*.dat(|.gz|.Z) *(/)' -- ffscan
-compctl -x 's[-]' -s " v v2 f s n eig1 eig2 disp proj 2d 3d filt extr over inpr h X nice b e dt tu w first last skip max nframes split" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-v]' -g '*.(trr|trj)(|.gz|.Z) *(/)' - 'c[-1,-v2]' -g '*.(trr|trj)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-eig1]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-eig2]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-disp]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-proj]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-2d]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-3d]' -g '*.(gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-filt]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-extr]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-over]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-inpr]' -g '*.xpm(|.gz|.Z) *(/)' -- g_anaeig
-compctl -x 's[-]' -s " f ac msd cc dist av ee g h X nice w notime b e n d bw errbar power nosubav oneacf acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-errbar]' -s " none stddev error 90" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac exp5 exp7" - 'c[-1,-f]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ac]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-msd]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-cc]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-dist]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-av]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ee]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' -- g_analyze
-compctl -x 's[-]' -s " f s n od ov of ot oh oc h X nice b e dt w type all binwidth chandler avercorr acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-type]' -s " angle dihedral improper ryckaert-bellemans" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac exp5 exp7" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-od]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ov]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-of]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ot]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oh]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oc]' -g '*.xvg(|.gz|.Z) *(/)' -- g_angle
-compctl -x 's[-]' -s " f n s o l d h X nice b e dt w blen tol noaver" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-l]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-d]' -g '*.xvg(|.gz|.Z) *(/)' -- g_bond
-compctl -x 's[-]' -s " f s n ol od oz ot otr otl ok okr okl oa h X nice b e dt tu na z" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-ol]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-od]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oz]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ot]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-otr]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-otl]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ok]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-okr]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-okl]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oa]' -g '*.pdb(|.gz|.Z) *(/)' -- g_bundle
-compctl -x 's[-]' -s " c f o p ss jc corr g h X nice b e dt w r0 phi psi omega rama viol all shift run maxchi nonormhisto ramomega bfact bmax acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-maxchi]' -s " 0 1 2 3 4 5 6" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac exp5 exp7" - 'c[-1,-c]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-p]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-ss]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-jc]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-corr]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' -- g_chi
-compctl -x 's[-]' -s " f s n dm o g dist ev sz tr ntr clid cl h X nice b e dt tu w dista nlevels keepfree cutoff nofit max skip av wcl nst rmsmin method binary M P seed niter kT" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-method]' -s " linkage jarvis-patrick monte-carlo diagonalization gromos" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-dm]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-dist]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ev]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-sz]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-tr]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-ntr]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-clid]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-cl]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' -- g_cluster
-compctl -x 's[-]' -s " f n o nc mc ac h X nice b e dt w cut nskip nlevels rgblo rgbhi" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-nc]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-mc]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ac]' -g '*.xvg(|.gz|.Z) *(/)' -- g_clustsize
-compctl -x 's[-]' -s " f1 f2 o n1 n2 h X nice one pbc" - 'c[-1,-f1]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-f2]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n1]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-n2]' -g '*.ndx(|.gz|.Z) *(/)' -- g_confrms
-compctl -x 's[-]' -s " f s n o v av l xpm xpma h X nice b e dt tu nofit ref mwa last" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-v]' -g '*.(trr|trj)(|.gz|.Z) *(/)' - 'c[-1,-av]' -g '*.(gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-l]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-xpm]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-xpma]' -g '*.xpm(|.gz|.Z) *(/)' -- g_covar
-compctl -x 's[-]' -s " f n s ei o h X nice b e dt w d sl number ed count" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-ei]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' -- g_density
-compctl -x 's[-]' -s " f d o c h X nice b e dt w fft nox1 eint bfit efit tail A tau1 tau2 eps0 epsRF fix ffn nsmooth" - 'c[-1,-ffn]' -s " none exp aexp exp_exp vac exp5 exp7" - 'c[-1,-f]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-d]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-c]' -g '*.xvg(|.gz|.Z) *(/)' -- g_dielectric
-compctl -x 's[-]' -s " f s o h X nice b e dt w sa mult" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.out(|.gz|.Z) *(/)' -- g_dih
-compctl -x 's[-]' -s " enx f s n o e a d c g q h X nice b e dt w mu mumax epsilonRF skip temp avercorr gkratom acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac exp5 exp7" - 'c[-1,-enx]' -g '*.(edr|ene)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-e]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-a]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-d]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-c]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-q]' -g '*.xvg(|.gz|.Z) *(/)' -- g_dipoles
-compctl -x 's[-]' -s " s f ds da dn dm dr l n h X nice b e dt w ntop" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-ds]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-da]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-dn]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-dm]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-dr]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-l]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' -- g_disre
-compctl -x 's[-]' -s " f s n o h X nice b e dt dist" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' -- g_dist
-compctl -x 's[-]' -s " f o n h X nice firstangle lastangle nframe maxangle trans head tail" - 'c[-1,-f]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' -- g_dyndom
-compctl -x 's[-]' -s " cp cs ci o p h X nice box nmol try seed vdwd shell" - 'c[-1,-cp]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-cs]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-ci]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-p]' -g '*.top(|.gz|.Z) *(/)' -- genbox
-compctl -x 's[-]' -s " f o trj h X nice nbox dist seed rot shuffle sort block nmolat maxrot renumber" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-trj]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' -- genconf
-compctl -x 's[-]' -s " f groups eref emat etot h X nice b e dt w sum skip nomean nlevels max min nocoul coulr coul14 nolj lj14 bham nofree temp" - 'c[-1,-f]' -g '*.(edr|ene)(|.gz|.Z) *(/)' - 'c[-1,-groups]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-eref]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-emat]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-etot]' -g '*.xvg(|.gz|.Z) *(/)' -- g_enemat
-compctl -x 's[-]' -s " f f2 s o viol pairs ora ort oda odr odt corr vis ravg h X nice b e w fee fetemp zero sum dp mutot skip aver nmol ndf fluc orinst acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac exp5 exp7" - 'c[-1,-f]' -g '*.(edr|ene)(|.gz|.Z) *(/)' - 'c[-1,-f2]' -g '*.(edr|ene)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-viol]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-pairs]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ora]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ort]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oda]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-odr]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-odt]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-corr]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-vis]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ravg]' -g '*.xvg(|.gz|.Z) *(/)' -- g_energy
-compctl -x 's[-]' -s " s n o g pot h X nice np pname pq nn nname nq rmin random seed" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-pot]' -g '*.pdb(|.gz|.Z) *(/)' -- genion
-compctl -x 's[-]' -s " f n o h X nice fc" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.itp(|.gz|.Z) *(/)' -- genpr
-compctl -x 's[-]' -s " f s o n h X nice b e dt w q p" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' -- g_gyrate
-compctl -x 's[-]' -s " f n nm s o h X nice b e dt w d sl" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-nm]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' -- g_h2order
-compctl -x 's[-]' -s " f s n g sel num ac dist ang hx hbn hbm da h X nice b e dt ins a r abin rbin nonitacc shell" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-sel]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-num]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ac]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-dist]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ang]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-hx]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-hbn]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-hbm]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-da]' -g '*.xvg(|.gz|.Z) *(/)' -- g_hbond
-compctl -x 's[-]' -s " s n f to cz co h X nice b e dt w r0 q noF db ev ahxstart ahxend" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-to]' -g '*.g87(|.gz|.Z) *(/)' - 'c[-1,-cz]' -g '*.(gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-co]' -g '*.(gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' -- g_helix
-compctl -x 's[-]' -s " f o h X nice b e dt w Elj Eqq Clj Cqq ligand" - 'c[-1,-f]' -g '*.(edr|ene)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' -- g_lie
-compctl -x 's[-]' -s " f s n mean frames no h X nice b e dt t nlevels" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-mean]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-frames]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-no]' -g '*.xvg(|.gz|.Z) *(/)' -- g_mdmat
-compctl -x 's[-]' -s " f s n od on o h X nice b e dt w matrix d pi" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-od]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-on]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.out(|.gz|.Z) *(/)' -- g_mindist
-compctl -x 's[-]' -s " f1 f2 o or n h X nice w ninterm first last nofit" - 'c[-1,-f1]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-f2]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-or]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' -- g_morph
-compctl -x 's[-]' -s " f s n o mol h X nice b e dt tu w type lateral ngroup nomw trestart beginfit endfit" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-type]' -s " no x y z" - 'c[-1,-lateral]' -s " no x y z" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-mol]' -g '*.xvg(|.gz|.Z) *(/)' -- g_msd
-compctl -x 's[-]' -s " f f2 s1 s2 c e e2 h X nice vdwfac bonlo bonhi tol lastener" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-f2]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s1]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-s2]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-c]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-e]' -g '*.(edr|ene)(|.gz|.Z) *(/)' - 'c[-1,-e2]' -g '*.(edr|ene)(|.gz|.Z) *(/)' -- gmxcheck
-compctl -x 's[-]' -s " s f e h X nice nonr" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-e]' -g '*.(edr|ene)(|.gz|.Z) *(/)' -- gmxdump
-compctl -x 's[-]' -s " f s o v h X nice nom first last" - 'c[-1,-f]' -g '*.mtx(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-v]' -g '*.(trr|trj)(|.gz|.Z) *(/)' -- g_nmeig
-compctl -x 's[-]' -s " v e s n o h X nice temp seed num first last" - 'c[-1,-v]' -g '*.(trr|trj)(|.gz|.Z) *(/)' - 'c[-1,-e]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' -- g_nmens
-compctl -x 's[-]' -s " f n s o od os h X nice b e dt w d sl szonly unsat" - 'c[-1,-d]' -s " z x y" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-od]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-os]' -g '*.xvg(|.gz|.Z) *(/)' -- g_order
-compctl -x 's[-]' -s " f n s o oc of h X nice b e dt w d sl cb ce tz spherical" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oc]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-of]' -g '*.xvg(|.gz|.Z) *(/)' -- g_potential
-compctl -x 's[-]' -s " f s o h X nice b e dt w" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' -- g_rama
-compctl -x 's[-]' -s " f s n o sq cn hq image h X nice b e dt w bin com cut fade grid nlevel wave" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-sq]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-cn]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-hq]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-image]' -g '*.xpm(|.gz|.Z) *(/)' -- g_rdf
-compctl -x 's[-]' -s " s f f2 n o mir a dist m bin bm h X nice b e dt tu w what nopbc nofit prev split skip skip2 max min bmax bmin nlevels" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-what]' -s " rmsd rho rhosc" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-f2]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-mir]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-a]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-dist]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-m]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-bin]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-bm]' -g '*.xpm(|.gz|.Z) *(/)' -- g_rms
-compctl -x 's[-]' -s " f s n equiv o rms scl mean nmr3 nmr6 noe h X nice b e dt w nlevels max nosumh" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-equiv]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-rms]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-scl]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-mean]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-nmr3]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-nmr6]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-noe]' -g '*.dat(|.gz|.Z) *(/)' -- g_rmsdist
-compctl -x 's[-]' -s " f s n q oq ox o od oc dir h X nice b e dt w res aniso" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-q]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-oq]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-ox]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-od]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oc]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-dir]' -g '*.log(|.gz|.Z) *(/)' -- g_rmsf
-compctl -x 's[-]' -s " f po c r n deshuf p pp o t h X nice nov time np shuffle sort normdumbds load maxwarn check14" - 'c[-1,-f]' -g '*.mdp(|.gz|.Z) *(/)' - 'c[-1,-po]' -g '*.mdp(|.gz|.Z) *(/)' - 'c[-1,-c]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-r]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-deshuf]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-p]' -g '*.top(|.gz|.Z) *(/)' - 'c[-1,-pp]' -g '*.top(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-t]' -g '*.(trr|trj)(|.gz|.Z) *(/)' -- grompp
-compctl -x 's[-]' -s " f s n o h X nice b e dt w d noaver acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac exp5 exp7" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' -- g_rotacf
-compctl -x 's[-]' -s " f s h X nice b e dt t sep" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' -- g_saltbr
-compctl -x 's[-]' -s " f s o r q ao n i h X nice b e dt w solsize ndots qmax minarea skip nopbc noprot dgs" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-r]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-q]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-ao]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-i]' -g '*.itp(|.gz|.Z) *(/)' -- g_sas
-compctl -x 's[-]' -s " f n s oa od od1 od2 h X nice b e dt w" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-oa]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-od]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-od1]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-od2]' -g '*.xvg(|.gz|.Z) *(/)' -- g_sgangle
-compctl -x 's[-]' -s " f s n o no ro co h X nice b e dt w com rmin rmax nbin" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-no]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ro]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-co]' -g '*.xvg(|.gz|.Z) *(/)' -- g_sorient
-compctl -x 's[-]' -s " f s n ot oa o of oc ov h X nice b e dt w mol k34 wt" - 'c[-1,-f]' -g '*.(trr|trj)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-ot]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oa]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-of]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oc]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ov]' -g '*.xvg(|.gz|.Z) *(/)' -- g_tcaf
-compctl -x 's[-]' -s " f s n ox ov of ob ot ekt ekr cv cf h X nice b e dt tu w com mol nojump nox noy noz len" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-ox]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ov]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-of]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ob]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ot]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ekt]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ekr]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-cv]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-cf]' -g '*.pdb(|.gz|.Z) *(/)' -- g_traj
-compctl -x 's[-]' -s " f s n o h X nice b e dt w mol acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac exp5 exp7" - 'c[-1,-f]' -g '*.(trr|trj)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' -- g_velacc
-compctl -x 's[-]' -s " f a h X nice b e dt" - 'c[-1,-f]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-a]' -g '*.dat(|.gz|.Z) *(/)' -- highway
-compctl -x 's[-]' -s " f n o h X nice" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.ndx(|.gz|.Z) *(/)' -- make_ndx
-compctl -x 's[-]' -s " s o x c e g dgdl table rerun ei eo j jo ffout devout runav pi po pd pn mtx h X nice deffnm np v nocompact multi glas ionize" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(trr|trj)(|.gz|.Z) *(/)' - 'c[-1,-x]' -g '*.xtc(|.gz|.Z) *(/)' - 'c[-1,-c]' -g '*.(gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-e]' -g '*.(edr|ene)(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-dgdl]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-table]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-rerun]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-ei]' -g '*.edi(|.gz|.Z) *(/)' - 'c[-1,-eo]' -g '*.edo(|.gz|.Z) *(/)' - 'c[-1,-j]' -g '*.gct(|.gz|.Z) *(/)' - 'c[-1,-jo]' -g '*.gct(|.gz|.Z) *(/)' - 'c[-1,-ffout]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-devout]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-runav]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-pi]' -g '*.ppa(|.gz|.Z) *(/)' - 'c[-1,-po]' -g '*.ppa(|.gz|.Z) *(/)' - 'c[-1,-pd]' -g '*.pdo(|.gz|.Z) *(/)' - 'c[-1,-pn]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-mtx]' -g '*.mtx(|.gz|.Z) *(/)' -- mdrun
-compctl -x 's[-]' -s " s n h X nice type" - 'c[-1,-type]' -s " angle g96-angle dihedral improper ryckaert-bellemans phi-psi" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' -- mk_angndx
-compctl -x 's[-]' -s " f s n h X nice b e dt" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' -- ngmx
-compctl -x 's[-]' -s " f o p i n q h X nice merge inter ss ter lys asp glu his angle dist posrefc una nosort H14 ignh alldih dummy heavyh deuterate" - 'c[-1,-dummy]' -s " none hydrogens aromatics" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-p]' -g '*.top(|.gz|.Z) *(/)' - 'c[-1,-i]' -g '*.itp(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-q]' -g '*.(gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' -- pdb2gmx
-compctl -x 's[-]' -s " s f n o h X nice b e dt" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' -- protonate
-compctl -x 's[-]' -s " s f n o h X nice time extend until zeroq nounconstrained" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(trr|trj)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' -- tpbconv
-compctl -x 's[-]' -s " o n h X nice tu b e dt prec novel settime nosort cat" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-o]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' -- trjcat
-compctl -x 's[-]' -s " f o s n fr h X nice b e tu w skip dt dump t0 timestep pbc ur center box shift fit pfit ndec novel force trunc exec app split sep" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-pbc]' -s " none whole inbox nojump" - 'c[-1,-ur]' -s " rect tric compact" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-fr]' -g '*.ndx(|.gz|.Z) *(/)' -- trjconv
-compctl -x 's[-]' -s " f s n o h X nice b e dt na da" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' -- trjorder
-compctl -x 's[-]' -s " f o h X nice r0 rot0 T nonn" - 'c[-1,-f]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.eps(|.gz|.Z) *(/)' -- wheel
-compctl -x 's[-]' -s " f o r h X nice scale nexcl H14 alldih nopairs name nopbc param noround kb kt kp" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.top(|.gz|.Z) *(/)' - 'c[-1,-r]' -g '*.rtp(|.gz|.Z) *(/)' -- x2top
-compctl -x 's[-]' -s " f f2 di do o xpm h X nice w noframe title yonce legend diag combine bx by rainbow gradient skip zeroline" - 'c[-1,-title]' -s " top once ylabel none" - 'c[-1,-legend]' -s " both first second none" - 'c[-1,-diag]' -s " first second none" - 'c[-1,-combine]' -s " halves add sub mult div" - 'c[-1,-rainbow]' -s " no blue red" - 'c[-1,-f]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-f2]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-di]' -g '*.m2p(|.gz|.Z) *(/)' - 'c[-1,-do]' -g '*.m2p(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.eps(|.gz|.Z) *(/)' - 'c[-1,-xpm]' -g '*.xpm(|.gz|.Z) *(/)' -- xpm2ps
-compctl -x 's[-]' -s " f s h X nice b e dt" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' -- xrama
+compctl -x 's[-]' -s " f ox od of g h nice free norms cutoff" - 'c[-1,-f]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-ox]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-od]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-of]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' -- anadock
+compctl -x 's[-]' -s " s g q d o n dom h nice noengh bm am pm rr ar er vm lm il dm im nm hm hb nobon nonb measure maxdist add vir sm" - 'c[-1,-sm]' -s " none tri tetra" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-q]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-d]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-dom]' -g '*.ndx(|.gz|.Z) *(/)' -- cdist
+compctl -x 's[-]' -s " g f d do c center n o keep viol h nice nf nit nov nochiral nopep lower weighted dump cubic explicit fit nbcheck nstprint ranlist noranlistfirst lowdev seed box grow" - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-d]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-do]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-c]' -g '*.(gro|g96|pdb|brk|xml|ent)(|.gz|.Z) *(/)' - 'c[-1,-center]' -g '*.(gro|g96|pdb|brk|xml|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-keep]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-viol]' -g '*.pdb(|.gz|.Z) *(/)' -- disco
+compctl -x 's[-]' -s " f s n ssdump map o sc a ta aa h nice b e dt tu w sss" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-ssdump]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-map]' -g '*.map(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-sc]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-a]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-ta]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-aa]' -g '*.xvg(|.gz|.Z) *(/)' -- do_dssp
+compctl -x 's[-]' -s " f n o bf h nice w ndef bt box angles d c center translate rotate princ scale density novol pbc mead grasp rvdw atom legend label" - 'c[-1,-bt]' -s " tric cubic dodecahedron octahedron" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|xml|ent)(|.gz|.Z) *(/)' - 'c[-1,-bf]' -g '*.dat(|.gz|.Z) *(/)' -- editconf
+compctl -x 's[-]' -s " f o h nice b e dt offset settime nosort scalefac noerror" - 'c[-1,-f]' -g '*.(edr|ene)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(edr|ene)(|.gz|.Z) *(/)' -- eneconv
+compctl -x 's[-]' -s " s g table parm ga c e o h nice tol fmax nocomb npow logeps v epot fepot pres fpres fmsf molsize nmol" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-table]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-parm]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-ga]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-c]' -g '*.gro(|.gz|.Z) *(/)' - 'c[-1,-e]' -g '*.(edr|ene)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(trr|trj)(|.gz|.Z) *(/)' -- ffscan
+compctl -x 's[-]' -s " v v2 f s n eig eig2 comp rmsf proj 2d 3d filt extr over inpr h nice b e dt tu w first last skip max nframes split" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-v]' -g '*.(trr|trj)(|.gz|.Z) *(/)' - 'c[-1,-v2]' -g '*.(trr|trj)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-eig]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-eig2]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-comp]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-rmsf]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-proj]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-2d]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-3d]' -g '*.(gro|g96|pdb|brk|xml|ent)(|.gz|.Z) *(/)' - 'c[-1,-filt]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-extr]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-over]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-inpr]' -g '*.xpm(|.gz|.Z) *(/)' -- g_anaeig
+compctl -x 's[-]' -s " f ac msd cc dist av ee g h nice w notime b e n d bw errbar filter power nosubav oneacf acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-errbar]' -s " none stddev error 90" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac exp5 exp7 exp9" - 'c[-1,-f]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ac]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-msd]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-cc]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-dist]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-av]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ee]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' -- g_analyze
+compctl -x 's[-]' -s " f s n od ov of ot oh oc h nice b e dt w type all binwidth chandler avercorr acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-type]' -s " angle dihedral improper ryckaert-bellemans" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac exp5 exp7 exp9" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-od]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ov]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-of]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ot]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oh]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oc]' -g '*.xvg(|.gz|.Z) *(/)' -- g_angle
+compctl -x 's[-]' -s " f n s o l d h nice b e dt w blen tol noaver noaverdist" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-l]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-d]' -g '*.xvg(|.gz|.Z) *(/)' -- g_bond
+compctl -x 's[-]' -s " f s n ol od oz ot otr otl ok okr okl oa h nice b e dt tu na z" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-ol]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-od]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oz]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ot]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-otr]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-otl]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ok]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-okr]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-okl]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oa]' -g '*.pdb(|.gz|.Z) *(/)' -- g_bundle
+compctl -x 's[-]' -s " s f o p ss jc corr g ot oh rt cp h nice b e dt w r0 phi psi omega rama viol all rad shift binwidth core_rotamer maxchi nonormhisto ramomega bfact chi_prod HChi bmax acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-maxchi]' -s " 0 1 2 3 4 5 6" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac exp5 exp7 exp9" - 'c[-1,-s]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-p]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-ss]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-jc]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-corr]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-ot]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oh]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-rt]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-cp]' -g '*.xvg(|.gz|.Z) *(/)' -- g_chi
+compctl -x 's[-]' -s " f s n dm o g dist ev sz tr ntr clid cl h nice b e dt tu w dista nlevels keepfree cutoff nofit max skip av wcl nst rmsmin method minstruct binary M P seed niter kT" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-method]' -s " linkage jarvis-patrick monte-carlo diagonalization gromos" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-dm]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-dist]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ev]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-sz]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-tr]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-ntr]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-clid]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-cl]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' -- g_cluster
+compctl -x 's[-]' -s " f s n o ow nc mc ac hc h nice b e dt tu w cut mol nskip nlevels rgblo rgbhi" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.tpr(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-ow]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-nc]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-mc]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ac]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-hc]' -g '*.xvg(|.gz|.Z) *(/)' -- g_clustsize
+compctl -x 's[-]' -s " f1 f2 o n1 n2 no h nice w one pbc nofit name bfac" - 'c[-1,-f1]' -g '*.(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-f2]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|xml|ent)(|.gz|.Z) *(/)' - 'c[-1,-n1]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-n2]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-no]' -g '*.ndx(|.gz|.Z) *(/)' -- g_confrms
+compctl -x 's[-]' -s " f s n o v av l ascii xpm xpma h nice b e dt tu nofit ref mwa last" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-v]' -g '*.(trr|trj)(|.gz|.Z) *(/)' - 'c[-1,-av]' -g '*.(gro|g96|pdb|brk|xml|ent)(|.gz|.Z) *(/)' - 'c[-1,-l]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-ascii]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-xpm]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-xpma]' -g '*.xpm(|.gz|.Z) *(/)' -- g_covar
+compctl -x 's[-]' -s " f n s ei o h nice b e dt w d sl number ed count" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-ei]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' -- g_density
+compctl -x 's[-]' -s " f d o c h nice b e dt w fft nox1 eint bfit efit tail A tau1 tau2 eps0 epsRF fix ffn nsmooth" - 'c[-1,-ffn]' -s " none exp aexp exp_exp vac exp5 exp7 exp9" - 'c[-1,-f]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-d]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-c]' -g '*.xvg(|.gz|.Z) *(/)' -- g_dielectric
+compctl -x 's[-]' -s " f s o h nice b e dt w sa mult" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.out(|.gz|.Z) *(/)' -- g_dih
+compctl -x 's[-]' -s " enx f s n o eps a d c g q h nice b e dt w mu mumax epsilonRF skip temp avercorr gkratom acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac exp5 exp7 exp9" - 'c[-1,-enx]' -g '*.(edr|ene)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-eps]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-a]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-d]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-c]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-q]' -g '*.xvg(|.gz|.Z) *(/)' -- g_dipoles
+compctl -x 's[-]' -s " s f ds da dn dm dr l n q h nice b e dt w ntop" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-ds]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-da]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-dn]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-dm]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-dr]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-l]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-q]' -g '*.pdb(|.gz|.Z) *(/)' -- g_disre
+compctl -x 's[-]' -s " f s n o h nice b e dt dist" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' -- g_dist
+compctl -x 's[-]' -s " f o n h nice firstangle lastangle nframe maxangle trans head tail" - 'c[-1,-f]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' -- g_dyndom
+compctl -x 's[-]' -s " f groups eref emat etot h nice b e dt w sum skip nomean nlevels max min nocoul coulr coul14 nolj lj14 bham nofree temp" - 'c[-1,-f]' -g '*.(edr|ene)(|.gz|.Z) *(/)' - 'c[-1,-groups]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-eref]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-emat]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-etot]' -g '*.xvg(|.gz|.Z) *(/)' -- g_enemat
+compctl -x 's[-]' -s " f f2 s o viol pairs ora ort oda odr odt corr vis ravg h nice b e w fee fetemp zero sum dp mutot skip aver nmol ndf fluc orinst acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac exp5 exp7 exp9" - 'c[-1,-f]' -g '*.(edr|ene)(|.gz|.Z) *(/)' - 'c[-1,-f2]' -g '*.(edr|ene)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-viol]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-pairs]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ora]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ort]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oda]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-odr]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-odt]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-corr]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-vis]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ravg]' -g '*.xvg(|.gz|.Z) *(/)' -- g_energy
+compctl -x 's[-]' -s " f s n ol oh h nice b e dt w nf all nonojump fit" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-ol]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-oh]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' -- g_filter
+compctl -x 's[-]' -s " f s o acf n h nice b e dt w q p moi acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac exp5 exp7 exp9" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-acf]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' -- g_gyrate
+compctl -x 's[-]' -s " f n nm s o h nice b e dt w d sl" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-nm]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' -- g_h2order
+compctl -x 's[-]' -s " f s n g sel num ac dist ang hx hbn hbm dan h nice b e dt ins a r noda abin rbin nonitacc contact shell dump max_hb nomerge" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-sel]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-num]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ac]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-dist]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ang]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-hx]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-hbn]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-hbm]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-dan]' -g '*.xvg(|.gz|.Z) *(/)' -- g_hbond
+compctl -x 's[-]' -s " s n f to cz co h nice b e dt w r0 q noF db ev ahxstart ahxend" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-to]' -g '*.g87(|.gz|.Z) *(/)' - 'c[-1,-cz]' -g '*.(gro|g96|pdb|brk|xml|ent)(|.gz|.Z) *(/)' - 'c[-1,-co]' -g '*.(gro|g96|pdb|brk|xml|ent)(|.gz|.Z) *(/)' -- g_helix
+compctl -x 's[-]' -s " f o h nice b e dt w Elj Eqq Clj Cqq ligand" - 'c[-1,-f]' -g '*.(edr|ene)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' -- g_lie
+compctl -x 's[-]' -s " f s n mean frames no h nice b e dt t nlevels" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-mean]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-frames]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-no]' -g '*.xvg(|.gz|.Z) *(/)' -- g_mdmat
+compctl -x 's[-]' -s " f s n od on o ox or h nice b e dt tu w matrix max d pi split" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-od]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-on]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.out(|.gz|.Z) *(/)' - 'c[-1,-ox]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-or]' -g '*.xvg(|.gz|.Z) *(/)' -- g_mindist
+compctl -x 's[-]' -s " f1 f2 o or n h nice w ninterm first last nofit" - 'c[-1,-f1]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-f2]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-or]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' -- g_morph
+compctl -x 's[-]' -s " f s n o mol h nice b e dt tu w type lateral ngroup nomw trestart beginfit endfit" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-type]' -s " no x y z" - 'c[-1,-lateral]' -s " no x y z" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-mol]' -g '*.xvg(|.gz|.Z) *(/)' -- g_msd
+compctl -x 's[-]' -s " f s o v h nice nom first last" - 'c[-1,-f]' -g '*.mtx(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-v]' -g '*.(trr|trj)(|.gz|.Z) *(/)' -- g_nmeig
+compctl -x 's[-]' -s " v e s n o h nice temp seed num first last" - 'c[-1,-v]' -g '*.(trr|trj)(|.gz|.Z) *(/)' - 'c[-1,-e]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' -- g_nmens
+compctl -x 's[-]' -s " f n s o od os h nice b e dt w d sl szonly unsat" - 'c[-1,-d]' -s " z x y" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-od]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-os]' -g '*.xvg(|.gz|.Z) *(/)' -- g_order
+compctl -x 's[-]' -s " f n s o oc of h nice b e dt w d sl cb ce tz spherical" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oc]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-of]' -g '*.xvg(|.gz|.Z) *(/)' -- g_potential
+compctl -x 's[-]' -s " f s o h nice b e dt w" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' -- g_rama
+compctl -x 's[-]' -s " f s n o sq cn hq h nice b e dt w bin com cut fade nlevel startq endq energy" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-sq]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-cn]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-hq]' -g '*.xvg(|.gz|.Z) *(/)' -- g_rdf
+compctl -x 's[-]' -s " s f f2 n o mir a dist m bin bm h nice b e dt tu w what nopbc fit prev split skip skip2 max min bmax bmin nlevels" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-what]' -s " rmsd rho rhosc" - 'c[-1,-fit]' -s " rot+trans translation none" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-f2]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-mir]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-a]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-dist]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-m]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-bin]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-bm]' -g '*.xpm(|.gz|.Z) *(/)' -- g_rms
+compctl -x 's[-]' -s " f s n equiv o rms scl mean nmr3 nmr6 noe h nice b e dt w nlevels max nosumh" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-equiv]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-rms]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-scl]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-mean]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-nmr3]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-nmr6]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-noe]' -g '*.dat(|.gz|.Z) *(/)' -- g_rmsdist
+compctl -x 's[-]' -s " f s n q oq ox o od oc dir h nice b e dt w res aniso" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-q]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-oq]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-ox]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-od]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oc]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-dir]' -g '*.log(|.gz|.Z) *(/)' -- g_rmsf
+compctl -x 's[-]' -s " f s n o h nice b e dt w d noaver acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac exp5 exp7 exp9" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' -- g_rotacf
+compctl -x 's[-]' -s " f s h nice b e dt t sep" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' -- g_saltbr
+compctl -x 's[-]' -s " f s o or oa q n i h nice b e dt w solsize ndots qmax f_index minarea nopbc noprot dgs" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-or]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oa]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-q]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-i]' -g '*.itp(|.gz|.Z) *(/)' -- g_sas
+compctl -x 's[-]' -s " f n s oa od od1 od2 h nice b e dt w" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-oa]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-od]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-od1]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-od2]' -g '*.xvg(|.gz|.Z) *(/)' -- g_sgangle
+compctl -x 's[-]' -s " f s n o no ro co h nice b e dt w com rmin rmax nbin pbc" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-no]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ro]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-co]' -g '*.xvg(|.gz|.Z) *(/)' -- g_sorient
+compctl -x 's[-]' -s " f s n ot oa o of oc ov h nice b e dt w mol k34 wt" - 'c[-1,-f]' -g '*.(trr|trj)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-ot]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oa]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-of]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oc]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ov]' -g '*.xvg(|.gz|.Z) *(/)' -- g_tcaf
+compctl -x 's[-]' -s " f s n ox ov of ob ot ekt ekr cv cf h nice b e dt tu w com mol nojump nox noy noz len scale" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-ox]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ov]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-of]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ob]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ot]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ekt]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ekr]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-cv]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-cf]' -g '*.pdb(|.gz|.Z) *(/)' -- g_traj
+compctl -x 's[-]' -s " f s n o h nice b e dt w mol acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac exp5 exp7 exp9" - 'c[-1,-f]' -g '*.(trr|trj)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' -- g_velacc
+compctl -x 's[-]' -s " o hist h nice w min max bins noprof temp flip tol" - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-hist]' -g '*.xvg(|.gz|.Z) *(/)' -- g_wham
+compctl -x 's[-]' -s " cp cs ci o p h nice box nmol try seed vdwd shell" - 'c[-1,-cp]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-cs]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-ci]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|xml|ent)(|.gz|.Z) *(/)' - 'c[-1,-p]' -g '*.top(|.gz|.Z) *(/)' -- genbox
+compctl -x 's[-]' -s " f o trj h nice nbox dist seed rot shuffle sort block nmolat maxrot renumber" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|xml|ent)(|.gz|.Z) *(/)' - 'c[-1,-trj]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' -- genconf
+compctl -x 's[-]' -s " s table n o g pot h nice np pname pq nn nname nq rmin random seed scale" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-table]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|xml|ent)(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-pot]' -g '*.pdb(|.gz|.Z) *(/)' -- genion
+compctl -x 's[-]' -s " f n o of h nice fc freeze" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.itp(|.gz|.Z) *(/)' - 'c[-1,-of]' -g '*.ndx(|.gz|.Z) *(/)' -- genpr
+compctl -x 's[-]' -s " f f2 s1 s2 c e e2 h nice vdwfac bonlo bonhi tol lastener" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-f2]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s1]' -g '*.(tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-s2]' -g '*.(tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-c]' -g '*.(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-e]' -g '*.(edr|ene)(|.gz|.Z) *(/)' - 'c[-1,-e2]' -g '*.(edr|ene)(|.gz|.Z) *(/)' -- gmxcheck
+compctl -x 's[-]' -s " s f e h nice nonr" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-e]' -g '*.(edr|ene)(|.gz|.Z) *(/)' -- gmxdump
+compctl -x 's[-]' -s " f po c r rb n deshuf p pp o t e h nice nov time np shuffle sort normdumbds load maxwarn check14 norenum" - 'c[-1,-f]' -g '*.mdp(|.gz|.Z) *(/)' - 'c[-1,-po]' -g '*.mdp(|.gz|.Z) *(/)' - 'c[-1,-c]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-r]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-rb]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-deshuf]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-p]' -g '*.top(|.gz|.Z) *(/)' - 'c[-1,-pp]' -g '*.top(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-t]' -g '*.(trr|trj)(|.gz|.Z) *(/)' - 'c[-1,-e]' -g '*.(edr|ene)(|.gz|.Z) *(/)' -- grompp
+compctl -x 's[-]' -s " f a h nice b e dt" - 'c[-1,-f]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-a]' -g '*.dat(|.gz|.Z) *(/)' -- highway
+compctl -x 's[-]' -s " f n o h nice natoms verbose" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.ndx(|.gz|.Z) *(/)' -- make_ndx
+compctl -x 's[-]' -s " s o x c e g dgdl field table rerun ei eo j jo ffout devout runav pi po pd pn mtx dn h nice deffnm np nt v nocompact multi glas ionize" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(trr|trj)(|.gz|.Z) *(/)' - 'c[-1,-x]' -g '*.xtc(|.gz|.Z) *(/)' - 'c[-1,-c]' -g '*.(gro|g96|pdb|brk|xml|ent)(|.gz|.Z) *(/)' - 'c[-1,-e]' -g '*.(edr|ene)(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-dgdl]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-field]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-table]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-rerun]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-ei]' -g '*.edi(|.gz|.Z) *(/)' - 'c[-1,-eo]' -g '*.edo(|.gz|.Z) *(/)' - 'c[-1,-j]' -g '*.gct(|.gz|.Z) *(/)' - 'c[-1,-jo]' -g '*.gct(|.gz|.Z) *(/)' - 'c[-1,-ffout]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-devout]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-runav]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-pi]' -g '*.ppa(|.gz|.Z) *(/)' - 'c[-1,-po]' -g '*.ppa(|.gz|.Z) *(/)' - 'c[-1,-pd]' -g '*.pdo(|.gz|.Z) *(/)' - 'c[-1,-pn]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-mtx]' -g '*.mtx(|.gz|.Z) *(/)' - 'c[-1,-dn]' -g '*.ndx(|.gz|.Z) *(/)' -- mdrun
+compctl -x 's[-]' -s " s n h nice type" - 'c[-1,-type]' -s " angle g96-angle dihedral improper ryckaert-bellemans phi-psi" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' -- mk_angndx
+compctl -x 's[-]' -s " f s n h nice b e dt" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' -- ngmx
+compctl -x 's[-]' -s " f o p i n q h nice merge ff water inter ss ter lys asp glu his angle dist una ignh missing posrefc dummy heavyh deuterate" - 'c[-1,-water]' -s " spc spce tip3p tip4p tip5p" - 'c[-1,-dummy]' -s " none hydrogens aromatics" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|xml|ent)(|.gz|.Z) *(/)' - 'c[-1,-p]' -g '*.top(|.gz|.Z) *(/)' - 'c[-1,-i]' -g '*.itp(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-q]' -g '*.(gro|g96|pdb|brk|xml|ent)(|.gz|.Z) *(/)' -- pdb2gmx
+compctl -x 's[-]' -s " s f n o h nice b e dt" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' -- protonate
+compctl -x 's[-]' -s " s f e n o h nice time extend until zeroq nounconstrained" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(trr|trj)(|.gz|.Z) *(/)' - 'c[-1,-e]' -g '*.(edr|ene)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' -- tpbconv
+compctl -x 's[-]' -s " f o n h nice tu b e dt prec novel settime nosort keeplast cat" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' -- trjcat
+compctl -x 's[-]' -s " f o s n fr h nice b e tu w skip dt dump t0 timestep pbc ur center box shift fit ndec novel force trunc exec app split sep ter" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-pbc]' -s " none whole inbox nojump cluster com" - 'c[-1,-ur]' -s " rect tric compact" - 'c[-1,-fit]' -s " none rot+trans translation progressive" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-fr]' -g '*.ndx(|.gz|.Z) *(/)' -- trjconv
+compctl -x 's[-]' -s " f s n o h nice b e dt na da" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' -- trjorder
+compctl -x 's[-]' -s " f o h nice r0 rot0 T nonn" - 'c[-1,-f]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.eps(|.gz|.Z) *(/)' -- wheel
+compctl -x 's[-]' -s " f o r h nice scale ff nexcl noH14 alldih remdih nopairs name nopbc param noround kb kt kp" - 'c[-1,-ff]' -s " G43a1 oplsaa gmx G43a2 G43b1" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.top(|.gz|.Z) *(/)' - 'c[-1,-r]' -g '*.rtp(|.gz|.Z) *(/)' -- x2top
+compctl -x 's[-]' -s " f f2 di do o xpm h nice w noframe title yonce legend diag combine bx by rainbow gradient skip zeroline legoffset" - 'c[-1,-title]' -s " top once ylabel none" - 'c[-1,-legend]' -s " both first second none" - 'c[-1,-diag]' -s " first second none" - 'c[-1,-combine]' -s " halves add sub mult div" - 'c[-1,-rainbow]' -s " no blue red" - 'c[-1,-f]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-f2]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-di]' -g '*.m2p(|.gz|.Z) *(/)' - 'c[-1,-do]' -g '*.m2p(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.eps(|.gz|.Z) *(/)' - 'c[-1,-xpm]' -g '*.xpm(|.gz|.Z) *(/)' -- xpm2ps
+compctl -x 's[-]' -s " f s h nice b e dt" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|xml)(|.gz|.Z) *(/)' -- xrama
<a href="http://www.gromacs.org/"><img SRC="images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>GROMACS<br>FAQ</h2><font size=-1><A HREF="online.html">Main Table of Contents</A></font><br><br></td>
</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1<br>
-Wed 27 Feb 2002</B></td></tr></TABLE>
+Sun 25 Jan 2004</B></td></tr></TABLE>
<HR>
<p>If you don't find the solution to your problem here, you could have a look in
<HTML>
<HEAD>
-<TITLE>GROMACS 3.1 Online Reference </TITLE>
+<TITLE>GROMACS 3.2 Online Reference </TITLE>
</HEAD>
<LINK rel=stylesheet href="online/style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<td ALIGN=LEFT VALIGN=TOP WIDTH=280>
<br><br>
<h2>
-GROMACS 3.1<br>
+GROMACS 3.2<br>
Online Reference</h2>
</td>
</TABLE></TD>
<td ALIGN=RIGHT VALIGN=BOTTOM WIDTH="*" NOSAVE>
-<B>VERSION 3.1<br>
-Wed 27 Feb 2002</B></td>
+<B>VERSION 3.2<br>
+Sun 25 Jan 2004</B></td>
</tr>
</table>
<multicol cols=5>
<A HREF="online/options.html">Options</a>
<br>
+<br><a href=online/anadock.html>anadock</a>
+<br><a href=online/cdist.html>cdist</a>
+<br><a href=online/disco.html>disco</a>
<br><a href=online/do_dssp.html>do_dssp</a>
<br><a href=online/editconf.html>editconf</a>
<br><a href=online/eneconv.html>eneconv</a>
<br><a href=online/g_disre.html>g_disre</a>
<br><a href=online/g_dist.html>g_dist</a>
<br><a href=online/g_dyndom.html>g_dyndom</a>
-<br><a href=online/genbox.html>genbox</a>
-<br><a href=online/genconf.html>genconf</a>
<br><a href=online/g_enemat.html>g_enemat</a>
<br><a href=online/g_energy.html>g_energy</a>
-<br><a href=online/genion.html>genion</a>
-<br><a href=online/genpr.html>genpr</a>
+<br><a href=online/g_filter.html>g_filter</a>
<br><a href=online/g_gyrate.html>g_gyrate</a>
<br><a href=online/g_h2order.html>g_h2order</a>
<br><a href=online/g_hbond.html>g_hbond</a>
<br><a href=online/g_mindist.html>g_mindist</a>
<br><a href=online/g_morph.html>g_morph</a>
<br><a href=online/g_msd.html>g_msd</a>
-<br><a href=online/gmxcheck.html>gmxcheck</a>
-<br><a href=online/gmxdump.html>gmxdump</a>
<br><a href=online/g_nmeig.html>g_nmeig</a>
<br><a href=online/g_nmens.html>g_nmens</a>
<br><a href=online/g_order.html>g_order</a>
<br><a href=online/g_rms.html>g_rms</a>
<br><a href=online/g_rmsdist.html>g_rmsdist</a>
<br><a href=online/g_rmsf.html>g_rmsf</a>
-<br><a href=online/grompp.html>grompp</a>
<br><a href=online/g_rotacf.html>g_rotacf</a>
<br><a href=online/g_saltbr.html>g_saltbr</a>
<br><a href=online/g_sas.html>g_sas</a>
<br><a href=online/g_tcaf.html>g_tcaf</a>
<br><a href=online/g_traj.html>g_traj</a>
<br><a href=online/g_velacc.html>g_velacc</a>
+<br><a href=online/g_wham.html>g_wham</a>
+<br><a href=online/genbox.html>genbox</a>
+<br><a href=online/genconf.html>genconf</a>
+<br><a href=online/genion.html>genion</a>
+<br><a href=online/genpr.html>genpr</a>
+<br><a href=online/gmxcheck.html>gmxcheck</a>
+<br><a href=online/gmxdump.html>gmxdump</a>
+<br><a href=online/grompp.html>grompp</a>
<br><a href=online/highway.html>highway</a>
<br><a href=online/make_ndx.html>make_ndx</a>
<br><a href=online/mdrun.html>mdrun</a>
<TR><TD><A HREF="online/grompp.html">grompp</A></TD><TD>makes a run input file</TD>
<TR><TD><A HREF="online/tpbconv.html">tpbconv</A></TD><TD>makes a run input file for restarting a crashed run</TD>
<TR><TD><A HREF="online/mdrun.html">mdrun</A></TD><TD>performs a simulation</TD>
-<TR><TD><A HREF="online/xmdrun.html">xmdrun</A></TD><TD>performs simulations with extra experimental features</TD>
</TABLE>
<A NAME="HNR3">
<TR><TD><A HREF="online/g_traj.html">g_traj</A></TD><TD>plots x, v and f of selected atoms/groups (and more) from a trajectory</TD>
<TR><TD><A HREF="online/g_analyze.html">g_analyze</A></TD><TD>analyzes data sets</TD>
<TR><TD><A HREF="online/trjorder.html">trjorder</A></TD><TD>orders molecules according to their distance to a group</TD>
+<TR><TD><A HREF="online/g_filter.html">g_filter</A></TD><TD>frequency filters trajectories, useful for making smooth movies</TD>
+<TR><TD><A HREF="online/g_lie.html">g_lie</A></TD><TD>free energy estimate from linear combinations</TD>
+<TR><TD><A HREF="online/g_dyndom.html">g_dyndom</A></TD><TD>interpolate and extrapolate structure rotations</TD>
+<TR><TD><A HREF="online/g_morph.html">g_morph</A></TD><TD>linear interpolation of conformations </TD>
+<TR><TD><A HREF="online/g_wham.html">g_wham</A></TD><TD>weighted histogram analysis after umbrella sampling</TD>
+<TR><TD><A HREF="online/ffscan.html">ffscan</A></TD><TD>scan and modify force field data for a single point energy calculation</TD>
+<TR><TD><A HREF="online/xpm2ps.html">xpm2ps</A></TD><TD>convert XPM (XPixelMap) file to postscript</TD>
</TABLE>
<A NAME="HNR7">
<TR><TD><A HREF="online/g_confrms.html">g_confrms</A></TD><TD>fits two structures and calculates the rmsd </TD>
<TR><TD><A HREF="online/g_cluster.html">g_cluster</A></TD><TD>clusters structures</TD>
<TR><TD><A HREF="online/g_rmsf.html">g_rmsf</A></TD><TD>calculates atomic fluctuations</TD>
+<TR><TD><A HREF="online/disco.html">disco</A></TD><TD>distance geometry calculation with the CONCOORD algorithm</TD>
+<TR><TD><A HREF="online/cdist.html">cdist</A></TD><TD>create input for disco</TD>
</TABLE>
<A NAME="HNR8">
<TR><TD><A HREF="online/g_sorient.html">g_sorient</A></TD><TD>analyzes solvent orientation around solutes</TD>
<TR><TD><A HREF="online/g_bundle.html">g_bundle</A></TD><TD>analyzes bundles of axes, e.g. helices</TD>
<TR><TD><A HREF="online/g_disre.html">g_disre</A></TD><TD>analyzes distance restraints</TD>
+<TR><TD><A HREF="online/g_clustsize.html">g_clustsize</A></TD><TD>calculate size distributions of atomic clusters</TD>
+<TR><TD><A HREF="online/disco.html">disco</A></TD><TD>distance geometry calculation with the CONCOORD algorithm</TD>
+<TR><TD><A HREF="online/cdist.html">cdist</A></TD><TD>create input for disco</TD>
+<TR><TD><A HREF="online/anadock.html">anadock</A></TD><TD>cluster structures from Autodock runs</TD>
</TABLE>
<A NAME="HNR12">
<TR><TD COLSPAN=2><b>Normal modes</b>
<TR><TD><A HREF="online/grompp.html">grompp</A></TD><TD>makes a run input file</TD>
<TR><TD><A HREF="online/mdrun.html">mdrun</A></TD><TD>finds a potential energy minimum</TD>
-<TR><TD><A HREF="online/nmrun.html">nmrun</A></TD><TD>calculates the Hessian</TD>
+<TR><TD><A HREF="online/mdrun.html">mdrun</A></TD><TD>calculates the Hessian</TD>
<TR><TD><A HREF="online/g_nmeig.html">g_nmeig</A></TD><TD>diagonalizes the Hessian </TD>
<TR><TD><A HREF="online/g_anaeig.html">g_anaeig</A></TD><TD>analyzes the normal modes</TD>
<TR><TD><A HREF="online/g_nmens.html">g_nmens</A></TD><TD>generates an ensemble of structures from the normal modes</TD>
#include <config.h>
#endif
+#include <gmx_ana.h>
/* This is just a wrapper binary.
#include <config.h>
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+#include <gmx_ana.h>
/* This is just a wrapper binary.
#include <config.h>
#endif
+#include <gmx_ana.h>
/* This is just a wrapper binary.
#include <config.h>
#endif
+#include <gmx_ana.h>
+
/* This is just a wrapper binary.
#include <config.h>
#endif
+#include <gmx_ana.h>
/* This is just a wrapper binary.
#include <config.h>
#endif
+#include <gmx_ana.h>
+
/* This is just a wrapper binary.
#include <config.h>
#endif
+#include <gmx_ana.h>
/* This is just a wrapper binary.
#include <config.h>
#endif
+#include <gmx_ana.h>
/* This is just a wrapper binary.
#include <config.h>
#endif
+#include <gmx_ana.h>
+
/* This is just a wrapper binary.
#include <config.h>
#endif
+#include <gmx_ana.h>
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/* This is just a wrapper binary.
#include <config.h>
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/* This is just a wrapper binary.
#include <config.h>
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+#include <gmx_ana.h>
/* This is just a wrapper binary.
#include <config.h>
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+#include <gmx_ana.h>
/* This is just a wrapper binary.
#include <config.h>
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+#include <gmx_ana.h>
/* This is just a wrapper binary.
#include <config.h>
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+#include <gmx_ana.h>
/* This is just a wrapper binary.
#include <config.h>
#endif
+#include <gmx_ana.h>
/* This is just a wrapper binary.
#include <config.h>
#endif
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/* This is just a wrapper binary.
#include <config.h>
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/* This is just a wrapper binary.
#include <config.h>
#endif
+#include <gmx_ana.h>
/* This is just a wrapper binary.
#include <config.h>
#endif
+#include <gmx_ana.h>
/* This is just a wrapper binary.
#include <config.h>
#endif
+#include <gmx_ana.h>
/* This is just a wrapper binary.
#include <config.h>
#endif
+#include <gmx_ana.h>
/* This is just a wrapper binary.
#include <config.h>
#endif
+#include <gmx_ana.h>
/* This is just a wrapper binary.
#include <config.h>
#endif
+#include <gmx_ana.h>
/* This is just a wrapper binary.
#include <config.h>
#endif
+#include <gmx_ana.h>
/* This is just a wrapper binary.
#include <config.h>
#endif
+#include <gmx_ana.h>
+
/* This is just a wrapper binary.
#include <config.h>
#endif
+#include <gmx_ana.h>
/* This is just a wrapper binary.
#include <config.h>
#endif
+#include <gmx_ana.h>
/* This is just a wrapper binary.
#include <config.h>
#endif
+#include <gmx_ana.h>
/* This is just a wrapper binary.
#include <config.h>
#endif
+#include <gmx_ana.h>
/* This is just a wrapper binary.
#include <config.h>
#endif
+#include <gmx_ana.h>
/* This is just a wrapper binary.
#include <config.h>
#endif
+#include <gmx_ana.h>
/* This is just a wrapper binary.
#include <config.h>
#endif
+#include <gmx_ana.h>
+
/* This is just a wrapper binary.
#include <config.h>
#endif
+#include <gmx_ana.h>
/* This is just a wrapper binary.
#include <config.h>
#endif
+#include <gmx_ana.h>
/* This is just a wrapper binary.
#include <config.h>
#endif
+#include <gmx_ana.h>
/* This is just a wrapper binary.
#include <config.h>
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+#include <gmx_ana.h>
/* This is just a wrapper binary.
#include <config.h>
#endif
+#include <gmx_ana.h>
/* This is just a wrapper binary.
#include <config.h>
#endif
+#include <gmx_ana.h>
/* This is just a wrapper binary.
#include <config.h>
#endif
+#include <gmx_ana.h>
/* This is just a wrapper binary.
#include <config.h>
#endif
+#include <gmx_ana.h>
/* This is just a wrapper binary.
#include <config.h>
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/* This is just a wrapper binary.
#include <config.h>
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/* This is just a wrapper binary.
#include <config.h>
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/* This is just a wrapper binary.
#include <config.h>
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/* This is just a wrapper binary.
#include <config.h>
#endif
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/* This is just a wrapper binary.
#include <config.h>
#endif
+#include <gmx_ana.h>
+
/* This is just a wrapper binary.
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff