"and free energy estimates are analysed, and for each cluster the",
"energy statistics are printed.[PAR]",
"An alternative approach to this is to cluster the structures first",
- "(using [TT]g_cluster[tt] and then sort the clusters on either lowest",
+ "using [TT]g_cluster[tt] and then sort the clusters on either lowest",
"energy or average energy."
};
t_filenm fnm[] = {
int main(int argc,char *argv[])
{
const char *desc[] = {
- "g_sigeps is a simple utility that converts c6/c12 or c6/cn combinations",
+ "[TT]g_sigeps[tt] is a simple utility that converts c6/c12 or c6/cn combinations",
"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."
const char *desc[] = {
"[TT]g_cluster[tt] can cluster structures with several different methods.",
"Distances between structures can be determined from a trajectory",
- "or read from an XPM matrix file with the [TT]-dm[tt] option.",
+ "or read from an [TT].xpm[tt] matrix file with the [TT]-dm[tt] option.",
"RMS deviation after fitting or RMS deviation of atom-pair distances",
"can be used to define the distance between structures.[PAR]",
"Compute partial densities across the box, using an index file.[PAR]",
"For the total density of NPT simulations, use [TT]g_energy[tt] instead.",
"[PAR]",
- "Densities in kg/m^3, number densities or electron densities can be",
+ "Densities are in kg/m^3, and number densities or electron densities can also be",
"calculated. For electron densities, a file describing the number of",
"electrons for each type of atom should be provided using [TT]-ei[tt].",
"It should look like:[BR]",
{
const char *desc[] = {
"[TT]g_disre[tt] computes violations of distance restraints.",
- "If necessary all protons can be added to a protein molecule ",
- "using the protonate program.[PAR]",
+ "If necessary, all protons can be added to a protein molecule ",
+ "using the [TT]g_protonate[tt] program.[PAR]",
"The program always",
"computes the instantaneous violations rather than time-averaged,",
"because this analysis is done from a trajectory file afterwards",
"Average, RMSD and drift are calculated with full precision from the",
"simulation (see printed manual). Drift is calculated by performing",
- "a LSQ fit of the data to a straight line. The reported total drift",
+ "a least-squares fit of the data to a straight line. The reported total drift",
"is the difference of the fit at the first and last point.",
"An error estimate of the average is given based on a block averages",
"over 5 blocks using the full precision averages. The error estimate",
"MD steps, or over many more points than the number of frames in",
"energy file. This makes the [TT]g_energy[tt] statistics output more accurate",
"than the [TT].xvg[tt] output. When exact averages are not present in the energy",
- "file the statistics mentioned above is simply over the single, per-frame",
+ "file the statistics mentioned above are simply over the single, per-frame",
"energy values.[PAR]",
- "The term fluctuation gives the RMSD around the LSQ fit.[PAR]",
+ "The term fluctuation gives the RMSD around the least-squares fit.[PAR]",
"Some fluctuation-dependent properties can be calculated provided",
"the correct energy terms are selected. The following properties",
"Option [TT]-oh[tt] writes a high-pass filtered trajectory.",
"The high-pass filtered coordinates are added to the coordinates",
"from the structure file. When using high-pass filtering use [TT]-fit[tt]",
- "or make sure you use a trajectory which has been fitted on",
+ "or make sure you use a trajectory that has been fitted on",
"the coordinates in the structure file."
};
int gmx_h2order(int argc,char *argv[])
{
const char *desc[] = {
- "Compute the orientation of water molecules with respect to the normal",
+ "[TT]g_h2order[tt] computes the orientation of water molecules with respect to the normal",
"of the box. The program determines the average cosine of the angle",
"between the dipole moment of water and an axis of the box. The box is",
"divided in slices and the average orientation per slice is printed.",
" in #nr slices."}
};
const char *bugs[] = {
- "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,"
+ "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."
};
int gmx_kinetics(int argc,char *argv[])
{
const char *desc[] = {
- "g_kinetics reads two [TT].xvg[tt] files, each one containing data for N replicas.",
+ "[TT]g_kinetics[tt] reads two [TT].xvg[tt] files, each one containing data for N replicas.",
"The first file contains the temperature of each replica at each timestep,",
"and the second contains real values that can be interpreted as",
"an indicator for folding. If the value in the file is larger than",
"The eigenvectors can be analyzed with [TT]g_anaeig[tt].",
"An ensemble of structures can be generated from the eigenvectors with",
"[TT]g_nmens[tt]. When mass weighting is used, the generated eigenvectors",
- "will be scaled back to plain cartesian coordinates before generating the",
- "output - in this case they will no longer be exactly orthogonal in the",
- "standard cartesian norm (But in the mass weighted norm they would be)."
+ "will be scaled back to plain Cartesian coordinates before generating the",
+ "output. In this case, they will no longer be exactly orthogonal in the",
+ "standard Cartesian norm, but in the mass-weighted norm they would be."
};
static gmx_bool bM=TRUE;
{
const char *desc[] = {
"[TT]g_nmens[tt] generates an ensemble around an average structure",
- "in a subspace which is defined by a set of normal modes (eigenvectors).",
+ "in a subspace that is defined by a set of normal modes (eigenvectors).",
"The eigenvectors are assumed to be mass-weighted.",
"The position along each eigenvector is randomly taken from a Gaussian",
"distribution with variance kT/eigenvalue.[PAR]",
const char *desc[] =
{
"[TT]g_nmtraj[tt] generates an virtual trajectory from an eigenvector, ",
- "corresponding to a harmonic cartesian oscillation around the average ",
+ "corresponding to a harmonic Cartesian oscillation around the average ",
"structure. The eigenvectors should normally be mass-weighted, but you can ",
"use non-weighted eigenvectors to generate orthogonal motions. ",
"The output frames are written as a trajectory file covering an entire period, and ",
"PDB format you can view it directly in PyMol and also render a photorealistic movie. ",
"Motion amplitudes are calculated from the eigenvalues and a preset temperature, ",
"assuming equipartition of the energy over all modes. To make the motion clearly visible ",
- "in PyMol you might want to amplify it by setting an unrealistic high temperature. ",
- "However, be aware that both the linear cartesian displacements and mass weighting will ",
+ "in PyMol you might want to amplify it by setting an unrealistically high temperature. ",
+ "However, be aware that both the linear Cartesian displacements and mass weighting will ",
"lead to serious structure deformation for high amplitudes - this is is simply a limitation ",
- "of the cartesian normal mode model. By default the selected eigenvector is set to 7, since ",
+ "of the Cartesian normal mode model. By default the selected eigenvector is set to 7, since ",
" the first six normal modes are the translational and rotational degrees of freedom."
};
int gmx_potential(int argc,char *argv[])
{
const char *desc[] = {
- "Compute the electrostatical potential across the box. The potential is",
+ "[TT]g_potential[tt] computes the electrostatical potential across the box. The potential is",
"calculated by first summing the charges per slice and then integrating",
"twice of this charge distribution. Periodic boundaries are not taken",
"into account. Reference of potential is taken to be the left side of",
"temperature factors and then it will also output average coordinates",
"and a [TT].pdb[tt] file with ANISOU records (corresonding to the [TT]-oq[tt]",
"or [TT]-ox[tt] option). Please note that the U values",
- "are orientation dependent, so before comparison with experimental data",
+ "are orientation-dependent, so before comparison with experimental data",
"you should verify that you fit to the experimental coordinates.[PAR]",
"When a [TT].pdb[tt] input file is passed to the program and the [TT]-aniso[tt]",
"flag is set",
const char *desc[] = {
"[TT]g_rotacf[tt] calculates the rotational correlation function",
"for molecules. Three atoms (i,j,k) must be given in the index",
- "file, defining two vectors ij and jk. The rotational acf",
+ "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",
"This will calculate the rotational correlation function using a first",
"order Legendre polynomial of the angle of a vector defined by the index",
"file. The correlation function will be fitted from 2.5 ps until 20.0 ps",
- "to a two parameter exponential.",
-
-
- ""
+ "to a two-parameter exponential."
};
static gmx_bool bVec = FALSE,bAver=TRUE;
const char *desc[] = {
"[TT]g_saltbr[tt] plots the distance between all combination of charged groups",
"as a function of time. The groups are combined in different ways.",
- "A minimum distance can be given, (eg. the cut-off), then groups",
+ "A minimum distance can be given, (ie. a cut-off), then groups",
"that are never closer than that distance will not be plotted.[BR]",
"Output will be in a number of fixed filenames, [TT]min-min.xvg[tt], [TT]plus-min.xvg[tt]",
"and [TT]plus-plus.xvg[tt], or files for every individual ion-pair if the [TT]-sep[tt]",
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff