# machine with no git.
#
# NOTE: when releasing the "-dev" suffix needs to be stripped off!
-set(PROJECT_VERSION "4.5.5-dev")
+set(PROJECT_VERSION "4.5.6-dev")
set(CUSTOM_VERSION_STRING ""
CACHE STRING "Custom version string (if empty, use hard-coded default)")
mark_as_advanced(CUSTOM_VERSION_STRING)
# It is a bit irritating, but this has to be set separately for now!
SET(CPACK_PACKAGE_VERSION_MAJOR "4")
SET(CPACK_PACKAGE_VERSION_MINOR "5")
-SET(CPACK_PACKAGE_VERSION_PATCH "5")
+SET(CPACK_PACKAGE_VERSION_PATCH "6")
# Cmake modules/macros are in a subdirectory to keep this file cleaner
# machine with no git.
#
# NOTE: when releasing the "-dev" suffix needs to be stripped off!
-AC_INIT(gromacs, 4.5.5-dev, [gmx-users@gromacs.org])
+AC_INIT(gromacs, 4.5.6-dev, [gmx-users@gromacs.org])
AC_CONFIG_SRCDIR(src/gmxlib/3dview.c)
AC_CONFIG_AUX_DIR(config)
AC_CANONICAL_HOST
-.TH do_dssp 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH do_dssp 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
do_dssp - assigns secondary structure and calculates solvent accessible surface area
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3do_dssp\fP
.BI "\-f" " traj.xtc "
-.TH editconf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH editconf 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
editconf - edits the box and writes subgroups
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3editconf\fP
.BI "\-f" " conf.gro "
.BI "\-resnr" " int "
.BI "\-[no]grasp" ""
.BI "\-rvdw" " real "
-.BI "\-sig56" " real "
+.BI "\-[no]sig56" ""
.BI "\-[no]vdwread" ""
.BI "\-[no]atom" ""
.BI "\-[no]legend" ""
Choose output from default index groups
.BI "\-bt" " enum" " triclinic"
- Box type for \-box and \-d: \fB triclinic\fR, \fB cubic\fR, \fB dodecahedron\fR or \fB octahedron\fR
+ Box type for \fB \-box\fR and \fB \-d\fR: \fB triclinic\fR, \fB cubic\fR, \fB dodecahedron\fR or \fB octahedron\fR
.BI "\-box" " vector" " 0 0 0"
Box vector lengths (a,b,c)
Distance between the solute and the box
.BI "\-[no]c" "no "
- Center molecule in box (implied by \-box and \-d)
+ Center molecule in box (implied by \fB \-box\fR and \fB \-d\fR)
.BI "\-center" " vector" " 0 0 0"
Coordinates of geometrical center
.BI "\-rvdw" " real" " 0.12 "
Default Van der Waals radius (in nm) if one can not be found in the database or if no parameters are present in the topology file
-.BI "\-sig56" " real" " 0 "
+.BI "\-[no]sig56" "no "
Use rmin/2 (minimum in the Van der Waals potential) rather than sigma/2
.BI "\-[no]vdwread" "no "
- Read the Van der Waals radii from the file vdwradii.dat rather than computing the radii based on the force field
+ Read the Van der Waals radii from the file \fB vdwradii.dat\fR rather than computing the radii based on the force field
.BI "\-[no]atom" "no "
Force B\-factor attachment per atom
-.TH eneconv 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH eneconv 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
eneconv - converts energy files
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3eneconv\fP
.BI "\-f" " ener.edr "
-.TH g_anadock 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_anadock 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_anadock - cluster structures from Autodock runs
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_anadock\fP
.BI "\-f" " eiwit.pdb "
-.TH g_anaeig 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_anaeig 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_anaeig - analyzes the eigenvectors
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_anaeig\fP
.BI "\-v" " eigenvec.trr "
-.TH g_analyze 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_analyze 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_analyze - analyzes data sets
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_analyze\fP
.BI "\-f" " graph.xvg "
\&Option \fB \-ac\fR produces the autocorrelation function(s).
+\&Be sure that the time interval between data points is
+\&much shorter than the time scale of the autocorrelation.
\&Option \fB \-cc\fR plots the resemblance of set i with a cosine of
\&i/2 periods. The formula is:
-2 (int0\-T y(t) cos(i pi t) dt)2 / int0\-T y(t) y(t) dt
+2 (integral from 0 to T of y(t) cos(i pi t) dt)2 / integral from 0 to T of y2(t) dt
\&This is useful for principal components obtained from covariance
\&analysis, since the principal components of random diffusion are
\&A set is divided in a number of blocks and averages are calculated for
\&each block. The error for the total average is calculated from
\&the variance between averages of the m blocks B_i as follows:
-\&error2 = Sum (B_i \- B)2 / (m*(m\-1)).
+\&error2 = sum (B_i \- B)2 / (m*(m\-1)).
\&These errors are plotted as a function of the block size.
\&Also an analytical block average curve is plotted, assuming
\&that the autocorrelation is a sum of two exponentials.
\&The analytical curve for the block average is:
-\&f(t) = sigma\fB *\fRsqrt(2/T ( alpha (tau1 ((exp(\-t/tau1) \- 1) tau1/t + 1)) +
+\&f(t) = sigma\fB *\fRsqrt(2/T ( alpha (tau_1 ((exp(\-t/tau_1) \- 1) tau_1/t + 1)) +
-\& (1\-alpha) (tau2 ((exp(\-t/tau2) \- 1) tau2/t + 1)))),
+\& (1\-alpha) (tau_2 ((exp(\-t/tau_2) \- 1) tau_2/t + 1)))),
where T is the total time.
-\&alpha, tau1 and tau2 are obtained by fitting f2(t) to error2.
+\&alpha, tau_1 and tau_2 are obtained by fitting f2(t) to error2.
\&When the actual block average is very close to the analytical curve,
-\&the error is sigma\fB *\fRsqrt(2/T (a tau1 + (1\-a) tau2)).
+\&the error is sigma\fB *\fRsqrt(2/T (a tau_1 + (1\-a) tau_2)).
\&The complete derivation is given in
\&B. Hess, J. Chem. Phys. 116:209\-217, 2002.
\&Option \fB \-gem\fR fits bimolecular rate constants ka and kb
\&(and optionally kD) to the hydrogen bond autocorrelation function
\&according to the reversible geminate recombination model. Removal of
-\&the ballistic component first is strongly adviced. The model is presented in
+\&the ballistic component first is strongly advised. The model is presented in
\&O. Markovitch, J. Chem. Phys. 129:084505, 2008.
Last time to read from set
.BI "\-n" " int" " 1"
- Read sets separated by &
+ Read this number of sets separated by &
.BI "\-[no]d" "no "
Use the derivative
Interpret second data set as error in the y values for integrating
.BI "\-[no]regression" "no "
- Perform a linear regression analysis on the data. If \fB \-xydy\fR is set a second set will be interpreted as the error bar in the Y value. Otherwise, if multiple data sets are present a multilinear regression will be performed yielding the constant A that minimize chi2 = (y \- A0 x0 \- A1 x1 \- ... \- AN xN)2 where now Y is the first data set in the input file and xi the others. Do read the information at the option \fB \-time\fR.
+ Perform a linear regression analysis on the data. If \fB \-xydy\fR is set a second set will be interpreted as the error bar in the Y value. Otherwise, if multiple data sets are present a multilinear regression will be performed yielding the constant A that minimize chi2 = (y \- A_0 x_0 \- A_1 x_1 \- ... \- A_N x_N)2 where now Y is the first data set in the input file and x_i the others. Do read the information at the option \fB \-time\fR.
.BI "\-[no]luzar" "no "
Do a Luzar and Chandler analysis on a correlation function and related as produced by \fB g_hbond\fR. When in addition the \fB \-xydy\fR flag is given the second and fourth column will be interpreted as errors in c(t) and n(t).
.BI "\-temp" " real" " 298.15"
- Temperature for the Luzar hydrogen bonding kinetics analysis
+ Temperature for the Luzar hydrogen bonding kinetics analysis (K)
.BI "\-fitstart" " real" " 1 "
Time (ps) from which to start fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation
Time (ps) where to stop fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation. Only with \fB \-gem\fR
.BI "\-smooth" " real" " \-1 "
- If = 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(\-x/tau)
+ If this value is = 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(\-x/tau)
.BI "\-filter" " real" " 0 "
- Print the high\-frequency fluctuation after filtering with a cosine filter of length
+ Print the high\-frequency fluctuation after filtering with a cosine filter of this length
.BI "\-[no]power" "no "
Fit data to: b ta
Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR, \fB exp9\fR or \fB erffit\fR
.BI "\-ncskip" " int" " 0"
- Skip N points in the output file of correlation functions
+ Skip this many points in the output file of correlation functions
.BI "\-beginfit" " real" " 0 "
Time where to begin the exponential fit of the correlation function
-.TH g_angle 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_angle 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_angle - calculates distributions and correlations for angles and dihedrals
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_angle\fP
.BI "\-f" " traj.xtc "
\&With option \fB \-or\fR a trajectory file is dumped containing cos and
\&sin of selected dihedral angles which subsequently can be used as
\&input for a PCA analysis using \fB g_covar\fR.
+
+
+\&Option \fB \-ot\fR plots when transitions occur between
+\&dihedral rotamers of multiplicity 3 and \fB \-oh\fR
+\&records a histogram of the times between such transitions,
+\&assuming the input trajectory frames are equally spaced in time.
.SH FILES
.BI "\-f" " traj.xtc"
.B Input
Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR, \fB exp9\fR or \fB erffit\fR
.BI "\-ncskip" " int" " 0"
- Skip N points in the output file of correlation functions
+ Skip this many points in the output file of correlation functions
.BI "\-beginfit" " real" " 0 "
Time where to begin the exponential fit of the correlation function
-.TH g_bar 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_bar 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_bar - calculates free energy difference estimates through Bennett's acceptance ratio
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_bar\fP
.BI "\-f" " dhdl.xvg "
-.TH g_bond 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_bond 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_bond - calculates distances between atoms
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_bond\fP
.BI "\-f" " traj.xtc "
Bond length. By default length of first bond
.BI "\-tol" " real" " 0.1 "
- Half width of distribution as fraction of blen
+ Half width of distribution as fraction of \fB \-blen\fR
.BI "\-[no]aver" "yes "
Average bond length distributions
-.TH g_bundle 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_bundle 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_bundle - analyzes bundles of axes, e.g. helices
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_bundle\fP
.BI "\-f" " traj.xtc "
-.TH g_chi 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_chi 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_chi - calculates everything you want to know about chi and other dihedrals
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_chi\fP
.BI "\-s" " conf.gro "
\&If option \fB \-corr\fR 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
+\&is C(t) = cos(chi(tau)) cos(chi(tau+t)). The use of cosines
\&rather than angles themselves, resolves the problem of periodicity.
\&(Van der Spoel & Berendsen (1997), Biophys. J. 72, 2032\-2041).
\&Separate files for each dihedral of each residue
\&All rotamers are taken as 3\-fold, except for omega 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
+\&to planar groups (i.e. chi_2 of aromatics, Asp and Asn; chi_3 of Glu
+\&and Gln; and chi_4 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 \fB \-core_rotamer\fR
\&The total number of rotamer transitions per timestep
\&(argument \fB \-ot\fR), the number of transitions per rotamer
\&(argument \fB \-rt\fR), and the 3J couplings (argument \fB \-jc\fR),
-\&can also be written to \fB .xvg\fR files.
+\&can also be written to \fB .xvg\fR files. Note that the analysis
+\&of rotamer transitions assumes that the supplied trajectory frames
+\&are equally spaced in time.
\&If \fB \-chi_prod\fR is set (and \fB \-maxchi\fR 0), cumulative rotamers, e.g.
-\&1+9(chi1\-1)+3(chi2\-1)+(chi3\-1) (if the residue has three 3\-fold
+\&1+9(chi_1\-1)+3(chi_2\-1)+(chi_3\-1) (if the residue has three 3\-fold
\&dihedrals and \fB \-maxchi\fR = 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
Output for omega dihedrals (peptide bonds)
.BI "\-[no]rama" "no "
- Generate phi/psi and chi1/chi2 Ramachandran plots
+ Generate phi/psi and chi_1/chi_2 Ramachandran plots
.BI "\-[no]viol" "no "
Write a file that gives 0 or 1 for violated Ramachandran angles
Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR, \fB exp9\fR or \fB erffit\fR
.BI "\-ncskip" " int" " 0"
- Skip N points in the output file of correlation functions
+ Skip this many points in the output file of correlation functions
.BI "\-beginfit" " real" " 0 "
Time where to begin the exponential fit of the correlation function
-.TH g_cluster 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_cluster 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_cluster - clusters structures
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_cluster\fP
.BI "\-f" " traj.xtc "
\&\fB \-cl\fR writes average (with option \fB \-av\fR) or central
\&structure of each cluster or writes numbered files with cluster members
\&for a selected set of clusters (with option \fB \-wcl\fR, depends on
-\&\fB \-nst\fR and \fB \-rmsmin\fR).
+\&\fB \-nst\fR and \fB \-rmsmin\fR). The center of a cluster is the
+\&structure with the smallest average RMSD from all other structures
+\&of the cluster.
.SH FILES
.BI "\-f" " traj.xtc"
Use RMSD of distances instead of RMS deviation
.BI "\-nlevels" " int" " 40"
- Discretize RMSD matrix in levels
+ Discretize RMSD matrix in this number of levels
.BI "\-cutoff" " real" " 0.1 "
RMSD cut\-off (nm) for two structures to be neighbor
Write average iso middle structure for each cluster
.BI "\-wcl" " int" " 0"
- Write all structures for first clusters to numbered files
+ Write the structures for this number of clusters to numbered files
.BI "\-nst" " int" " 1"
- Only write all structures if more than per cluster
+ Only write all structures if more than this number of structures per cluster
.BI "\-rmsmin" " real" " 0 "
minimum rms difference with rest of cluster for writing structures
-.TH g_clustsize 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_clustsize 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_clustsize - calculate size distributions of atomic clusters
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_clustsize\fP
.BI "\-f" " traj.xtc "
-.TH g_confrms 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_confrms 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_confrms - fits two structures and calculates the rmsd
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_confrms\fP
.BI "\-f1" " conf1.gro "
-.TH g_covar 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_covar 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_covar - calculates and diagonalizes the covariance matrix
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_covar\fP
.BI "\-f" " traj.xtc "
-.TH g_current 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_current 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_current - calculate current autocorrelation function of system
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_current\fP
.BI "\-s" " topol.tpr "
\&Option \fB \-eps\fR controls the dielectric constant of the surrounding medium for simulations using
-\&a Reaction Field or dipole corrections of the Ewald summation (eps=0 corresponds to
+\&a Reaction Field or dipole corrections of the Ewald summation (\fB \-eps\fR=0 corresponds to
\&tin\-foil boundary conditions).
\&
Removes jumps of atoms across the box.
.BI "\-eps" " real" " 0 "
- Dielectric constant of the surrounding medium. eps=0.0 corresponds to eps=infinity (tin\-foil boundary conditions).
+ Dielectric constant of the surrounding medium. The value zero corresponds to infinity (tin\-foil boundary conditions).
.BI "\-bfit" " real" " 100 "
Begin of the fit of the straight line to the MSD of the translational fraction of the dipole moment.
-.TH g_density 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_density 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_density - calculates the density of the system
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_density\fP
.BI "\-f" " traj.xtc "
Take the normal on the membrane in direction X, Y or Z.
.BI "\-sl" " int" " 50"
- Divide the box in nr slices.
+ Divide the box in this number of slices.
.BI "\-dens" " enum" " mass"
Density: \fB mass\fR, \fB number\fR, \fB charge\fR or \fB electron\fR
.BI "\-ng" " int" " 1"
- Number of groups to compute densities of
+ Number of groups of which to compute densities.
.BI "\-[no]symm" "no "
Symmetrize the density along the axis, with respect to the center. Useful for bilayers.
-.TH g_densmap 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_densmap 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_densmap - calculates 2D planar or axial-radial density maps
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_densmap\fP
.BI "\-f" " traj.xtc "
-.TH g_densorder 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_densorder 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_densorder - calculate surface fluctuations
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_densorder\fP
.BI "\-s" " topol.tpr "
-.TH g_dielectric 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_dielectric 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_dielectric - calculates frequency dependent dielectric constants
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_dielectric\fP
.BI "\-f" " dipcorr.xvg "
\&\fB g_dielectric\fR calculates frequency dependent dielectric constants
\&from the autocorrelation function of the total dipole moment in
\&your simulation. This ACF can be generated by \fB g_dipoles\fR.
-\&For an estimate of the error you can run g_statistics on the
-\&ACF, and use the output thus generated for this program.
\&The functional forms of the available functions are:
-\&One parameter: y = Exp[\-a1 x],
+\&One parameter: y = exp(\-a_1 x),
-\&Two parameters: y = a2 Exp[\-a1 x],
+\&Two parameters: y = a_2 exp(\-a_1 x),
-\&Three parameters: y = a2 Exp[\-a1 x] + (1 \- a2) Exp[\-a3 x].
+\&Three parameters: y = a_2 exp(\-a_1 x) + (1 \- a_2) exp(\-a_3 x).
\&Start values for the fit procedure can be given on the command line.
\&It is also possible to fix parameters at their start value, use \fB \-fix\fR
-.TH g_dih 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_dih 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_dih - analyzes dihedral transitions
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_dih\fP
.BI "\-f" " traj.xtc "
-.TH g_dipoles 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_dipoles 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_dipoles - computes the total dipole plus fluctuations
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_dipoles\fP
.BI "\-en" " ener.edr "
\&The file \fB Mtot.xvg\fR contains the total dipole moment of a frame, the
\&components as well as the norm of the vector.
-\&The file \fB aver.xvg\fR contains |Mu|2 and | Mu |2 during the
+\&The file \fB aver.xvg\fR contains |mu|2 and |mu|2 during the
\&simulation.
\&The file \fB dipdist.xvg\fR contains the distribution of dipole moments during
\&the simulation
\&EXAMPLES
-\&\fB g_dipoles \-corr mol \-P1 \-o dip_sqr \-mu 2.273 \-mumax 5.0 \-nofft\fR
+\&\fB g_dipoles \-corr mol \-P 1 \-o dip_sqr \-mu 2.273 \-mumax 5.0\fR
\&This will calculate the autocorrelation function of the molecular
\&dipoles using a first order Legendre polynomial of the angle of the
\&dipole vector and itself a time t later. For this calculation 1001
\&frames will be used. Further, the dielectric constant will be calculated
-\&using an epsilonRF of infinity (default), temperature of 300 K (default) and
+\&using an \fB \-epsilonRF\fR of infinity (default), temperature of 300 K (default) and
\&an average dipole moment of the molecule of 2.273 (SPC). For the
\&distribution function a maximum of 5.0 will be used.
.SH FILES
dipole of a single molecule (in Debye)
.BI "\-mumax" " real" " 5 "
- max dipole in Debye (for histrogram)
+ max dipole in Debye (for histogram)
.BI "\-epsilonRF" " real" " 0 "
epsilon of the reaction field used during the simulation, needed for dielectric constant calculation. WARNING: 0.0 means infinity (default)
Correlation function to calculate: \fB none\fR, \fB mol\fR, \fB molsep\fR or \fB total\fR
.BI "\-[no]pairs" "yes "
- Calculate |cos theta| between all pairs of molecules. May be slow
+ Calculate |cos(theta)| between all pairs of molecules. May be slow
.BI "\-ncos" " int" " 1"
- Must be 1 or 2. Determines whether the cos is computed between all molecules in one group, or between molecules in two different groups. This turns on the \fB \-gkr\fR flag.
+ Must be 1 or 2. Determines whether the cos(theta) is computed between all molecules in one group, or between molecules in two different groups. This turns on the \fB \-g\fR flag.
.BI "\-axis" " string" " Z"
Take the normal on the computational box in direction X, Y or Z.
.BI "\-sl" " int" " 10"
- Divide the box in nr slices.
+ Divide the box into this number of slices.
.BI "\-gkratom" " int" " 0"
Use the n\-th atom of a molecule (starting from 1) to calculate the distance between molecules rather than the center of charge (when 0) in the calculation of distance dependent Kirkwood factors
Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR, \fB exp9\fR or \fB erffit\fR
.BI "\-ncskip" " int" " 0"
- Skip N points in the output file of correlation functions
+ Skip this many points in the output file of correlation functions
.BI "\-beginfit" " real" " 0 "
Time where to begin the exponential fit of the correlation function
-.TH g_disre 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_disre 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_disre - analyzes distance restraints
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_disre\fP
.BI "\-s" " topol.tpr "
-.TH g_dist 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_dist 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_dist - calculates the distances between the centers of mass of two groups
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_dist\fP
.BI "\-f" " traj.xtc "
\&With options \fB \-lt\fR and \fB \-dist\fR the number of contacts
\&of all atoms in group 2 that are closer than a certain distance
\&to the center of mass of group 1 are plotted as a function of the time
-\&that the contact was continously present.
+\&that the contact was continuously present.
\&Other programs that calculate distances are \fB g_mindist\fR
-.TH g_dyndom 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_dyndom 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_dyndom - interpolate and extrapolate structure rotations
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_dyndom\fP
.BI "\-f" " dyndom.pdb "
-.TH g_enemat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_enemat 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_enemat - extracts an energy matrix from an energy file
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_enemat\fP
.BI "\-f" " ener.edr "
\&An approximation of the free energy can be calculated using:
-\&E(free) = E0 + kT log( exp((E\-E0)/kT) ), where ''
+\&E_free = E_0 + kT log(exp((E\-E_0)/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)
-.TH g_energy 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_energy 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_energy - writes energies to xvg files and displays averages
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_energy\fP
.BI "\-f" " ener.edr "
.BI "\-skip" " int "
.BI "\-[no]aver" ""
.BI "\-nmol" " int "
+.BI "\-[no]fluct_props" ""
+.BI "\-[no]driftcorr" ""
.BI "\-[no]fluc" ""
.BI "\-[no]orinst" ""
.BI "\-[no]ovec" ""
\&The term fluctuation gives the RMSD around the least\-squares fit.
-\&When the \fB \-viol\fR option is set, the time averaged
+\&Some fluctuation\-dependent properties can be calculated provided
+\&the correct energy terms are selected, and that the command line option
+\&\fB \-fluct_props\fR is given. The following properties
+\&will be computed:
+
+\&Property Energy terms needed
+
+\&\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-
+
+\&Heat capacity C_p (NPT sims): Enthalpy, Temp
+
+\&Heat capacity C_v (NVT sims): Etot, Temp
+
+\&Thermal expansion coeff. (NPT): Enthalpy, Vol, Temp
+
+\&Isothermal compressibility: Vol, Temp
+
+\&Adiabatic bulk modulus: Vol, Temp
+
+\&\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-
+
+\&You always need to set the number of molecules \fB \-nmol\fR.
+\&The C_p/C_v computations do \fB not\fR include any corrections
+\&for quantum effects. Use the \fB g_dos\fR program if you need that (and you do).
+
+When the \fB \-viol\fR option is set, the time averaged
\&violations are plotted and the running time\-averaged and
\&instantaneous sum of violations are recalculated. Additionally
\&running time\-averaged and instantaneous distances between
\&With \fB \-fee\fR 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 A = A(N,V,T) \- A_idealgas(N,V,T) = kT ln(exp(U_pot/kT))
-\& Delta G = G(N,p,T) \- G_idgas(N,p,T) = kT ln e(Upot/kT)
+\& Delta G = G(N,p,T) \- G_idealgas(N,p,T) = kT ln(exp(U_pot/kT))
\&where k is Boltzmann's constant, T is set by \fB \-fetemp\fR and
\&the average is over the ensemble (or time in a trajectory).
\&and using the potential energy. This also allows for an entropy
\&estimate using:
-\& Delta S(N,V,T) = S(N,V,T) \- S_idgas(N,V,T) = (Upot \- Delta A)/T
+\& Delta S(N,V,T) = S(N,V,T) \- S_idealgas(N,V,T) = (U_pot \- Delta A)/T
-\& Delta S(N,p,T) = S(N,p,T) \- S_idgas(N,p,T) = (Upot + pV \- Delta G)/T
+\& Delta S(N,p,T) = S(N,p,T) \- S_idealgas(N,p,T) = (U_pot + pV \- Delta G)/T
\&
\&When a second energy file is specified (\fB \-f2\fR), a free energy
-\&difference is calculated dF = \-kT ln e \-(EB\-EA)/kT A ,
-\&where EA and EB are the energies from the first and second energy
+\&difference is calculated
+ dF = \-kT ln(exp(\-(E_B\-E_A)/kT)_A) ,
+\&where E_A and E_B are the energies from the first and second energy
\&files, and the average is over the ensemble A. The running average
\&of the free energy difference is printed to a file specified by \fB \-ravg\fR.
\&\fB Note\fR that the energies must both be calculated from the same trajectory.
.BI "\-nmol" " int" " 1"
Number of molecules in your sample: the energies are divided by this number
+.BI "\-[no]fluct_props" "no "
+ Compute properties based on energy fluctuations, like heat capacity
+
+.BI "\-[no]driftcorr" "no "
+ Useful only for calculations of fluctuation properties. The drift in the observables will be subtracted before computing the fluctuation properties.
+
.BI "\-[no]fluc" "no "
Calculate autocorrelation of energy fluctuations rather than energy itself
Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR, \fB exp9\fR or \fB erffit\fR
.BI "\-ncskip" " int" " 0"
- Skip N points in the output file of correlation functions
+ Skip this many points in the output file of correlation functions
.BI "\-beginfit" " real" " 0 "
Time where to begin the exponential fit of the correlation function
-.TH g_filter 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_filter 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_filter - frequency filters trajectories, useful for making smooth movies
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_filter\fP
.BI "\-f" " traj.xtc "
-.TH g_gyrate 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_gyrate 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_gyrate - calculates the radius of gyration
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_gyrate\fP
.BI "\-f" " traj.xtc "
Calculate the moments of inertia (defined by the principal axes).
.BI "\-nz" " int" " 0"
- Calculate the 2D radii of gyration of slices along the z\-axis
+ Calculate the 2D radii of gyration of this number of slices along the z\-axis
.BI "\-acflen" " int" " \-1"
Length of the ACF, default is half the number of frames
Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR, \fB exp9\fR or \fB erffit\fR
.BI "\-ncskip" " int" " 0"
- Skip N points in the output file of correlation functions
+ Skip this many points in the output file of correlation functions
.BI "\-beginfit" " real" " 0 "
Time where to begin the exponential fit of the correlation function
-.TH g_h2order 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_h2order 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_h2order - computes the orientation of water molecules
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_h2order\fP
.BI "\-f" " traj.xtc "
Take the normal on the membrane in direction X, Y or Z.
.BI "\-sl" " int" " 0"
- Calculate order parameter as function of boxlength, dividing the box in nr slices.
+ Calculate order parameter as function of boxlength, dividing the box in this number of slices.
.SH KNOWN PROBLEMS
\- The program assigns whole water molecules to a slice, based on the first atom of three in the index file group. It assumes an order O,H,H. Name is not important, but the order is. If this demand is not met, assigning molecules to slices is different.
-.TH g_hbond 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_hbond 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_hbond - computes and analyzes hydrogen bonds
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_hbond\fP
.BI "\-f" " traj.xtc "
Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR, \fB exp9\fR or \fB erffit\fR
.BI "\-ncskip" " int" " 0"
- Skip N points in the output file of correlation functions
+ Skip this many points in the output file of correlation functions
.BI "\-beginfit" " real" " 0 "
Time where to begin the exponential fit of the correlation function
-.TH g_helix 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_helix 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_helix - calculates basic properties of alpha helices
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_helix\fP
.BI "\-s" " topol.tpr "
\&\fB 1.\fR Helix radius (file \fB radius.xvg\fR). This is merely the
\&RMS deviation in two dimensions for all Calpha atoms.
-\&it is calced as sqrt((SUM i(x2(i)+y2(i)))/N), where N is the number
+\&it is calculated as sqrt((sum_i (x2(i)+y2(i)))/N) where N is the number
\&of backbone atoms. For an ideal helix the radius is 0.23 nm
\&\fB 2.\fR Twist (file \fB twist.xvg\fR). The average helical angle per
-.TH g_helixorient 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_helixorient 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_helixorient - calculates local pitch/bending/rotation/orientation inside helices
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_helixorient\fP
.BI "\-s" " topol.tpr "
-.TH g_hydorder 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_hydorder 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
-g_hydorder
-.B VERSION 4.5.4-dev-20110404-bc5695c
+g_hydorder - computes tetrahedrality parameters around a given atom
+
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_hydorder\fP
.BI "\-f" " traj.xtc "
.BI "\-tblock" " int "
.BI "\-nlevel" " int "
.SH DESCRIPTION
-\&The tetrahedrality order parameters can be determined
-\&around an atom. Both angle an distance order parameters are calculated. See
+\&g_hydorder computes the tetrahedrality order parameters around a
+\&given atom. Both angle an distance order parameters are calculated. See
\&P.\-L. Chau and A.J. Hardwick, Mol. Phys., 93, (1998), 511\-518.
\&for more details.
This application calculates the orderparameter in a 3d\-mesh in the box, and
-.TH g_lie 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_lie 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_lie - free energy estimate from linear combinations
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_lie\fP
.BI "\-f" " ener.edr "
-.TH g_mdmat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_mdmat 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_mdmat - calculates residue contact maps
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_mdmat\fP
.BI "\-f" " traj.xtc "
trunc distance
.BI "\-nlevels" " int" " 40"
- Discretize distance in levels
+ Discretize distance in this number of levels
.SH SEE ALSO
.BR gromacs(7)
-.TH g_membed 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_membed 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_membed - embeds a protein into a lipid bilayer
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_membed\fP
.BI "\-f" " into_mem.tpr "
-.TH g_mindist 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_mindist 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_mindist - calculates the minimum distance between two groups
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_mindist\fP
.BI "\-f" " traj.xtc "
\&(between any pair of atoms from the respective groups)
\&and the number of contacts within a given
\&distance are written to two separate output files.
-\&With the \fB \-group\fR option a contact of an atom an other group
+\&With the \fB \-group\fR option a contact of an atom in another group
\&with multiple atoms in the first group is counted as one contact
\&instead of as multiple contacts.
\&With \fB \-or\fR, minimum distances to each residue in the first
-.TH g_morph 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_morph 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_morph - linear interpolation of conformations
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_morph\fP
.BI "\-f1" " conf1.gro "
\&interpolating: 0 corresponds to input structure 1 while
\&1 corresponds to input structure 2.
\&If you specify \fB \-first\fR 0 or \fB \-last\fR 1 extrapolation will be
-\&on the path from input structure x1 to x2. In general, the coordinates
-\&of the intermediate x(i) out of N total intermidates correspond to:
+\&on the path from input structure x_1 to x_2. In general, the coordinates
+\&of the intermediate x(i) out of N total intermediates correspond to:
-\&x(i) = x1 + (first+(i/(N\-1))*(last\-first))*(x2\-x1)
+\&x(i) = x_1 + (first+(i/(N\-1))*(last\-first))*(x_2\-x_1)
\&Finally the RMSD with respect to both input structures can be computed
Number of intermediates
.BI "\-first" " real" " 0 "
- Corresponds to first generated structure (0 is input x0, see above)
+ Corresponds to first generated structure (0 is input x_1, see above)
.BI "\-last" " real" " 1 "
- Corresponds to last generated structure (1 is input x1, see above)
+ Corresponds to last generated structure (1 is input x_2, see above)
.BI "\-[no]fit" "yes "
Do a least squares fit of the second to the first structure before interpolating
-.TH g_msd 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_msd 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_msd - calculates mean square displacements
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_msd\fP
.BI "\-f" " traj.xtc "
-.TH g_nmeig 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_nmeig 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_nmeig - diagonalizes the Hessian
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_nmeig\fP
.BI "\-f" " hessian.mtx "
-.TH g_nmens 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_nmens 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_nmens - generates an ensemble of structures from the normal modes
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_nmens\fP
.BI "\-v" " eigenvec.trr "
-.TH g_nmtraj 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_nmtraj 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_nmtraj - generate a virtual trajectory from an eigenvector
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_nmtraj\fP
.BI "\-s" " topol.tpr "
String of phases (default is 0.0)
.BI "\-temp" " real" " 300 "
- Temperature in Kelvin
+ Temperature (K)
.BI "\-amplitude" " real" " 0.25 "
Amplitude for modes with eigenvalue=0
-.TH g_options 1 "Sun 10 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110410-e5eb052-dirty"
+.TH g_options 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_options
-.B VERSION 4.5.4-dev-20110410-e5eb052-dirty
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_options\fP
.BI "\-[no]h" ""
-.TH g_order 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_order 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_order - computes the order parameter per atom for carbon tails
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_order\fP
.BI "\-f" " traj.xtc "
Direction of the normal on the membrane: \fB z\fR, \fB x\fR or \fB y\fR
.BI "\-sl" " int" " 1"
- Calculate order parameter as function of box length, dividing the box in nr slices.
+ Calculate order parameter as function of box length, dividing the box into this number of slices.
.BI "\-[no]szonly" "no "
Only give Sz element of order tensor. (axis can be specified with \fB \-d\fR)
-.TH g_pme_error 1 "Sun 10 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110410-e5eb052-dirty"
+.TH g_pme_error 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_pme_error - estimates the error of using PME with a given input file
-.B VERSION 4.5.4-dev-20110410-e5eb052-dirty
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_pme_error\fP
.BI "\-s" " topol.tpr "
-.TH g_polystat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_polystat 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_polystat - calculates static properties of polymers
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_polystat\fP
.BI "\-s" " topol.tpr "
-.TH g_potential 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_potential 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_potential - calculates the electrostatic potential across the box
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_potential\fP
.BI "\-f" " traj.xtc "
Take the normal on the membrane in direction X, Y or Z.
.BI "\-sl" " int" " 10"
- Calculate potential as function of boxlength, dividing the box in nr slices.
+ Calculate potential as function of boxlength, dividing the box in this number of slices.
.BI "\-cb" " int" " 0"
- Discard first nr slices of box for integration
+ Discard this number of first slices of box for integration
.BI "\-ce" " int" " 0"
- Discard last nr slices of box for integration
+ Discard this number of last slices of box for integration
.BI "\-tz" " real" " 0 "
- Translate all coordinates distance in the direction of the box
+ Translate all coordinates by this distance in the direction of the box
.BI "\-[no]spherical" "no "
Calculate spherical thingie
-.TH g_principal 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_principal 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_principal - calculates axes of inertia for a group of atoms
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_principal\fP
.BI "\-f" " traj.xtc "
-.TH g_protonate 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_protonate 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_protonate - protonates structures
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_protonate\fP
.BI "\-s" " topol.tpr "
.BI "\-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
+.SH KNOWN PROBLEMS
+\- For the moment, only .pdb files are accepted to the \-s flag
+
.SH SEE ALSO
.BR gromacs(7)
-.TH g_rama 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_rama 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_rama - computes Ramachandran plots
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_rama\fP
.BI "\-f" " traj.xtc "
-.TH g_rdf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_rdf 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_rdf - calculates radial distribution functions
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_rdf\fP
.BI "\-f" " traj.xtc "
-.TH g_rms 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_rms 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_rms - calculates rmsd's with a reference structure and rmsd matrices
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_rms\fP
.BI "\-s" " topol.tpr "
-.TH g_rmsdist 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_rmsdist 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_rmsdist - calculates atom pair distances averaged with power \-2, \-3 or \-6
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_rmsdist\fP
.BI "\-f" " traj.xtc "
xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
.BI "\-nlevels" " int" " 40"
- Discretize rms in levels
+ Discretize RMS in this number of levels
.BI "\-max" " real" " \-1 "
Maximum level in matrices
.BI "\-[no]sumh" "yes "
- average distance over equivalent hydrogens
+ Average distance over equivalent hydrogens
.BI "\-[no]pbc" "yes "
Use periodic boundary conditions when computing distances
-.TH g_rmsf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_rmsf 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_rmsf - calculates atomic fluctuations
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_rmsf\fP
.BI "\-f" " traj.xtc "
-.TH g_rotacf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_rotacf 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_rotacf - calculates the rotational correlation function for molecules
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_rotacf\fP
.BI "\-f" " traj.xtc "
.BI "\-endfit" " real "
.SH DESCRIPTION
\&\fB g_rotacf\fR calculates the rotational correlation function
-\&for molecules. Three atoms (i,j,k) must be given in the index
+\&for molecules. Atom triplets (i,j,k) must be given in the index
\&file, defining two vectors ij and jk. The rotational ACF
\&is calculated as the autocorrelation function of the vector
\&n = ij x jk, i.e. the cross product of the two vectors.
\&Since three atoms span a plane, the order of the three atoms
-\&does not matter. Optionally, controlled by the \fB \-d\fR switch, you can
+\&does not matter. Optionally, by invoking the \fB \-d\fR switch, you can
\&calculate the rotational correlation function for linear molecules
-\&by specifying two atoms (i,j) in the index file.
+\&by specifying atom pairs (i,j) in the index file.
\&
Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR, \fB exp9\fR or \fB erffit\fR
.BI "\-ncskip" " int" " 0"
- Skip N points in the output file of correlation functions
+ Skip this many points in the output file of correlation functions
.BI "\-beginfit" " real" " 0 "
Time where to begin the exponential fit of the correlation function
-.TH g_rotmat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_rotmat 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_rotmat - plots the rotation matrix for fitting to a reference structure
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_rotmat\fP
.BI "\-f" " traj.xtc "
-.TH g_saltbr 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_saltbr 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_saltbr - computes salt bridges
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_saltbr\fP
.BI "\-f" " traj.xtc "
Only use frame when t MOD dt = first time (ps)
.BI "\-t" " real" " 1000 "
- trunc distance
+ Groups that are never closer than this distance are not plotted
.BI "\-[no]sep" "no "
Use separate files for each interaction (may be MANY)
-.TH g_sas 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_sas 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_sas - computes solvent accessible surface area
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_sas\fP
.BI "\-f" " traj.xtc "
.BI "\-[no]prot" ""
.BI "\-dgs" " real "
.SH DESCRIPTION
-\&\fB g_sas\fR computes hydrophobic, hydrophilic and total solvent accessible surface area.
+\&\fB g_sas\fR computes hydrophobic, hydrophilic and total solvent
+\&accessible surface area. See Eisenhaber F, Lijnzaad P, Argos P,
+\&Sander C, & Scharf M (1995) J. Comput. Chem. 16, 273\-284.
\&As a side effect, the Connolly surface can be generated as well in
-\&a \fB .pdb\fR file where the nodes are represented as atoms and the vertices
-\&connecting the nearest nodes as CONECT records.
+\&a \fB .pdb\fR file where the nodes are represented as atoms and the
+\&vertice connecting the nearest nodes as CONECT records.
\&The program will ask for a group for the surface calculation
\&and a group for the output. The calculation group should always
\&consists of all the non\-solvent atoms in the system.
\&this can be turned off using the \fB \-nopbc\fR option.
-\&With the \fB \-tv\fR option the total volume and density of the molecule can be
-\&computed.
+\&With the \fB \-tv\fR option the total volume and density of the
+\&molecule can be computed.
\&Please consider whether the normal probe radius is appropriate
\&in this case or whether you would rather use e.g. 0. It is good
\&to keep in mind that the results for volume and density are very
-.TH g_select 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_select 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_select - selects groups of atoms based on flexible textual selections
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_select\fP
.BI "\-f" " traj.xtc "
\&analysis programs to calculate more complex things.
\&Any combination of the output options is possible, but note
\&that \fB \-om\fR only operates on the first selection.
+\&\fB \-os\fR is the default output option if none is selected.
\&With \fB \-os\fR, calculates the number of positions in each
Use periodic boundary conditions for distance calculation
.BI "\-select" " string" " "
- Selection string (use 'help' for help)
+ Selection string (use 'help' for help). Note that the whole selection string will need to be quoted so that your shell will pass it in as a string. Example: \fB g_select \-select '"Nearby water" resname SOL and within 0.25 of group Protein'\fR
.BI "\-selrpos" " enum" " atom"
Selection reference position: \fB atom\fR, \fB res_com\fR, \fB res_cog\fR, \fB mol_com\fR, \fB mol_cog\fR, \fB whole_res_com\fR, \fB whole_res_cog\fR, \fB whole_mol_com\fR, \fB whole_mol_cog\fR, \fB part_res_com\fR, \fB part_res_cog\fR, \fB part_mol_com\fR, \fB part_mol_cog\fR, \fB dyn_res_com\fR, \fB dyn_res_cog\fR, \fB dyn_mol_com\fR or \fB dyn_mol_cog\fR
-.TH g_sgangle 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_sgangle 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_sgangle - computes the angle and distance between two groups
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_sgangle\fP
.BI "\-f" " traj.xtc "
-.TH g_sham 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_sham 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_sham - read/write xmgr and xvgr data sets
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_sham\fP
.BI "\-f" " graph.xvg "
Protein data bank file
.BI "\-mdata" " mapdata.xvg"
-.B Output, Opt.
+.B Input, Opt.
xvgr/xmgr file
.BI "\-g" " shamlog.log"
Tolerance on time in appropriate units (usually ps)
.BI "\-n" " int" " 1"
- Read sets separated by &
+ Read this number of sets separated by lines containing only an ampersand
.BI "\-[no]d" "no "
Use the derivative
-.TH g_sigeps 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_sigeps 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_sigeps - convert c6/12 or c6/cn combinations to and from sigma/epsilon
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_sigeps\fP
.BI "\-o" " potje.xvg "
xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
.BI "\-c6" " real" " 0.001 "
- c6
+ C6
.BI "\-cn" " real" " 1e\-06 "
- constant for repulsion
+ Constant for repulsion
.BI "\-pow" " int" " 12"
- power of the repulsion term
+ Power of the repulsion term
.BI "\-sig" " real" " 0.3 "
- sig
+ sigma
.BI "\-eps" " real" " 1 "
- eps
+ epsilon
.BI "\-A" " real" " 100000"
Buckingham A
-.TH g_sorient 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_sorient 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_sorient - analyzes solvent orientation around solutes
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_sorient\fP
.BI "\-f" " traj.xtc "
\&reference positions to the first atom of each solvent molecule:
-\&theta1: the angle with the vector from the first atom of the solvent
+\&theta_1: the angle with the vector from the first atom of the solvent
\&molecule to the midpoint between atoms 2 and 3.
-\&theta2: the angle with the normal of the solvent plane, defined by the
+\&theta_2: the angle with the normal of the solvent plane, defined by the
\&same three atoms, or, when the option \fB \-v23\fR is set,
\&the angle with the vector between atoms 2 and 3.
\&considered for \fB \-o\fR and \fB \-no\fR each frame.
-\&\fB \-o\fR: distribtion of cos(theta1) for rmin=r=rmax.
+\&\fB \-o\fR: distribtion of cos(theta_1) for rmin=r=rmax.
-\&\fB \-no\fR: distribution of cos(theta2) for rmin=r=rmax.
+\&\fB \-no\fR: distribution of cos(theta_2) for rmin=r=rmax.
-\&\fB \-ro\fR: cos(theta1) and 3cos2(theta2)\-1 as a function of the
+\&\fB \-ro\fR: cos(theta_1) and 3cos(2theta_2)\-1 as a function of the
\&distance.
\&\fB \-co\fR: the sum over all solvent molecules within distance r
-\&of cos(theta1) and 3cos2(theta2)\-1 as a function of r.
+\&of cos(theta_1) and 3cos(2(theta_2)\-1) as a function of r.
\&\fB \-rc\fR: the distribution of the solvent molecules as a function of r
-.TH g_spatial 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_spatial 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_spatial - calculates the spatial distribution function
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_spatial\fP
.BI "\-s" " topol.tpr "
Do not display this number of outer cubes (positive values may reduce boundary speckles; \-1 ensures outer surface is visible)
.BI "\-bin" " real" " 0.05 "
- Width of the bins in nm
+ Width of the bins (nm)
.BI "\-nab" " int" " 4"
Number of additional bins to ensure proper memory allocation
-.TH g_spol 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_spol 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_spol - analyzes solvent dipole orientation and polarization around solutes
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_spol\fP
.BI "\-f" " traj.xtc "
-.TH g_tcaf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_tcaf 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_tcaf - calculates viscosities of liquids
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_tcaf\fP
.BI "\-f" " traj.trr "
\¬ independent). For each k\-vector the sine and cosine are used, in
\&combination with the velocity in 2 perpendicular directions. This gives
\&a total of 16*2*2=64 transverse currents. One autocorrelation is
-\&calculated fitted for each k\-vector, which gives 16 TCAF's. Each of
-\&these TCAF's is fitted to f(t) = exp(\-v)(cosh(Wv) + 1/W sinh(Wv)),
+\&calculated fitted for each k\-vector, which gives 16 TCAFs. Each of
+\&these TCAFs is fitted to f(t) = exp(\-v)(cosh(Wv) + 1/W sinh(Wv)),
\&v = \-t/(2 tau), W = sqrt(1 \- 4 tau eta/rho k2), which gives 16 values of tau
-\&and eta. The fit weights decay with time as exp(\-t/wt), and the TCAF and
-\&fit are calculated up to time 5*wt.
+\&and eta. The fit weights decay exponentially with time constant w (given with \fB \-wt\fR) as exp(\-t/w), and the TCAF and
+\&fit are calculated up to time 5*w.
\&The eta values should be fitted to 1 \- a eta(k) k2, from which
\&one can estimate the shear viscosity at k=0.
\&When the box is cubic, one can use the option \fB \-oc\fR, which
-\&averages the TCAF's over all k\-vectors with the same length.
-\&This results in more accurate tcaf's.
-\&Both the cubic TCAF's and fits are written to \fB \-oc\fR
+\&averages the TCAFs over all k\-vectors with the same length.
+\&This results in more accurate TCAFs.
+\&Both the cubic TCAFs and fits are written to \fB \-oc\fR
\&The cubic eta estimates are also written to \fB \-ov\fR.
\&The k\-dependent viscosities in the \fB \-ov\fR file should be
-\&fitted to eta(k) = eta0 (1 \- a k2) to obtain the viscosity at
+\&fitted to eta(k) = eta_0 (1 \- a k2) to obtain the viscosity at
\&infinite wavelength.
xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
.BI "\-[no]mol" "no "
- Calculate tcaf of molecules
+ Calculate TCAF of molecules
.BI "\-[no]k34" "no "
Also use k=(3,0,0) and k=(4,0,0)
Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR, \fB exp9\fR or \fB erffit\fR
.BI "\-ncskip" " int" " 0"
- Skip N points in the output file of correlation functions
+ Skip this many points in the output file of correlation functions
.BI "\-beginfit" " real" " 0 "
Time where to begin the exponential fit of the correlation function
-.TH g_traj 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_traj 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_traj - plots x, v and f of selected atoms/groups (and more) from a trajectory
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_traj\fP
.BI "\-f" " traj.xtc "
-.TH g_tune_pme 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_tune_pme 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_tune_pme - time mdrun as a function of PME nodes to optimize settings
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_tune_pme\fP
.BI "\-p" " perf.out "
If non\-negative, perform this many steps in the real run (overwrites nsteps from \fB .tpr\fR, add \fB .cpt\fR steps)
.BI "\-[no]launch" "no "
- Lauch the real simulation after optimization
+ Launch the real simulation after optimization
.BI "\-deffnm" " string" " "
Set the default filename for all file options at launch time
Do multiple simulations in parallel
.BI "\-replex" " int" " 0"
- Attempt replica exchange every steps
+ Attempt replica exchange periodically with this period (steps)
.BI "\-reseed" " int" " \-1"
Seed for replica exchange, \-1 is generate a seed
-.TH g_vanhove 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_vanhove 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_vanhove - calculates Van Hove displacement functions
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_vanhove\fP
.BI "\-f" " traj.xtc "
.BI "\-ft" " int "
.SH DESCRIPTION
\&\fB g_vanhove\fR computes the Van Hove correlation function.
-\&The Van Hove G(r,t) is the probability that a particle that is at r0
-\&at time zero can be found at position r0+r at time t.
+\&The Van Hove G(r,t) is the probability that a particle that is at r_0
+\&at time zero can be found at position r_0+r at time t.
\&\fB g_vanhove\fR determines G not for a vector r, but for the length of r.
\&Thus it gives the probability that a particle moves a distance of r
\&in time t.
-.TH g_velacc 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_velacc 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_velacc - calculates velocity autocorrelation functions
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_velacc\fP
.BI "\-f" " traj.trr "
\&With option \fB \-mol\fR the velocity autocorrelation function of
\&molecules is calculated. In this case the index group should consist
\&of molecule numbers instead of atom numbers.
+
+
+\&Be sure that your trajectory contains frames with velocity information
+\&(i.e. \fB nstvout\fR was set in your original \fB .mdp\fR file),
+\&and that the time interval between data collection points is
+\&much shorter than the time scale of the autocorrelation.
.SH FILES
.BI "\-f" " traj.trr"
.B Input
Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR, \fB exp9\fR or \fB erffit\fR
.BI "\-ncskip" " int" " 0"
- Skip N points in the output file of correlation functions
+ Skip this many points in the output file of correlation functions
.BI "\-beginfit" " real" " 0 "
Time where to begin the exponential fit of the correlation function
-.TH g_wham 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_wham 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_wham - weighted histogram analysis after umbrella sampling
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_wham\fP
.BI "\-ix" " pullx\-files.dat "
\&to the file defined with \fB \-oiact\fR. In verbose mode, all
\&autocorrelation functions (ACFs) are written to \fB hist_autocorr.xvg\fR.
\&Because the IACTs can be severely underestimated in case of limited
-\&sampling, option \fB \-acsig\fR allows to smooth the IACTs along the
+\&sampling, option \fB \-acsig\fR allows one to smooth the IACTs along the
\&reaction coordinate with a Gaussian (sigma provided with \fB \-acsig\fR,
\&see output in \fB iact.xvg\fR). Note that the IACTs are estimated by simple
\&integration of the ACFs while the ACFs are larger 0.05.
-.TH g_wheel 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_wheel 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_wheel - plots helical wheels
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_wheel\fP
.BI "\-f" " nnnice.dat "
-.TH g_x2top 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_x2top 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_x2top - generates a primitive topology from coordinates
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_x2top\fP
.BI "\-f" " conf.gro "
-.TH g_xrama 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH g_xrama 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
g_xrama - shows animated Ramachandran plots
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3g_xrama\fP
.BI "\-f" " traj.xtc "
-.TH genbox 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH genbox 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
genbox - solvates a system
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3genbox\fP
.BI "\-cp" " protein.gro "
Set the nicelevel
.BI "\-box" " vector" " 0 0 0"
- box size
+ Box size
.BI "\-nmol" " int" " 0"
- no of extra molecules to insert
+ Number of extra molecules to insert
.BI "\-try" " int" " 10"
- try inserting \fB \-nmol\fR times \fB \-try\fR times
+ Try inserting \fB \-nmol\fR times \fB \-try\fR times
.BI "\-seed" " int" " 1997"
- random generator seed
+ Random generator seed
.BI "\-vdwd" " real" " 0.105 "
- default vdwaals distance
+ Default van der Waals distance
.BI "\-shell" " real" " 0 "
- thickness of optional water layer around solute
+ Thickness of optional water layer around solute
.BI "\-maxsol" " int" " 0"
- maximum number of solvent molecules to add if they fit in the box. If zero (default) this is ignored
+ Maximum number of solvent molecules to add if they fit in the box. If zero (default) this is ignored
.BI "\-[no]vel" "no "
- keep velocities from input solute and solvent
+ Keep velocities from input solute and solvent
.SH KNOWN PROBLEMS
\- Molecules must be whole in the initial configurations.
-.TH genconf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH genconf 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
genconf - multiplies a conformation in 'random' orientations
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3genconf\fP
.BI "\-f" " conf.gro "
-.TH genion 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH genion 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
genion - generates mono atomic ions on energetically favorable positions
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3genion\fP
.BI "\-s" " topol.tpr "
-.TH genrestr 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH genrestr 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
genrestr - generates position restraints or distance restraints for index groups
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3genrestr\fP
.BI "\-f" " conf.gro "
Set the nicelevel
.BI "\-fc" " vector" " 1000 1000 1000"
- force constants (kJ/mol nm2)
+ Force constants (kJ/mol nm2)
.BI "\-freeze" " real" " 0 "
- if the \fB \-of\fR 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
+ If the \fB \-of\fR 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
.BI "\-[no]disre" "no "
Generate a distance restraint matrix for all the atoms in index
-.TH gmxcheck 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH gmxcheck 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
gmxcheck - checks and compares files
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3gmxcheck\fP
.BI "\-f" " traj.xtc "
-.TH gmxdump 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH gmxdump 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
gmxdump - makes binary files human readable
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3gmxdump\fP
.BI "\-s" " topol.tpr "
.BI "\-[no]sys" "no "
List the atoms and bonded interactions for the whole system instead of for each molecule type
+.SH KNOWN PROBLEMS
+\- Position restraint output from \-sys \-s is broken
+
.SH SEE ALSO
.BR gromacs(7)
-.TH grompp 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH grompp 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
grompp - makes a run input file
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3grompp\fP
.BI "\-f" " grompp.mdp "
-.TH make_edi 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH make_edi 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
make_edi - generate input files for essential dynamics sampling
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3make_edi\fP
.BI "\-f" " eigenvec.trr "
-.TH make_ndx 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH make_ndx 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
make_ndx - makes index files
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3make_ndx\fP
.BI "\-f" " conf.gro "
-.TH mdrun 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH mdrun 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
mdrun - performs a simulation, do a normal mode analysis or an energy minimization
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3mdrun\fP
.BI "\-s" " topol.tpr "
.BI "\-xvg" " enum "
.BI "\-[no]pd" ""
.BI "\-dd" " vector "
+.BI "\-nt" " int "
.BI "\-npme" " int "
.BI "\-ddorder" " enum "
.BI "\-[no]ddcheck" ""
.BI "\-dd" " vector" " 0 0 0"
Domain decomposition grid, 0 is optimize
+.BI "\-nt" " int" " 0"
+ Number of threads to start (0 is guess)
+
.BI "\-npme" " int" " \-1"
Number of separate nodes to be used for PME, \-1 is guess
Do multiple simulations in parallel
.BI "\-replex" " int" " 0"
- Attempt replica exchange every steps
+ Attempt replica exchange periodically with this period (steps)
.BI "\-reseed" " int" " \-1"
Seed for replica exchange, \-1 is generate a seed
-.TH mk_angndx 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH mk_angndx 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
mk_angndx - generates index files for g_angle
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3mk_angndx\fP
.BI "\-s" " topol.tpr "
Include angles with atoms with mass 1.5
.BI "\-hq" " real" " \-1 "
- Ignore angles with atoms with mass 1.5 and |q| hq
+ Ignore angles with atoms with mass 1.5 and magnitude of their charge less than this value
.SH SEE ALSO
.BR gromacs(7)
-.TH ngmx 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH ngmx 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
ngmx - displays a trajectory
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3ngmx\fP
.BI "\-f" " traj.xtc "
-.TH pdb2gmx 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH pdb2gmx 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
-pdb2gmx - converts pdb files to topology and coordinate files
+pdb2gmx - converts coordinate files to topology and FF-compliant coordinate files
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3pdb2gmx\fP
.BI "\-f" " eiwit.pdb "
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-chainsep" " enum "
+.BI "\-merge" " enum "
.BI "\-ff" " string "
.BI "\-water" " enum "
.BI "\-[no]inter" ""
\&\fB pdb2gmx\fR will search for force fields by looking for
\&a \fB forcefield.itp\fR file in subdirectories \fB forcefield.ff\fR
-\&of the current working directory and of the Gromacs library directory
+\&of the current working directory and of the GROMACS library directory
\&as inferred from the path of the binary or the \fB GMXLIB\fR environment
\&variable.
\&By default the forcefield selection is interactive,
\&After choosing a force field, all files will be read only from
\&the corresponding force field directory.
\&If you want to modify or add a residue types, you can copy the force
-\&field directory from the Gromacs library directory to your current
+\&field directory from the GROMACS library directory to your current
\&working directory. If you want to add new protein residue types,
\&you will need to modify \fB residuetypes.dat\fR in the library directory
\&or copy the whole library directory to a local directory and set
\&The program has limited intelligence, it reads a number of database
\&files, that allow it to make special bonds (Cys\-Cys, Heme\-His, etc.),
\&if necessary this can be done manually. The program can prompt the
-\&user to select which kind of LYS, ASP, GLU, CYS or HIS residue she
-\&wants. For LYS the choice is between neutral (two protons on NZ) or
-\&protonated (three protons, default), for ASP and GLU unprotonated
-\&(default) or protonated, for HIS the proton can be either on ND1,
+\&user to select which kind of LYS, ASP, GLU, CYS or HIS residue is
+\&desired. For Lys the choice is between neutral (two protons on NZ) or
+\&protonated (three protons, default), for Asp and Glu unprotonated
+\&(default) or protonated, for His the proton can be either on ND1,
\&on NE2 or on both. By default these selections are done automatically.
\&For His, this is based on an optimal hydrogen bonding
\&conformation. Hydrogen bonds are defined based on a simple geometric
\&\fB \-dist\fR respectively.
+\&The protonation state of N\- and C\-termini can be chosen interactively
+\&with the \fB \-ter\fR flag. Default termini are ionized (NH3+ and COO\-),
+\&respectively. Some force fields support zwitterionic forms for chains of
+\&one residue, but for polypeptides these options should NOT be selected.
+\&The AMBER force fields have unique forms for the terminal residues,
+\&and these are incompatible with the \fB \-ter\fR mechanism. You need
+\&to prefix your N\- or C\-terminal residue names with "N" or "C"
+\&respectively to use these forms, making sure you preserve the format
+\&of the coordinate file. Alternatively, use named terminating residues
+\&(e.g. ACE, NME).
+
+
\&The separation of chains is not entirely trivial since the markup
\&in user\-generated PDB files frequently varies and sometimes it
\&is desirable to merge entries across a TER record, for instance
\&two protein chains or if you have a HEME group bound to a protein.
\&In such cases multiple chains should be contained in a single
\&\fB moleculetype\fR definition.
-\&To handle this, \fB pdb2gmx\fR has an option \fB \-chainsep\fR so you can
-\&choose whether a new chain should start when we find a TER record,
-\&when the chain id changes, combinations of either or both of these
-\&or fully interactively.
+\&To handle this, \fB pdb2gmx\fR uses two separate options.
+\&First, \fB \-chainsep\fR allows you to choose when a new chemical chain should
+\&start, and termini added when applicable. This can be done based on the
+\&existence of TER records, when the chain id changes, or combinations of either
+\&or both of these. You can also do the selection fully interactively.
+\&In addition, there is a \fB \-merge\fR option that controls how multiple chains
+\&are merged into one moleculetype, after adding all the chemical termini (or not).
+\&This can be turned off (no merging), all non\-water chains can be merged into a
+\&single molecule, or the selection can be done interactively.
\&\fB pdb2gmx\fR will also check the occupancy field of the \fB .pdb\fR file.
Set the nicelevel
.BI "\-chainsep" " enum" " id_or_ter"
- Condition in PDB files when a new chain and molecule_type should be started: \fB id_or_ter\fR, \fB id_and_ter\fR, \fB ter\fR, \fB id\fR or \fB interactive\fR
+ Condition in PDB files when a new chain should be started (adding termini): \fB id_or_ter\fR, \fB id_and_ter\fR, \fB ter\fR, \fB id\fR or \fB interactive\fR
+
+.BI "\-merge" " enum" " no"
+ Merge multiple chains into a single [moleculetype]: \fB no\fR, \fB all\fR or \fB interactive\fR
.BI "\-ff" " string" " select"
Force field, interactive by default. Use \fB \-h\fR for information.
Interactive SS bridge selection
.BI "\-[no]ter" "no "
- Interactive termini selection, iso charged
+ Interactive termini selection, instead of charged (default)
.BI "\-[no]lys" "no "
- Interactive lysine selection, iso charged
+ Interactive lysine selection, instead of charged
.BI "\-[no]arg" "no "
- Interactive arginine selection, iso charged
+ Interactive arginine selection, instead of charged
.BI "\-[no]asp" "no "
- Interactive aspartic Acid selection, iso charged
+ Interactive aspartic acid selection, instead of charged
.BI "\-[no]glu" "no "
- Interactive glutamic Acid selection, iso charged
+ Interactive glutamic acid selection, instead of charged
.BI "\-[no]gln" "no "
- Interactive glutamine selection, iso neutral
+ Interactive glutamine selection, instead of neutral
.BI "\-[no]his" "no "
- Interactive histidine selection, iso checking H\-bonds
+ Interactive histidine selection, instead of checking H\-bonds
.BI "\-angle" " real" " 135 "
Minimum hydrogen\-donor\-acceptor angle for a H\-bond (degrees)
-.TH tpbconv 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH tpbconv 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
tpbconv - makes a run input file for restarting a crashed run
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3tpbconv\fP
.BI "\-s" " topol.tpr "
-.TH trjcat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH trjcat 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
trjcat - concatenates trajectory files
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3trjcat\fP
.BI "\-f" " traj.xtc "
-.TH trjconv 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH trjconv 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
trjconv - converts and manipulates trajectory files
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3trjconv\fP
.BI "\-f" " traj.xtc "
\&Option \fB \-pbc\fR sets the type of periodic boundary condition
\&treatment:
-\&\fB * mol\fR puts the center of mass of molecules in the box.
+\&\fB * mol\fR puts the center of mass of molecules in the box,
+\&and requires a run input file to be supplied with \fB \-s\fR.
\&\fB * res\fR puts the center of mass of residues in the box.
\&\fB rect\fR is the ordinary brick shape.
\&\fB tric\fR is the triclinic unit cell.
\&\fB compact\fR puts all atoms at the closest distance from the center
-\&of the box. This can be useful for visualizing e.g. truncated
-\&octahedra. The center for options \fB tric\fR and \fB compact\fR
+\&of the box. This can be useful for visualizing e.g. truncated octahedra
+\&or rhombic dodecahedra. The center for options \fB tric\fR and \fB compact\fR
\&is \fB tric\fR (see below), unless the option \fB \-boxcenter\fR
\&is set differently.
\&want all molecules in the box after the centering.
+\&It is not always possible to use combinations of \fB \-pbc\fR,
+\&\fB \-fit\fR, \fB \-ur\fR and \fB \-center\fR to do exactly what
+\&you want in one call to \fB trjconv\fR. Consider using multiple
+\&calls, and check out the GROMACS website for suggestions.
+
+
\&With \fB \-dt\fR, it is possible to reduce the number of
\&frames in the output. This option relies on the accuracy of the times
\&in your input trajectory, so if these are inaccurate use the
-.TH trjorder 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH trjorder 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
trjorder - orders molecules according to their distance to a group
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3trjorder\fP
.BI "\-f" " traj.xtc "
-.TH xpm2ps 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.TH xpm2ps 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
.SH NAME
xpm2ps - converts XPM matrices to encapsulated postscript (or XPM)
-.B VERSION 4.5.4-dev-20110404-bc5695c
+.B VERSION 4.5.6
.SH SYNOPSIS
\f3xpm2ps\fP
.BI "\-f" " root.xpm "
.\" ========================================================================
.\"
.IX Title "GROMACS 7"
-.TH GROMACS 7 "2008-10-12" "gromacs" "GROMACS suite, Version 4.0"
+.TH GROMACS 7 "2013-01-18" "gromacs" "GROMACS suite, Version 4.5.6"
.SH "NAME"
gromacs \- molecular dynamics simulation suite
.SH "DESCRIPTION"
_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 -mead -bf -h -version -nice -w -ndef -bt -box -angles -d -c -center -aligncenter -align -translate -rotate -princ -scale -density -pbc -grasp -rvdw -sig56 -vdwread -atom -legend -label -conect' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -n -o -mead -bf -h -version -nice -w -ndef -bt -box -angles -d -c -center -aligncenter -align -translate -rotate -princ -scale -density -pbc -resnr -grasp -rvdw -sig56 -vdwread -atom -legend -label -conect' -- $c)); return 0; fi
case "$p" in
-bt) COMPREPLY=( $(compgen -W ' triclinic cubic dodecahedron octahedron ' -- $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
_eneconv_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -o -h -version -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 -version -nice -b -e -dt -offset -settime -nosort -rmdh -scalefac -noerror' -- $c)); return 0; fi
case "$p" in
-f) COMPREPLY=( $(compgen -X '!*.edr*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.edr*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-xvg) COMPREPLY=( $(compgen -W ' xmgrace xmgr none ' -- $c ));;
-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 exp9 ' -- $c ));;
+-fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 exp9 erffit ' -- $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 ));;
-xvg) COMPREPLY=( $(compgen -W ' xmgrace xmgr none ' -- $c ));;
-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 exp9 ' -- $c ));;
+-fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 exp9 erffit ' -- $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|cpt|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 ));;
-od) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
_g_bar_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -o -oi -oh -g -h -version -nice -w -xvg -b -e -temp -prec -nbmin -nbmax -nbin' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -g -o -oi -oh -h -version -nice -w -xvg -b -e -temp -prec -nbmin -nbmax -nbin' -- $c)); return 0; fi
case "$p" in
-xvg) COMPREPLY=( $(compgen -W ' xmgrace xmgr none ' -- $c ));;
-f) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-g) COMPREPLY=( $(compgen -X '!*.edr*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-oi) 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 ));;
--g) COMPREPLY=( $(compgen -X '!*.edr*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
esac }
complete -F _g_bar_compl g_bar
shopt -s extglob
-xvg) COMPREPLY=( $(compgen -W ' xmgrace xmgr none ' -- $c ));;
-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 exp9 ' -- $c ));;
+-fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 exp9 erffit ' -- $c ));;
-s) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|cpt|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 $c ));;
_g_cluster_compl() {
local p c
COMPREPLY=() c=${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 -version -nice -b -e -dt -tu -w -xvg -dista -nlevels -cutoff -nofit -max -skip -av -wcl -nst -rmsmin -method -minstruct -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 -version -nice -b -e -dt -tu -w -xvg -dista -nlevels -cutoff -nofit -max -skip -av -wcl -nst -rmsmin -method -minstruct -binary -M -P -seed -niter -kT -nopbc' -- $c)); return 0; fi
case "$p" in
-tu) COMPREPLY=( $(compgen -W ' fs ps ns us ms s ' -- $c ));;
-xvg) COMPREPLY=( $(compgen -W ' xmgrace xmgr none ' -- $c ));;
esac }
complete -F _g_densmap_compl g_densmap
shopt -s extglob
+_g_densorder_compl() {
+local p c
+COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -s -f -n -o -or -og -Spect -h -version -nice -b -e -dt -w -1d -bw -bwn -order -axis -method -d1 -d2 -tblock -nlevel' -- $c)); return 0; fi
+case "$p" in
+-method) COMPREPLY=( $(compgen -W ' bisect functional ' -- $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|cpt|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 '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-or) COMPREPLY=( $(compgen -X '!*.out*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-og) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-Spect) COMPREPLY=( $(compgen -X '!*.out*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac }
+complete -F _g_densorder_compl g_densorder
+shopt -s extglob
_g_dielectric_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -d -o -c -h -version -nice -b -e -dt -w -xvg -fft -nox1 -eint -bfit -efit -tail -A -tau1 -tau2 -eps0 -epsRF -fix -ffn -nsmooth' -- $c)); return 0; fi
case "$p" in
-xvg) COMPREPLY=( $(compgen -W ' xmgrace xmgr none ' -- $c ));;
--ffn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 exp9 ' -- $c ));;
+-ffn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 exp9 erffit ' -- $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 ));;
-xvg) COMPREPLY=( $(compgen -W ' xmgrace xmgr none ' -- $c ));;
-corr) COMPREPLY=( $(compgen -W ' none mol molsep total ' -- $c ));;
-P) COMPREPLY=( $(compgen -W ' 0 1 2 3 ' -- $c ));;
--fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 exp9 ' -- $c ));;
+-fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 exp9 erffit ' -- $c ));;
-en) COMPREPLY=( $(compgen -X '!*.edr*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|cpt|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 $c ));;
esac }
complete -F _g_dist_compl g_dist
shopt -s extglob
+_g_dos_compl() {
+local p c
+COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -vacf -mvacf -dos -g -h -version -nice -b -e -dt -w -xvg -nov -recip -abs -normdos -T -acflen -nonormalize -P -fitfn -ncskip -beginfit -endfit' -- $c)); return 0; fi
+case "$p" in
+-xvg) COMPREPLY=( $(compgen -W ' xmgrace xmgr none ' -- $c ));;
+-P) COMPREPLY=( $(compgen -W ' 0 1 2 3 ' -- $c ));;
+-fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 exp9 erffit ' -- $c ));;
+-f) COMPREPLY=( $(compgen -X '!*.+(trr|cpt|trj)*(.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 ));;
+-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-vacf) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-mvacf) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-dos) 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 $c ));;
+esac }
+complete -F _g_dos_compl g_dos
+shopt -s extglob
_g_dyndom_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
esac }
complete -F _g_dyndom_compl g_dyndom
shopt -s extglob
+_genbox_compl() {
+local p c
+COMPREPLY=() c=${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 -version -nice -box -nmol -try -seed -vdwd -shell -maxsol -vel' -- $c)); return 0; fi
+case "$p" in
+-cp) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-cs) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-ci) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-o) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|esp|xyz)*(.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 -version -nice -nbox -dist -seed -rot -shuffle -sort -block -nmolat -maxrot -norenumber' -- $c)); return 0; fi
+case "$p" in
+-f) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-o) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|esp|xyz)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-trj) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|cpt|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=${COMP_WORDS[COMP_CWORD-1]}
_g_energy_compl() {
local p c
COMPREPLY=() c=${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 -oten -corr -vis -ravg -h -version -nice -b -e -w -xvg -fee -fetemp -zero -sum -dp -nbmin -nbmax -mutot -skip -aver -nmol -nconstr -fluc -orinst -ovec -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 -oten -corr -vis -ravg -odh -h -version -nice -b -e -w -xvg -fee -fetemp -zero -sum -dp -nbmin -nbmax -mutot -skip -aver -nmol -fluct_props -driftcorr -fluc -orinst -ovec -acflen -nonormalize -P -fitfn -ncskip -beginfit -endfit' -- $c)); return 0; fi
case "$p" in
-xvg) COMPREPLY=( $(compgen -W ' xmgrace xmgr none ' -- $c ));;
-P) COMPREPLY=( $(compgen -W ' 0 1 2 3 ' -- $c ));;
--fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 exp9 ' -- $c ));;
+-fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 exp9 erffit ' -- $c ));;
-f) COMPREPLY=( $(compgen -X '!*.edr*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-f2) COMPREPLY=( $(compgen -X '!*.edr*(.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 ));;
-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 ));;
+-odh) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
esac }
complete -F _g_energy_compl g_energy
shopt -s extglob
+_genion_compl() {
+local p c
+COMPREPLY=() c=${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 -p -h -version -nice -xvg -np -pname -pq -nn -nname -nq -rmin -norandom -seed -scale -conc -neutral' -- $c)); return 0; fi
+case "$p" in
+-xvg) COMPREPLY=( $(compgen -W ' xmgrace xmgr none ' -- $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.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|ent|esp|xyz)*(.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 ));;
+-p) COMPREPLY=( $(compgen -X '!*.top*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac }
+complete -F _genion_compl genion
+shopt -s extglob
+_genrestr_compl() {
+local p c
+COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -n -o -of -h -version -nice -fc -freeze -disre -disre_dist -disre_frac -disre_up2 -cutoff -constr' -- $c)); return 0; fi
+case "$p" in
+-f) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|esp|xyz|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 '!*.itp*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-of) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac }
+complete -F _genrestr_compl genrestr
+shopt -s extglob
_g_filter_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
case "$p" in
-xvg) COMPREPLY=( $(compgen -W ' xmgrace xmgr none ' -- $c ));;
-P) COMPREPLY=( $(compgen -W ' 0 1 2 3 ' -- $c ));;
--fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 exp9 ' -- $c ));;
+-fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 exp9 erffit ' -- $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|cpt|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 ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
_g_hbond_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -num -g -ac -dist -ang -hx -hbn -hbm -don -dan -life -nhbdist -h -version -nice -b -e -dt -xvg -a -r -noda -r2 -abin -rbin -nonitacc -contact -shell -fitstart -fitstart -temp -smooth -dump -max_hb -nomerge -geminate -diff -acflen -nonormalize -P -fitfn -ncskip -beginfit -endfit' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -num -g -ac -dist -ang -hx -hbn -hbm -don -dan -life -nhbdist -h -version -nice -b -e -dt -tu -xvg -a -r -noda -r2 -abin -rbin -nonitacc -contact -shell -fitstart -fitstart -temp -smooth -dump -max_hb -nomerge -geminate -diff -acflen -nonormalize -P -fitfn -ncskip -beginfit -endfit' -- $c)); return 0; fi
case "$p" in
+-tu) COMPREPLY=( $(compgen -W ' fs ps ns us ms s ' -- $c ));;
-xvg) COMPREPLY=( $(compgen -W ' xmgrace xmgr none ' -- $c ));;
-geminate) COMPREPLY=( $(compgen -W ' none dd ad aa a4 ' -- $c ));;
-P) COMPREPLY=( $(compgen -W ' 0 1 2 3 ' -- $c ));;
--fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 exp9 ' -- $c ));;
+-fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 exp9 erffit ' -- $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|cpt|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 ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
esac }
complete -F _g_helixorient_compl g_helixorient
shopt -s extglob
+_g_hydorder_compl() {
+local p c
+COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -n -s -o -or -Spect -h -version -nice -b -e -dt -w -d -bw -sgang1 -sgang2 -tblock -nlevel' -- $c)); return 0; fi
+case "$p" in
+-d) COMPREPLY=( $(compgen -W ' z x y ' -- $c ));;
+-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|cpt|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 ));;
+-o) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-or) COMPREPLY=( $(compgen -X '!*.out*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-Spect) COMPREPLY=( $(compgen -X '!*.out*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac }
+complete -F _g_hydorder_compl g_hydorder
+shopt -s extglob
_g_lie_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
_g_membed_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -n -p -o -x -cpi -cpo -c -e -g -ei -rerun -table -tablep -tableb -dhdl -field -table -tablep -tableb -rerun -tpi -tpid -ei -eo -j -jo -ffout -devout -runav -px -pf -mtx -dn -h -version -nice -deffnm -xvg -xyinit -xyend -zinit -zend -nxy -nz -rad -pieces -asymmetry -ndiff -maxwarn -nocompact -v' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -n -p -o -x -cpi -cpo -c -e -g -ei -rerun -table -tablep -tableb -dhdl -field -table -tablep -tableb -rerun -tpi -tpid -ei -eo -j -jo -ffout -devout -runav -px -pf -mtx -dn -multidir -h -version -nice -deffnm -xvg -xyinit -xyend -zinit -zend -nxy -nz -rad -pieces -asymmetry -ndiff -maxwarn -nocompact -v' -- $c)); return 0; fi
case "$p" in
-xvg) COMPREPLY=( $(compgen -W ' xmgrace xmgr none ' -- $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-pf) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-mtx) COMPREPLY=( $(compgen -X '!*.mtx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-dn) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-multidir) COMPREPLY=( $(compgen -X '!*.rundir*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
esac }
complete -F _g_membed_compl g_membed
shopt -s extglob
esac }
complete -F _g_msd_compl g_msd
shopt -s extglob
+_gmxcheck_compl() {
+local p c
+COMPREPLY=() c=${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 -n -m -h -version -nice -vdwfac -bonlo -bonhi -rmsd -tol -abstol -ab -lastener' -- $c)); return 0; fi
+case "$p" in
+-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|cpt|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-f2) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|cpt|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*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-e2) COMPREPLY=( $(compgen -X '!*.edr*(.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 '!*.tex*(.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 -cp -p -mtx -om -h -version -nice -nonr -sys' -- $c)); return 0; fi
+case "$p" in
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|cpt|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-e) COMPREPLY=( $(compgen -X '!*.edr*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-cp) COMPREPLY=( $(compgen -X '!*.cpt*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-p) COMPREPLY=( $(compgen -X '!*.top*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-mtx) COMPREPLY=( $(compgen -X '!*.mtx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-om) COMPREPLY=( $(compgen -X '!*.mdp*(.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 -of -ol -v -h -version -nice -xvg -nom -first -last' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -of -ol -qc -v -h -version -nice -xvg -nom -first -last -T -constr' -- $c)); return 0; fi
case "$p" in
-xvg) COMPREPLY=( $(compgen -W ' xmgrace xmgr none ' -- $c ));;
-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)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-of) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-ol) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-qc) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-v) COMPREPLY=( $(compgen -X '!*.+(trr|cpt|trj)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
esac }
complete -F _g_nmeig_compl g_nmeig
esac }
complete -F _g_nmtraj_compl g_nmtraj
shopt -s extglob
+_g_options_compl() {
+local p c
+COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -h -version -nice' -- $c)); return 0; fi
+case "$p" in
+esac }
+complete -F _g_options_compl g_options
+shopt -s extglob
_g_order_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
esac }
complete -F _g_order_compl g_order
shopt -s extglob
+_g_pme_error_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 -so -h -version -nice -beta -tune -self -seed -v' -- $c)); return 0; fi
+case "$p" in
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-o) COMPREPLY=( $(compgen -X '!*.out*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-so) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac }
+complete -F _g_pme_error_compl g_pme_error
+shopt -s extglob
_g_polystat_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
esac }
complete -F _g_rmsf_compl g_rmsf
shopt -s extglob
+_grompp_compl() {
+local p c
+COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -po -c -r -rb -n -p -pp -o -t -e -h -version -nice -v -time -normvsbds -maxwarn -zero -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|esp|xyz|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-r) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-rb) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|esp|xyz|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 ));;
+-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|cpt|trj)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-e) COMPREPLY=( $(compgen -X '!*.edr*(.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=${COMP_WORDS[COMP_CWORD-1]}
case "$p" in
-xvg) COMPREPLY=( $(compgen -W ' xmgrace xmgr none ' -- $c ));;
-P) COMPREPLY=( $(compgen -W ' 0 1 2 3 ' -- $c ));;
--fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 exp9 ' -- $c ));;
+-fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 exp9 erffit ' -- $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|cpt|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 ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
esac }
complete -F _g_sas_compl g_sas
shopt -s extglob
-_g_sdf_compl() {
-local p c
-COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -n -s -o -r -h -version -nice -b -e -dt -mode -triangle -dtri -bin -grid' -- $c)); return 0; fi
-case "$p" in
--f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|cpt|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 ));;
--o) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--r) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|esp|xyz)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
-complete -F _g_sdf_compl g_sdf
-shopt -s extglob
_g_select_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
case "$p" in
-xvg) COMPREPLY=( $(compgen -W ' xmgrace xmgr none ' -- $c ));;
-P) COMPREPLY=( $(compgen -W ' 0 1 2 3 ' -- $c ));;
--fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 exp9 ' -- $c ));;
+-fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 exp9 erffit ' -- $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(trr|cpt|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 ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
_g_traj_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -ox -oxt -ov -of -ob -ot -ekt -ekr -vd -cv -cf -av -af -h -version -nice -b -e -dt -tu -w -xvg -com -nopbc -mol -nojump -nox -noy -noz -ng -len -fp -bin -scale' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -s -n -ox -oxt -ov -of -ob -ot -ekt -ekr -vd -cv -cf -av -af -h -version -nice -b -e -dt -tu -w -xvg -com -nopbc -mol -nojump -nox -noy -noz -ng -len -fp -bin -ctime -scale' -- $c)); return 0; fi
case "$p" in
-tu) COMPREPLY=( $(compgen -W ' fs ps ns us ms s ' -- $c ));;
-xvg) COMPREPLY=( $(compgen -W ' xmgrace xmgr none ' -- $c ));;
_g_tune_pme_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -p -err -so -s -o -x -cpi -cpo -c -e -g -dhdl -field -table -tablep -tableb -rerun -tpi -tpid -ei -eo -j -jo -ffout -devout -runav -px -pf -mtx -dn -bo -bx -bcpo -bc -be -bg -beo -bdhdl -bfield -btpi -btpid -bjo -bffout -bdevout -brunav -bpx -bpf -bmtx -bdn -h -version -nice -xvg -np -npstring -nt -r -max -min -npme -upfac -downfac -ntpr -four -steps -resetstep -simsteps -launch -deffnm -ddorder -noddcheck -rdd -rcon -dlb -dds -gcom -v -nocompact -seppot -pforce -reprod -cpt -cpnum -noappend -maxh -multi -replex -reseed -ionize' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -p -err -so -s -o -x -cpi -cpo -c -e -g -dhdl -field -table -tablep -tableb -rerun -tpi -tpid -ei -eo -j -jo -ffout -devout -runav -px -pf -mtx -dn -bo -bx -bcpo -bc -be -bg -beo -bdhdl -bfield -btpi -btpid -bjo -bffout -bdevout -brunav -bpx -bpf -bmtx -bdn -h -version -nice -xvg -np -npstring -nt -r -max -min -npme -fix -upfac -downfac -ntpr -four -steps -resetstep -simsteps -launch -deffnm -ddorder -noddcheck -rdd -rcon -dlb -dds -gcom -v -nocompact -seppot -pforce -reprod -cpt -cpnum -noappend -maxh -multi -replex -reseed -ionize' -- $c)); return 0; fi
case "$p" in
-xvg) COMPREPLY=( $(compgen -W ' xmgrace xmgr none ' -- $c ));;
-npstring) COMPREPLY=( $(compgen -W ' -np -n none ' -- $c ));;
case "$p" in
-xvg) COMPREPLY=( $(compgen -W ' xmgrace xmgr none ' -- $c ));;
-P) COMPREPLY=( $(compgen -W ' 0 1 2 3 ' -- $c ));;
--fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 exp9 ' -- $c ));;
+-fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 exp9 erffit ' -- $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(trr|cpt|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 ));;
-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
_g_wham_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -ix -if -it -ip -o -hist -bsres -bsprof -tab -wcorr -h -version -nice -xvg -min -max -noauto -bins -temp -tol -v -b -e -dt -histonly -boundsonly -nolog -unit -zprof0 -cycl -alpha -flip -hist-eq -nBootstrap -bs-dt -bs-seed -nohistbs -histbs-block -vbs' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -ix -if -it -ip -o -hist -oiact -iiact -bsres -bsprof -tab -h -version -nice -xvg -min -max -noauto -bins -temp -tol -v -b -e -dt -histonly -boundsonly -nolog -unit -zprof0 -cycl -sym -ac -acsig -ac-trestart -nBootstrap -bs-method -bs-tau -bs-seed -histbs-block -vbs' -- $c)); return 0; fi
case "$p" in
-xvg) COMPREPLY=( $(compgen -W ' xmgrace xmgr none ' -- $c ));;
-unit) COMPREPLY=( $(compgen -W ' kJ kCal kT ' -- $c ));;
--cycl) COMPREPLY=( $(compgen -W ' no yes weighted ' -- $c ));;
+-bs-method) COMPREPLY=( $(compgen -W ' b-hist hist traj traj-gauss ' -- $c ));;
-ix) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-if) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-it) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-ip) 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 ));;
-hist) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-oiact) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-iiact) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-bsres) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-bsprof) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-tab) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--wcorr) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
esac }
complete -F _g_wham_compl g_wham
shopt -s extglob
esac }
complete -F _g_xrama_compl g_xrama
shopt -s extglob
-_genbox_compl() {
-local p c
-COMPREPLY=() c=${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 -version -nice -box -nmol -try -seed -vdwd -shell -maxsol -vel' -- $c)); return 0; fi
-case "$p" in
--cp) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--cs) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--ci) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--o) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|esp|xyz)*(.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 -version -nice -nbox -dist -seed -rot -shuffle -sort -block -nmolat -maxrot -norenumber' -- $c)); return 0; fi
-case "$p" in
--f) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--o) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|esp|xyz)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--trj) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|cpt|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 -p -h -version -nice -xvg -np -pname -pq -nn -nname -nq -rmin -norandom -seed -scale -conc -neutral' -- $c)); return 0; fi
-case "$p" in
--xvg) COMPREPLY=( $(compgen -W ' xmgrace xmgr none ' -- $c ));;
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.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|ent|esp|xyz)*(.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 ));;
--p) COMPREPLY=( $(compgen -X '!*.top*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
-complete -F _genion_compl genion
-shopt -s extglob
-_genrestr_compl() {
-local p c
-COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -n -o -of -h -version -nice -fc -freeze -disre -disre_dist -disre_frac -disre_up2 -cutoff -constr' -- $c)); return 0; fi
-case "$p" in
--f) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|esp|xyz|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 '!*.itp*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--of) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
-complete -F _genrestr_compl genrestr
-shopt -s extglob
-_gmxcheck_compl() {
-local p c
-COMPREPLY=() c=${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 -n -m -h -version -nice -vdwfac -bonlo -bonhi -rmsd -tol -abstol -ab -lastener' -- $c)); return 0; fi
-case "$p" in
--f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|cpt|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--f2) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|cpt|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*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--e2) COMPREPLY=( $(compgen -X '!*.edr*(.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 '!*.tex*(.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 -cp -p -mtx -om -h -version -nice -nonr -sys' -- $c)); return 0; fi
-case "$p" in
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|cpt|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--e) COMPREPLY=( $(compgen -X '!*.edr*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--cp) COMPREPLY=( $(compgen -X '!*.cpt*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--p) COMPREPLY=( $(compgen -X '!*.top*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--mtx) COMPREPLY=( $(compgen -X '!*.mtx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--om) COMPREPLY=( $(compgen -X '!*.mdp*(.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 -p -pp -o -t -e -h -version -nice -v -time -normvsbds -maxwarn -zero -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|esp|xyz|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--r) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--rb) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|esp|xyz|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 ));;
--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|cpt|trj)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--e) COMPREPLY=( $(compgen -X '!*.edr*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
-complete -F _grompp_compl grompp
-shopt -s extglob
_make_edi_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -eig -s -n -tar -ori -o -h -version -nice -xvg -mon -linfix -linacc -flood -radfix -radacc -radcon -outfrq -slope -maxedsteps -deltaF0 -deltaF -tau -eqsteps -Eflnull -T -alpha -linstep -accdir -radstep -restrain -hessian -harmonic' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -eig -s -n -tar -ori -o -h -version -nice -xvg -mon -linfix -linacc -radfix -radacc -radcon -flood -outfrq -slope -linstep -accdir -radstep -maxedsteps -eqsteps -deltaF0 -deltaF -tau -Eflnull -T -alpha -restrain -hessian -harmonic -constF' -- $c)); return 0; fi
case "$p" in
-xvg) COMPREPLY=( $(compgen -W ' xmgrace xmgr none ' -- $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(trr|cpt|trj)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
_mdrun_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -s -o -x -cpi -cpo -c -e -g -dhdl -field -table -tablep -tableb -rerun -tpi -tpid -ei -eo -j -jo -ffout -devout -runav -px -pf -mtx -dn -h -version -nice -deffnm -xvg -pd -dd -nt -npme -ddorder -noddcheck -rdd -rcon -dlb -dds -gcom -v -nocompact -seppot -pforce -reprod -cpt -cpnum -noappend -maxh -multi -replex -reseed -ionize' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -s -o -x -cpi -cpo -c -e -g -dhdl -field -table -tablep -tableb -rerun -tpi -tpid -ei -eo -j -jo -ffout -devout -runav -px -pf -mtx -dn -multidir -h -version -nice -deffnm -xvg -pd -dd -nt -npme -ddorder -noddcheck -rdd -rcon -dlb -dds -gcom -v -nocompact -seppot -pforce -reprod -cpt -cpnum -noappend -maxh -multi -replex -reseed -ionize' -- $c)); return 0; fi
case "$p" in
-xvg) COMPREPLY=( $(compgen -W ' xmgrace xmgr none ' -- $c ));;
-ddorder) COMPREPLY=( $(compgen -W ' interleave pp_pme cartesian ' -- $c ));;
-pf) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-mtx) COMPREPLY=( $(compgen -X '!*.mtx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-dn) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-multidir) COMPREPLY=( $(compgen -X '!*.rundir*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
esac }
complete -F _mdrun_compl mdrun
shopt -s extglob
_pdb2gmx_compl() {
local p c
COMPREPLY=() c=${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 -version -nice -chainsep -ff -water -inter -ss -ter -lys -arg -asp -glu -gln -his -angle -dist -una -ignh -missing -v -posrefc -vsite -heavyh -deuterate -nochargegrp -nocmap -renum -rtpres' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -o -p -i -n -q -h -version -nice -chainsep -merge -ff -water -inter -ss -ter -lys -arg -asp -glu -gln -his -angle -dist -una -ignh -missing -v -posrefc -vsite -heavyh -deuterate -nochargegrp -nocmap -renum -rtpres' -- $c)); return 0; fi
case "$p" in
-chainsep) COMPREPLY=( $(compgen -W ' id_or_ter id_and_ter ter id interactive ' -- $c ));;
+-merge) COMPREPLY=( $(compgen -W ' no all interactive ' -- $c ));;
-water) COMPREPLY=( $(compgen -W ' select none spc spce tip3p tip4p tip5p ' -- $c ));;
-vsite) COMPREPLY=( $(compgen -W ' none hydrogens aromatics ' -- $c ));;
-f) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
_trjconv_compl() {
local p c
COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -o -s -n -fr -sub -drop -h -version -nice -b -e -tu -w -xvg -skip -dt -round -dump -t0 -timestep -pbc -ur -center -boxcenter -box -trans -shift -fit -ndec -novel -force -trunc -exec -app -split -sep -nzero -dropunder -dropover -conect' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W ' -f -o -s -n -fr -sub -drop -h -version -nice -b -e -tu -w -xvg -skip -dt -round -dump -t0 -timestep -pbc -ur -center -boxcenter -box -clustercenter -trans -shift -fit -ndec -novel -force -trunc -exec -app -split -sep -nzero -dropunder -dropover -conect' -- $c)); return 0; fi
case "$p" in
-tu) COMPREPLY=( $(compgen -W ' fs ps ns us ms s ' -- $c ));;
-xvg) COMPREPLY=( $(compgen -W ' xmgrace xmgr none ' -- $c ));;
complete do_dssp "n/-tu/( fs ps ns us ms s)/" "n/-xvg/( xmgrace xmgr none)/" "n/-f/f:*.{xtc,trr,cpt,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 version nice b e dt tu w xvg sss)/"
-complete editconf "n/-bt/( triclinic cubic dodecahedron octahedron)/" "n/-f/f:*.{gro,g96,pdb,brk,ent,esp,xyz,tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,ent,esp,xyz}{,.gz,.Z}/" "n/-mead/f:*.pqr{,.gz,.Z}/" "n/-bf/f:*.dat{,.gz,.Z}/" "c/-/( f n o mead bf h version nice w ndef bt box angles d c center aligncenter align translate rotate princ scale density pbc grasp rvdw sig56 vdwread atom legend label conect)/"
-complete eneconv "n/-f/f:*.edr{,.gz,.Z}/" "n/-o/f:*.edr{,.gz,.Z}/" "c/-/( f o h version nice b e dt offset settime nosort scalefac noerror)/"
+complete editconf "n/-bt/( triclinic cubic dodecahedron octahedron)/" "n/-f/f:*.{gro,g96,pdb,brk,ent,esp,xyz,tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,ent,esp,xyz}{,.gz,.Z}/" "n/-mead/f:*.pqr{,.gz,.Z}/" "n/-bf/f:*.dat{,.gz,.Z}/" "c/-/( f n o mead bf h version nice w ndef bt box angles d c center aligncenter align translate rotate princ scale density pbc resnr grasp rvdw sig56 vdwread atom legend label conect)/"
+complete eneconv "n/-f/f:*.edr{,.gz,.Z}/" "n/-o/f:*.edr{,.gz,.Z}/" "c/-/( f o h version nice b e dt offset settime nosort rmdh scalefac noerror)/"
complete g_anadock "n/-xvg/( xmgrace xmgr none)/" "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 version nice xvg free norms cutoff)/"
complete g_anaeig "n/-tu/( fs ps ns us ms s)/" "n/-xvg/( xmgrace xmgr none)/" "n/-v/f:*.{trr,cpt,trj}{,.gz,.Z}/" "n/-v2/f:*.{trr,cpt,trj}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,cpt,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/-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,ent,esp,xyz}{,.gz,.Z}/" "n/-filt/f:*.{xtc,trr,cpt,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-extr/f:*.{xtc,trr,cpt,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 version nice b e dt tu w xvg first last skip max nframes split entropy temp nevskip)/"
-complete g_analyze "n/-xvg/( xmgrace xmgr none)/" "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/-bal/f:*.xvg{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "c/-/( f ac msd cc dist av ee bal g h version nice w xvg notime b e n d bw errbar integrate aver_start xydy regression luzar temp fitstart fitend smooth filter power nosubav oneacf acflen nonormalize P fitfn ncskip beginfit endfit)/"
-complete g_angle "n/-xvg/( xmgrace xmgr none)/" "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,cpt,trj,gro,g96,pdb,g87}{,.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}/" "n/-or/f:*.trr{,.gz,.Z}/" "c/-/( f n od ov of ot oh oc or h version nice b e dt w xvg type all binwidth noperiodic chandler avercorr acflen nonormalize P fitfn ncskip beginfit endfit)/"
-complete g_bar "n/-xvg/( xmgrace xmgr none)/" "n/-f/f:*.xvg{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-oi/f:*.xvg{,.gz,.Z}/" "n/-oh/f:*.xvg{,.gz,.Z}/" "n/-g/f:*.edr{,.gz,.Z}/" "c/-/( f o oi oh g h version nice w xvg b e temp prec nbmin nbmax nbin)/"
+complete g_analyze "n/-xvg/( xmgrace xmgr none)/" "n/-errbar/( none stddev error 90)/" "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7 exp9 erffit)/" "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/-bal/f:*.xvg{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "c/-/( f ac msd cc dist av ee bal g h version nice w xvg notime b e n d bw errbar integrate aver_start xydy regression luzar temp fitstart fitend smooth filter power nosubav oneacf acflen nonormalize P fitfn ncskip beginfit endfit)/"
+complete g_angle "n/-xvg/( xmgrace xmgr none)/" "n/-type/( angle dihedral improper ryckaert-bellemans)/" "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7 exp9 erffit)/" "n/-f/f:*.{xtc,trr,cpt,trj,gro,g96,pdb,g87}{,.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}/" "n/-or/f:*.trr{,.gz,.Z}/" "c/-/( f n od ov of ot oh oc or h version nice b e dt w xvg type all binwidth noperiodic chandler avercorr acflen nonormalize P fitfn ncskip beginfit endfit)/"
+complete g_bar "n/-xvg/( xmgrace xmgr none)/" "n/-f/f:*.xvg{,.gz,.Z}/" "n/-g/f:*.edr{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-oi/f:*.xvg{,.gz,.Z}/" "n/-oh/f:*.xvg{,.gz,.Z}/" "c/-/( f g o oi oh h version nice w xvg b e temp prec nbmin nbmax nbin)/"
complete g_bond "n/-xvg/( xmgrace xmgr none)/" "n/-f/f:*.{xtc,trr,cpt,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 version nice b e dt w xvg blen tol noaver noaverdist)/"
complete g_bundle "n/-tu/( fs ps ns us ms s)/" "n/-xvg/( xmgrace xmgr none)/" "n/-f/f:*.{xtc,trr,cpt,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 version nice b e dt tu xvg na z)/"
-complete g_chi "n/-xvg/( xmgrace xmgr none)/" "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,esp,xyz,tpr,tpb,tpa}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,cpt,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 version nice b e dt w xvg r0 phi psi omega rama viol noperiodic 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/( fs ps ns us ms s)/" "n/-xvg/( xmgrace xmgr none)/" "n/-method/( linkage jarvis-patrick monte-carlo diagonalization gromos)/" "n/-f/f:*.{xtc,trr,cpt,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,cpt,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "c/-/( f s n dm o g dist ev sz tr ntr clid cl h version nice b e dt tu w xvg dista nlevels cutoff nofit max skip av wcl nst rmsmin method minstruct binary M P seed niter kT)/"
+complete g_chi "n/-xvg/( xmgrace xmgr none)/" "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 erffit)/" "n/-s/f:*.{gro,g96,pdb,brk,ent,esp,xyz,tpr,tpb,tpa}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,cpt,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 version nice b e dt w xvg r0 phi psi omega rama viol noperiodic 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/( fs ps ns us ms s)/" "n/-xvg/( xmgrace xmgr none)/" "n/-method/( linkage jarvis-patrick monte-carlo diagonalization gromos)/" "n/-f/f:*.{xtc,trr,cpt,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,cpt,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "c/-/( f s n dm o g dist ev sz tr ntr clid cl h version nice b e dt tu w xvg dista nlevels cutoff nofit max skip av wcl nst rmsmin method minstruct binary M P seed niter kT nopbc)/"
complete g_clustsize "n/-tu/( fs ps ns us ms s)/" "n/-xvg/( xmgrace xmgr none)/" "n/-f/f:*.{xtc,trr,cpt,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}/" "n/-temp/f:*.xvg{,.gz,.Z}/" "n/-mcn/f:*.ndx{,.gz,.Z}/" "c/-/( f s n o ow nc mc ac hc temp mcn h version nice b e dt tu w xvg cut mol nopbc nskip nlevels ndf 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,esp,xyz,tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,ent,esp,xyz}{,.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 version nice w one nomw pbc nofit name label bfac)/"
complete g_covar "n/-tu/( fs ps ns us ms s)/" "n/-xvg/( xmgrace xmgr none)/" "n/-f/f:*.{xtc,trr,cpt,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,cpt,trj}{,.gz,.Z}/" "n/-av/f:*.{gro,g96,pdb,brk,ent,esp,xyz}{,.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 version nice b e dt tu xvg nofit ref mwa last nopbc)/"
complete g_current "n/-xvg/( xmgrace xmgr none)/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,cpt,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-caf/f:*.xvg{,.gz,.Z}/" "n/-dsp/f:*.xvg{,.gz,.Z}/" "n/-md/f:*.xvg{,.gz,.Z}/" "n/-mj/f:*.xvg{,.gz,.Z}/" "n/-mc/f:*.xvg{,.gz,.Z}/" "c/-/( s n f o caf dsp md mj mc h version nice b e dt w xvg sh nonojump eps bfit efit bvit evit tr temp)/"
complete g_density "n/-xvg/( xmgrace xmgr none)/" "n/-dens/( mass number charge electron)/" "n/-f/f:*.{xtc,trr,cpt,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 version nice b e dt w xvg d sl dens ng symm center)/"
complete g_densmap "n/-aver/( z y x)/" "n/-unit/( nm-3 nm-2 count)/" "n/-f/f:*.{xtc,trr,cpt,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:*.dat{,.gz,.Z}/" "n/-o/f:*.xpm{,.gz,.Z}/" "c/-/( f s n od o h version nice b e dt w bin aver xmin xmax n1 n2 amax rmax mirror sums unit dmin dmax)/"
-complete g_dielectric "n/-xvg/( xmgrace xmgr none)/" "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 version nice b e dt w xvg fft nox1 eint bfit efit tail A tau1 tau2 eps0 epsRF fix ffn nsmooth)/"
+complete g_densorder "n/-method/( bisect functional)/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,cpt,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.dat{,.gz,.Z}/" "n/-or/f:*.out{,.gz,.Z}/" "n/-og/f:*.xpm{,.gz,.Z}/" "n/-Spect/f:*.out{,.gz,.Z}/" "c/-/( s f n o or og Spect h version nice b e dt w 1d bw bwn order axis method d1 d2 tblock nlevel)/"
+complete g_dielectric "n/-xvg/( xmgrace xmgr none)/" "n/-ffn/( none exp aexp exp_exp vac exp5 exp7 exp9 erffit)/" "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 version nice b e dt w xvg fft nox1 eint bfit efit tail A tau1 tau2 eps0 epsRF fix ffn nsmooth)/"
complete g_dih "n/-f/f:*.{xtc,trr,cpt,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 version nice b e dt w sa mult)/"
-complete g_dipoles "n/-xvg/( xmgrace xmgr none)/" "n/-corr/( none mol molsep total)/" "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7 exp9)/" "n/-en/f:*.edr{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,cpt,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/-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/-adip/f:*.xvg{,.gz,.Z}/" "n/-dip3d/f:*.xvg{,.gz,.Z}/" "n/-cos/f:*.xvg{,.gz,.Z}/" "n/-cmap/f:*.xpm{,.gz,.Z}/" "n/-q/f:*.xvg{,.gz,.Z}/" "n/-slab/f:*.xvg{,.gz,.Z}/" "c/-/( en f s n o eps a d c g adip dip3d cos cmap q slab h version nice b e dt w xvg mu mumax epsilonRF skip temp corr nopairs ncos axis sl gkratom gkratom2 rcmax phi nlevels ndegrees acflen nonormalize P fitfn ncskip beginfit endfit)/"
+complete g_dipoles "n/-xvg/( xmgrace xmgr none)/" "n/-corr/( none mol molsep total)/" "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7 exp9 erffit)/" "n/-en/f:*.edr{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,cpt,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/-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/-adip/f:*.xvg{,.gz,.Z}/" "n/-dip3d/f:*.xvg{,.gz,.Z}/" "n/-cos/f:*.xvg{,.gz,.Z}/" "n/-cmap/f:*.xpm{,.gz,.Z}/" "n/-q/f:*.xvg{,.gz,.Z}/" "n/-slab/f:*.xvg{,.gz,.Z}/" "c/-/( en f s n o eps a d c g adip dip3d cos cmap q slab h version nice b e dt w xvg mu mumax epsilonRF skip temp corr nopairs ncos axis sl gkratom gkratom2 rcmax phi nlevels ndegrees acflen nonormalize P fitfn ncskip beginfit endfit)/"
complete g_disre "n/-xvg/( xmgrace xmgr none)/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,cpt,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}/" "n/-c/f:*.ndx{,.gz,.Z}/" "n/-x/f:*.xpm{,.gz,.Z}/" "c/-/( s f ds da dn dm dr l n q c x h version nice b e dt w xvg ntop maxdr nlevels nothird)/"
complete g_dist "n/-xvg/( xmgrace xmgr none)/" "n/-f/f:*.{xtc,trr,cpt,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/-lt/f:*.xvg{,.gz,.Z}/" "c/-/( f s n o lt h version nice b e dt xvg dist)/"
+complete g_dos "n/-xvg/( xmgrace xmgr none)/" "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7 exp9 erffit)/" "n/-f/f:*.{trr,cpt,trj}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-vacf/f:*.xvg{,.gz,.Z}/" "n/-mvacf/f:*.xvg{,.gz,.Z}/" "n/-dos/f:*.xvg{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "c/-/( f s n vacf mvacf dos g h version nice b e dt w xvg nov recip abs normdos T acflen nonormalize P fitfn ncskip beginfit endfit)/"
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 version nice firstangle lastangle nframe maxangle trans head tail)/"
+complete genbox "n/-cp/f:*.{gro,g96,pdb,brk,ent,esp,xyz,tpr,tpb,tpa}{,.gz,.Z}/" "n/-cs/f:*.{gro,g96,pdb,brk,ent,esp,xyz,tpr,tpb,tpa}{,.gz,.Z}/" "n/-ci/f:*.{gro,g96,pdb,brk,ent,esp,xyz,tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,ent,esp,xyz}{,.gz,.Z}/" "n/-p/f:*.top{,.gz,.Z}/" "c/-/( cp cs ci o p h version nice box nmol try seed vdwd shell maxsol vel)/"
+complete genconf "n/-f/f:*.{gro,g96,pdb,brk,ent,esp,xyz,tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,ent,esp,xyz}{,.gz,.Z}/" "n/-trj/f:*.{xtc,trr,cpt,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "c/-/( f o trj h version nice nbox dist seed rot shuffle sort block nmolat maxrot norenumber)/"
complete g_enemat "n/-xvg/( xmgrace xmgr none)/" "n/-f/f:*.edr{,.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 version nice b e dt w xvg sum skip nomean nlevels max min nocoul coulr coul14 nolj lj lj14 bhamsr bhamlr nofree temp)/"
-complete g_energy "n/-xvg/( xmgrace xmgr none)/" "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7 exp9)/" "n/-f/f:*.edr{,.gz,.Z}/" "n/-f2/f:*.edr{,.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/-oten/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 oten corr vis ravg h version nice b e w xvg fee fetemp zero sum dp nbmin nbmax mutot skip aver nmol nconstr fluc orinst ovec acflen nonormalize P fitfn ncskip beginfit endfit)/"
+complete g_energy "n/-xvg/( xmgrace xmgr none)/" "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7 exp9 erffit)/" "n/-f/f:*.edr{,.gz,.Z}/" "n/-f2/f:*.edr{,.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/-oten/f:*.xvg{,.gz,.Z}/" "n/-corr/f:*.xvg{,.gz,.Z}/" "n/-vis/f:*.xvg{,.gz,.Z}/" "n/-ravg/f:*.xvg{,.gz,.Z}/" "n/-odh/f:*.xvg{,.gz,.Z}/" "c/-/( f f2 s o viol pairs ora ort oda odr odt oten corr vis ravg odh h version nice b e w xvg fee fetemp zero sum dp nbmin nbmax mutot skip aver nmol fluct_props driftcorr fluc orinst ovec acflen nonormalize P fitfn ncskip beginfit endfit)/"
+complete genion "n/-xvg/( xmgrace xmgr none)/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-table/f:*.xvg{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,ent,esp,xyz}{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "n/-pot/f:*.pdb{,.gz,.Z}/" "n/-p/f:*.top{,.gz,.Z}/" "c/-/( s table n o g pot p h version nice xvg np pname pq nn nname nq rmin norandom seed scale conc neutral)/"
+complete genrestr "n/-f/f:*.{gro,g96,pdb,brk,ent,esp,xyz,tpr,tpb,tpa}{,.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 version nice fc freeze disre disre_dist disre_frac disre_up2 cutoff constr)/"
complete g_filter "n/-f/f:*.{xtc,trr,cpt,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:*.{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 version nice b e dt w nf all nonojump fit)/"
-complete g_gyrate "n/-xvg/( xmgrace xmgr none)/" "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7 exp9)/" "n/-f/f:*.{xtc,trr,cpt,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/-acf/f:*.xvg{,.gz,.Z}/" "c/-/( f s n o acf h version nice b e dt w xvg nmol q p moi nz acflen nonormalize P fitfn ncskip beginfit endfit)/"
+complete g_gyrate "n/-xvg/( xmgrace xmgr none)/" "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7 exp9 erffit)/" "n/-f/f:*.{xtc,trr,cpt,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/-acf/f:*.xvg{,.gz,.Z}/" "c/-/( f s n o acf h version nice b e dt w xvg nmol q p moi nz acflen nonormalize P fitfn ncskip beginfit endfit)/"
complete g_h2order "n/-xvg/( xmgrace xmgr none)/" "n/-f/f:*.{xtc,trr,cpt,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 version nice b e dt w xvg d sl)/"
-complete g_hbond "n/-xvg/( xmgrace xmgr none)/" "n/-geminate/( none dd ad aa a4)/" "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7 exp9)/" "n/-f/f:*.{xtc,trr,cpt,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-num/f:*.xvg{,.gz,.Z}/" "n/-g/f:*.log{,.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/-don/f:*.xvg{,.gz,.Z}/" "n/-dan/f:*.xvg{,.gz,.Z}/" "n/-life/f:*.xvg{,.gz,.Z}/" "n/-nhbdist/f:*.xvg{,.gz,.Z}/" "c/-/( f s n num g ac dist ang hx hbn hbm don dan life nhbdist h version nice b e dt xvg a r noda r2 abin rbin nonitacc contact shell fitstart fitstart temp smooth dump max_hb nomerge geminate diff acflen nonormalize P fitfn ncskip beginfit endfit)/"
+complete g_hbond "n/-tu/( fs ps ns us ms s)/" "n/-xvg/( xmgrace xmgr none)/" "n/-geminate/( none dd ad aa a4)/" "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7 exp9 erffit)/" "n/-f/f:*.{xtc,trr,cpt,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-num/f:*.xvg{,.gz,.Z}/" "n/-g/f:*.log{,.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/-don/f:*.xvg{,.gz,.Z}/" "n/-dan/f:*.xvg{,.gz,.Z}/" "n/-life/f:*.xvg{,.gz,.Z}/" "n/-nhbdist/f:*.xvg{,.gz,.Z}/" "c/-/( f s n num g ac dist ang hx hbn hbm don dan life nhbdist h version nice b e dt tu xvg a r noda r2 abin rbin nonitacc contact shell fitstart fitstart temp smooth dump max_hb nomerge geminate diff acflen nonormalize P fitfn ncskip beginfit endfit)/"
complete g_helix "n/-prop/( RAD TWIST RISE LEN NHX DIP RMS CPHI RMSA PHI PSI HB3 HB4 HB5 CD222)/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,cpt,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-to/f:*.g87{,.gz,.Z}/" "n/-cz/f:*.{gro,g96,pdb,brk,ent,esp,xyz}{,.gz,.Z}/" "n/-co/f:*.{gro,g96,pdb,brk,ent,esp,xyz}{,.gz,.Z}/" "c/-/( s n f to cz co h version nice b e dt w r0 q noF db prop ev ahxstart ahxend)/"
complete g_helixorient "n/-xvg/( xmgrace xmgr none)/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,cpt,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-oaxis/f:*.dat{,.gz,.Z}/" "n/-ocenter/f:*.dat{,.gz,.Z}/" "n/-orise/f:*.xvg{,.gz,.Z}/" "n/-oradius/f:*.xvg{,.gz,.Z}/" "n/-otwist/f:*.xvg{,.gz,.Z}/" "n/-obending/f:*.xvg{,.gz,.Z}/" "n/-otilt/f:*.xvg{,.gz,.Z}/" "n/-orot/f:*.xvg{,.gz,.Z}/" "c/-/( s f n oaxis ocenter orise oradius otwist obending otilt orot h version nice b e dt xvg sidechain incremental)/"
+complete g_hydorder "n/-d/( z x y)/" "n/-f/f:*.{xtc,trr,cpt,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.xpm{,.gz,.Z}/" "n/-or/f:*.out{,.gz,.Z}/" "n/-Spect/f:*.out{,.gz,.Z}/" "c/-/( f n s o or Spect h version nice b e dt w d bw sgang1 sgang2 tblock nlevel)/"
complete g_lie "n/-xvg/( xmgrace xmgr none)/" "n/-f/f:*.edr{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "c/-/( f o h version nice b e dt w xvg Elj Eqq Clj Cqq ligand)/"
complete g_mdmat "n/-xvg/( xmgrace xmgr none)/" "n/-f/f:*.{xtc,trr,cpt,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 version nice b e dt xvg t nlevels)/"
-complete g_membed "n/-xvg/( xmgrace xmgr none)/" "n/-f/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-p/f:*.top{,.gz,.Z}/" "n/-o/f:*.{trr,cpt,trj}{,.gz,.Z}/" "n/-x/f:*.xtc{,.gz,.Z}/" "n/-cpi/f:*.cpt{,.gz,.Z}/" "n/-cpo/f:*.cpt{,.gz,.Z}/" "n/-c/f:*.{gro,g96,pdb,brk,ent,esp,xyz}{,.gz,.Z}/" "n/-e/f:*.edr{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "n/-ei/f:*.edi{,.gz,.Z}/" "n/-rerun/f:*.{xtc,trr,cpt,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-table/f:*.xvg{,.gz,.Z}/" "n/-tablep/f:*.xvg{,.gz,.Z}/" "n/-tableb/f:*.xvg{,.gz,.Z}/" "n/-dhdl/f:*.xvg{,.gz,.Z}/" "n/-field/f:*.xvg{,.gz,.Z}/" "n/-table/f:*.xvg{,.gz,.Z}/" "n/-tablep/f:*.xvg{,.gz,.Z}/" "n/-tableb/f:*.xvg{,.gz,.Z}/" "n/-rerun/f:*.{xtc,trr,cpt,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-tpi/f:*.xvg{,.gz,.Z}/" "n/-tpid/f:*.xvg{,.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/-px/f:*.xvg{,.gz,.Z}/" "n/-pf/f:*.xvg{,.gz,.Z}/" "n/-mtx/f:*.mtx{,.gz,.Z}/" "n/-dn/f:*.ndx{,.gz,.Z}/" "c/-/( f n p o x cpi cpo c e g ei rerun table tablep tableb dhdl field table tablep tableb rerun tpi tpid ei eo j jo ffout devout runav px pf mtx dn h version nice deffnm xvg xyinit xyend zinit zend nxy nz rad pieces asymmetry ndiff maxwarn nocompact v)/"
+complete g_membed "n/-xvg/( xmgrace xmgr none)/" "n/-f/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-p/f:*.top{,.gz,.Z}/" "n/-o/f:*.{trr,cpt,trj}{,.gz,.Z}/" "n/-x/f:*.xtc{,.gz,.Z}/" "n/-cpi/f:*.cpt{,.gz,.Z}/" "n/-cpo/f:*.cpt{,.gz,.Z}/" "n/-c/f:*.{gro,g96,pdb,brk,ent,esp,xyz}{,.gz,.Z}/" "n/-e/f:*.edr{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "n/-ei/f:*.edi{,.gz,.Z}/" "n/-rerun/f:*.{xtc,trr,cpt,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-table/f:*.xvg{,.gz,.Z}/" "n/-tablep/f:*.xvg{,.gz,.Z}/" "n/-tableb/f:*.xvg{,.gz,.Z}/" "n/-dhdl/f:*.xvg{,.gz,.Z}/" "n/-field/f:*.xvg{,.gz,.Z}/" "n/-table/f:*.xvg{,.gz,.Z}/" "n/-tablep/f:*.xvg{,.gz,.Z}/" "n/-tableb/f:*.xvg{,.gz,.Z}/" "n/-rerun/f:*.{xtc,trr,cpt,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-tpi/f:*.xvg{,.gz,.Z}/" "n/-tpid/f:*.xvg{,.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/-px/f:*.xvg{,.gz,.Z}/" "n/-pf/f:*.xvg{,.gz,.Z}/" "n/-mtx/f:*.mtx{,.gz,.Z}/" "n/-dn/f:*.ndx{,.gz,.Z}/" "n/-multidir/f:*.rundir{,.gz,.Z}/" "c/-/( f n p o x cpi cpo c e g ei rerun table tablep tableb dhdl field table tablep tableb rerun tpi tpid ei eo j jo ffout devout runav px pf mtx dn multidir h version nice deffnm xvg xyinit xyend zinit zend nxy nz rad pieces asymmetry ndiff maxwarn nocompact v)/"
complete g_mindist "n/-tu/( fs ps ns us ms s)/" "n/-xvg/( xmgrace xmgr none)/" "n/-f/f:*.{xtc,trr,cpt,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}/" "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 version nice b e dt tu w xvg matrix max d group pi split ng nopbc respertime printresname)/"
complete g_morph "n/-xvg/( xmgrace xmgr none)/" "n/-f1/f:*.{gro,g96,pdb,brk,ent,esp,xyz,tpr,tpb,tpa}{,.gz,.Z}/" "n/-f2/f:*.{gro,g96,pdb,brk,ent,esp,xyz,tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.{xtc,trr,cpt,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 version nice w xvg ninterm first last nofit)/"
complete g_msd "n/-tu/( fs ps ns us ms s)/" "n/-xvg/( xmgrace xmgr none)/" "n/-type/( no x y z)/" "n/-lateral/( no x y z)/" "n/-f/f:*.{xtc,trr,cpt,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}/" "n/-pdb/f:*.pdb{,.gz,.Z}/" "c/-/( f s n o mol pdb h version nice b e tu w xvg type lateral ten ngroup nomw rmcomm tpdb trestart beginfit endfit)/"
-complete g_nmeig "n/-xvg/( xmgrace xmgr none)/" "n/-f/f:*.mtx{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-of/f:*.xvg{,.gz,.Z}/" "n/-ol/f:*.xvg{,.gz,.Z}/" "n/-v/f:*.{trr,cpt,trj}{,.gz,.Z}/" "c/-/( f s of ol v h version nice xvg nom first last)/"
+complete gmxcheck "n/-f/f:*.{xtc,trr,cpt,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-f2/f:*.{xtc,trr,cpt,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{,.gz,.Z}/" "n/-e2/f:*.edr{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-m/f:*.tex{,.gz,.Z}/" "c/-/( f f2 s1 s2 c e e2 n m h version nice vdwfac bonlo bonhi rmsd tol abstol ab lastener)/"
+complete gmxdump "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,cpt,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-e/f:*.edr{,.gz,.Z}/" "n/-cp/f:*.cpt{,.gz,.Z}/" "n/-p/f:*.top{,.gz,.Z}/" "n/-mtx/f:*.mtx{,.gz,.Z}/" "n/-om/f:*.mdp{,.gz,.Z}/" "c/-/( s f e cp p mtx om h version nice nonr sys)/"
+complete g_nmeig "n/-xvg/( xmgrace xmgr none)/" "n/-f/f:*.mtx{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-of/f:*.xvg{,.gz,.Z}/" "n/-ol/f:*.xvg{,.gz,.Z}/" "n/-qc/f:*.xvg{,.gz,.Z}/" "n/-v/f:*.{trr,cpt,trj}{,.gz,.Z}/" "c/-/( f s of ol qc v h version nice xvg nom first last T constr)/"
complete g_nmens "n/-xvg/( xmgrace xmgr none)/" "n/-v/f:*.{trr,cpt,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 version nice xvg temp seed num first last)/"
complete g_nmtraj "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-v/f:*.{trr,cpt,trj}{,.gz,.Z}/" "n/-o/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "c/-/( s v o h version nice eignr phases temp amplitude nframes)/"
+complete g_options "c/-/( h version nice)/"
complete g_order "n/-xvg/( xmgrace xmgr none)/" "n/-d/( z x y)/" "n/-f/f:*.{xtc,trr,cpt,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-nr/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/-ob/f:*.pdb{,.gz,.Z}/" "n/-os/f:*.xvg{,.gz,.Z}/" "n/-Sg/f:*.xvg{,.gz,.Z}/" "n/-Sk/f:*.xvg{,.gz,.Z}/" "n/-Sgsl/f:*.xvg{,.gz,.Z}/" "n/-Sksl/f:*.xvg{,.gz,.Z}/" "c/-/( f n nr s o od ob os Sg Sk Sgsl Sksl h version nice b e dt w xvg d sl szonly unsat permolecule radial calcdist)/"
+complete g_pme_error "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.out{,.gz,.Z}/" "n/-so/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "c/-/( s o so h version nice beta tune self seed v)/"
complete g_polystat "n/-tu/( fs ps ns us ms s)/" "n/-xvg/( xmgrace xmgr none)/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,cpt,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-v/f:*.xvg{,.gz,.Z}/" "n/-p/f:*.xvg{,.gz,.Z}/" "n/-i/f:*.xvg{,.gz,.Z}/" "c/-/( s f n o v p i h version nice b e dt tu w xvg nomw pc)/"
complete g_potential "n/-xvg/( xmgrace xmgr none)/" "n/-f/f:*.{xtc,trr,cpt,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 version nice b e dt w xvg d sl cb ce tz spherical ng correct)/"
complete g_principal "n/-tu/( fs ps ns us ms s)/" "n/-f/f:*.{xtc,trr,cpt,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/-a1/f:*.dat{,.gz,.Z}/" "n/-a2/f:*.dat{,.gz,.Z}/" "n/-a3/f:*.dat{,.gz,.Z}/" "n/-om/f:*.dat{,.gz,.Z}/" "c/-/( f s n a1 a2 a3 om h version nice b e dt tu w foo)/"
complete g_rms "n/-tu/( fs ps ns us ms s)/" "n/-xvg/( xmgrace xmgr none)/" "n/-what/( rmsd rho rhosc)/" "n/-fit/( rot+trans translation none)/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,cpt,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-f2/f:*.{xtc,trr,cpt,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 version nice b e dt tu w xvg what nopbc fit prev split skip skip2 max min bmax bmin nomw nlevels ng)/"
complete g_rmsdist "n/-xvg/( xmgrace xmgr none)/" "n/-f/f:*.{xtc,trr,cpt,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 version nice b e dt w xvg nlevels max nosumh nopbc)/"
complete g_rmsf "n/-xvg/( xmgrace xmgr none)/" "n/-f/f:*.{xtc,trr,cpt,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 version nice b e dt w xvg res aniso nofit)/"
-complete g_rotacf "n/-xvg/( xmgrace xmgr none)/" "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7 exp9)/" "n/-f/f:*.{xtc,trr,cpt,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 version nice b e dt w xvg d noaver acflen nonormalize P fitfn ncskip beginfit endfit)/"
+complete grompp "n/-f/f:*.mdp{,.gz,.Z}/" "n/-po/f:*.mdp{,.gz,.Z}/" "n/-c/f:*.{gro,g96,pdb,brk,ent,esp,xyz,tpr,tpb,tpa}{,.gz,.Z}/" "n/-r/f:*.{gro,g96,pdb,brk,ent,esp,xyz,tpr,tpb,tpa}{,.gz,.Z}/" "n/-rb/f:*.{gro,g96,pdb,brk,ent,esp,xyz,tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/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,cpt,trj}{,.gz,.Z}/" "n/-e/f:*.edr{,.gz,.Z}/" "c/-/( f po c r rb n p pp o t e h version nice v time normvsbds maxwarn zero norenum)/"
+complete g_rotacf "n/-xvg/( xmgrace xmgr none)/" "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7 exp9 erffit)/" "n/-f/f:*.{xtc,trr,cpt,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 version nice b e dt w xvg d noaver acflen nonormalize P fitfn ncskip beginfit endfit)/"
complete g_rotmat "n/-xvg/( xmgrace xmgr none)/" "n/-ref/( none xyz xy)/" "n/-f/f:*.{xtc,trr,cpt,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}/" "c/-/( f s n o h version nice b e dt w xvg ref skip fitxy nomw)/"
complete g_saltbr "n/-f/f:*.{xtc,trr,cpt,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "c/-/( f s h version nice b e dt t sep)/"
complete g_sas "n/-xvg/( xmgrace xmgr none)/" "n/-f/f:*.{xtc,trr,cpt,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/-or/f:*.xvg{,.gz,.Z}/" "n/-oa/f:*.xvg{,.gz,.Z}/" "n/-tv/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 tv q n i h version nice b e dt w xvg probe ndots qmax f_index minarea nopbc noprot dgs)/"
-complete g_sdf "n/-f/f:*.{xtc,trr,cpt,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:*.dat{,.gz,.Z}/" "n/-r/f:*.{gro,g96,pdb,brk,ent,esp,xyz}{,.gz,.Z}/" "c/-/( f n s o r h version nice b e dt mode triangle dtri bin grid)/"
complete g_select "n/-xvg/( xmgrace xmgr none)/" "n/-selrpos/( atom res_com res_cog mol_com mol_cog whole_res_com whole_res_cog whole_mol_com whole_mol_cog part_res_com part_res_cog part_mol_com part_mol_cog dyn_res_com dyn_res_cog dyn_mol_com dyn_mol_cog)/" "n/-seltype/( atom res_com res_cog mol_com mol_cog whole_res_com whole_res_cog whole_mol_com whole_mol_cog part_res_com part_res_cog part_mol_com part_mol_cog dyn_res_com dyn_res_cog dyn_mol_com dyn_mol_cog)/" "n/-resnr/( number index)/" "n/-f/f:*.{xtc,trr,cpt,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-sf/f:*.dat{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-os/f:*.xvg{,.gz,.Z}/" "n/-oc/f:*.xvg{,.gz,.Z}/" "n/-oi/f:*.dat{,.gz,.Z}/" "n/-om/f:*.dat{,.gz,.Z}/" "n/-on/f:*.ndx{,.gz,.Z}/" "c/-/( f s sf n os oc oi om on h version nice b e dt xvg normpbc nopbc select selrpos seltype dump norm cfnorm resnr)/"
complete g_sgangle "n/-xvg/( xmgrace xmgr none)/" "n/-f/f:*.{xtc,trr,cpt,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 version nice b e dt w xvg one z)/"
complete g_sham "n/-xvg/( xmgrace xmgr none)/" "n/-f/f:*.xvg{,.gz,.Z}/" "n/-ge/f:*.xvg{,.gz,.Z}/" "n/-ene/f:*.xvg{,.gz,.Z}/" "n/-dist/f:*.xvg{,.gz,.Z}/" "n/-histo/f:*.xvg{,.gz,.Z}/" "n/-bin/f:*.ndx{,.gz,.Z}/" "n/-lp/f:*.xpm{,.gz,.Z}/" "n/-ls/f:*.xpm{,.gz,.Z}/" "n/-lsh/f:*.xpm{,.gz,.Z}/" "n/-lss/f:*.xpm{,.gz,.Z}/" "n/-map/f:*.xpm{,.gz,.Z}/" "n/-ls3/f:*.pdb{,.gz,.Z}/" "n/-mdata/f:*.xvg{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "c/-/( f ge ene dist histo bin lp ls lsh lss map ls3 mdata g h version nice w xvg notime b e ttol n d bw nosham tsham pmin dim ngrid xmin xmax pmax gmax emin emax nlevels mname)/"
complete g_sorient "n/-xvg/( xmgrace xmgr none)/" "n/-f/f:*.{xtc,trr,cpt,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}/" "n/-rc/f:*.xvg{,.gz,.Z}/" "c/-/( f s n o no ro co rc h version nice b e dt w xvg com v23 rmin rmax cbin rbin pbc)/"
complete g_spatial "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,cpt,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "c/-/( s f n h version nice b e dt w pbc nodiv ign bin nab)/"
complete g_spol "n/-xvg/( xmgrace xmgr none)/" "n/-f/f:*.{xtc,trr,cpt,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 version nice b e dt w xvg com refat rmin rmax dip bw)/"
-complete g_tcaf "n/-xvg/( xmgrace xmgr none)/" "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7 exp9)/" "n/-f/f:*.{trr,cpt,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 version nice b e dt w xvg mol k34 wt acflen nonormalize P fitfn ncskip beginfit endfit)/"
-complete g_traj "n/-tu/( fs ps ns us ms s)/" "n/-xvg/( xmgrace xmgr none)/" "n/-f/f:*.{xtc,trr,cpt,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/-oxt/f:*.{xtc,trr,cpt,trj,gro,g96,pdb,g87}{,.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/-vd/f:*.xvg{,.gz,.Z}/" "n/-cv/f:*.pdb{,.gz,.Z}/" "n/-cf/f:*.pdb{,.gz,.Z}/" "n/-av/f:*.xvg{,.gz,.Z}/" "n/-af/f:*.xvg{,.gz,.Z}/" "c/-/( f s n ox oxt ov of ob ot ekt ekr vd cv cf av af h version nice b e dt tu w xvg com nopbc mol nojump nox noy noz ng len fp bin scale)/"
-complete g_tune_pme "n/-xvg/( xmgrace xmgr none)/" "n/-npstring/( -np -n none)/" "n/-npme/( auto all subset)/" "n/-ddorder/( interleave pp_pme cartesian)/" "n/-dlb/( auto no yes)/" "n/-p/f:*.out{,.gz,.Z}/" "n/-err/f:*.log{,.gz,.Z}/" "n/-so/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.{trr,cpt,trj}{,.gz,.Z}/" "n/-x/f:*.xtc{,.gz,.Z}/" "n/-cpi/f:*.cpt{,.gz,.Z}/" "n/-cpo/f:*.cpt{,.gz,.Z}/" "n/-c/f:*.{gro,g96,pdb,brk,ent,esp,xyz}{,.gz,.Z}/" "n/-e/f:*.edr{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "n/-dhdl/f:*.xvg{,.gz,.Z}/" "n/-field/f:*.xvg{,.gz,.Z}/" "n/-table/f:*.xvg{,.gz,.Z}/" "n/-tablep/f:*.xvg{,.gz,.Z}/" "n/-tableb/f:*.xvg{,.gz,.Z}/" "n/-rerun/f:*.{xtc,trr,cpt,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-tpi/f:*.xvg{,.gz,.Z}/" "n/-tpid/f:*.xvg{,.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/-px/f:*.xvg{,.gz,.Z}/" "n/-pf/f:*.xvg{,.gz,.Z}/" "n/-mtx/f:*.mtx{,.gz,.Z}/" "n/-dn/f:*.ndx{,.gz,.Z}/" "n/-bo/f:*.{trr,cpt,trj}{,.gz,.Z}/" "n/-bx/f:*.xtc{,.gz,.Z}/" "n/-bcpo/f:*.cpt{,.gz,.Z}/" "n/-bc/f:*.{gro,g96,pdb,brk,ent,esp,xyz}{,.gz,.Z}/" "n/-be/f:*.edr{,.gz,.Z}/" "n/-bg/f:*.log{,.gz,.Z}/" "n/-beo/f:*.edo{,.gz,.Z}/" "n/-bdhdl/f:*.xvg{,.gz,.Z}/" "n/-bfield/f:*.xvg{,.gz,.Z}/" "n/-btpi/f:*.xvg{,.gz,.Z}/" "n/-btpid/f:*.xvg{,.gz,.Z}/" "n/-bjo/f:*.gct{,.gz,.Z}/" "n/-bffout/f:*.xvg{,.gz,.Z}/" "n/-bdevout/f:*.xvg{,.gz,.Z}/" "n/-brunav/f:*.xvg{,.gz,.Z}/" "n/-bpx/f:*.xvg{,.gz,.Z}/" "n/-bpf/f:*.xvg{,.gz,.Z}/" "n/-bmtx/f:*.mtx{,.gz,.Z}/" "n/-bdn/f:*.ndx{,.gz,.Z}/" "c/-/( p err so s o x cpi cpo c e g dhdl field table tablep tableb rerun tpi tpid ei eo j jo ffout devout runav px pf mtx dn bo bx bcpo bc be bg beo bdhdl bfield btpi btpid bjo bffout bdevout brunav bpx bpf bmtx bdn h version nice xvg np npstring nt r max min npme upfac downfac ntpr four steps resetstep simsteps launch deffnm ddorder noddcheck rdd rcon dlb dds gcom v nocompact seppot pforce reprod cpt cpnum noappend maxh multi replex reseed ionize)/"
+complete g_tcaf "n/-xvg/( xmgrace xmgr none)/" "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7 exp9 erffit)/" "n/-f/f:*.{trr,cpt,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 version nice b e dt w xvg mol k34 wt acflen nonormalize P fitfn ncskip beginfit endfit)/"
+complete g_traj "n/-tu/( fs ps ns us ms s)/" "n/-xvg/( xmgrace xmgr none)/" "n/-f/f:*.{xtc,trr,cpt,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/-oxt/f:*.{xtc,trr,cpt,trj,gro,g96,pdb,g87}{,.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/-vd/f:*.xvg{,.gz,.Z}/" "n/-cv/f:*.pdb{,.gz,.Z}/" "n/-cf/f:*.pdb{,.gz,.Z}/" "n/-av/f:*.xvg{,.gz,.Z}/" "n/-af/f:*.xvg{,.gz,.Z}/" "c/-/( f s n ox oxt ov of ob ot ekt ekr vd cv cf av af h version nice b e dt tu w xvg com nopbc mol nojump nox noy noz ng len fp bin ctime scale)/"
+complete g_tune_pme "n/-xvg/( xmgrace xmgr none)/" "n/-npstring/( -np -n none)/" "n/-npme/( auto all subset)/" "n/-ddorder/( interleave pp_pme cartesian)/" "n/-dlb/( auto no yes)/" "n/-p/f:*.out{,.gz,.Z}/" "n/-err/f:*.log{,.gz,.Z}/" "n/-so/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.{trr,cpt,trj}{,.gz,.Z}/" "n/-x/f:*.xtc{,.gz,.Z}/" "n/-cpi/f:*.cpt{,.gz,.Z}/" "n/-cpo/f:*.cpt{,.gz,.Z}/" "n/-c/f:*.{gro,g96,pdb,brk,ent,esp,xyz}{,.gz,.Z}/" "n/-e/f:*.edr{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "n/-dhdl/f:*.xvg{,.gz,.Z}/" "n/-field/f:*.xvg{,.gz,.Z}/" "n/-table/f:*.xvg{,.gz,.Z}/" "n/-tablep/f:*.xvg{,.gz,.Z}/" "n/-tableb/f:*.xvg{,.gz,.Z}/" "n/-rerun/f:*.{xtc,trr,cpt,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-tpi/f:*.xvg{,.gz,.Z}/" "n/-tpid/f:*.xvg{,.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/-px/f:*.xvg{,.gz,.Z}/" "n/-pf/f:*.xvg{,.gz,.Z}/" "n/-mtx/f:*.mtx{,.gz,.Z}/" "n/-dn/f:*.ndx{,.gz,.Z}/" "n/-bo/f:*.{trr,cpt,trj}{,.gz,.Z}/" "n/-bx/f:*.xtc{,.gz,.Z}/" "n/-bcpo/f:*.cpt{,.gz,.Z}/" "n/-bc/f:*.{gro,g96,pdb,brk,ent,esp,xyz}{,.gz,.Z}/" "n/-be/f:*.edr{,.gz,.Z}/" "n/-bg/f:*.log{,.gz,.Z}/" "n/-beo/f:*.edo{,.gz,.Z}/" "n/-bdhdl/f:*.xvg{,.gz,.Z}/" "n/-bfield/f:*.xvg{,.gz,.Z}/" "n/-btpi/f:*.xvg{,.gz,.Z}/" "n/-btpid/f:*.xvg{,.gz,.Z}/" "n/-bjo/f:*.gct{,.gz,.Z}/" "n/-bffout/f:*.xvg{,.gz,.Z}/" "n/-bdevout/f:*.xvg{,.gz,.Z}/" "n/-brunav/f:*.xvg{,.gz,.Z}/" "n/-bpx/f:*.xvg{,.gz,.Z}/" "n/-bpf/f:*.xvg{,.gz,.Z}/" "n/-bmtx/f:*.mtx{,.gz,.Z}/" "n/-bdn/f:*.ndx{,.gz,.Z}/" "c/-/( p err so s o x cpi cpo c e g dhdl field table tablep tableb rerun tpi tpid ei eo j jo ffout devout runav px pf mtx dn bo bx bcpo bc be bg beo bdhdl bfield btpi btpid bjo bffout bdevout brunav bpx bpf bmtx bdn h version nice xvg np npstring nt r max min npme fix upfac downfac ntpr four steps resetstep simsteps launch deffnm ddorder noddcheck rdd rcon dlb dds gcom v nocompact seppot pforce reprod cpt cpnum noappend maxh multi replex reseed ionize)/"
complete g_vanhove "n/-xvg/( xmgrace xmgr none)/" "n/-f/f:*.{xtc,trr,cpt,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/-om/f:*.xpm{,.gz,.Z}/" "n/-or/f:*.xvg{,.gz,.Z}/" "n/-ot/f:*.xvg{,.gz,.Z}/" "c/-/( f s n om or ot h version nice b e dt w xvg sqrt fm rmax rbin mmax nlevels nr fr rt ft)/"
-complete g_velacc "n/-xvg/( xmgrace xmgr none)/" "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7 exp9)/" "n/-f/f:*.{trr,cpt,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 version nice b e dt w xvg m mol acflen nonormalize P fitfn ncskip beginfit endfit)/"
-complete g_wham "n/-xvg/( xmgrace xmgr none)/" "n/-unit/( kJ kCal kT)/" "n/-cycl/( no yes weighted)/" "n/-ix/f:*.dat{,.gz,.Z}/" "n/-if/f:*.dat{,.gz,.Z}/" "n/-it/f:*.dat{,.gz,.Z}/" "n/-ip/f:*.dat{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-hist/f:*.xvg{,.gz,.Z}/" "n/-bsres/f:*.xvg{,.gz,.Z}/" "n/-bsprof/f:*.xvg{,.gz,.Z}/" "n/-tab/f:*.dat{,.gz,.Z}/" "n/-wcorr/f:*.xvg{,.gz,.Z}/" "c/-/( ix if it ip o hist bsres bsprof tab wcorr h version nice xvg min max noauto bins temp tol v b e dt histonly boundsonly nolog unit zprof0 cycl alpha flip hist-eq nBootstrap bs-dt bs-seed nohistbs histbs-block vbs)/"
+complete g_velacc "n/-xvg/( xmgrace xmgr none)/" "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7 exp9 erffit)/" "n/-f/f:*.{trr,cpt,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 version nice b e dt w xvg m mol acflen nonormalize P fitfn ncskip beginfit endfit)/"
+complete g_wham "n/-xvg/( xmgrace xmgr none)/" "n/-unit/( kJ kCal kT)/" "n/-bs-method/( b-hist hist traj traj-gauss)/" "n/-ix/f:*.dat{,.gz,.Z}/" "n/-if/f:*.dat{,.gz,.Z}/" "n/-it/f:*.dat{,.gz,.Z}/" "n/-ip/f:*.dat{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-hist/f:*.xvg{,.gz,.Z}/" "n/-oiact/f:*.xvg{,.gz,.Z}/" "n/-iiact/f:*.dat{,.gz,.Z}/" "n/-bsres/f:*.xvg{,.gz,.Z}/" "n/-bsprof/f:*.xvg{,.gz,.Z}/" "n/-tab/f:*.dat{,.gz,.Z}/" "c/-/( ix if it ip o hist oiact iiact bsres bsprof tab h version nice xvg min max noauto bins temp tol v b e dt histonly boundsonly nolog unit zprof0 cycl sym ac acsig ac-trestart nBootstrap bs-method bs-tau bs-seed histbs-block vbs)/"
complete g_wheel "n/-f/f:*.dat{,.gz,.Z}/" "n/-o/f:*.eps{,.gz,.Z}/" "c/-/( f o h version nice r0 rot0 T nonn)/"
complete g_x2top "n/-f/f:*.{gro,g96,pdb,brk,ent,esp,xyz,tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.top{,.gz,.Z}/" "n/-r/f:*.rtp{,.gz,.Z}/" "c/-/( f o r h version nice ff v nexcl noH14 alldih remdih nopairs name nopbc pdbq noparam noround kb kt kp)/"
complete g_xrama "n/-f/f:*.{xtc,trr,cpt,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "c/-/( f s h version nice b e dt)/"
-complete genbox "n/-cp/f:*.{gro,g96,pdb,brk,ent,esp,xyz,tpr,tpb,tpa}{,.gz,.Z}/" "n/-cs/f:*.{gro,g96,pdb,brk,ent,esp,xyz,tpr,tpb,tpa}{,.gz,.Z}/" "n/-ci/f:*.{gro,g96,pdb,brk,ent,esp,xyz,tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,ent,esp,xyz}{,.gz,.Z}/" "n/-p/f:*.top{,.gz,.Z}/" "c/-/( cp cs ci o p h version nice box nmol try seed vdwd shell maxsol vel)/"
-complete genconf "n/-f/f:*.{gro,g96,pdb,brk,ent,esp,xyz,tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,ent,esp,xyz}{,.gz,.Z}/" "n/-trj/f:*.{xtc,trr,cpt,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "c/-/( f o trj h version nice nbox dist seed rot shuffle sort block nmolat maxrot norenumber)/"
-complete genion "n/-xvg/( xmgrace xmgr none)/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-table/f:*.xvg{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,ent,esp,xyz}{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "n/-pot/f:*.pdb{,.gz,.Z}/" "n/-p/f:*.top{,.gz,.Z}/" "c/-/( s table n o g pot p h version nice xvg np pname pq nn nname nq rmin norandom seed scale conc neutral)/"
-complete genrestr "n/-f/f:*.{gro,g96,pdb,brk,ent,esp,xyz,tpr,tpb,tpa}{,.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 version nice fc freeze disre disre_dist disre_frac disre_up2 cutoff constr)/"
-complete gmxcheck "n/-f/f:*.{xtc,trr,cpt,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-f2/f:*.{xtc,trr,cpt,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{,.gz,.Z}/" "n/-e2/f:*.edr{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-m/f:*.tex{,.gz,.Z}/" "c/-/( f f2 s1 s2 c e e2 n m h version nice vdwfac bonlo bonhi rmsd tol abstol ab lastener)/"
-complete gmxdump "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,cpt,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-e/f:*.edr{,.gz,.Z}/" "n/-cp/f:*.cpt{,.gz,.Z}/" "n/-p/f:*.top{,.gz,.Z}/" "n/-mtx/f:*.mtx{,.gz,.Z}/" "n/-om/f:*.mdp{,.gz,.Z}/" "c/-/( s f e cp p mtx om h version nice nonr sys)/"
-complete grompp "n/-f/f:*.mdp{,.gz,.Z}/" "n/-po/f:*.mdp{,.gz,.Z}/" "n/-c/f:*.{gro,g96,pdb,brk,ent,esp,xyz,tpr,tpb,tpa}{,.gz,.Z}/" "n/-r/f:*.{gro,g96,pdb,brk,ent,esp,xyz,tpr,tpb,tpa}{,.gz,.Z}/" "n/-rb/f:*.{gro,g96,pdb,brk,ent,esp,xyz,tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/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,cpt,trj}{,.gz,.Z}/" "n/-e/f:*.edr{,.gz,.Z}/" "c/-/( f po c r rb n p pp o t e h version nice v time normvsbds maxwarn zero norenum)/"
-complete make_edi "n/-xvg/( xmgrace xmgr none)/" "n/-f/f:*.{trr,cpt,trj}{,.gz,.Z}/" "n/-eig/f:*.xvg{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-tar/f:*.{gro,g96,pdb,brk,ent,esp,xyz,tpr,tpb,tpa}{,.gz,.Z}/" "n/-ori/f:*.{gro,g96,pdb,brk,ent,esp,xyz,tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.edi{,.gz,.Z}/" "c/-/( f eig s n tar ori o h version nice xvg mon linfix linacc flood radfix radacc radcon outfrq slope maxedsteps deltaF0 deltaF tau eqsteps Eflnull T alpha linstep accdir radstep restrain hessian harmonic)/"
+complete make_edi "n/-xvg/( xmgrace xmgr none)/" "n/-f/f:*.{trr,cpt,trj}{,.gz,.Z}/" "n/-eig/f:*.xvg{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-tar/f:*.{gro,g96,pdb,brk,ent,esp,xyz,tpr,tpb,tpa}{,.gz,.Z}/" "n/-ori/f:*.{gro,g96,pdb,brk,ent,esp,xyz,tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.edi{,.gz,.Z}/" "c/-/( f eig s n tar ori o h version nice xvg mon linfix linacc radfix radacc radcon flood outfrq slope linstep accdir radstep maxedsteps eqsteps deltaF0 deltaF tau Eflnull T alpha restrain hessian harmonic constF)/"
complete make_ndx "n/-f/f:*.{gro,g96,pdb,brk,ent,esp,xyz,tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.ndx{,.gz,.Z}/" "c/-/( f n o h version nice natoms)/"
-complete mdrun "n/-xvg/( xmgrace xmgr none)/" "n/-ddorder/( interleave pp_pme cartesian)/" "n/-dlb/( auto no yes)/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.{trr,cpt,trj}{,.gz,.Z}/" "n/-x/f:*.xtc{,.gz,.Z}/" "n/-cpi/f:*.cpt{,.gz,.Z}/" "n/-cpo/f:*.cpt{,.gz,.Z}/" "n/-c/f:*.{gro,g96,pdb,brk,ent,esp,xyz}{,.gz,.Z}/" "n/-e/f:*.edr{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "n/-dhdl/f:*.xvg{,.gz,.Z}/" "n/-field/f:*.xvg{,.gz,.Z}/" "n/-table/f:*.xvg{,.gz,.Z}/" "n/-tablep/f:*.xvg{,.gz,.Z}/" "n/-tableb/f:*.xvg{,.gz,.Z}/" "n/-rerun/f:*.{xtc,trr,cpt,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-tpi/f:*.xvg{,.gz,.Z}/" "n/-tpid/f:*.xvg{,.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/-px/f:*.xvg{,.gz,.Z}/" "n/-pf/f:*.xvg{,.gz,.Z}/" "n/-mtx/f:*.mtx{,.gz,.Z}/" "n/-dn/f:*.ndx{,.gz,.Z}/" "c/-/( s o x cpi cpo c e g dhdl field table tablep tableb rerun tpi tpid ei eo j jo ffout devout runav px pf mtx dn h version nice deffnm xvg pd dd nt npme ddorder noddcheck rdd rcon dlb dds gcom v nocompact seppot pforce reprod cpt cpnum noappend maxh multi replex reseed ionize)/"
+complete mdrun "n/-xvg/( xmgrace xmgr none)/" "n/-ddorder/( interleave pp_pme cartesian)/" "n/-dlb/( auto no yes)/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.{trr,cpt,trj}{,.gz,.Z}/" "n/-x/f:*.xtc{,.gz,.Z}/" "n/-cpi/f:*.cpt{,.gz,.Z}/" "n/-cpo/f:*.cpt{,.gz,.Z}/" "n/-c/f:*.{gro,g96,pdb,brk,ent,esp,xyz}{,.gz,.Z}/" "n/-e/f:*.edr{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "n/-dhdl/f:*.xvg{,.gz,.Z}/" "n/-field/f:*.xvg{,.gz,.Z}/" "n/-table/f:*.xvg{,.gz,.Z}/" "n/-tablep/f:*.xvg{,.gz,.Z}/" "n/-tableb/f:*.xvg{,.gz,.Z}/" "n/-rerun/f:*.{xtc,trr,cpt,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-tpi/f:*.xvg{,.gz,.Z}/" "n/-tpid/f:*.xvg{,.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/-px/f:*.xvg{,.gz,.Z}/" "n/-pf/f:*.xvg{,.gz,.Z}/" "n/-mtx/f:*.mtx{,.gz,.Z}/" "n/-dn/f:*.ndx{,.gz,.Z}/" "n/-multidir/f:*.rundir{,.gz,.Z}/" "c/-/( s o x cpi cpo c e g dhdl field table tablep tableb rerun tpi tpid ei eo j jo ffout devout runav px pf mtx dn multidir h version nice deffnm xvg pd dd nt npme ddorder noddcheck rdd rcon dlb dds gcom v nocompact seppot pforce reprod cpt cpnum noappend maxh multi replex reseed ionize)/"
complete mk_angndx "n/-type/( angle dihedral improper ryckaert-bellemans)/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "c/-/( s n h version nice type nohyd hq)/"
complete ngmx "n/-f/f:*.{xtc,trr,cpt,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 version nice b e dt)/"
-complete pdb2gmx "n/-chainsep/( id_or_ter id_and_ter ter id interactive)/" "n/-water/( select none spc spce tip3p tip4p tip5p)/" "n/-vsite/( none hydrogens aromatics)/" "n/-f/f:*.{gro,g96,pdb,brk,ent,esp,xyz,tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,ent,esp,xyz}{,.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,esp,xyz}{,.gz,.Z}/" "c/-/( f o p i n q h version nice chainsep ff water inter ss ter lys arg asp glu gln his angle dist una ignh missing v posrefc vsite heavyh deuterate nochargegrp nocmap renum rtpres)/"
+complete pdb2gmx "n/-chainsep/( id_or_ter id_and_ter ter id interactive)/" "n/-merge/( no all interactive)/" "n/-water/( select none spc spce tip3p tip4p tip5p)/" "n/-vsite/( none hydrogens aromatics)/" "n/-f/f:*.{gro,g96,pdb,brk,ent,esp,xyz,tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,ent,esp,xyz}{,.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,esp,xyz}{,.gz,.Z}/" "c/-/( f o p i n q h version nice chainsep merge ff water inter ss ter lys arg asp glu gln his angle dist una ignh missing v posrefc vsite heavyh deuterate nochargegrp nocmap renum rtpres)/"
complete tpbconv "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-f/f:*.{trr,cpt,trj}{,.gz,.Z}/" "n/-e/f:*.edr{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "c/-/( s f e n o h version nice extend until nsteps time zeroq novel nocont)/"
complete trjcat "n/-tu/( fs ps ns us ms s)/" "n/-xvg/( xmgrace xmgr none)/" "n/-f/f:*.{xtc,trr,cpt,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}/" "n/-demux/f:*.xvg{,.gz,.Z}/" "c/-/( f o n demux h version nice tu xvg b e dt prec novel settime nosort keeplast overwrite cat)/"
-complete trjconv "n/-tu/( fs ps ns us ms s)/" "n/-xvg/( xmgrace xmgr none)/" "n/-pbc/( none mol res atom nojump cluster whole)/" "n/-ur/( rect tric compact)/" "n/-boxcenter/( tric rect zero)/" "n/-fit/( none rot+trans rotxy+transxy translation transxy progressive)/" "n/-f/f:*.{xtc,trr,cpt,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}/" "n/-sub/f:*.ndx{,.gz,.Z}/" "n/-drop/f:*.xvg{,.gz,.Z}/" "c/-/( f o s n fr sub drop h version nice b e tu w xvg skip dt round dump t0 timestep pbc ur center boxcenter box trans shift fit ndec novel force trunc exec app split sep nzero dropunder dropover conect)/"
+complete trjconv "n/-tu/( fs ps ns us ms s)/" "n/-xvg/( xmgrace xmgr none)/" "n/-pbc/( none mol res atom nojump cluster whole)/" "n/-ur/( rect tric compact)/" "n/-boxcenter/( tric rect zero)/" "n/-fit/( none rot+trans rotxy+transxy translation transxy progressive)/" "n/-f/f:*.{xtc,trr,cpt,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}/" "n/-sub/f:*.ndx{,.gz,.Z}/" "n/-drop/f:*.xvg{,.gz,.Z}/" "c/-/( f o s n fr sub drop h version nice b e tu w xvg skip dt round dump t0 timestep pbc ur center boxcenter box clustercenter trans shift fit ndec novel force trunc exec app split sep nzero dropunder dropover conect)/"
complete trjorder "n/-xvg/( xmgrace xmgr none)/" "n/-f/f:*.{xtc,trr,cpt,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}/" "n/-nshell/f:*.xvg{,.gz,.Z}/" "c/-/( f s n o nshell h version nice b e dt xvg na da com r z)/"
complete xpm2ps "n/-title/( top once ylabel none)/" "n/-legend/( both first second none)/" "n/-diag/( first second none)/" "n/-rainbow/( no blue red)/" "n/-combine/( halves add sub mult div)/" "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 version nice w noframe title yonce legend diag size bx by rainbow gradient skip zeroline legoffset combine cmin cmax)/"
compctl -x 's[-]' -s " f s n ssdump map o sc a ta aa h version nice b e dt tu w xvg sss" - 'c[-1,-tu]' -s " fs ps ns us ms s" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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 mead bf h version nice w ndef bt box angles d c center aligncenter align translate rotate princ scale density pbc grasp rvdw sig56 vdwread atom legend label conect" - 'c[-1,-bt]' -s " triclinic cubic dodecahedron octahedron" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz)(|.gz|.Z) *(/)' - 'c[-1,-mead]' -g '*.pqr(|.gz|.Z) *(/)' - 'c[-1,-bf]' -g '*.dat(|.gz|.Z) *(/)' -- editconf
-compctl -x 's[-]' -s " f o h version nice b e dt offset settime nosort scalefac noerror" - 'c[-1,-f]' -g '*.edr(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.edr(|.gz|.Z) *(/)' -- eneconv
+compctl -x 's[-]' -s " f n o mead bf h version nice w ndef bt box angles d c center aligncenter align translate rotate princ scale density pbc resnr grasp rvdw sig56 vdwread atom legend label conect" - 'c[-1,-bt]' -s " triclinic cubic dodecahedron octahedron" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz)(|.gz|.Z) *(/)' - 'c[-1,-mead]' -g '*.pqr(|.gz|.Z) *(/)' - 'c[-1,-bf]' -g '*.dat(|.gz|.Z) *(/)' -- editconf
+compctl -x 's[-]' -s " f o h version nice b e dt offset settime nosort rmdh scalefac noerror" - 'c[-1,-f]' -g '*.edr(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.edr(|.gz|.Z) *(/)' -- eneconv
compctl -x 's[-]' -s " f ox od of g h version nice xvg free norms cutoff" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - '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) *(/)' -- g_anadock
compctl -x 's[-]' -s " v v2 f s n eig eig2 comp rmsf proj 2d 3d filt extr over inpr h version nice b e dt tu w xvg first last skip max nframes split entropy temp nevskip" - 'c[-1,-tu]' -s " fs ps ns us ms s" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-v]' -g '*.(trr|cpt|trj)(|.gz|.Z) *(/)' - 'c[-1,-v2]' -g '*.(trr|cpt|trj)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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,-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|ent|esp|xyz)(|.gz|.Z) *(/)' - 'c[-1,-filt]' -g '*.(xtc|trr|cpt|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-extr]' -g '*.(xtc|trr|cpt|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 bal g h version nice w xvg notime b e n d bw errbar integrate aver_start xydy regression luzar temp fitstart fitend smooth filter power nosubav oneacf acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - '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,-bal]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' -- g_analyze
-compctl -x 's[-]' -s " f n od ov of ot oh oc or h version nice b e dt w xvg type all binwidth noperiodic chandler avercorr acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - '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|cpt|trj|gro|g96|pdb|g87)(|.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) *(/)' - 'c[-1,-or]' -g '*.trr(|.gz|.Z) *(/)' -- g_angle
-compctl -x 's[-]' -s " f o oi oh g h version nice w xvg b e temp prec nbmin nbmax nbin" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-f]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oi]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oh]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.edr(|.gz|.Z) *(/)' -- g_bar
+compctl -x 's[-]' -s " f ac msd cc dist av ee bal g h version nice w xvg notime b e n d bw errbar integrate aver_start xydy regression luzar temp fitstart fitend smooth filter power nosubav oneacf acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - '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 erffit" - '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,-bal]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' -- g_analyze
+compctl -x 's[-]' -s " f n od ov of ot oh oc or h version nice b e dt w xvg type all binwidth noperiodic chandler avercorr acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - '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 erffit" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|trj|gro|g96|pdb|g87)(|.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) *(/)' - 'c[-1,-or]' -g '*.trr(|.gz|.Z) *(/)' -- g_angle
+compctl -x 's[-]' -s " f g o oi oh h version nice w xvg b e temp prec nbmin nbmax nbin" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-f]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.edr(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oi]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oh]' -g '*.xvg(|.gz|.Z) *(/)' -- g_bar
compctl -x 's[-]' -s " f n s o l d h version nice b e dt w xvg blen tol noaver noaverdist" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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 version nice b e dt tu xvg na z" - 'c[-1,-tu]' -s " fs ps ns us ms s" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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 " s f o p ss jc corr g ot oh rt cp h version nice b e dt w xvg r0 phi psi omega rama viol noperiodic all rad shift binwidth core_rotamer maxchi nonormhisto ramomega bfact chi_prod HChi bmax acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - '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|esp|xyz|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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 version nice b e dt tu w xvg dista nlevels cutoff nofit max skip av wcl nst rmsmin method minstruct binary M P seed niter kT" - 'c[-1,-tu]' -s " fs ps ns us ms s" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-method]' -s " linkage jarvis-patrick monte-carlo diagonalization gromos" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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|cpt|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' -- g_cluster
+compctl -x 's[-]' -s " s f o p ss jc corr g ot oh rt cp h version nice b e dt w xvg r0 phi psi omega rama viol noperiodic all rad shift binwidth core_rotamer maxchi nonormhisto ramomega bfact chi_prod HChi bmax acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - '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 erffit" - 'c[-1,-s]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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 version nice b e dt tu w xvg dista nlevels cutoff nofit max skip av wcl nst rmsmin method minstruct binary M P seed niter kT nopbc" - 'c[-1,-tu]' -s " fs ps ns us ms s" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-method]' -s " linkage jarvis-patrick monte-carlo diagonalization gromos" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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|cpt|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' -- g_cluster
compctl -x 's[-]' -s " f s n o ow nc mc ac hc temp mcn h version nice b e dt tu w xvg cut mol nopbc nskip nlevels ndf rgblo rgbhi" - 'c[-1,-tu]' -s " fs ps ns us ms s" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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) *(/)' - 'c[-1,-temp]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-mcn]' -g '*.ndx(|.gz|.Z) *(/)' -- g_clustsize
compctl -x 's[-]' -s " f1 f2 o n1 n2 no h version nice w one nomw pbc nofit name label bfac" - 'c[-1,-f1]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-f2]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz)(|.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 version nice b e dt tu xvg nofit ref mwa last nopbc" - 'c[-1,-tu]' -s " fs ps ns us ms s" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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|cpt|trj)(|.gz|.Z) *(/)' - 'c[-1,-av]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz)(|.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 " s n f o caf dsp md mj mc h version nice b e dt w xvg sh nonojump eps bfit efit bvit evit tr temp" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|cpt|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-caf]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-dsp]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-md]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-mj]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-mc]' -g '*.xvg(|.gz|.Z) *(/)' -- g_current
compctl -x 's[-]' -s " f n s ei o h version nice b e dt w xvg d sl dens ng symm center" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-dens]' -s " mass number charge electron" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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 s n od o h version nice b e dt w bin aver xmin xmax n1 n2 amax rmax mirror sums unit dmin dmax" - 'c[-1,-aver]' -s " z y x" - 'c[-1,-unit]' -s " nm-3 nm-2 count" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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 '*.dat(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xpm(|.gz|.Z) *(/)' -- g_densmap
-compctl -x 's[-]' -s " f d o c h version nice b e dt w xvg fft nox1 eint bfit efit tail A tau1 tau2 eps0 epsRF fix ffn nsmooth" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - '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 " s f n o or og Spect h version nice b e dt w 1d bw bwn order axis method d1 d2 tblock nlevel" - 'c[-1,-method]' -s " bisect functional" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|cpt|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-or]' -g '*.out(|.gz|.Z) *(/)' - 'c[-1,-og]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-Spect]' -g '*.out(|.gz|.Z) *(/)' -- g_densorder
+compctl -x 's[-]' -s " f d o c h version nice b e dt w xvg fft nox1 eint bfit efit tail A tau1 tau2 eps0 epsRF fix ffn nsmooth" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-ffn]' -s " none exp aexp exp_exp vac exp5 exp7 exp9 erffit" - '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 version nice b e dt w sa mult" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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 " en f s n o eps a d c g adip dip3d cos cmap q slab h version nice b e dt w xvg mu mumax epsilonRF skip temp corr nopairs ncos axis sl gkratom gkratom2 rcmax phi nlevels ndegrees acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-corr]' -s " none mol molsep total" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac exp5 exp7 exp9" - 'c[-1,-en]' -g '*.edr(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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,-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,-adip]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-dip3d]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-cos]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-cmap]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-q]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-slab]' -g '*.xvg(|.gz|.Z) *(/)' -- g_dipoles
+compctl -x 's[-]' -s " en f s n o eps a d c g adip dip3d cos cmap q slab h version nice b e dt w xvg mu mumax epsilonRF skip temp corr nopairs ncos axis sl gkratom gkratom2 rcmax phi nlevels ndegrees acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-corr]' -s " none mol molsep total" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac exp5 exp7 exp9 erffit" - 'c[-1,-en]' -g '*.edr(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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,-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,-adip]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-dip3d]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-cos]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-cmap]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-q]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-slab]' -g '*.xvg(|.gz|.Z) *(/)' -- g_dipoles
compctl -x 's[-]' -s " s f ds da dn dm dr l n q c x h version nice b e dt w xvg ntop maxdr nlevels nothird" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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) *(/)' - 'c[-1,-c]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-x]' -g '*.xpm(|.gz|.Z) *(/)' -- g_disre
compctl -x 's[-]' -s " f s n o lt h version nice b e dt xvg dist" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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,-lt]' -g '*.xvg(|.gz|.Z) *(/)' -- g_dist
+compctl -x 's[-]' -s " f s n vacf mvacf dos g h version nice b e dt w xvg nov recip abs normdos T acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac exp5 exp7 exp9 erffit" - 'c[-1,-f]' -g '*.(trr|cpt|trj)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-vacf]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-mvacf]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-dos]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' -- g_dos
compctl -x 's[-]' -s " f o n h version 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 version nice box nmol try seed vdwd shell maxsol vel" - 'c[-1,-cp]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-cs]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-ci]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz)(|.gz|.Z) *(/)' - 'c[-1,-p]' -g '*.top(|.gz|.Z) *(/)' -- genbox
+compctl -x 's[-]' -s " f o trj h version nice nbox dist seed rot shuffle sort block nmolat maxrot norenumber" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz)(|.gz|.Z) *(/)' - 'c[-1,-trj]' -g '*.(xtc|trr|cpt|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' -- genconf
compctl -x 's[-]' -s " f groups eref emat etot h version nice b e dt w xvg sum skip nomean nlevels max min nocoul coulr coul14 nolj lj lj14 bhamsr bhamlr nofree temp" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-f]' -g '*.edr(|.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 oten corr vis ravg h version nice b e w xvg fee fetemp zero sum dp nbmin nbmax mutot skip aver nmol nconstr fluc orinst ovec acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - '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(|.gz|.Z) *(/)' - 'c[-1,-f2]' -g '*.edr(|.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,-oten]' -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 f2 s o viol pairs ora ort oda odr odt oten corr vis ravg odh h version nice b e w xvg fee fetemp zero sum dp nbmin nbmax mutot skip aver nmol fluct_props driftcorr fluc orinst ovec acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac exp5 exp7 exp9 erffit" - 'c[-1,-f]' -g '*.edr(|.gz|.Z) *(/)' - 'c[-1,-f2]' -g '*.edr(|.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,-oten]' -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) *(/)' - 'c[-1,-odh]' -g '*.xvg(|.gz|.Z) *(/)' -- g_energy
+compctl -x 's[-]' -s " s table n o g pot p h version nice xvg np pname pq nn nname nq rmin norandom seed scale conc neutral" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-table]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz)(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-pot]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-p]' -g '*.top(|.gz|.Z) *(/)' -- genion
+compctl -x 's[-]' -s " f n o of h version nice fc freeze disre disre_dist disre_frac disre_up2 cutoff constr" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.itp(|.gz|.Z) *(/)' - 'c[-1,-of]' -g '*.ndx(|.gz|.Z) *(/)' -- genrestr
compctl -x 's[-]' -s " f s n ol oh h version nice b e dt w nf all nonojump fit" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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 '*.(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 n o acf h version nice b e dt w xvg nmol q p moi nz acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - '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|cpt|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,-acf]' -g '*.xvg(|.gz|.Z) *(/)' -- g_gyrate
+compctl -x 's[-]' -s " f s n o acf h version nice b e dt w xvg nmol q p moi nz acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac exp5 exp7 exp9 erffit" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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,-acf]' -g '*.xvg(|.gz|.Z) *(/)' -- g_gyrate
compctl -x 's[-]' -s " f n nm s o h version nice b e dt w xvg d sl" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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 num g ac dist ang hx hbn hbm don dan life nhbdist h version nice b e dt xvg a r noda r2 abin rbin nonitacc contact shell fitstart fitstart temp smooth dump max_hb nomerge geminate diff acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-geminate]' -s " none dd ad aa a4" - '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|cpt|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,-num]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.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,-don]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-dan]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-life]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-nhbdist]' -g '*.xvg(|.gz|.Z) *(/)' -- g_hbond
+compctl -x 's[-]' -s " f s n num g ac dist ang hx hbn hbm don dan life nhbdist h version nice b e dt tu xvg a r noda r2 abin rbin nonitacc contact shell fitstart fitstart temp smooth dump max_hb nomerge geminate diff acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-tu]' -s " fs ps ns us ms s" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-geminate]' -s " none dd ad aa a4" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac exp5 exp7 exp9 erffit" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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,-num]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.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,-don]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-dan]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-life]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-nhbdist]' -g '*.xvg(|.gz|.Z) *(/)' -- g_hbond
compctl -x 's[-]' -s " s n f to cz co h version nice b e dt w r0 q noF db prop ev ahxstart ahxend" - 'c[-1,-prop]' -s " RAD TWIST RISE LEN NHX DIP RMS CPHI RMSA PHI PSI HB3 HB4 HB5 CD222" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|cpt|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-to]' -g '*.g87(|.gz|.Z) *(/)' - 'c[-1,-cz]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz)(|.gz|.Z) *(/)' - 'c[-1,-co]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz)(|.gz|.Z) *(/)' -- g_helix
compctl -x 's[-]' -s " s f n oaxis ocenter orise oradius otwist obending otilt orot h version nice b e dt xvg sidechain incremental" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|cpt|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-oaxis]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-ocenter]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-orise]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oradius]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-otwist]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-obending]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-otilt]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-orot]' -g '*.xvg(|.gz|.Z) *(/)' -- g_helixorient
+compctl -x 's[-]' -s " f n s o or Spect h version nice b e dt w d bw sgang1 sgang2 tblock nlevel" - 'c[-1,-d]' -s " z x y" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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 '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-or]' -g '*.out(|.gz|.Z) *(/)' - 'c[-1,-Spect]' -g '*.out(|.gz|.Z) *(/)' -- g_hydorder
compctl -x 's[-]' -s " f o h version nice b e dt w xvg Elj Eqq Clj Cqq ligand" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-f]' -g '*.edr(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' -- g_lie
compctl -x 's[-]' -s " f s n mean frames no h version nice b e dt xvg t nlevels" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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 n p o x cpi cpo c e g ei rerun table tablep tableb dhdl field table tablep tableb rerun tpi tpid ei eo j jo ffout devout runav px pf mtx dn h version nice deffnm xvg xyinit xyend zinit zend nxy nz rad pieces asymmetry ndiff maxwarn nocompact v" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-f]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-p]' -g '*.top(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(trr|cpt|trj)(|.gz|.Z) *(/)' - 'c[-1,-x]' -g '*.xtc(|.gz|.Z) *(/)' - 'c[-1,-cpi]' -g '*.cpt(|.gz|.Z) *(/)' - 'c[-1,-cpo]' -g '*.cpt(|.gz|.Z) *(/)' - 'c[-1,-c]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz)(|.gz|.Z) *(/)' - 'c[-1,-e]' -g '*.edr(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-ei]' -g '*.edi(|.gz|.Z) *(/)' - 'c[-1,-rerun]' -g '*.(xtc|trr|cpt|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-table]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-tablep]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-tableb]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-dhdl]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-field]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-table]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-tablep]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-tableb]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-rerun]' -g '*.(xtc|trr|cpt|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-tpi]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-tpid]' -g '*.xvg(|.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,-px]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-pf]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-mtx]' -g '*.mtx(|.gz|.Z) *(/)' - 'c[-1,-dn]' -g '*.ndx(|.gz|.Z) *(/)' -- g_membed
+compctl -x 's[-]' -s " f n p o x cpi cpo c e g ei rerun table tablep tableb dhdl field table tablep tableb rerun tpi tpid ei eo j jo ffout devout runav px pf mtx dn multidir h version nice deffnm xvg xyinit xyend zinit zend nxy nz rad pieces asymmetry ndiff maxwarn nocompact v" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-f]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-p]' -g '*.top(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(trr|cpt|trj)(|.gz|.Z) *(/)' - 'c[-1,-x]' -g '*.xtc(|.gz|.Z) *(/)' - 'c[-1,-cpi]' -g '*.cpt(|.gz|.Z) *(/)' - 'c[-1,-cpo]' -g '*.cpt(|.gz|.Z) *(/)' - 'c[-1,-c]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz)(|.gz|.Z) *(/)' - 'c[-1,-e]' -g '*.edr(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-ei]' -g '*.edi(|.gz|.Z) *(/)' - 'c[-1,-rerun]' -g '*.(xtc|trr|cpt|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-table]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-tablep]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-tableb]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-dhdl]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-field]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-table]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-tablep]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-tableb]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-rerun]' -g '*.(xtc|trr|cpt|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-tpi]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-tpid]' -g '*.xvg(|.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,-px]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-pf]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-mtx]' -g '*.mtx(|.gz|.Z) *(/)' - 'c[-1,-dn]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-multidir]' -g '*.rundir(|.gz|.Z) *(/)' -- g_membed
compctl -x 's[-]' -s " f s n od on o ox or h version nice b e dt tu w xvg matrix max d group pi split ng nopbc respertime printresname" - 'c[-1,-tu]' -s " fs ps ns us ms s" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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) *(/)' - '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 version nice w xvg ninterm first last nofit" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-f1]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-f2]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(xtc|trr|cpt|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 pdb h version nice b e tu w xvg type lateral ten ngroup nomw rmcomm tpdb trestart beginfit endfit" - 'c[-1,-tu]' -s " fs ps ns us ms s" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-type]' -s " no x y z" - 'c[-1,-lateral]' -s " no x y z" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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) *(/)' - 'c[-1,-pdb]' -g '*.pdb(|.gz|.Z) *(/)' -- g_msd
-compctl -x 's[-]' -s " f s of ol v h version nice xvg nom first last" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-f]' -g '*.mtx(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-of]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ol]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-v]' -g '*.(trr|cpt|trj)(|.gz|.Z) *(/)' -- g_nmeig
+compctl -x 's[-]' -s " f f2 s1 s2 c e e2 n m h version nice vdwfac bonlo bonhi rmsd tol abstol ab lastener" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-f2]' -g '*.(xtc|trr|cpt|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(|.gz|.Z) *(/)' - 'c[-1,-e2]' -g '*.edr(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-m]' -g '*.tex(|.gz|.Z) *(/)' -- gmxcheck
+compctl -x 's[-]' -s " s f e cp p mtx om h version nice nonr sys" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|cpt|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-e]' -g '*.edr(|.gz|.Z) *(/)' - 'c[-1,-cp]' -g '*.cpt(|.gz|.Z) *(/)' - 'c[-1,-p]' -g '*.top(|.gz|.Z) *(/)' - 'c[-1,-mtx]' -g '*.mtx(|.gz|.Z) *(/)' - 'c[-1,-om]' -g '*.mdp(|.gz|.Z) *(/)' -- gmxdump
+compctl -x 's[-]' -s " f s of ol qc v h version nice xvg nom first last T constr" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-f]' -g '*.mtx(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-of]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ol]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-qc]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-v]' -g '*.(trr|cpt|trj)(|.gz|.Z) *(/)' -- g_nmeig
compctl -x 's[-]' -s " v e s n o h version nice xvg temp seed num first last" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-v]' -g '*.(trr|cpt|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 " s v o h version nice eignr phases temp amplitude nframes" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-v]' -g '*.(trr|cpt|trj)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' -- g_nmtraj
+compctl -x 's[-]' -s " h version nice" -- g_options
compctl -x 's[-]' -s " f n nr s o od ob os Sg Sk Sgsl Sksl h version nice b e dt w xvg d sl szonly unsat permolecule radial calcdist" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-d]' -s " z x y" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-nr]' -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,-ob]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-os]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-Sg]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-Sk]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-Sgsl]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-Sksl]' -g '*.xvg(|.gz|.Z) *(/)' -- g_order
+compctl -x 's[-]' -s " s o so h version nice beta tune self seed v" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.out(|.gz|.Z) *(/)' - 'c[-1,-so]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' -- g_pme_error
compctl -x 's[-]' -s " s f n o v p i h version nice b e dt tu w xvg nomw pc" - 'c[-1,-tu]' -s " fs ps ns us ms s" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|cpt|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-v]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-p]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-i]' -g '*.xvg(|.gz|.Z) *(/)' -- g_polystat
compctl -x 's[-]' -s " f n s o oc of h version nice b e dt w xvg d sl cb ce tz spherical ng correct" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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 n a1 a2 a3 om h version nice b e dt tu w foo" - 'c[-1,-tu]' -s " fs ps ns us ms s" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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,-a1]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-a2]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-a3]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-om]' -g '*.dat(|.gz|.Z) *(/)' -- g_principal
compctl -x 's[-]' -s " s f f2 n o mir a dist m bin bm h version nice b e dt tu w xvg what nopbc fit prev split skip skip2 max min bmax bmin nomw nlevels ng" - 'c[-1,-tu]' -s " fs ps ns us ms s" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-what]' -s " rmsd rho rhosc" - 'c[-1,-fit]' -s " rot+trans translation none" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|cpt|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-f2]' -g '*.(xtc|trr|cpt|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 version nice b e dt w xvg nlevels max nosumh nopbc" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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 version nice b e dt w xvg res aniso nofit" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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 s n o h version nice b e dt w xvg d noaver acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - '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|cpt|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 po c r rb n p pp o t e h version nice v time normvsbds maxwarn zero norenum" - 'c[-1,-f]' -g '*.mdp(|.gz|.Z) *(/)' - 'c[-1,-po]' -g '*.mdp(|.gz|.Z) *(/)' - 'c[-1,-c]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-r]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-rb]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -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|cpt|trj)(|.gz|.Z) *(/)' - 'c[-1,-e]' -g '*.edr(|.gz|.Z) *(/)' -- grompp
+compctl -x 's[-]' -s " f s n o h version nice b e dt w xvg d noaver acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac exp5 exp7 exp9 erffit" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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 n o h version nice b e dt w xvg ref skip fitxy nomw" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-ref]' -s " none xyz xy" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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) *(/)' -- g_rotmat
compctl -x 's[-]' -s " f s h version nice b e dt t sep" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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 or oa tv q n i h version nice b e dt w xvg probe ndots qmax f_index minarea nopbc noprot dgs" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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,-or]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oa]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-tv]' -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 o r h version nice b e dt mode triangle dtri bin grid" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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 '*.dat(|.gz|.Z) *(/)' - 'c[-1,-r]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz)(|.gz|.Z) *(/)' -- g_sdf
compctl -x 's[-]' -s " f s sf n os oc oi om on h version nice b e dt xvg normpbc nopbc select selrpos seltype dump norm cfnorm resnr" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-selrpos]' -s " atom res_com res_cog mol_com mol_cog whole_res_com whole_res_cog whole_mol_com whole_mol_cog part_res_com part_res_cog part_mol_com part_mol_cog dyn_res_com dyn_res_cog dyn_mol_com dyn_mol_cog" - 'c[-1,-seltype]' -s " atom res_com res_cog mol_com mol_cog whole_res_com whole_res_cog whole_mol_com whole_mol_cog part_res_com part_res_cog part_mol_com part_mol_cog dyn_res_com dyn_res_cog dyn_mol_com dyn_mol_cog" - 'c[-1,-resnr]' -s " number index" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-sf]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-os]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oc]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oi]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-om]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-on]' -g '*.ndx(|.gz|.Z) *(/)' -- g_select
compctl -x 's[-]' -s " f n s oa od od1 od2 h version nice b e dt w xvg one z" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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 ge ene dist histo bin lp ls lsh lss map ls3 mdata g h version nice w xvg notime b e ttol n d bw nosham tsham pmin dim ngrid xmin xmax pmax gmax emin emax nlevels mname" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-f]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ge]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ene]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-dist]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-histo]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-bin]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-lp]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-ls]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-lsh]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-lss]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-map]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-ls3]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-mdata]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' -- g_sham
compctl -x 's[-]' -s " f s n o no ro co rc h version nice b e dt w xvg com v23 rmin rmax cbin rbin pbc" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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) *(/)' - 'c[-1,-rc]' -g '*.xvg(|.gz|.Z) *(/)' -- g_sorient
compctl -x 's[-]' -s " s f n h version nice b e dt w pbc nodiv ign bin nab" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|cpt|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' -- g_spatial
compctl -x 's[-]' -s " f s n o h version nice b e dt w xvg com refat rmin rmax dip bw" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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_spol
-compctl -x 's[-]' -s " f s n ot oa o of oc ov h version nice b e dt w xvg mol k34 wt acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - '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|cpt|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 oxt ov of ob ot ekt ekr vd cv cf av af h version nice b e dt tu w xvg com nopbc mol nojump nox noy noz ng len fp bin scale" - 'c[-1,-tu]' -s " fs ps ns us ms s" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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,-oxt]' -g '*.(xtc|trr|cpt|trj|gro|g96|pdb|g87)(|.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,-vd]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-cv]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-cf]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-av]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-af]' -g '*.xvg(|.gz|.Z) *(/)' -- g_traj
-compctl -x 's[-]' -s " p err so s o x cpi cpo c e g dhdl field table tablep tableb rerun tpi tpid ei eo j jo ffout devout runav px pf mtx dn bo bx bcpo bc be bg beo bdhdl bfield btpi btpid bjo bffout bdevout brunav bpx bpf bmtx bdn h version nice xvg np npstring nt r max min npme upfac downfac ntpr four steps resetstep simsteps launch deffnm ddorder noddcheck rdd rcon dlb dds gcom v nocompact seppot pforce reprod cpt cpnum noappend maxh multi replex reseed ionize" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-npstring]' -s " -np -n none" - 'c[-1,-npme]' -s " auto all subset" - 'c[-1,-ddorder]' -s " interleave pp_pme cartesian" - 'c[-1,-dlb]' -s " auto no yes" - 'c[-1,-p]' -g '*.out(|.gz|.Z) *(/)' - 'c[-1,-err]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-so]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(trr|cpt|trj)(|.gz|.Z) *(/)' - 'c[-1,-x]' -g '*.xtc(|.gz|.Z) *(/)' - 'c[-1,-cpi]' -g '*.cpt(|.gz|.Z) *(/)' - 'c[-1,-cpo]' -g '*.cpt(|.gz|.Z) *(/)' - 'c[-1,-c]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz)(|.gz|.Z) *(/)' - 'c[-1,-e]' -g '*.edr(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-dhdl]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-field]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-table]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-tablep]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-tableb]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-rerun]' -g '*.(xtc|trr|cpt|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-tpi]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-tpid]' -g '*.xvg(|.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,-px]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-pf]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-mtx]' -g '*.mtx(|.gz|.Z) *(/)' - 'c[-1,-dn]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-bo]' -g '*.(trr|cpt|trj)(|.gz|.Z) *(/)' - 'c[-1,-bx]' -g '*.xtc(|.gz|.Z) *(/)' - 'c[-1,-bcpo]' -g '*.cpt(|.gz|.Z) *(/)' - 'c[-1,-bc]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz)(|.gz|.Z) *(/)' - 'c[-1,-be]' -g '*.edr(|.gz|.Z) *(/)' - 'c[-1,-bg]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-beo]' -g '*.edo(|.gz|.Z) *(/)' - 'c[-1,-bdhdl]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-bfield]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-btpi]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-btpid]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-bjo]' -g '*.gct(|.gz|.Z) *(/)' - 'c[-1,-bffout]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-bdevout]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-brunav]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-bpx]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-bpf]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-bmtx]' -g '*.mtx(|.gz|.Z) *(/)' - 'c[-1,-bdn]' -g '*.ndx(|.gz|.Z) *(/)' -- g_tune_pme
+compctl -x 's[-]' -s " f s n ot oa o of oc ov h version nice b e dt w xvg mol k34 wt acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac exp5 exp7 exp9 erffit" - 'c[-1,-f]' -g '*.(trr|cpt|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 oxt ov of ob ot ekt ekr vd cv cf av af h version nice b e dt tu w xvg com nopbc mol nojump nox noy noz ng len fp bin ctime scale" - 'c[-1,-tu]' -s " fs ps ns us ms s" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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,-oxt]' -g '*.(xtc|trr|cpt|trj|gro|g96|pdb|g87)(|.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,-vd]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-cv]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-cf]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-av]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-af]' -g '*.xvg(|.gz|.Z) *(/)' -- g_traj
+compctl -x 's[-]' -s " p err so s o x cpi cpo c e g dhdl field table tablep tableb rerun tpi tpid ei eo j jo ffout devout runav px pf mtx dn bo bx bcpo bc be bg beo bdhdl bfield btpi btpid bjo bffout bdevout brunav bpx bpf bmtx bdn h version nice xvg np npstring nt r max min npme fix upfac downfac ntpr four steps resetstep simsteps launch deffnm ddorder noddcheck rdd rcon dlb dds gcom v nocompact seppot pforce reprod cpt cpnum noappend maxh multi replex reseed ionize" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-npstring]' -s " -np -n none" - 'c[-1,-npme]' -s " auto all subset" - 'c[-1,-ddorder]' -s " interleave pp_pme cartesian" - 'c[-1,-dlb]' -s " auto no yes" - 'c[-1,-p]' -g '*.out(|.gz|.Z) *(/)' - 'c[-1,-err]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-so]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(trr|cpt|trj)(|.gz|.Z) *(/)' - 'c[-1,-x]' -g '*.xtc(|.gz|.Z) *(/)' - 'c[-1,-cpi]' -g '*.cpt(|.gz|.Z) *(/)' - 'c[-1,-cpo]' -g '*.cpt(|.gz|.Z) *(/)' - 'c[-1,-c]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz)(|.gz|.Z) *(/)' - 'c[-1,-e]' -g '*.edr(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-dhdl]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-field]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-table]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-tablep]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-tableb]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-rerun]' -g '*.(xtc|trr|cpt|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-tpi]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-tpid]' -g '*.xvg(|.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,-px]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-pf]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-mtx]' -g '*.mtx(|.gz|.Z) *(/)' - 'c[-1,-dn]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-bo]' -g '*.(trr|cpt|trj)(|.gz|.Z) *(/)' - 'c[-1,-bx]' -g '*.xtc(|.gz|.Z) *(/)' - 'c[-1,-bcpo]' -g '*.cpt(|.gz|.Z) *(/)' - 'c[-1,-bc]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz)(|.gz|.Z) *(/)' - 'c[-1,-be]' -g '*.edr(|.gz|.Z) *(/)' - 'c[-1,-bg]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-beo]' -g '*.edo(|.gz|.Z) *(/)' - 'c[-1,-bdhdl]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-bfield]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-btpi]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-btpid]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-bjo]' -g '*.gct(|.gz|.Z) *(/)' - 'c[-1,-bffout]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-bdevout]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-brunav]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-bpx]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-bpf]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-bmtx]' -g '*.mtx(|.gz|.Z) *(/)' - 'c[-1,-bdn]' -g '*.ndx(|.gz|.Z) *(/)' -- g_tune_pme
compctl -x 's[-]' -s " f s n om or ot h version nice b e dt w xvg sqrt fm rmax rbin mmax nlevels nr fr rt ft" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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,-om]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-or]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ot]' -g '*.xvg(|.gz|.Z) *(/)' -- g_vanhove
-compctl -x 's[-]' -s " f s n o h version nice b e dt w xvg m mol acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - '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|cpt|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 " ix if it ip o hist bsres bsprof tab wcorr h version nice xvg min max noauto bins temp tol v b e dt histonly boundsonly nolog unit zprof0 cycl alpha flip hist-eq nBootstrap bs-dt bs-seed nohistbs histbs-block vbs" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-unit]' -s " kJ kCal kT" - 'c[-1,-cycl]' -s " no yes weighted" - 'c[-1,-ix]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-if]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-it]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-ip]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-hist]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-bsres]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-bsprof]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-tab]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-wcorr]' -g '*.xvg(|.gz|.Z) *(/)' -- g_wham
+compctl -x 's[-]' -s " f s n o h version nice b e dt w xvg m mol acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac exp5 exp7 exp9 erffit" - 'c[-1,-f]' -g '*.(trr|cpt|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 " ix if it ip o hist oiact iiact bsres bsprof tab h version nice xvg min max noauto bins temp tol v b e dt histonly boundsonly nolog unit zprof0 cycl sym ac acsig ac-trestart nBootstrap bs-method bs-tau bs-seed histbs-block vbs" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-unit]' -s " kJ kCal kT" - 'c[-1,-bs-method]' -s " b-hist hist traj traj-gauss" - 'c[-1,-ix]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-if]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-it]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-ip]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-hist]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oiact]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-iiact]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-bsres]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-bsprof]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-tab]' -g '*.dat(|.gz|.Z) *(/)' -- g_wham
compctl -x 's[-]' -s " f o h version nice r0 rot0 T nonn" - 'c[-1,-f]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.eps(|.gz|.Z) *(/)' -- g_wheel
compctl -x 's[-]' -s " f o r h version nice ff v nexcl noH14 alldih remdih nopairs name nopbc pdbq noparam noround kb kt kp" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.top(|.gz|.Z) *(/)' - 'c[-1,-r]' -g '*.rtp(|.gz|.Z) *(/)' -- g_x2top
compctl -x 's[-]' -s " f s h version nice b e dt" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' -- g_xrama
-compctl -x 's[-]' -s " cp cs ci o p h version nice box nmol try seed vdwd shell maxsol vel" - 'c[-1,-cp]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-cs]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-ci]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz)(|.gz|.Z) *(/)' - 'c[-1,-p]' -g '*.top(|.gz|.Z) *(/)' -- genbox
-compctl -x 's[-]' -s " f o trj h version nice nbox dist seed rot shuffle sort block nmolat maxrot norenumber" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz)(|.gz|.Z) *(/)' - 'c[-1,-trj]' -g '*.(xtc|trr|cpt|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' -- genconf
-compctl -x 's[-]' -s " s table n o g pot p h version nice xvg np pname pq nn nname nq rmin norandom seed scale conc neutral" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-table]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz)(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-pot]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-p]' -g '*.top(|.gz|.Z) *(/)' -- genion
-compctl -x 's[-]' -s " f n o of h version nice fc freeze disre disre_dist disre_frac disre_up2 cutoff constr" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.itp(|.gz|.Z) *(/)' - 'c[-1,-of]' -g '*.ndx(|.gz|.Z) *(/)' -- genrestr
-compctl -x 's[-]' -s " f f2 s1 s2 c e e2 n m h version nice vdwfac bonlo bonhi rmsd tol abstol ab lastener" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-f2]' -g '*.(xtc|trr|cpt|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(|.gz|.Z) *(/)' - 'c[-1,-e2]' -g '*.edr(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-m]' -g '*.tex(|.gz|.Z) *(/)' -- gmxcheck
-compctl -x 's[-]' -s " s f e cp p mtx om h version nice nonr sys" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|cpt|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-e]' -g '*.edr(|.gz|.Z) *(/)' - 'c[-1,-cp]' -g '*.cpt(|.gz|.Z) *(/)' - 'c[-1,-p]' -g '*.top(|.gz|.Z) *(/)' - 'c[-1,-mtx]' -g '*.mtx(|.gz|.Z) *(/)' - 'c[-1,-om]' -g '*.mdp(|.gz|.Z) *(/)' -- gmxdump
-compctl -x 's[-]' -s " f po c r rb n p pp o t e h version nice v time normvsbds maxwarn zero norenum" - 'c[-1,-f]' -g '*.mdp(|.gz|.Z) *(/)' - 'c[-1,-po]' -g '*.mdp(|.gz|.Z) *(/)' - 'c[-1,-c]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-r]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-rb]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -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|cpt|trj)(|.gz|.Z) *(/)' - 'c[-1,-e]' -g '*.edr(|.gz|.Z) *(/)' -- grompp
-compctl -x 's[-]' -s " f eig s n tar ori o h version nice xvg mon linfix linacc flood radfix radacc radcon outfrq slope maxedsteps deltaF0 deltaF tau eqsteps Eflnull T alpha linstep accdir radstep restrain hessian harmonic" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-f]' -g '*.(trr|cpt|trj)(|.gz|.Z) *(/)' - 'c[-1,-eig]' -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,-tar]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-ori]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.edi(|.gz|.Z) *(/)' -- make_edi
+compctl -x 's[-]' -s " f eig s n tar ori o h version nice xvg mon linfix linacc radfix radacc radcon flood outfrq slope linstep accdir radstep maxedsteps eqsteps deltaF0 deltaF tau Eflnull T alpha restrain hessian harmonic constF" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-f]' -g '*.(trr|cpt|trj)(|.gz|.Z) *(/)' - 'c[-1,-eig]' -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,-tar]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-ori]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.edi(|.gz|.Z) *(/)' -- make_edi
compctl -x 's[-]' -s " f n o h version nice natoms" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz|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 cpi cpo c e g dhdl field table tablep tableb rerun tpi tpid ei eo j jo ffout devout runav px pf mtx dn h version nice deffnm xvg pd dd nt npme ddorder noddcheck rdd rcon dlb dds gcom v nocompact seppot pforce reprod cpt cpnum noappend maxh multi replex reseed ionize" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-ddorder]' -s " interleave pp_pme cartesian" - 'c[-1,-dlb]' -s " auto no yes" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(trr|cpt|trj)(|.gz|.Z) *(/)' - 'c[-1,-x]' -g '*.xtc(|.gz|.Z) *(/)' - 'c[-1,-cpi]' -g '*.cpt(|.gz|.Z) *(/)' - 'c[-1,-cpo]' -g '*.cpt(|.gz|.Z) *(/)' - 'c[-1,-c]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz)(|.gz|.Z) *(/)' - 'c[-1,-e]' -g '*.edr(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-dhdl]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-field]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-table]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-tablep]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-tableb]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-rerun]' -g '*.(xtc|trr|cpt|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-tpi]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-tpid]' -g '*.xvg(|.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,-px]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-pf]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-mtx]' -g '*.mtx(|.gz|.Z) *(/)' - 'c[-1,-dn]' -g '*.ndx(|.gz|.Z) *(/)' -- mdrun
+compctl -x 's[-]' -s " s o x cpi cpo c e g dhdl field table tablep tableb rerun tpi tpid ei eo j jo ffout devout runav px pf mtx dn multidir h version nice deffnm xvg pd dd nt npme ddorder noddcheck rdd rcon dlb dds gcom v nocompact seppot pforce reprod cpt cpnum noappend maxh multi replex reseed ionize" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-ddorder]' -s " interleave pp_pme cartesian" - 'c[-1,-dlb]' -s " auto no yes" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(trr|cpt|trj)(|.gz|.Z) *(/)' - 'c[-1,-x]' -g '*.xtc(|.gz|.Z) *(/)' - 'c[-1,-cpi]' -g '*.cpt(|.gz|.Z) *(/)' - 'c[-1,-cpo]' -g '*.cpt(|.gz|.Z) *(/)' - 'c[-1,-c]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz)(|.gz|.Z) *(/)' - 'c[-1,-e]' -g '*.edr(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-dhdl]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-field]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-table]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-tablep]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-tableb]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-rerun]' -g '*.(xtc|trr|cpt|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-tpi]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-tpid]' -g '*.xvg(|.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,-px]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-pf]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-mtx]' -g '*.mtx(|.gz|.Z) *(/)' - 'c[-1,-dn]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-multidir]' -g '*.rundir(|.gz|.Z) *(/)' -- mdrun
compctl -x 's[-]' -s " s n h version nice type nohyd hq" - 'c[-1,-type]' -s " angle dihedral improper ryckaert-bellemans" - '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 version nice b e dt" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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 version nice chainsep ff water inter ss ter lys arg asp glu gln his angle dist una ignh missing v posrefc vsite heavyh deuterate nochargegrp nocmap renum rtpres" - 'c[-1,-chainsep]' -s " id_or_ter id_and_ter ter id interactive" - 'c[-1,-water]' -s " select none spc spce tip3p tip4p tip5p" - 'c[-1,-vsite]' -s " none hydrogens aromatics" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz)(|.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|esp|xyz)(|.gz|.Z) *(/)' -- pdb2gmx
+compctl -x 's[-]' -s " f o p i n q h version nice chainsep merge ff water inter ss ter lys arg asp glu gln his angle dist una ignh missing v posrefc vsite heavyh deuterate nochargegrp nocmap renum rtpres" - 'c[-1,-chainsep]' -s " id_or_ter id_and_ter ter id interactive" - 'c[-1,-merge]' -s " no all interactive" - 'c[-1,-water]' -s " select none spc spce tip3p tip4p tip5p" - 'c[-1,-vsite]' -s " none hydrogens aromatics" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|ent|esp|xyz)(|.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|esp|xyz)(|.gz|.Z) *(/)' -- pdb2gmx
compctl -x 's[-]' -s " s f e n o h version nice extend until nsteps time zeroq novel nocont" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(trr|cpt|trj)(|.gz|.Z) *(/)' - 'c[-1,-e]' -g '*.edr(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' -- tpbconv
compctl -x 's[-]' -s " f o n demux h version nice tu xvg b e dt prec novel settime nosort keeplast overwrite cat" - 'c[-1,-tu]' -s " fs ps ns us ms s" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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) *(/)' - 'c[-1,-demux]' -g '*.xvg(|.gz|.Z) *(/)' -- trjcat
-compctl -x 's[-]' -s " f o s n fr sub drop h version nice b e tu w xvg skip dt round dump t0 timestep pbc ur center boxcenter box trans shift fit ndec novel force trunc exec app split sep nzero dropunder dropover conect" - 'c[-1,-tu]' -s " fs ps ns us ms s" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-pbc]' -s " none mol res atom nojump cluster whole" - 'c[-1,-ur]' -s " rect tric compact" - 'c[-1,-boxcenter]' -s " tric rect zero" - 'c[-1,-fit]' -s " none rot+trans rotxy+transxy translation transxy progressive" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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) *(/)' - 'c[-1,-sub]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-drop]' -g '*.xvg(|.gz|.Z) *(/)' -- trjconv
+compctl -x 's[-]' -s " f o s n fr sub drop h version nice b e tu w xvg skip dt round dump t0 timestep pbc ur center boxcenter box clustercenter trans shift fit ndec novel force trunc exec app split sep nzero dropunder dropover conect" - 'c[-1,-tu]' -s " fs ps ns us ms s" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-pbc]' -s " none mol res atom nojump cluster whole" - 'c[-1,-ur]' -s " rect tric compact" - 'c[-1,-boxcenter]' -s " tric rect zero" - 'c[-1,-fit]' -s " none rot+trans rotxy+transxy translation transxy progressive" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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) *(/)' - 'c[-1,-sub]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-drop]' -g '*.xvg(|.gz|.Z) *(/)' -- trjconv
compctl -x 's[-]' -s " f s n o nshell h version nice b e dt xvg na da com r z" - 'c[-1,-xvg]' -s " xmgrace xmgr none" - 'c[-1,-f]' -g '*.(xtc|trr|cpt|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) *(/)' - 'c[-1,-nshell]' -g '*.xvg(|.gz|.Z) *(/)' -- trjorder
compctl -x 's[-]' -s " f f2 di do o xpm h version nice w noframe title yonce legend diag size bx by rainbow gradient skip zeroline legoffset combine cmin cmax" - '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,-rainbow]' -s " no blue red" - 'c[-1,-combine]' -s " halves add sub mult div" - '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
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff