int main (int argc,char *argv[])
{
const char *desc[] = {
- "[TT]protonate[tt] reads (a) conformation(s) and adds all missing",
- "hydrogens as defined in [TT]ffgmx2.hdb[tt]. If only [TT]-s[tt] is",
+ "g_protonate reads (a) conformation(s) and adds all missing",
+ "hydrogens as defined in [TT]gmx2.ff/aminoacids.hdb[tt]. If only [TT]-s[tt] is",
"specified, this conformation will be protonated, if also [TT]-f[tt]",
"is specified, the conformation(s) will be read from this file",
"which can be either a single conformation or a trajectory.",
int main(int argc,char *argv[])
{
const char *desc[] = {
- "xrama shows a Ramachandran movie, that is, it shows",
+ "g_xrama shows a Ramachandran movie, that is, it shows",
"the Phi/Psi angles as a function of time in an X-Window.[PAR]"
"Static Phi/Psi plots for printing can be made with g_rama.[PAR]",
"Some of the more common X command line options can be used:[BR]",
- "-bg, -fg change colors, -font fontname, changes the font."
+ "[TT]-bg[tt], [TT]-fg[tt] change colors, [TT]-font fontname[tt], changes the font."
};
output_env_t oenv;
int main(int argc,char *argv[])
{
const char *desc[] = {
- "Sigeps is a simple utility that converts c6/c12 or c6/cn combinations",
+ "g_sigeps 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."
int gmx_anaeig(int argc,char *argv[])
{
static const char *desc[] = {
- "[TT]g_anaeig[tt] analyzes eigenvectors. The eigenvectors can be of a",
+ "g_anaeig analyzes eigenvectors. The eigenvectors can be of a",
"covariance matrix ([TT]g_covar[tt]) or of a Normal Modes analysis",
"([TT]g_nmeig[tt]).[PAR]",
static const char *desc[] = {
"g_angle computes the angle distribution for a number of angles",
"or dihedrals. This way you can check whether your simulation",
- "is correct. With option -ov you can plot the average angle of",
- "a group of angles as a function of time. With the -all option",
+ "is correct. With option [TT]-ov[tt] you can plot the average angle of",
+ "a group of angles as a function of time. With the [TT]-all[tt] option",
"the first graph is the average, the rest are the individual angles.[PAR]",
- "With the -of option g_angle also calculates the fraction of trans",
+ "With the [TT]-of[tt] option, g_angle also calculates the fraction of trans",
"dihedrals (only for dihedrals) as function of time, but this is",
"probably only fun for a selected few.[PAR]",
- "With option -oc a dihedral correlation function is calculated.[PAR]",
- "It should be noted that the indexfile should contain",
+ "With option [TT]-oc[tt] a dihedral correlation function is calculated.[PAR]",
+ "It should be noted that the index file should contain",
"atom-triples for angles or atom-quadruplets for dihedrals.",
"If this is not the case, the program will crash.[PAR]",
"With option [TT]-or[tt] a trajectory file is dumped containing cos and",
"Every individual BAR free energy difference relies on two ",
"simulations at different states: say state A and state B, as",
- "controlled by a parameter 'lambda' (see the mdp parameter",
- "'init_lambda'). The BAR method calculates a ratio of weighted",
+ "controlled by a parameter, lambda (see the mdp parameter",
+ "[TT]init_lambda[tt]). 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 linearly depend on lambda",
"(in which case we can extrapolate the derivative of the Hamiltonian",
- "w.r.t. lambda, as is the default when 'free_energy' is on), the",
- "energy differences to the other state need to be calculated",
+ "with respect to lambda, as is the default when [TT]free_energy[tt] is on),",
+ "the energy differences to the other state need to be calculated",
"explicitly during the simulation. This can be controlled with",
- "the mdp option 'foreign_lambda'.[PAR]",
+ "the mdp option [TT]foreign_lambda[tt].[PAR]",
"Input option [TT]-f[tt] expects multiple dhdl files. ",
"Two types of input files are supported:[BR]",
- "* Files with only one y-value, for such files it is assumed ",
- "that the y-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.",
+ "[TT]*[tt] Files with only one y-value, for such files it is assumed ",
+ " that the y-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.",
"[BR]",
- "* Files with more than one y-value. The files should have columns ",
- "with dH/dlambda and Delta lambda. The lambda values are inferred ",
- "from the legends: ",
- "lambda of the simulation from the legend of dH/dlambda ",
- "and the foreign lambda's from the legends of Delta H.[BR]",
+ "[TT]*[tt] Files with more than one y-value. The files should have columns ",
+ " with dH/dlambda and Delta lambda. The lambda values are inferred ",
+ " from the legends: lambda of the simulation from the legend of dH/dlambda ",
+ " and the foreign lambda's from the legends of Delta H.[PAR]",
"The lambda of the simulation is parsed from dhdl.xvg file's legend ",
- "containing the string 'dH', the foreign lambda's from the legend ",
+ "containing the string 'dH', the foreign lambdas from the legend ",
"containing the capitalized letters 'D' and 'H'. The temperature ",
"is parsed from the legend line containing 'T ='.[PAR]",
"The input option [TT]-g[tt] expects multiple .edr files. ",
"These can contain either lists of energy differences (see the",
"mdp option separate_dhdl_file), or a series of histograms",
- "(see the mdp options dh_hist_size and dh_hist_spacing).",
+ "(see the mdp options [TT]dh_hist_size[tt] and [TT]dh_hist_spacing[tt]).",
"The temperature and lambda values are automatically deduced from",
"the ener.edr file.[PAR]"
"difference estimates and phase space overlap measures in units of ",
"kT (together with their computed error estimate). The printed ",
"values are:[BR]",
- "* lam_A: the lambda values for point A.[BR]",
- "* lam_B: the lambda values for point B.[BR]",
- "* DG: the free energy estimate.[BR]",
- "* s_A: an estimate of the relative entropy of B in A.[BR]",
- "* s_A: an estimate of the relative entropy of A in B.[BR]",
- "* stdev: an estimate expected per-sample standard deviation.[PAR]",
+ "[TT]*[tt] lam_A: the lambda values for point A.[BR]",
+ "[TT]*[tt] lam_B: the lambda values for point B.[BR]",
+ "[TT]*[tt] DG: the free energy estimate.[BR]",
+ "[TT]*[tt] s_A: an estimate of the relative entropy of B in A.[BR]",
+ "[TT]*[tt] s_A: an estimate of the relative entropy of A in B.[BR]",
+ "[TT]*[tt] stdev: an estimate expected per-sample standard deviation.[PAR]",
"The relative entropy of both states in each other's ensemble can be ",
"interpreted as a measure of phase space overlap: ",
"Wu & Kofke, J. Chem. Phys. 123 084109 (2009) for more information.",
"[PAR]",
"The estimate of the expected per-sample standard deviation, as given ",
- "in Bennett's original BAR paper: ",
- "Bennett, J. Comp. Phys. 22, p 245 (1976), Eq. 10 gives an estimate ",
- "of the quality of sampling (not directly of the actual statistical ",
- "error, because it assumes independent samples).[PAR]",
+ "in Bennett's original BAR paper: Bennett, J. Comp. Phys. 22, p 245 (1976).",
+ "Eq. 10 therein gives an estimate of the quality of sampling (not directly",
+ "of the actual statistical error, because it assumes independent samples).[PAR]",
"To get a visual estimate of the phase space overlap, use the ",
- "-oh option to write series of histograms, together with the ",
- "-nbin option.[PAR]"
+ "[TT]-oh[tt] option to write series of histograms, together with the ",
+ "[TT]-nbin[tt] option.[PAR]"
};
static real begin=0,end=-1,temp=-1;
int nd=2,nbmin=5,nbmax=5;
{
const char *desc[] = {
"g_bond makes a distribution of bond lengths. If all is well a",
- "gaussian distribution should be made when using a harmonic potential.",
+ "Gaussian distribution should be made when using a harmonic potential.",
"Bonds are read from a single group in the index file in order i1-j1",
"i2-j2 through in-jn.[PAR]",
"[TT]-tol[tt] gives the half-width of the distribution as a fraction",
"calculate dihedral autocorrelation functions. The function used",
"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), [BB]Biophys. J. 72[bb], 2032-2041).",
+ "(Van der Spoel & Berendsen (1997), Biophys. J. 72, 2032-2041).",
"Separate files for each dihedral of each residue",
"(corr(dihedral)(RESIDUE)(nresnr).xvg) are output, as well as a",
"file containing the information for all residues (argument of [TT]-corr[tt]).[PAR]",
"rotamers per nanosecond, and the order parameter S2 of each dihedral.[BR]",
"(d) a table for each residue of the rotamer occupancy.[BR]",
"All rotamers are taken as 3-fold, except for omegas and chi-dihedrals",
- "to planar groups (i.e. chi2 of aromatics asp and asn, chi3 of glu",
- "and gln, and chi4 of arg), which are 2-fold. \"rotamer 0\" means ",
+ "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 [TT]-core_rotamer[tt][PAR]",
{
const char *desc[] = {
"This program computes the size distributions of molecular/atomic clusters in",
- "the gas phase. The output is given in the form of a XPM file.",
- "The total number of clusters is written to a XVG file.[PAR]",
+ "the gas phase. The output is given in the form of an .xpm file.",
+ "The total number of clusters is written to an .xvg file.[PAR]",
"When the [TT]-mol[tt] option is given clusters will be made out of",
"molecules rather than atoms, which allows clustering of large molecules.",
"In this case an index file would still contain atom numbers",
"that the particles are free to move. If you are using constraints,",
"please correct the temperature. For instance water simulated with SHAKE",
"or SETTLE will yield a temperature that is 1.5 times too low. You can",
- "compensate for this with the -ndf option. Remember to take the removal",
+ "compensate for this with the [TT]-ndf[tt] option. Remember to take the removal",
"of center of mass motion into account.[PAR]",
"The [TT]-mc[tt] option will produce an index file containing the",
"atom numbers of the largest cluster."
{
const char *desc[] = {
"g_confrms computes the root mean square deviation (RMSD) of two",
- "structures after LSQ fitting the second structure on the first one.",
+ "structures after least-squares fitting the second structure on the first one.",
"The two structures do NOT need to have the same number of atoms,",
"only the two index groups used for the fit need to be identical.",
"With [TT]-name[tt] only matching atom names from the selected groups",
int gmx_covar(int argc,char *argv[])
{
const char *desc[] = {
- "[TT]g_covar[tt] calculates and diagonalizes the (mass-weighted)",
+ "g_covar calculates and diagonalizes the (mass-weighted)",
"covariance matrix.",
"All structures are fitted to the structure in the structure file.",
"When this is not a run input file periodicity will not be taken into",
"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]",
- " 2[BR]",
- " atomname = nrelectrons[BR]",
- " atomname = nrelectrons[BR]",
+ " [TT]2[tt][BR]",
+ " [TT]atomname = nrelectrons[tt][BR]",
+ " [TT]atomname = nrelectrons[tt][BR]",
"The first line contains the number of lines to read from the file.",
"There should be one line for each unique atom name in your system.",
"The number of electrons for each atom is modified by its atomic",
int gmx_dielectric(int argc,char *argv[])
{
const char *desc[] = {
- "dielectric calculates frequency dependent dielectric constants",
+ "g_dielectric calculates frequency dependent dielectric constants",
"from the autocorrelation function of the total dipole moment in",
"your simulation. This ACF can be generated by g_dipoles.",
"For an estimate of the error you can run g_statistics on the",
"the dipoles divided by the distance to the third power.[PAR]",
"[PAR]",
"EXAMPLES[PAR]",
- "g_dipoles -corr mol -P1 -o dip_sqr -mu 2.273 -mumax 5.0 -nofft[PAR]",
+ "[TT]g_dipoles -corr mol -P1 -o dip_sqr -mu 2.273 -mumax 5.0 -nofft[tt][PAR]",
"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",
"the time averaged values per restraint are given in the log file.[PAR]",
"An index file may be used to select specific restraints for",
"printing.[PAR]",
- "When the optional[TT]-q[tt] flag is given a pdb file coloured by the",
+ "When the optional [TT]-q[tt] flag is given a pdb file coloured by the",
"amount of average violations.[PAR]",
"When the [TT]-c[tt] option is given, an index file will be read",
"containing the frames in your trajectory corresponding to the clusters",
{
const char *desc[] = {
"g_dyndom reads a pdb file output from DynDom",
- "http://www.cmp.uea.ac.uk/dyndom/",
- "It reads the coordinates, and the coordinates of the rotation axis",
- "furthermore it reads an index file containing the domains.",
+ "(http://www.cmp.uea.ac.uk/dyndom/).",
+ "It reads the coordinates, the coordinates of the rotation axis,",
+ "and an index file containing the domains.",
"Furthermore it takes the first and last atom of the arrow file",
"as command line arguments (head and tail) and",
"finally it takes the translation vector (given in DynDom info file)",
int gmx_genbox(int argc,char *argv[])
{
const char *desc[] = {
- "Genbox can do one of 3 things:[PAR]",
+ "genbox can do one of 3 things:[PAR]",
- "1) Generate a box of solvent. Specify -cs and -box. Or specify -cs and",
- "-cp with a structure file with a box, but without atoms.[PAR]",
+ "1) Generate a box of solvent. Specify [TT]-cs[tt] and [TT]-box[tt]. Or specify [TT]-cs[tt] and",
+ "[TT]-cp[tt] with a structure file with a box, but without atoms.[PAR]",
- "2) Solvate a solute configuration, eg. a protein, in a bath of solvent ",
+ "2) Solvate a solute configuration, e.g. a protein, in a bath of solvent ",
"molecules. Specify [TT]-cp[tt] (solute) and [TT]-cs[tt] (solvent). ",
"The box specified in the solute coordinate file ([TT]-cp[tt]) is used,",
"unless [TT]-box[tt] is set.",
"to change the box dimensions and center the solute.",
"Solvent molecules are removed from the box where the ",
"distance between any atom of the solute molecule(s) and any atom of ",
- "the solvent molecule is less than the sum of the VanderWaals radii of ",
- "both atoms. A database ([TT]vdwradii.dat[tt]) of VanderWaals radii is ",
- "read by the program, atoms not in the database are ",
+ "the solvent molecule is less than the sum of the van der Waals radii of ",
+ "both atoms. A database ([TT]vdwradii.dat[tt]) of van der Waals radii is ",
+ "read by the program, and atoms not in the database are ",
"assigned a default distance [TT]-vdwd[tt].",
"Note that this option will also influence the distances between",
"solvent molecules if they contain atoms that are not in the database.",
"at random positions.",
"The program iterates until [TT]nmol[tt] molecules",
"have been inserted in the box. To test whether an insertion is ",
- "successful the same VanderWaals criterium is used as for removal of ",
+ "successful the same van der Waals criterium is used as for removal of ",
"solvent molecules. When no appropriately ",
"sized holes (holes that can hold an extra molecule) are available the ",
"program tries for [TT]-nmol[tt] * [TT]-try[tt] times before giving up. ",
- "Increase -try if you have several small holes to fill.[PAR]",
+ "Increase [TT]-try[tt] if you have several small holes to fill.[PAR]",
"The default solvent is Simple Point Charge water (SPC), with coordinates ",
"from [TT]$GMXLIB/spc216.gro[tt]. These coordinates can also be used",
"longest molecule axis along a box edge. This way the amount of solvent",
"molecules necessary is reduced.",
"It should be kept in mind that this only works for",
- "short simulations, as eg. an alpha-helical peptide in solution can ",
+ "short simulations, as e.g. an alpha-helical peptide in solution can ",
"rotate over 90 degrees, within 500 ps. In general it is therefore ",
"better to make a more or less cubic box.[PAR]",
- "Setting -shell larger than zero will place a layer of water of",
+ "Setting [TT]-shell[tt] larger than zero will place a layer of water of",
"the specified thickness (nm) around the solute. Hint: it is a good",
"idea to put the protein in the center of a box first (using editconf).",
"[PAR]",
const char *desc[] = {
"Compute the orientation of water molecules with respect to the normal",
"of the box. The program determines the average cosine of the angle",
- "between de dipole moment of water and an axis of the box. The box is",
+ "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.",
"Each water molecule is assigned to a slice, per time frame, based on the",
- "position of the oxygen. When -nm is used the angle between the water",
+ "position of the oxygen. When [TT]-nm[tt] is used, the angle between the water",
"dipole and the axis from the center of mass to the oxygen is calculated",
"instead of the angle between the dipole and a box axis."
};
"identical or non-overlapping. All hydrogen bonds between the two",
"groups are analyzed.[PAR]",
- "If you set -shell, you will be asked for an additional index group",
+ "If you set [TT]-shell[tt], you will be asked for an additional index group",
"which should contain exactly one atom. In this case, only hydrogen",
"bonds between atoms within the shell distance from the one atom are",
"considered.[PAR]",
{
const char *desc[] = {
"g_mdmat makes distance matrices consisting of the smallest distance",
- "between residue pairs. With -frames these distance matrices can be",
- "stored as a function",
- "of time, to be able to see differences in tertiary structure as a",
- "funcion of time. If you choose your options unwise, this may generate",
- "a large output file. Default only an averaged matrix over the whole",
+ "between residue pairs. With [TT]-frames[tt], these distance matrices can be",
+ "stored in order to see differences in tertiary structure as a",
+ "function of time. If you choose your options unwisely, this may generate",
+ "a large output file. By default, only an averaged matrix over the whole",
"trajectory is output.",
"Also a count of the number of different atomic contacts between",
"residues over the whole trajectory can be made.",
"orientation. Box size should be taken from the membrane structure file. The corresponding topology",
"files should also be merged. Consecutively, create a tpr file (input for g_membed) from these files,"
"with the following options included in the mdp file.\n",
- " - integrator = md\n",
- " - energygrp = Protein (or other group that you want to insert)\n",
- " - freezegrps = Protein\n",
- " - freezedim = Y Y Y\n",
- " - energygrp_excl = Protein Protein\n",
+ " - [TT]integrator = md[tt][BR]",
+ " - [TT]energygrp = Protein[tt] (or other group that you want to insert)[BR]",
+ " - [TT]freezegrps = Protein[tt][BR]",
+ " - [TT]freezedim = Y Y Y[tt][BR]",
+ " - [TT]energygrp_excl = Protein Protein[tt][BR]",
"The output is a structure file containing the protein embedded in the membrane. If a topology",
"file is provided, the number of lipid and ",
"solvent molecules will be updated to match the new structure file.\n",
"create intermediates. Of course these are completely unphysical, but",
"that you may try to justify yourself. Output is in the form of a ",
"generic trajectory. The number of intermediates can be controlled with",
- "the -ninterm flag. The first and last flag correspond to the way of",
+ "the [TT]-ninterm[tt] flag. The first and last flag correspond to the way of",
"interpolating: 0 corresponds to input structure 1 while",
"1 corresponds to input structure 2.",
"If you specify first < 0 or last > 1 extrapolation will be",
int gmx_nmens(int argc,char *argv[])
{
const char *desc[] = {
- "[TT]g_nmens[tt] generates an ensemble around an average structure",
+ "g_nmens generates an ensemble around an average structure",
"in a subspace which 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",
{
const char *desc[] =
{
- "[TT]g_nmtraj[tt] generates an virtual trajectory from an eigenvector, ",
+ "g_nmtraj generates an virtual trajectory from an eigenvector, ",
"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. ",
"parameters however, which only work for water anyway).[PAR]",
"The program can also give all",
"diagonal elements of the order tensor and even calculate the deuterium",
- "order parameter Scd (default). If the option -szonly is given, only one",
- "order tensor component (specified by the -d option) is given and the",
- "order parameter per slice is calculated as well. If -szonly is not",
+ "order parameter Scd (default). If the option [TT]-szonly[tt] is given, only one",
+ "order tensor component (specified by the [TT]-d[tt] option) is given and the",
+ "order parameter per slice is calculated as well. If [TT]-szonly[tt] is not",
"selected, all diagonal elements and the deuterium order parameter is",
"given.[PAR]"
"The tetrahedrality order parameters can be determined",
"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",
- "the box. It's also possible to calculate the potential in spherical",
+ "the box. It is also possible to calculate the potential in spherical",
"coordinates as function of r by calculating a charge distribution in",
"spherical slices and twice integrating them. epsilon_r is taken as 1,",
- "2 is more appropriate in many cases."
+ "but 2 is more appropriate in many cases."
};
output_env_t oenv;
static int axis = 2; /* normal to memb. default z */
"coordinates.[PAR]",
"With the option [TT]-od[tt] the root mean square deviation with",
"respect to the reference structure is calculated.[PAR]",
- "With the option [TT]aniso[tt] g_rmsf will compute anisotropic",
+ "With the option [TT]-aniso[tt], g_rmsf will compute anisotropic",
"temperature factors and then it will also output average coordinates",
"and a pdb file with ANISOU records (corresonding to the [TT]-oq[tt]",
"or [TT]-ox[tt] option). Please note that the U values",
"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 -d switch, you can",
+ "does not matter. Optionally, controlled by the [TT]-d[tt] switch, you can",
"calculate the rotational correlation function for linear molecules",
"by specifying two atoms (i,j) in the index file.",
"[PAR]",
"EXAMPLES[PAR]",
- "g_rotacf -P 1 -nparm 2 -fft -n index -o rotacf-x-P1",
- "-fa expfit-x-P1 -beginfit 2.5 -endfit 20.0[PAR]",
+ "[TT]g_rotacf -P 1 -nparm 2 -fft -n index -o rotacf-x-P1",
+ "-fa expfit-x-P1 -beginfit 2.5 -endfit 20.0[tt][PAR]",
"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 till 20.0 ps",
+ "file. The correlation function will be fitted from 2.5 ps until 20.0 ps",
"to a two parameter exponential.",
"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",
"approximate, in e.g. ice Ih one can easily fit water molecules in the",
- "pores which would yield too low volume, too high surface area and too",
- "high density."
+ "pores which would yield a volume that is too low, and surface area and density",
+ "that are both too high."
};
output_env_t oenv;
"Compute the angle and distance between two groups. ",
"The groups are defined by a number of atoms given in an index file and",
"may be two or three atoms in size.",
- "If -one is set, only one group should be specified in the index",
+ "If [TT]-one[tt] is set, only one group should be specified in the index",
"file and the angle between this group at time 0 and t will be computed.",
"The angles calculated depend on the order in which the atoms are ",
"given. Giving for instance 5 6 will rotate the vector 5-6 with ",
"The cos of the angle is calculated, using the inproduct of the two",
"normalized vectors.[PAR]",
"Here is what some of the file options do:[BR]",
- "-oa: Angle between the two groups specified in the index file. If a group contains three atoms the normal to the plane defined by those three atoms will be used. If a group contains two atoms, the vector defined by those two atoms will be used.[BR]",
- "-od: Distance between two groups. Distance is taken from the center of one group to the center of the other group.[BR]",
- "-od1: If one plane and one vector is given, the distances for each of the atoms from the center of the plane is given separately.[BR]",
- "-od2: For two planes this option has no meaning."
+ "[TT]-oa[tt]: Angle between the two groups specified in the index file. If a group contains three atoms the normal to the plane defined by those three atoms will be used. If a group contains two atoms, the vector defined by those two atoms will be used.[BR]",
+ "[TT]-od[tt]: Distance between two groups. Distance is taken from the center of one group to the center of the other group.[BR]",
+ "[TT]-od1[tt]: If one plane and one vector is given, the distances for each of the atoms from the center of the plane is given separately.[BR]",
+ "[TT]-od2[tt]: For two planes this option has no meaning."
};
output_env_t oenv;
const char *desc[] = {
"g_spatial calculates the spatial distribution function and ",
"outputs it in a form that can be read by VMD as Gaussian98 cube format. ",
- "This was developed from template.c (gromacs-3.3). ",
+ "This was developed from template.c (GROMACS-3.3). ",
"For a system of 32K atoms and a 50ns trajectory, the SDF can be generated ",
"in about 30 minutes, with most of the time dedicated to the two runs through ",
"trjconv that are required to center everything properly. ",
"3. trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans \n",
"4. run g_spatial on the xtc output of step #3. \n",
"5. Load grid.cube into VMD and view as an isosurface. \n",
- "*** Systems such as micelles will require trjconv -pbc cluster between steps 1 and 2\n",
+ "*** Systems such as micelles will require [TT]trjconv -pbc cluster[tt] between steps 1 and 2\n",
"WARNINGS: \n",
"The SDF will be generated for a cube that contains all bins that have some non-zero occupancy. ",
- "However, the preparatory -fit rot+trans option to trjconv implies that your system will be rotating ",
+ "However, the preparatory [TT]-fit rot+trans[tt] option to trjconv implies that your system will be rotating ",
"and translating in space (in order that the selected group does not). Therefore the values that are ",
"returned will only be valid for some region around your central group/coordinate that has full overlap ",
"with system volume throughout the entire translated/rotated system over the course of the trajectory. ",
"It is up to the user to ensure that this is the case. \n",
"BUGS: \n",
"When the allocated memory is not large enough, a segmentation fault may occur. This is usually detected ",
- "and the program is halted prior to the fault while displaying a warning message suggesting the use of the -nab ",
+ "and the program is halted prior to the fault while displaying a warning message suggesting the use of the [TT]-nab[tt] ",
"option. However, the program does not detect all such events. If you encounter a segmentation fault, run it again ",
- "with an increased -nab value. \n",
+ "with an increased [TT]-nab[tt] value. \n",
"RISKY OPTIONS: \n",
"To reduce the amount of space and time required, you can output only the coords ",
"that are going to be used in the first and subsequent run through trjconv. ",
- "However, be sure to set the -nab option to a sufficiently high value since ",
- "memory is allocated for cube bins based on the initial coords and the -nab ",
+ "However, be sure to set the [TT]-nab[tt] option to a sufficiently high value since ",
+ "memory is allocated for cube bins based on the initial coords and the [TT]-nab[tt] ",
"(Number of Additional Bins) option value. \n"
};
int gmx_wheel(int argc,char *argv[])
{
const char *desc[] = {
- "wheel plots a helical wheel representation of your sequence.",
+ "g_wheel plots a helical wheel representation of your sequence.",
"The input sequence is in the .dat file where the first line contains",
"the number of residues and each consecutive line contains a residue"
"name."
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff