-.TH do_dssp 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH do_dssp 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
do_dssp - assigns secondary structure and calculates solvent accessible surface area
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3do_dssp\fP
.BI "\-f" " traj.xtc "
-.TH editconf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH editconf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
editconf - edits the box and writes subgroups
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3editconf\fP
.BI "\-f" " conf.gro "
-.TH eneconv 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH eneconv 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
eneconv - converts energy files
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3eneconv\fP
.BI "\-f" " ener.edr "
-.TH g_anadock 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_anadock 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_anadock - cluster structures from Autodock runs
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_anadock\fP
.BI "\-f" " eiwit.pdb "
-.TH g_anaeig 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_anaeig 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_anaeig - analyzes the eigenvectors
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_anaeig\fP
.BI "\-v" " eigenvec.trr "
-.TH g_analyze 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_analyze 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_analyze - analyzes data sets
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_analyze\fP
.BI "\-f" " graph.xvg "
\&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 [GRK]pi[grk] t) dt)2 / int0\-T y(t) y(t) dt
+2 (int0\-T y(t) cos(i pi t) dt)2 / int0\-T y(t) y(t) dt
\&This is useful for principal components obtained from covariance
\&analysis, since the principal components of random diffusion are
\&that the autocorrelation is a sum of two exponentials.
\&The analytical curve for the block average is:
-\&f(t) = [GRK]sigma[grk]\fB *\fRsqrt(2/T ( [GRK]alpha[grk] ([GRK]tau[grk]1 ((exp(\-t/[GRK]tau[grk]1) \- 1) [GRK]tau[grk]1/t + 1)) +
+\&f(t) = sigma\fB *\fRsqrt(2/T ( alpha (tau1 ((exp(\-t/tau1) \- 1) tau1/t + 1)) +
-\& (1\-[GRK]alpha[grk]) ([GRK]tau[grk]2 ((exp(\-t/[GRK]tau[grk]2) \- 1) [GRK]tau[grk]2/t + 1)))),
+\& (1\-alpha) (tau2 ((exp(\-t/tau2) \- 1) tau2/t + 1)))),
where T is the total time.
-\&[GRK]alpha[grk], [GRK]tau[grk]1 and [GRK]tau[grk]2 are obtained by fitting f2(t) to error2.
+\&alpha, tau1 and tau2 are obtained by fitting f2(t) to error2.
\&When the actual block average is very close to the analytical curve,
-\&the error is [GRK]sigma[grk]\fB *\fRsqrt(2/T (a [GRK]tau[grk]1 + (1\-a) [GRK]tau[grk]2)).
+\&the error is sigma\fB *\fRsqrt(2/T (a tau1 + (1\-a) tau2)).
\&The complete derivation is given in
\&B. Hess, J. Chem. Phys. 116:209\-217, 2002.
\&Option \fB \-filter\fR prints the RMS high\-frequency fluctuation
\&of each set and over all sets with respect to a filtered average.
-\&The filter is proportional to cos([GRK]pi[grk] t/len) where t goes from \-len/2
+\&The filter is proportional to cos(pi t/len) where t goes from \-len/2
\&to len/2. len is supplied with the option \fB \-filter\fR.
\&This filter reduces oscillations with period len/2 and len by a factor
\&of 0.79 and 0.33 respectively.
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 [GRK]chi[grk]2 = (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 \- 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.
.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).
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/[GRK]tau[grk])
+ If = 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
-.TH g_angle 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_angle 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_angle - calculates distributions and correlations for angles and dihedrals
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_angle\fP
.BI "\-f" " traj.xtc "
-.TH g_bar 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_bar 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_bar - calculates free energy difference estimates through Bennett's acceptance ratio
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_bar\fP
.BI "\-f" " dhdl.xvg "
\&Every individual BAR free energy difference relies on two
\&simulations at different states: say state A and state B, as
-\&controlled by a parameter, [GRK]lambda[grk] (see the \fB .mdp\fR parameter
+\&controlled by a parameter, lambda (see the \fB .mdp\fR parameter
\&\fB init_lambda\fR). The BAR method calculates a ratio of weighted
\&average of the Hamiltonian difference of state B given state A and
-\&vice versa. If the Hamiltonian does not depend linearly on [GRK]lambda[grk]
+\&vice versa. If the Hamiltonian does not depend linearly on lambda
\&(in which case we can extrapolate the derivative of the Hamiltonian
-\&with respect to [GRK]lambda[grk], as is the default when \fB free_energy\fR is on),
+\&with respect to lambda, as is the default when \fB free_energy\fR is on),
\&the energy differences to the other state need to be calculated
\&explicitly during the simulation. This can be controlled with
\&the \fB .mdp\fR option \fB foreign_lambda\fR.
\&Two types of input files are supported:
\&\fB *\fR Files with only one \fI y\fR\-value, for such files it is assumed
-\& that the \fI y\fR\-value is dH/d[GRK]lambda[grk] and that the Hamiltonian depends
-\& linearly on [GRK]lambda[grk]. The [GRK]lambda[grk] value of the simulation is inferred
+\& that the \fI y\fR\-value is dH/dlambda and that the Hamiltonian depends
+\& linearly on lambda. The lambda value of the simulation is inferred
\& from the subtitle (if present), otherwise from a number in the
\& subdirectory in the file name.
\&
\&\fB *\fR Files with more than one \fI y\fR\-value. The files should have columns
-\& with dH/d[GRK]lambda[grk] and [GRK]Delta[grk][GRK]lambda[grk]. The [GRK]lambda[grk] values are inferred
-\& from the legends: [GRK]lambda[grk] of the simulation from the legend of dH/d[GRK]lambda[grk]
-\& and the foreign [GRK]lambda[grk] values from the legends of Delta H.
+\& with dH/dlambda and Deltalambda. The lambda values are inferred
+\& from the legends: lambda of the simulation from the legend of dH/dlambda
+\& and the foreign lambda values from the legends of Delta H.
-\&The [GRK]lambda[grk] of the simulation is parsed from \fB dhdl.xvg\fR file's legend
-\&containing the string 'dH', the foreign [GRK]lambda[grk] values from the legend
+\&The lambda of the simulation is parsed from \fB dhdl.xvg\fR file's legend
+\&containing the string 'dH', the foreign lambda values from the legend
\&containing the capitalized letters 'D' and 'H'. The temperature
\&is parsed from the legend line containing 'T ='.
\&These can contain either lists of energy differences (see the
\&\fB .mdp\fR option \fB separate_dhdl_file\fR), or a series of histograms
\&(see the \fB .mdp\fR options \fB dh_hist_size\fR and \fB dh_hist_spacing\fR).
-\&The temperature and [GRK]lambda[grk] values are automatically deduced from
+\&The temperature and lambda values are automatically deduced from
\&the \fB ener.edr\fR file.
The free energy estimates are determined using BAR with bisection,
\&\fB g_bar\fR tries to aggregate samples with the same 'native' and 'foreign'
-\&[GRK]lambda[grk] values, but always assumes independent samples. \fB Note\fR that
+\&lambda values, but always assumes independent samples. \fB Note\fR that
\&when aggregating energy differences/derivatives with different
\&sampling intervals, this is almost certainly not correct. Usually
\&subsequent energies are correlated and different time intervals mean
\&kT (together with their computed error estimate). The printed
\&values are:
-\&\fB *\fR lam_A: the [GRK]lambda[grk] values for point A.
+\&\fB *\fR lam_A: the lambda values for point A.
-\&\fB *\fR lam_B: the [GRK]lambda[grk] values for point B.
+\&\fB *\fR lam_B: the lambda values for point B.
\&\fB *\fR DG: the free energy estimate.
-.TH g_bond 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_bond 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_bond - calculates distances between atoms
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_bond\fP
.BI "\-f" " traj.xtc "
-.TH g_bundle 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_bundle 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_bundle - analyzes bundles of axes, e.g. helices
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_bundle\fP
.BI "\-f" " traj.xtc "
-.TH g_chi 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_chi 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_chi - calculates everything you want to know about chi and other dihedrals
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_chi\fP
.BI "\-s" " conf.gro "
.BI "\-beginfit" " real "
.BI "\-endfit" " real "
.SH DESCRIPTION
-\&\fB g_chi\fR computes [GRK]phi[grk], [GRK]psi[grk], [GRK]omega[grk], and [GRK]chi[grk] dihedrals for all your
+\&\fB g_chi\fR computes phi, psi, omega, and chi dihedrals for all your
\&amino acid backbone and sidechains.
\&It can compute dihedral angle as a function of time, and as
\&histogram distributions.
\&If option \fB \-corr\fR is given, the program will
\&calculate dihedral autocorrelation functions. The function used
-\&is C(t) = cos([GRK]chi[grk]([GRK]tau[grk])) cos([GRK]chi[grk]([GRK]tau[grk]+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
\&(d) a table for each residue of the rotamer occupancy.
-\&All rotamers are taken as 3\-fold, except for [GRK]omega[grk] and [GRK]chi[grk] dihedrals
-\&to planar groups (i.e. [GRK]chi[grk]2 of aromatics, Asp and Asn; [GRK]chi[grk]3 of Glu
-\&and Gln; and [GRK]chi[grk]4 of Arg), which are 2\-fold. "rotamer 0" means
+\&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
\&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
\&If \fB \-chi_prod\fR is set (and \fB \-maxchi\fR 0), cumulative rotamers, e.g.
-\&1+9([GRK]chi[grk]1\-1)+3([GRK]chi[grk]2\-1)+([GRK]chi[grk]3\-1) (if the residue has three 3\-fold
+\&1+9(chi1\-1)+3(chi2\-1)+(chi3\-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
\&and their occupancies to \fB histo\-chiproduct(RESIDUE)(nresnr).xvg\fR.
-\&The option \fB \-r\fR generates a contour plot of the average [GRK]omega[grk] angle
-\&as a function of the [GRK]phi[grk] and [GRK]psi[grk] angles, that is, in a Ramachandran plot
-\&the average [GRK]omega[grk] angle is plotted using color coding.
+\&The option \fB \-r\fR generates a contour plot of the average omega angle
+\&as a function of the phi and psi angles, that is, in a Ramachandran plot
+\&the average omega angle is plotted using color coding.
.SH FILES
.BI "\-s" " conf.gro"
.B Input
starting residue
.BI "\-[no]phi" "no "
- Output for [GRK]phi[grk] dihedral angles
+ Output for phi dihedral angles
.BI "\-[no]psi" "no "
- Output for [GRK]psi[grk] dihedral angles
+ Output for psi dihedral angles
.BI "\-[no]omega" "no "
- Output for [GRK]omega[grk] dihedrals (peptide bonds)
+ Output for omega dihedrals (peptide bonds)
.BI "\-[no]rama" "no "
- Generate [GRK]phi[grk]/[GRK]psi[grk] and [GRK]chi[grk]1/[GRK]chi[grk]2 Ramachandran plots
+ Generate phi/psi and chi1/chi2 Ramachandran plots
.BI "\-[no]viol" "no "
Write a file that gives 0 or 1 for violated Ramachandran angles
in angle vs time files, use radians rather than degrees.
.BI "\-[no]shift" "no "
- Compute chemical shifts from [GRK]phi[grk]/[GRK]psi[grk] angles
+ Compute chemical shifts from phi/psi angles
.BI "\-binwidth" " int" " 1"
bin width for histograms (degrees)
only the central \fB \-core_rotamer\fR*(360/multiplicity) belongs to each rotamer (the rest is assigned to rotamer 0)
.BI "\-maxchi" " enum" " 0"
- calculate first ndih [GRK]chi[grk] dihedrals: \fB 0\fR, \fB 1\fR, \fB 2\fR, \fB 3\fR, \fB 4\fR, \fB 5\fR or \fB 6\fR
+ calculate first ndih chi dihedrals: \fB 0\fR, \fB 1\fR, \fB 2\fR, \fB 3\fR, \fB 4\fR, \fB 5\fR or \fB 6\fR
.BI "\-[no]normhisto" "yes "
Normalize histograms
.SH KNOWN PROBLEMS
\- Produces MANY output files (up to about 4 times the number of residues in the protein, twice that if autocorrelation functions are calculated). Typically several hundred files are output.
-\- [GRK]phi[grk] and [GRK]psi[grk] dihedrals are calculated in a non\-standard way, using H\-N\-CA\-C for [GRK]phi[grk] instead of C(\-)\-N\-CA\-C, and N\-CA\-C\-O for [GRK]psi[grk] instead of N\-CA\-C\-N(+). This causes (usually small) discrepancies with the output of other tools like \fB g_rama\fR.
+\- phi and psi dihedrals are calculated in a non\-standard way, using H\-N\-CA\-C for phi instead of C(\-)\-N\-CA\-C, and N\-CA\-C\-O for psi instead of N\-CA\-C\-N(+). This causes (usually small) discrepancies with the output of other tools like \fB g_rama\fR.
\- \fB \-r0\fR option does not work properly
-.TH g_cluster 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_cluster 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_cluster - clusters structures
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_cluster\fP
.BI "\-f" " traj.xtc "
-.TH g_clustsize 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_clustsize 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_clustsize - calculate size distributions of atomic clusters
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_clustsize\fP
.BI "\-f" " traj.xtc "
-.TH g_confrms 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_confrms 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_confrms - fits two structures and calculates the rmsd
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_confrms\fP
.BI "\-f1" " conf1.gro "
-.TH g_covar 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_covar 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_covar - calculates and diagonalizes the covariance matrix
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_covar\fP
.BI "\-f" " traj.xtc "
-.TH g_current 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_current 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_current - calculate current autocorrelation function of system
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_current\fP
.BI "\-s" " topol.tpr "
-.TH g_density 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_density 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_density - calculates the density of the system
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_density\fP
.BI "\-f" " traj.xtc "
-.TH g_densmap 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_densmap 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_densmap - calculates 2D planar or axial-radial density maps
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_densmap\fP
.BI "\-f" " traj.xtc "
--- /dev/null
+.TH g_densorder 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
+.SH NAME
+g_densorder - calculate surface fluctuations
+
+.B VERSION 4.5.4-dev-20110404-bc5695c
+.SH SYNOPSIS
+\f3g_densorder\fP
+.BI "\-s" " topol.tpr "
+.BI "\-f" " traj.xtc "
+.BI "\-n" " index.ndx "
+.BI "\-o" " Density4D.dat "
+.BI "\-or" " hello.out "
+.BI "\-og" " interface.xpm "
+.BI "\-Spect" " intfspect.out "
+.BI "\-[no]h" ""
+.BI "\-[no]version" ""
+.BI "\-nice" " int "
+.BI "\-b" " time "
+.BI "\-e" " time "
+.BI "\-dt" " time "
+.BI "\-[no]w" ""
+.BI "\-[no]1d" ""
+.BI "\-bw" " real "
+.BI "\-bwn" " real "
+.BI "\-order" " int "
+.BI "\-axis" " string "
+.BI "\-method" " enum "
+.BI "\-d1" " real "
+.BI "\-d2" " real "
+.BI "\-tblock" " int "
+.BI "\-nlevel" " int "
+.SH DESCRIPTION
+\&A small program to reduce a two\-phase density distribution
+\&along an axis, computed over a MD trajectory
+\&to 2D surfaces fluctuating in time, by a fit to
+\&a functional profile for interfacial densities
+\&A time\-averaged spatial representation of the
+\&interfaces can be output with the option \-tavg
+.SH FILES
+.BI "\-s" " topol.tpr"
+.B Input
+ Run input file: tpr tpb tpa
+
+.BI "\-f" " traj.xtc"
+.B Input
+ Trajectory: xtc trr trj gro g96 pdb cpt
+
+.BI "\-n" " index.ndx"
+.B Input
+ Index file
+
+.BI "\-o" " Density4D.dat"
+.B Output, Opt.
+ Generic data file
+
+.BI "\-or" " hello.out"
+.B Output, Opt., Mult.
+ Generic output file
+
+.BI "\-og" " interface.xpm"
+.B Output, Opt., Mult.
+ X PixMap compatible matrix file
+
+.BI "\-Spect" " intfspect.out"
+.B Output, Opt., Mult.
+ Generic output file
+
+.SH OTHER OPTIONS
+.BI "\-[no]h" "no "
+ Print help info and quit
+
+.BI "\-[no]version" "no "
+ Print version info and quit
+
+.BI "\-nice" " int" " 0"
+ Set the nicelevel
+
+.BI "\-b" " time" " 0 "
+ First frame (ps) to read from trajectory
+
+.BI "\-e" " time" " 0 "
+ Last frame (ps) to read from trajectory
+
+.BI "\-dt" " time" " 0 "
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "\-[no]w" "no "
+ View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files
+
+.BI "\-[no]1d" "no "
+ Pseudo\-1d interface geometry
+
+.BI "\-bw" " real" " 0.2 "
+ Binwidth of density distribution tangential to interface
+
+.BI "\-bwn" " real" " 0.05 "
+ Binwidth of density distribution normal to interface
+
+.BI "\-order" " int" " 0"
+ Order of Gaussian filter, order 0 equates to NO filtering
+
+.BI "\-axis" " string" " Z"
+ Axis Direction \- X, Y or Z
+
+.BI "\-method" " enum" " bisect"
+ Interface location method: \fB bisect\fR or \fB functional\fR
+
+.BI "\-d1" " real" " 0 "
+ Bulk density phase 1 (at small z)
+
+.BI "\-d2" " real" " 1000 "
+ Bulk density phase 2 (at large z)
+
+.BI "\-tblock" " int" " 100"
+ Number of frames in one time\-block average
+
+.BI "\-nlevel" " int" " 100"
+ Number of Height levels in 2D \- XPixMaps
+
+.SH SEE ALSO
+.BR gromacs(7)
+
+More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.
-.TH g_dielectric 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_dielectric 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_dielectric - calculates frequency dependent dielectric constants
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_dielectric\fP
.BI "\-f" " dipcorr.xvg "
Start value for fit parameter A
.BI "\-tau1" " real" " 10 "
- Start value for fit parameter [GRK]tau[grk]1
+ Start value for fit parameter tau1
.BI "\-tau2" " real" " 1 "
- Start value for fit parameter [GRK]tau[grk]2
+ Start value for fit parameter tau2
.BI "\-eps0" " real" " 80 "
- [GRK]epsilon[grk]0 of your liquid
+ epsilon0 of your liquid
.BI "\-epsRF" " real" " 78.5 "
- [GRK]epsilon[grk] of the reaction field used in your simulation. A value of 0 means infinity.
+ epsilon of the reaction field used in your simulation. A value of 0 means infinity.
.BI "\-fix" " int" " 0"
Fix parameters at their start values, A (2), tau1 (1), or tau2 (4)
-.TH g_dih 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_dih 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_dih - analyzes dihedral transitions
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_dih\fP
.BI "\-f" " traj.xtc "
-.TH g_dipoles 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_dipoles 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_dipoles - computes the total dipole plus fluctuations
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_dipoles\fP
.BI "\-en" " ener.edr "
\&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 [GRK]epsilon[grk]RF of infinity (default), temperature of 300 K (default) and
+\&using an epsilonRF 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
Correlation function to calculate: \fB none\fR, \fB mol\fR, \fB molsep\fR or \fB total\fR
.BI "\-[no]pairs" "yes "
- Calculate |cos [GRK]theta[grk]| 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.
-.TH g_disre 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_disre 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_disre - analyzes distance restraints
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_disre\fP
.BI "\-s" " topol.tpr "
-.TH g_dist 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_dist 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_dist - calculates the distances between the centers of mass of two groups
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_dist\fP
.BI "\-f" " traj.xtc "
-.TH g_dyndom 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_dyndom 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_dyndom - interpolate and extrapolate structure rotations
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_dyndom\fP
.BI "\-f" " dyndom.pdb "
-.TH g_enemat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_enemat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_enemat - extracts an energy matrix from an energy file
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_enemat\fP
.BI "\-f" " ener.edr "
-.TH g_energy 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_energy 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_energy - writes energies to xvg files and displays averages
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_energy\fP
.BI "\-f" " ener.edr "
\&With \fB \-fee\fR an estimate is calculated for the free\-energy
\&difference with an ideal gas state:
-\& [GRK]Delta[grk] A = A(N,V,T) \- A_idgas(N,V,T) = kT ln e(Upot/kT)
+\& Delta A = A(N,V,T) \- A_idgas(N,V,T) = kT ln e(Upot/kT)
-\& [GRK]Delta[grk] G = G(N,p,T) \- G_idgas(N,p,T) = kT ln e(Upot/kT)
+\& Delta G = G(N,p,T) \- G_idgas(N,p,T) = kT ln e(Upot/kT)
\&where k is Boltzmann's constant, T is set by \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:
-\& [GRK]Delta[grk] S(N,V,T) = S(N,V,T) \- S_idgas(N,V,T) = (Upot \- [GRK]Delta[grk] A)/T
+\& Delta S(N,V,T) = S(N,V,T) \- S_idgas(N,V,T) = (Upot \- Delta A)/T
-\& [GRK]Delta[grk] S(N,p,T) = S(N,p,T) \- S_idgas(N,p,T) = (Upot + pV \- [GRK]Delta[grk] G)/T
+\& Delta S(N,p,T) = S(N,p,T) \- S_idgas(N,p,T) = (Upot + pV \- Delta G)/T
\&
-.TH g_filter 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_filter 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_filter - frequency filters trajectories, useful for making smooth movies
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_filter\fP
.BI "\-f" " traj.xtc "
.BI "\-[no]fit" ""
.SH DESCRIPTION
\&\fB g_filter\fR performs frequency filtering on a trajectory.
-\&The filter shape is cos([GRK]pi[grk] t/A) + 1 from \-A to +A, where A is given
+\&The filter shape is cos(pi t/A) + 1 from \-A to +A, where A is given
\&by the option \fB \-nf\fR times the time step in the input trajectory.
\&This filter reduces fluctuations with period A by 85%, with period
\&2*A by 50% and with period 3*A by 17% for low\-pass filtering.
-.TH g_gyrate 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_gyrate 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_gyrate - calculates the radius of gyration
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_gyrate\fP
.BI "\-f" " traj.xtc "
-.TH g_h2order 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_h2order 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_h2order - computes the orientation of water molecules
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_h2order\fP
.BI "\-f" " traj.xtc "
-.TH g_hbond 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_hbond 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_hbond - computes and analyzes hydrogen bonds
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_hbond\fP
.BI "\-f" " traj.xtc "
Temperature (K) for computing the Gibbs energy corresponding to HB breaking and reforming
.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/[GRK]tau[grk])
+ If = 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(\-x/tau)
.BI "\-dump" " int" " 0"
Dump the first N hydrogen bond ACFs in a single \fB .xvg\fR file for debugging
-.TH g_helix 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_helix 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_helix - calculates basic properties of alpha helices
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_helix\fP
.BI "\-s" " topol.tpr "
.SH DESCRIPTION
\&\fB g_helix\fR computes all kinds of helix properties. First, the peptide
\&is checked to find the longest helical part, as determined by
-\&hydrogen bonds and [GRK]phi[grk]/[GRK]psi[grk] angles.
+\&hydrogen bonds and phi/psi angles.
\&That bit is fitted
\&to an ideal helix around the \fI z\fR\-axis and centered around the origin.
\&Then the following properties are computed:
\&\fB 1.\fR Helix radius (file \fB radius.xvg\fR). This is merely the
-\&RMS deviation in two dimensions for all C[GRK]alpha[grk] atoms.
+\&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
\&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
-\&residue is calculated. For an [GRK]alpha[grk]\-helix it is 100 degrees,
+\&residue is calculated. For an alpha\-helix it is 100 degrees,
\&for 3\-10 helices it will be smaller, and
\&for 5\-helices it will be larger.
\&\fB 3.\fR Rise per residue (file \fB rise.xvg\fR). The helical rise per
-\&residue is plotted as the difference in \fI z\fR\-coordinate between C[GRK]alpha[grk]
+\&residue is plotted as the difference in \fI z\fR\-coordinate between Calpha
\&atoms. For an ideal helix, this is 0.15 nm
\&\fB 4.\fR Total helix length (file \fB len\-ahx.xvg\fR). The total length
\&\fB 6.\fR Helix dipole, backbone only (file \fB dip\-ahx.xvg\fR).
-\&\fB 7.\fR RMS deviation from ideal helix, calculated for the C[GRK]alpha[grk]
+\&\fB 7.\fR RMS deviation from ideal helix, calculated for the Calpha
\&atoms only (file \fB rms\-ahx.xvg\fR).
-\&\fB 8.\fR Average C[GRK]alpha[grk] \- C[GRK]alpha[grk] dihedral angle (file \fB phi\-ahx.xvg\fR).
+\&\fB 8.\fR Average Calpha \- Calpha dihedral angle (file \fB phi\-ahx.xvg\fR).
-\&\fB 9.\fR Average [GRK]phi[grk] and [GRK]psi[grk] angles (file \fB phipsi.xvg\fR).
+\&\fB 9.\fR Average phi and psi angles (file \fB phipsi.xvg\fR).
\&\fB 10.\fR Ellipticity at 222 nm according to Hirst and Brooks.
\&
-.TH g_helixorient 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_helixorient 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_helixorient - calculates local pitch/bending/rotation/orientation inside helices
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_helixorient\fP
.BI "\-s" " topol.tpr "
.SH DESCRIPTION
\&\fB g_helixorient\fR calculates the coordinates and direction of the average
\&axis inside an alpha helix, and the direction/vectors of both the
-\&C[GRK]alpha[grk] and (optionally) a sidechain atom relative to the axis.
+\&Calpha and (optionally) a sidechain atom relative to the axis.
-\&As input, you need to specify an index group with C[GRK]alpha[grk] atoms
-\&corresponding to an [GRK]alpha[grk]\-helix of continuous residues. Sidechain
+\&As input, you need to specify an index group with Calpha atoms
+\&corresponding to an alpha\-helix of continuous residues. Sidechain
\&directions require a second index group of the same size, containing
\&the heavy atom in each residue that should represent the sidechain.
\&\fB Note\fR that this program does not do any fitting of structures.
-\&We need four C[GRK]alpha[grk] coordinates to define the local direction of the helix
+\&We need four Calpha coordinates to define the local direction of the helix
\&axis.
\&The tilt/rotation is calculated from Euler rotations, where we define
-\&the helix axis as the local \fI x\fR\-axis, the residues/C[GRK]alpha[grk] vector as \fI y\fR, and the
+\&the helix axis as the local \fI x\fR\-axis, the residues/Calpha vector as \fI y\fR, and the
\&\fI z\fR\-axis from their cross product. We use the Euler Y\-Z\-X rotation, meaning
\&we first tilt the helix axis (1) around and (2) orthogonal to the residues
\&vector, and finally apply the (3) rotation around it. For debugging or other
-.TH g_lie 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_lie 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_lie - free energy estimate from linear combinations
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_lie\fP
.BI "\-f" " ener.edr "
-.TH g_mdmat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_mdmat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_mdmat - calculates residue contact maps
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_mdmat\fP
.BI "\-f" " traj.xtc "
-.TH g_membed 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_membed 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_membed - embeds a protein into a lipid bilayer
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.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-20110404-3c0e5ec"
+.TH g_mindist 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_mindist - calculates the minimum distance between two groups
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_mindist\fP
.BI "\-f" " traj.xtc "
-.TH g_morph 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_morph 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_morph - linear interpolation of conformations
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_morph\fP
.BI "\-f1" " conf1.gro "
-.TH g_msd 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_msd 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_msd - calculates mean square displacements
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_msd\fP
.BI "\-f" " traj.xtc "
-.TH g_nmeig 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_nmeig 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_nmeig - diagonalizes the Hessian
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_nmeig\fP
.BI "\-f" " hessian.mtx "
-.TH g_nmens 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_nmens 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_nmens - generates an ensemble of structures from the normal modes
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_nmens\fP
.BI "\-v" " eigenvec.trr "
-.TH g_nmtraj 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_nmtraj 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_nmtraj - generate a virtual trajectory from an eigenvector
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_nmtraj\fP
.BI "\-s" " topol.tpr "
-.TH g_order 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_order 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_order - computes the order parameter per atom for carbon tails
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_order\fP
.BI "\-f" " traj.xtc "
-.TH g_polystat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_polystat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_polystat - calculates static properties of polymers
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_polystat\fP
.BI "\-s" " topol.tpr "
-.TH g_potential 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_potential 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_potential - calculates the electrostatic potential across the box
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_potential\fP
.BI "\-f" " traj.xtc "
-.TH g_principal 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_principal 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_principal - calculates axes of inertia for a group of atoms
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_principal\fP
.BI "\-f" " traj.xtc "
-.TH g_protonate 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_protonate 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_protonate - protonates structures
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_protonate\fP
.BI "\-s" " topol.tpr "
-.TH g_rama 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_rama 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_rama - computes Ramachandran plots
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_rama\fP
.BI "\-f" " traj.xtc "
.BI "\-[no]w" ""
.BI "\-xvg" " enum "
.SH DESCRIPTION
-\&\fB g_rama\fR selects the [GRK]phi[grk]/[GRK]psi[grk] dihedral combinations from your topology file
+\&\fB g_rama\fR selects the phi/psi dihedral combinations from your topology file
\&and computes these as a function of time.
\&Using simple Unix tools such as \fI grep\fR you can select out
\&specific residues.
-.TH g_rdf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_rdf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_rdf - calculates radial distribution functions
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_rdf\fP
.BI "\-f" " traj.xtc "
-.TH g_rms 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_rms 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_rms - calculates rmsd's with a reference structure and rmsd matrices
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_rms\fP
.BI "\-s" " topol.tpr "
.BI "\-ng" " int "
.SH DESCRIPTION
\&\fB g_rms\fR compares two structures by computing the root mean square
-\&deviation (RMSD), the size\-independent [GRK]rho[grk] similarity parameter
-\&(\fB rho\fR) or the scaled [GRK]rho[grk] (\fB rhosc\fR),
+\&deviation (RMSD), the size\-independent rho similarity parameter
+\&(\fB rho\fR) or the scaled rho (\fB rhosc\fR),
\&see Maiorov & Crippen, Proteins \fB 22\fR, 273 (1995).
\&This is selected by \fB \-what\fR.
-.TH g_rmsdist 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_rmsdist 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_rmsdist - calculates atom pair distances averaged with power \-2, \-3 or \-6
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_rmsdist\fP
.BI "\-f" " traj.xtc "
-.TH g_rmsf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_rmsf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_rmsf - calculates atomic fluctuations
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_rmsf\fP
.BI "\-f" " traj.xtc "
-.TH g_rotacf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_rotacf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_rotacf - calculates the rotational correlation function for molecules
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_rotacf\fP
.BI "\-f" " traj.xtc "
-.TH g_rotmat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_rotmat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_rotmat - plots the rotation matrix for fitting to a reference structure
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_rotmat\fP
.BI "\-f" " traj.xtc "
-.TH g_saltbr 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_saltbr 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_saltbr - computes salt bridges
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_saltbr\fP
.BI "\-f" " traj.xtc "
-.TH g_sas 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_sas 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_sas - computes solvent accessible surface area
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_sas\fP
.BI "\-f" " traj.xtc "
-.TH g_select 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_select 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_select - selects groups of atoms based on flexible textual selections
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_select\fP
.BI "\-f" " traj.xtc "
-.TH g_sgangle 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_sgangle 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_sgangle - computes the angle and distance between two groups
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_sgangle\fP
.BI "\-f" " traj.xtc "
-.TH g_sham 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_sham 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_sham - read/write xmgr and xvgr data sets
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_sham\fP
.BI "\-f" " graph.xvg "
-.TH g_sigeps 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_sigeps 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_sigeps - convert c6/12 or c6/cn combinations to and from sigma/epsilon
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_sigeps\fP
.BI "\-o" " potje.xvg "
.BI "\-sigfac" " real "
.SH DESCRIPTION
\&\fB g_sigeps\fR is a simple utility that converts C6/C12 or C6/Cn combinations
-\&to [GRK]sigma[grk] and [GRK]epsilon[grk], or vice versa. It can also plot the potential
+\&to sigma and epsilon, or vice versa. It can also plot the potential
\&in file. In addition, it makes an approximation of a Buckingham potential
\&to a Lennard\-Jones potential.
.SH FILES
-.TH g_sorient 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_sorient 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_sorient - analyzes solvent orientation around solutes
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_sorient\fP
.BI "\-f" " traj.xtc "
\&reference positions to the first atom of each solvent molecule:
-\&[GRK]theta[grk]1: the angle with the vector from the first atom of the solvent
+\&theta1: the angle with the vector from the first atom of the solvent
\&molecule to the midpoint between atoms 2 and 3.
-\&[GRK]theta[grk]2: the angle with the normal of the solvent plane, defined by the
+\&theta2: 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([GRK]theta[grk]1) for rmin=r=rmax.
+\&\fB \-o\fR: distribtion of cos(theta1) for rmin=r=rmax.
-\&\fB \-no\fR: distribution of cos([GRK]theta[grk]2) for rmin=r=rmax.
+\&\fB \-no\fR: distribution of cos(theta2) for rmin=r=rmax.
-\&\fB \-ro\fR: cos([GRK]theta[grk]1) and 3cos2([GRK]theta[grk]2)\-1 as a function of the
+\&\fB \-ro\fR: cos(theta1) and 3cos2(theta2)\-1 as a function of the
\&distance.
\&\fB \-co\fR: the sum over all solvent molecules within distance r
-\&of cos([GRK]theta[grk]1) and 3cos2([GRK]theta[grk]2)\-1 as a function of r.
+\&of cos(theta1) and 3cos2(theta2)\-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-20110404-3c0e5ec"
+.TH g_spatial 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_spatial - calculates the spatial distribution function
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_spatial\fP
.BI "\-s" " topol.tpr "
-.TH g_spol 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_spol 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_spol - analyzes solvent dipole orientation and polarization around solutes
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_spol\fP
.BI "\-f" " traj.xtc "
-.TH g_tcaf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_tcaf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_tcaf - calculates viscosities of liquids
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_tcaf\fP
.BI "\-f" " traj.trr "
.BI "\-endfit" " real "
.SH DESCRIPTION
\&\fB g_tcaf\fR computes tranverse current autocorrelations.
-\&These are used to estimate the shear viscosity, [GRK]eta[grk].
+\&These are used to estimate the shear viscosity, eta.
\&For details see: Palmer, Phys. Rev. E 49 (1994) pp 359\-366.
\&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)),
-\&v = \-t/(2 [GRK]tau[grk]), W = sqrt(1 \- 4 [GRK]tau[grk] [GRK]eta[grk]/[GRK]rho[grk] k2), which gives 16 values of [GRK]tau[grk]
-\&and [GRK]eta[grk]. The fit weights decay with time as exp(\-t/wt), and the TCAF and
+\&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.
-\&The [GRK]eta[grk] values should be fitted to 1 \- a [GRK]eta[grk](k) k2, from which
+\&The eta values should be fitted to 1 \- a eta(k) k2, from which
\&one can estimate the shear viscosity at k=0.
\&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
-\&The cubic [GRK]eta[grk] estimates are also written to \fB \-ov\fR.
+\&The cubic eta estimates are also written to \fB \-ov\fR.
\&With option \fB \-mol\fR, the transverse current is determined of
\&The k\-dependent viscosities in the \fB \-ov\fR file should be
-\&fitted to [GRK]eta[grk](k) = [GRK]eta[grk]0 (1 \- a k2) to obtain the viscosity at
+\&fitted to eta(k) = eta0 (1 \- a k2) to obtain the viscosity at
\&infinite wavelength.
-.TH g_traj 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_traj 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_traj - plots x, v and f of selected atoms/groups (and more) from a trajectory
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.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-20110404-3c0e5ec"
+.TH g_tune_pme 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_tune_pme - time mdrun as a function of PME nodes to optimize settings
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_tune_pme\fP
.BI "\-p" " perf.out "
-.TH g_vanhove 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_vanhove 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_vanhove - calculates Van Hove displacement functions
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_vanhove\fP
.BI "\-f" " traj.xtc "
-.TH g_velacc 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_velacc 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_velacc - calculates velocity autocorrelation functions
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_velacc\fP
.BI "\-f" " traj.trr "
-.TH g_wham 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_wham 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_wham - weighted histogram analysis after umbrella sampling
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_wham\fP
.BI "\-ix" " pullx\-files.dat "
\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-
\&With \fB \-ac\fR, \fB g_wham\fR estimates the integrated autocorrelation
-\&time (IACT) [GRK]tau[grk] for each umbrella window and weights the respective
-\&window with 1/[1+2*[GRK]tau[grk]/dt]. The IACTs are written
+\&time (IACT) tau for each umbrella window and weights the respective
+\&window with 1/[1+2*tau/dt]. The IACTs are written
\&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
-\&reaction coordinate with a Gaussian ([GRK]sigma[grk] provided with \fB \-acsig\fR,
+\&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.
\&If you prefer to compute the IACTs by a more sophisticated (but possibly
Calculate integrated autocorrelation times and use in wham
.BI "\-acsig" " real" " 0 "
- Smooth autocorrelation times along reaction coordinate with Gaussian of this [GRK]sigma[grk]
+ Smooth autocorrelation times along reaction coordinate with Gaussian of this sigma
.BI "\-ac\-trestart" " real" " 1 "
When computing autocorrelation functions, restart computing every .. (ps)
-.TH g_wheel 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_wheel 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_wheel - plots helical wheels
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_wheel\fP
.BI "\-f" " nnnice.dat "
-.TH g_x2top 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_x2top 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_x2top - generates a primitive topology from coordinates
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_x2top\fP
.BI "\-f" " conf.gro "
-.TH g_xrama 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH g_xrama 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_xrama - shows animated Ramachandran plots
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_xrama\fP
.BI "\-f" " traj.xtc "
-.TH genbox 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH genbox 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
genbox - solvates a system
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3genbox\fP
.BI "\-cp" " protein.gro "
-.TH genconf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH genconf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
genconf - multiplies a conformation in 'random' orientations
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3genconf\fP
.BI "\-f" " conf.gro "
-.TH genion 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH genion 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
genion - generates mono atomic ions on energetically favorable positions
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3genion\fP
.BI "\-s" " topol.tpr "
-.TH genrestr 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH genrestr 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
genrestr - generates position restraints or distance restraints for index groups
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3genrestr\fP
.BI "\-f" " conf.gro "
\&With the \fB \-disre\fR option, half a matrix of distance restraints
\&is generated instead of position restraints. With this matrix, that
-\&one typically would apply to C[GRK]alpha[grk] atoms in a protein, one can
+\&one typically would apply to Calpha atoms in a protein, one can
\&maintain the overall conformation of a protein without tieing it to
\&a specific position (as with position restraints).
.SH FILES
-.TH gmxcheck 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH gmxcheck 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
gmxcheck - checks and compares files
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3gmxcheck\fP
.BI "\-f" " traj.xtc "
-.TH gmxdump 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH gmxdump 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
gmxdump - makes binary files human readable
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3gmxdump\fP
.BI "\-s" " topol.tpr "
-.TH grompp 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH grompp 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
grompp - makes a run input file
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3grompp\fP
.BI "\-f" " grompp.mdp "
-.TH make_edi 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH make_edi 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
make_edi - generate input files for essential dynamics sampling
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3make_edi\fP
.BI "\-f" " eigenvec.trr "
\&It can be changed with \fB \-ori\fR to an arbitrary position in configurational space.
\&With \fB \-tau\fR, \fB \-deltaF0\fR, and \fB \-Eflnull\fR you control the flooding behaviour.
\&Efl is the flooding strength, it is updated according to the rule of adaptive flooding.
-\&Tau is the time constant of adaptive flooding, high [GRK]tau[grk] means slow adaption (i.e. growth).
+\&Tau is the time constant of adaptive flooding, high tau means slow adaption (i.e. growth).
\&DeltaF0 is the flooding strength you want to reach after tau ps of simulation.
\&To use constant Efl set \fB \-tau\fR to zero.
\&
\&\fB \-alpha\fR is a fudge parameter to control the width of the flooding potential. A value of 2 has been found
\&to give good results for most standard cases in flooding of proteins.
-\&[GRK]alpha[grk] basically accounts for incomplete sampling, if you sampled further the width of the ensemble would
-\&increase, this is mimicked by [GRK]alpha[grk] 1.
-\&For restraining, [GRK]alpha[grk] 1 can give you smaller width in the restraining potential.
+\&alpha basically accounts for incomplete sampling, if you sampled further the width of the ensemble would
+\&increase, this is mimicked by alpha 1.
+\&For restraining, alpha 1 can give you smaller width in the restraining potential.
\&
-.TH make_ndx 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH make_ndx 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
make_ndx - makes index files
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3make_ndx\fP
.BI "\-f" " conf.gro "
-.TH mdrun 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH mdrun 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
mdrun - performs a simulation, do a normal mode analysis or an energy minimization
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3mdrun\fP
.BI "\-s" " topol.tpr "
-.TH mk_angndx 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH mk_angndx 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
mk_angndx - generates index files for g_angle
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3mk_angndx\fP
.BI "\-s" " topol.tpr "
-.TH ngmx 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH ngmx 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
ngmx - displays a trajectory
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3ngmx\fP
.BI "\-f" " traj.xtc "
-.TH pdb2gmx 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH pdb2gmx 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
pdb2gmx - converts pdb files to topology and coordinate files
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3pdb2gmx\fP
.BI "\-f" " eiwit.pdb "
-.TH tpbconv 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH tpbconv 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
tpbconv - makes a run input file for restarting a crashed run
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3tpbconv\fP
.BI "\-s" " topol.tpr "
\&\fB 3.\fR by creating a \fB .tpx\fR file for a subset of your original
\&tpx file, which is useful when you want to remove the solvent from
-\&your \fB .tpx\fR file, or when you want to make e.g. a pure C[GRK]alpha[grk] \fB .tpx\fR file.
+\&your \fB .tpx\fR file, or when you want to make e.g. a pure Calpha \fB .tpx\fR file.
\&Note that you may need to use \fB \-nsteps \-1\fR (or similar) to get
\&this to work.
\&\fB WARNING: this \fB .tpx\fR file is not fully functional\fR.
-.TH trjcat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH trjcat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
trjcat - concatenates trajectory files
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3trjcat\fP
.BI "\-f" " traj.xtc "
-.TH trjconv 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH trjconv 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
trjconv - converts and manipulates trajectory files
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3trjconv\fP
.BI "\-f" " traj.xtc "
-.TH trjorder 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH trjorder 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
trjorder - orders molecules according to their distance to a group
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3trjorder\fP
.BI "\-f" " traj.xtc "
-.TH xpm2ps 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
+.TH xpm2ps 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
xpm2ps - converts XPM matrices to encapsulated postscript (or XPM)
-.B VERSION 4.5.4-dev-20110404-3c0e5ec
+.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3xpm2ps\fP
.BI "\-f" " root.xpm "
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff