user-guide/plotje.gif
user-guide/xvgr.gif
conf.py
+ links.dat
)
set(SPHINX_INPUT_FILES ${SPHINX_CONFIG_VARS_FILE})
foreach(_file ${SPHINX_SOURCE_FILES})
file(MAKE_DIRECTORY ${OUTPUT_DIR}/programs)
file(COPY ${SOURCE_HTML_DIR}/header.html.in DESTINATION .)
file(COPY ${SOURCE_HTML_DIR}/footer.html DESTINATION .)
-file(COPY ${SOURCE_HTML_DIR}/links.dat DESTINATION .)
# This is generated by gmx help -export html
set(HEADER_FILE header.html)
list(APPEND deps
${CMAKE_CURRENT_SOURCE_DIR}/BuildHtmlHelp.cmake
${CMAKE_CURRENT_SOURCE_DIR}/header.html.in
- ${CMAKE_CURRENT_SOURCE_DIR}/links.dat
)
gmx_add_custom_output_target(html OUTPUT STAMP
int main(int argc,char *argv[])
{
static char *desc[] = {
- "[TT]gmxdump[tt] reads a run input file ([TT].tpr[tt]),",
- "a trajectory ([TT].trr[tt]/[TT].xtc[tt]) or an energy",
- "file ([TT].edr[tt]) and prints that to standard",
+ "[TT]gmxdump[tt] reads a run input file ([REF].tpr[ref]),",
+ "a trajectory ([REF].trr[ref]/[REF].xtc[ref]) or an energy",
+ "file ([REF].edr[ref]) and prints that to standard",
"output in a readable format. This program is essential for",
"checking your run input file in case of problems.[PAR]"
};
"reference molecule. ",
"The Volume of the SDF grid will be V=x*y*z (nm^3). ",
"Use [TT]-bin[tt] to set the binwidth for grid.[PAR]",
- "The output will be a binary 3D-grid file ([TT]gom_plt.dat[tt]) in the [TT].plt[tt] format that can be be",
+ "The output will be a binary 3D-grid file ([TT]gom_plt.dat[tt]) in the [REF].plt[ref] format that can be be",
"read directly by gOpenMol. ",
- "The option [TT]-r[tt] will generate a [TT].gro[tt] file with the reference molecule(s) transferred to",
+ "The option [TT]-r[tt] will generate a [REF].gro[ref] file with the reference molecule(s) transferred to",
"the SDF coordinate system. Load this file into gOpenMol and display the",
"SDF as a contour plot (see http://www.csc.fi/gopenmol/index.phtml for ",
"further documentation). [PAR]",
if (module->second->shortDescription() != NULL)
{
std::string linkName("[gmx-" + module->first + "]");
- std::string targetName(
- formatString("%s-%s", program, module->first.c_str()));
+ const char *name = module->first.c_str();
+ std::string reference(
+ formatString(":doc:`%s %s <%s-%s>`", program, name, program, name));
std::string displayName(
- formatString("[TT]%s %s[tt]", program, module->first.c_str()));
- links->addLink(linkName, targetName, displayName);
+ formatString("[TT]%s %s[tt]", program, name));
+ links->addLink(linkName, reference, displayName);
}
}
}
const CommandLineHelpModuleImpl &helpModule)
: links_(eHelpOutputFormat_Rst)
{
-#if 0 // TODO: Investigate how these links can be made to work again.
File linksFile("links.dat", "r");
std::string line;
while (linksFile.readLine(&line))
{
- links_.addLink(line, "../online/" + line, line);
+ links_.addLink("[REF]." + line + "[ref]",
+ formatString(":ref:`.%s <%s>`", line.c_str(), line.c_str()),
+ line);
+ links_.addLink("[REF]" + line + "[ref]", formatString(":ref:`%s`", line.c_str()), line);
}
linksFile.close();
-#endif
initProgramLinks(&links_, helpModule);
}
{
options.addOption(
gmx::BooleanOption("w").store(&bView)
- .description("View output [TT].xvg[tt], [TT].xpm[tt], "
- "[TT].eps[tt] and [TT].pdb[tt] files"));
+ .description("View output [REF].xvg[ref], [REF].xpm[ref], "
+ "[REF].eps[ref] and [REF].pdb[ref] files"));
}
bool bXvgr = false;
"eigenvector [TT]-first[tt] will be written unless [TT]-first[tt] and",
"[TT]-last[tt] have been set explicitly, in which case all eigenvectors",
"will be written to separate files. Chain identifiers will be added",
- "when writing a [TT].pdb[tt] file with two or three structures (you",
- "can use [TT]rasmol -nmrpdb[tt] to view such a [TT].pdb[tt] file).[PAR]",
+ "when writing a [REF].pdb[ref] file with two or three structures (you",
+ "can use [TT]rasmol -nmrpdb[tt] to view such a [REF].pdb[ref] file).[PAR]",
" Overlap calculations between covariance analysis:[BR]",
" [BB]Note:[bb] the analysis should use the same fitting structure[PAR]",
"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 [TT].mdp[tt] parameter",
+ "controlled by a parameter, [GRK]lambda[grk] (see the [REF].mdp[ref] 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.",
"The energy differences to the other state must be calculated",
"explicitly during the simulation. This can be done with",
- "the [TT].mdp[tt] option [TT]foreign_lambda[tt].[PAR]",
+ "the [REF].mdp[ref] option [TT]foreign_lambda[tt].[PAR]",
"Input option [TT]-f[tt] expects multiple [TT]dhdl.xvg[tt] files. ",
"Two types of input files are supported:[BR]",
"capitalized letters 'D' and 'H'. The temperature is parsed from ",
"the legend line containing 'T ='.[PAR]",
- "The input option [TT]-g[tt] expects multiple [TT].edr[tt] files. ",
+ "The input option [TT]-g[tt] expects multiple [REF].edr[ref] files. ",
"These can contain either lists of energy differences (see the ",
- "[TT].mdp[tt] option [TT]separate_dhdl_file[tt]), or a series of ",
- "histograms (see the [TT].mdp[tt] options [TT]dh_hist_size[tt] and ",
+ "[REF].mdp[ref] option [TT]separate_dhdl_file[tt]), or a series of ",
+ "histograms (see the [REF].mdp[ref] options [TT]dh_hist_size[tt] and ",
"[TT]dh_hist_spacing[tt]).", "The temperature and [GRK]lambda[grk] ",
"values are automatically deduced from the [TT]ener.edr[tt] file.[PAR]",
- "In addition to the [TT].mdp[tt] option [TT]foreign_lambda[tt], ",
+ "In addition to the [REF].mdp[ref] option [TT]foreign_lambda[tt], ",
"the energy difference can also be extrapolated from the ",
"dH/d[GRK]lambda[grk] values. This is done with the[TT]-extp[tt]",
"option, which assumes that the system's Hamiltonian depends linearly",
"[PAR]",
"With option [TT]-oa[tt] the top, mid (or kink when [TT]-ok[tt] is set)",
"and bottom points of each axis",
- "are written to a [TT].pdb[tt] file each frame. The residue numbers correspond",
+ "are written to a [REF].pdb[ref] file each frame. The residue numbers correspond",
"to the axis numbers. When viewing this file with Rasmol, use the",
"command line option [TT]-nmrpdb[tt], and type [TT]set axis true[tt] to",
"display the reference axis."
"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]",
- "The S^2 order parameters are also output to an [TT].xvg[tt] file",
- "(argument [TT]-o[tt] ) and optionally as a [TT].pdb[tt] file with",
+ "The S^2 order parameters are also output to an [REF].xvg[ref] file",
+ "(argument [TT]-o[tt] ) and optionally as a [REF].pdb[ref] file with",
"the S^2 values as B-factor (argument [TT]-p[tt]). ",
"The total number of rotamer transitions per timestep",
"(argument [TT]-ot[tt]), the number of transitions per rotamer",
"(argument [TT]-rt[tt]), and the ^3J couplings (argument [TT]-jc[tt]), ",
- "can also be written to [TT].xvg[tt] files. Note that the analysis",
+ "can also be written to [REF].xvg[ref] files. Note that the analysis",
"of rotamer transitions assumes that the supplied trajectory frames",
"are equally spaced in time.[PAR]",
{ "-normhisto", FALSE, etBOOL, {&bNormHisto},
"Normalize histograms" },
{ "-ramomega", FALSE, etBOOL, {&bRamOmega},
- "compute average omega as a function of [GRK]phi[grk]/[GRK]psi[grk] and plot it in an [TT].xpm[tt] plot" },
+ "compute average omega as a function of [GRK]phi[grk]/[GRK]psi[grk] and plot it in an [REF].xpm[ref] plot" },
{ "-bfact", FALSE, etREAL, {&bfac_init},
- "B-factor value for [TT].pdb[tt] file for atoms with no calculated dihedral order parameter"},
+ "B-factor value for [REF].pdb[ref] file for atoms with no calculated dihedral order parameter"},
{ "-chi_prod", FALSE, etBOOL, {&bChiProduct},
"compute a single cumulative rotamer for each residue"},
{ "-HChi", FALSE, etBOOL, {&bHChi},
const char *desc[] = {
"[THISMODULE] can cluster structures using several different methods.",
"Distances between structures can be determined from a trajectory",
- "or read from an [TT].xpm[tt] matrix file with the [TT]-dm[tt] option.",
+ "or read from an [REF].xpm[ref] 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]",
"ensemble of simulations or a pulling simulation. Obviously the user",
"has to prepare the trajectory well (e.g. by not superimposing frames).",
"The final result can be inspect visually by looking at the matrix",
- "[TT].xpm[tt] file, which should vary smoothly from bottom to top.[PAR]",
+ "[REF].xpm[ref] file, which should vary smoothly from bottom to top.[PAR]",
"diagonalization: diagonalize the RMSD matrix.[PAR]",
{ "-method", FALSE, etENUM, {methodname},
"Method for cluster determination" },
{ "-minstruct", FALSE, etINT, {&minstruct},
- "Minimum number of structures in cluster for coloring in the [TT].xpm[tt] file" },
+ "Minimum number of structures in cluster for coloring in the [REF].xpm[ref] file" },
{ "-binary", FALSE, etBOOL, {&bBinary},
"Treat the RMSD matrix as consisting of 0 and 1, where the cut-off "
"is given by [TT]-cutoff[tt]" },
{
if (bTPRwarn)
{
- printf("You need a [TT].tpr[tt] file to analyse temperatures\n");
+ printf("You need a [REF].tpr[ref] file to analyse temperatures\n");
bTPRwarn = FALSE;
}
}
{
const char *desc[] = {
"[THISMODULE] computes the size distributions of molecular/atomic clusters in",
- "the gas phase. The output is given in the form of an [TT].xpm[tt] file.",
- "The total number of clusters is written to an [TT].xvg[tt] file.[PAR]",
+ "the gas phase. The output is given in the form of an [REF].xpm[ref] file.",
+ "The total number of clusters is written to an [REF].xvg[ref] 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",
"or your calculation will die with a SEGV.[PAR]",
"When velocities are present in your trajectory, the temperature of",
- "the largest cluster will be printed in a separate [TT].xvg[tt] file assuming",
+ "the largest cluster will be printed in a separate [REF].xvg[ref] file assuming",
"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",
{ "-cut", FALSE, etREAL, {&cutoff},
"Largest distance (nm) to be considered in a cluster" },
{ "-mol", FALSE, etBOOL, {&bMol},
- "Cluster molecules rather than atoms (needs [TT].tpr[tt] file)" },
+ "Cluster molecules rather than atoms (needs [REF].tpr[ref] file)" },
{ "-pbc", FALSE, etBOOL, {&bPBC},
"Use periodic boundary conditions" },
{ "-nskip", FALSE, etINT, {&nskip},
"Number of frames to skip between writing" },
{ "-nlevels", FALSE, etINT, {&nlevels},
- "Number of levels of grey in [TT].xpm[tt] output" },
+ "Number of levels of grey in [REF].xpm[ref] output" },
{ "-ndf", FALSE, etINT, {&ndf},
"Number of degrees of freedom of the entire system for temperature calculation. If not set, the number of atoms times three is used." },
{ "-rgblo", FALSE, etRVEC, {rlo},
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
"will be used for the fit and RMSD calculation. This can be useful ",
"when comparing mutants of a protein.",
"[PAR]",
- "The superimposed structures are written to file. In a [TT].pdb[tt] file",
+ "The superimposed structures are written to file. In a [REF].pdb[ref] file",
"the two structures will be written as separate models",
- "(use [TT]rasmol -nmrpdb[tt]). Also in a [TT].pdb[tt] file, B-factors",
+ "(use [TT]rasmol -nmrpdb[tt]). Also in a [REF].pdb[ref] file, B-factors",
"calculated from the atomic MSD values can be written with [TT]-bfac[tt].",
};
static gmx_bool bOne = FALSE, bRmpbc = FALSE, bMW = TRUE, bName = FALSE,
"Option [TT]-ascii[tt] writes the whole covariance matrix to",
"an ASCII file. The order of the elements is: x1x1, x1y1, x1z1, x1x2, ...",
"[PAR]",
- "Option [TT]-xpm[tt] writes the whole covariance matrix to an [TT].xpm[tt] file.",
+ "Option [TT]-xpm[tt] writes the whole covariance matrix to an [REF].xpm[ref] file.",
"[PAR]",
- "Option [TT]-xpma[tt] writes the atomic covariance matrix to an [TT].xpm[tt] file,",
+ "Option [TT]-xpma[tt] writes the atomic covariance matrix to an [REF].xpm[ref] file,",
"i.e. for each atom pair the sum of the xx, yy and zz covariances is",
"written.",
"[PAR]",
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const char *desc[] = {
"[THISMODULE] computes 2D number-density maps.",
"It can make planar and axial-radial density maps.",
- "The output [TT].xpm[tt] file can be visualized with for instance xv",
+ "The output [REF].xpm[ref] file can be visualized with for instance xv",
"and can be converted to postscript with [TT]xpm2ps[tt].",
- "Optionally, output can be in text form to a [TT].dat[tt] file with [TT]-od[tt], instead of the usual [TT].xpm[tt] file with [TT]-o[tt].",
+ "Optionally, output can be in text form to a [REF].dat[ref] file with [TT]-od[tt], instead of the usual [REF].xpm[ref] file with [TT]-o[tt].",
"[PAR]",
"The default analysis is a 2-D number-density map for a selected",
"group of atoms in the x-y plane.",
{ "-rcmax", FALSE, etREAL, {&rcmax},
"Maximum distance to use in the dipole orientation distribution (with ncos == 2). If zero, a criterion based on the box length will be used." },
{ "-phi", FALSE, etBOOL, {&bPhi},
- "Plot the 'torsion angle' defined as the rotation of the two dipole vectors around the distance vector between the two molecules in the [TT].xpm[tt] file from the [TT]-cmap[tt] option. By default the cosine of the angle between the dipoles is plotted." },
+ "Plot the 'torsion angle' defined as the rotation of the two dipole vectors around the distance vector between the two molecules in the [REF].xpm[ref] file from the [TT]-cmap[tt] option. By default the cosine of the angle between the dipoles is plotted." },
{ "-nlevels", FALSE, etINT, {&nlevels},
"Number of colors in the cmap output" },
{ "-ndegrees", FALSE, etINT, {&ndegrees},
"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 [TT].pdb[tt] file coloured by the",
+ "When the optional [TT]-q[tt] flag is given a [REF].pdb[ref] 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",
"Even newer versions (which at the time of writing are not yet released)",
"are assumed to have the same syntax as 2.0.0.[PAR]",
"The structure assignment for each residue and time is written to an",
- "[TT].xpm[tt] matrix file. This file can be visualized with for instance",
+ "[REF].xpm[ref] matrix file. This file can be visualized with for instance",
"[TT]xv[tt] and can be converted to postscript with [TT]xpm2ps[tt].",
- "Individual chains are separated by light grey lines in the [TT].xpm[tt] and",
+ "Individual chains are separated by light grey lines in the [REF].xpm[ref] and",
"postscript files.",
"The number of residues with each secondary structure type and the",
"total secondary structure ([TT]-sss[tt]) count as a function of",
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int gmx_dyndom(int argc, char *argv[])
{
const char *desc[] = {
- "[THISMODULE] reads a [TT].pdb[tt] file output from DynDom",
+ "[THISMODULE] reads a [REF].pdb[ref] file output from DynDom",
"(http://www.cmp.uea.ac.uk/dyndom/).",
"It reads the coordinates, the coordinates of the rotation axis,",
"and an index file containing the domains.",
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
const char *desc[] =
{
- "[THISMODULE] converts generic structure format to [TT].gro[tt], [TT].g96[tt]",
- "or [TT].pdb[tt].",
+ "[THISMODULE] converts generic structure format to [REF].gro[ref], [TT].g96[tt]",
+ "or [REF].pdb[ref].",
"[PAR]",
"The box can be modified with options [TT]-box[tt], [TT]-d[tt] and",
"[TT]-angles[tt]. Both [TT]-box[tt] and [TT]-d[tt]",
"[PAR]",
"Scaling is applied before any of the other operations are",
"performed. Boxes and coordinates can be scaled to give a certain density (option",
- "[TT]-density[tt]). Note that this may be inaccurate in case a [TT].gro[tt]",
+ "[TT]-density[tt]). Note that this may be inaccurate in case a [REF].gro[ref]",
"file is given as input. A special feature of the scaling option is that when the",
"factor -1 is given in one dimension, one obtains a mirror image,",
"mirrored in one of the planes. When one uses -1 in three dimensions, ",
"It is important that the box vectors at the bottom of your input file",
"are correct when the periodicity is to be removed.",
"[PAR]",
- "When writing [TT].pdb[tt] files, B-factors can be",
+ "When writing [REF].pdb[ref] files, B-factors can be",
"added with the [TT]-bf[tt] option. B-factors are read",
"from a file with with following format: first line states number of",
"entries in the file, next lines state an index",
"a row of CA atoms with B-factors ranging from the minimum to the",
"maximum value found, effectively making a legend for viewing.",
"[PAR]",
- "With the option [TT]-mead[tt] a special [TT].pdb[tt] ([TT].pqr[tt])",
+ "With the option [TT]-mead[tt] a special [REF].pdb[ref] ([REF].pqr[ref])",
"file for the MEAD electrostatics",
"program (Poisson-Boltzmann solver) can be made. A further prerequisite",
"is that the input file is a run input file.",
"with an optional center of rotation specified by [TT]-aligncenter[tt].",
"[PAR]",
"Finally, with option [TT]-label[tt], [TT]editconf[tt] can add a chain identifier",
- "to a [TT].pdb[tt] file, which can be useful for analysis with e.g. Rasmol.",
+ "to a [REF].pdb[ref] file, which can be useful for analysis with e.g. Rasmol.",
"[PAR]",
"To convert a truncated octrahedron file produced by a package which uses",
"a cubic box with the corners cut off (such as GROMOS), use:[BR]",
{
"-conect", FALSE, etBOOL,
{ &bCONECT },
- "Add CONECT records to a [TT].pdb[tt] file when written. Can only be done when a topology is present"
+ "Add CONECT records to a [REF].pdb[ref] file when written. Can only be done when a topology is present"
}
};
#define NPA asize(pa)
"[BB]Note[bb] that in most cases the energy files contains averages over all",
"MD steps, or over many more points than the number of frames in",
"energy file. This makes the [THISMODULE] statistics output more accurate",
- "than the [TT].xvg[tt] output. When exact averages are not present in the energy",
+ "than the [REF].xvg[ref] output. When exact averages are not present in the energy",
"file, the statistics mentioned above are simply over the single, per-frame",
"energy values.[PAR]",
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{ "-rmin", FALSE, etREAL, {&rmin}, "Minimum distance between ions" },
{ "-seed", FALSE, etINT, {&seed}, "Seed for random number generator" },
{ "-conc", FALSE, etREAL, {&conc},
- "Specify salt concentration (mol/liter). This will add sufficient ions to reach up to the specified concentration as computed from the volume of the cell in the input [TT].tpr[tt] file. Overrides the [TT]-np[tt] and [TT]-nn[tt] options." },
+ "Specify salt concentration (mol/liter). This will add sufficient ions to reach up to the specified concentration as computed from the volume of the cell in the input [REF].tpr[ref] file. Overrides the [TT]-np[tt] and [TT]-nn[tt] options." },
{ "-neutral", FALSE, etBOOL, {&bNeutral}, "This option will add enough ions to neutralize the system. These ions are added on top of those specified with [TT]-np[tt]/[TT]-nn[tt] or [TT]-conc[tt]. "}
};
t_topology top;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
"or construct a suitable index group to provide",
"as input to [THISMODULE].[PAR]",
"The [TT]-of[tt] option produces an index file that can be used for",
- "freezing atoms. In this case, the input file must be a [TT].pdb[tt] file.[PAR]",
+ "freezing atoms. In this case, the input file must be a [REF].pdb[ref] file.[PAR]",
"With the [TT]-disre[tt] 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",
{ "-smooth", FALSE, etREAL, {&smooth_tail_start},
"If >= 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(-x/[GRK]tau[grk])" },
{ "-dump", FALSE, etINT, {&nDump},
- "Dump the first N hydrogen bond ACFs in a single [TT].xvg[tt] file for debugging" },
+ "Dump the first N hydrogen bond ACFs in a single [REF].xvg[ref] file for debugging" },
{ "-max_hb", FALSE, etREAL, {&maxnhb},
"Theoretical maximum number of hydrogen bonds used for normalizing HB autocorrelation function. Can be useful in case the program estimates it wrongly" },
{ "-merge", FALSE, etBOOL, {&bMerge},
"To utilize [TT]g_lie[tt] correctly, two simulations are required: one with the",
"molecule of interest bound to its receptor and one with the molecule in water.",
"Both need to utilize [TT]energygrps[tt] such that Coul-SR(A-B), LJ-SR(A-B), etc. terms",
- "are written to the [TT].edr[tt] file. Values from the molecule-in-water simulation",
+ "are written to the [REF].edr[ref] file. Values from the molecule-in-water simulation",
"are necessary for supplying suitable values for -Elj and -Eqq."
};
static real lie_lj = 0, lie_qq = 0, fac_lj = 0.181, fac_qq = 0.5;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
"[TT]-radcon[tt]: perform acceptance radius contraction along selected eigenvectors",
"towards a target structure specified with [TT]-tar[tt].[PAR]",
"NOTE: each eigenvector can be selected only once. [PAR]",
- "[TT]-outfrq[tt]: frequency (in steps) of writing out projections etc. to [TT].xvg[tt] file[PAR]",
+ "[TT]-outfrq[tt]: frequency (in steps) of writing out projections etc. to [REF].xvg[ref] file[PAR]",
"[TT]-slope[tt]: minimal slope in acceptance radius expansion. A new expansion",
"cycle will be started if the spontaneous increase of the radius (in nm/step)",
"is less than the value specified.[PAR]",
"lower as in a free MD simulation, especially on a large number of ranks and/or",
"when the ED group contains a lot of atoms. [PAR]",
"Please also note that if your ED group contains more than a single protein,",
- "then the [TT].tpr[tt] file must contain the correct PBC representation of the ED group.",
+ "then the [REF].tpr[ref] file must contain the correct PBC representation of the ED group.",
"Take a look on the initial RMSD from the reference structure, which is printed",
"out at the start of the simulation; if this is much higher than expected, one",
"of the ED molecules might be shifted by a box vector. [PAR]",
- "All ED-related output of [TT]mdrun[tt] (specify with [TT]-eo[tt]) is written to a [TT].xvg[tt] file",
+ "All ED-related output of [TT]mdrun[tt] (specify with [TT]-eo[tt]) is written to a [REF].xvg[ref] file",
"as a function of time in intervals of OUTFRQ steps.[PAR]",
"[BB]Note[bb] that you can impose multiple ED constraints and flooding potentials in",
- "a single simulation (on different molecules) if several [TT].edi[tt] files were concatenated",
- "first. The constraints are applied in the order they appear in the [TT].edi[tt] file. ",
- "Depending on what was specified in the [TT].edi[tt] input file, the output file contains for each ED dataset[PAR]",
+ "a single simulation (on different molecules) if several [REF].edi[ref] files were concatenated",
+ "first. The constraints are applied in the order they appear in the [REF].edi[ref] file. ",
+ "Depending on what was specified in the [REF].edi[ref] input file, the output file contains for each ED dataset[PAR]",
"[TT]*[tt] the RMSD of the fitted molecule to the reference structure (for atoms involved in fitting prior to calculating the ED constraints)[BR]",
"[TT]*[tt] projections of the positions onto selected eigenvectors[BR]",
"[PAR][PAR]",
"[PAR]",
"RESTART and FLOODING:",
"If you want to restart a crashed flooding simulation please find the values deltaF and Efl in",
- "the output file and manually put them into the [TT].edi[tt] file under DELTA_F0 and EFL_NULL."
+ "the output file and manually put them into the [REF].edi[ref] file under DELTA_F0 and EFL_NULL."
};
/* Save all the params in this struct and then save it in an edi file.
{ "-flood", FALSE, etSTR, {&evSelections[2]},
"Indices of eigenvectors for flooding"},
{ "-outfrq", FALSE, etINT, {&edi_params.outfrq},
- "Freqency (in steps) of writing output in [TT].xvg[tt] file" },
+ "Freqency (in steps) of writing output in [REF].xvg[ref] file" },
{ "-slope", FALSE, etREAL, { &edi_params.slope},
"Minimal slope in acceptance radius expansion"},
{ "-linstep", FALSE, etSTR, {&evParams[0]},
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
static const char *desc[] = {
"[THISMODULE] makes an index file for calculation of",
- "angle distributions etc. It uses a run input file ([TT].tpx[tt]) for the",
+ "angle distributions etc. It uses a run input file ([REF].tpx[ref]) for the",
"definitions of the angles, dihedrals etc."
};
static const char *opt[] = { NULL, "angle", "dihedral", "improper", "ryckaert-bellemans", NULL };
"Note that this diffusion coefficient and error estimate are only",
"accurate when the MSD is completely linear between",
"[TT]-beginfit[tt] and [TT]-endfit[tt].[PAR]",
- "Option [TT]-pdb[tt] writes a [TT].pdb[tt] file with the coordinates of the frame",
+ "Option [TT]-pdb[tt] writes a [REF].pdb[ref] file with the coordinates of the frame",
"at time [TT]-tpdb[tt] with in the B-factor field the square root of",
"the diffusion coefficient of the molecule.",
"This option implies option [TT]-mol[tt]."
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
t_pargs pa[] = {
{ "-beta", FALSE, etREAL, {&user_beta},
- "If positive, overwrite ewald_beta from [TT].tpr[tt] file with this value" },
+ "If positive, overwrite ewald_beta from [REF].tpr[ref] file with this value" },
{ "-tune", FALSE, etBOOL, {&bTUNE},
"Tune the splitting parameter such that the error is equally distributed between real and reciprocal space" },
{ "-self", FALSE, etREAL, {&fracself},
"are usually all trans and therefore only every second bond aligns.",
"The persistence length is defined as number of bonds where",
"the average cos reaches a value of 1/e. This point is determined",
- "by a linear interpolation of log(<cos>)."
+ "by a linear interpolation of [LOG]<cos>[log]."
};
static gmx_bool bMW = TRUE, bPC = FALSE;
t_pargs pa[] = {
"Option [TT]-prev[tt] produces the comparison with a previous frame",
"the specified number of frames ago.[PAR]",
- "Option [TT]-m[tt] produces a matrix in [TT].xpm[tt] format of",
+ "Option [TT]-m[tt] produces a matrix in [REF].xpm[ref] format of",
"comparison values of each structure in the trajectory with respect to",
"each other structure. This file can be visualized with for instance",
"[TT]xv[tt] and can be converted to postscript with [gmx-xpm2ps].[PAR]",
"Option [TT]-mw[tt] controls whether mass weighting is done or not.",
"If you select the option (default) and ",
- "supply a valid [TT].tpr[tt] file masses will be taken from there, ",
+ "supply a valid [REF].tpr[ref] file masses will be taken from there, ",
"otherwise the masses will be deduced from the [TT]atommass.dat[tt] file in",
"[TT]GMXLIB[tt]. This is fine for proteins, but not",
"necessarily for other molecules. A default mass of 12.011 amu (carbon)",
"deviation) of atomic positions in the trajectory (supplied with [TT]-f[tt])",
"after (optionally) fitting to a reference frame (supplied with [TT]-s[tt]).[PAR]",
"With option [TT]-oq[tt] the RMSF values are converted to B-factor",
- "values, which are written to a [TT].pdb[tt] file with the coordinates, of the",
- "structure file, or of a [TT].pdb[tt] file when [TT]-q[tt] is specified.",
+ "values, which are written to a [REF].pdb[ref] file with the coordinates, of the",
+ "structure file, or of a [REF].pdb[ref] file when [TT]-q[tt] is specified.",
"Option [TT]-ox[tt] writes the B-factors to a file with the average",
"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], [THISMODULE] will compute anisotropic",
"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]",
+ "and a [REF].pdb[ref] 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",
"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]",
+ "When a [REF].pdb[ref] input file is passed to the program and the [TT]-aniso[tt]",
"flag is set",
"a correlation plot of the Uij will be created, if any anisotropic",
- "temperature factors are present in the [TT].pdb[tt] file.[PAR]",
+ "temperature factors are present in the [REF].pdb[ref] file.[PAR]",
"With option [TT]-dir[tt] the average MSF (3x3) matrix is diagonalized.",
"This shows the directions in which the atoms fluctuate the most and",
"the least."
{
const char *desc[] = {
"[THISMODULE] makes multi-dimensional free-energy, enthalpy and entropy plots.",
- "[THISMODULE] reads one or more [TT].xvg[tt] files and analyzes data sets.",
+ "[THISMODULE] reads one or more [REF].xvg[ref] files and analyzes data sets.",
"The basic purpose of [THISMODULE] is to plot Gibbs free energy landscapes",
"(option [TT]-ls[tt])",
"by Bolzmann inverting multi-dimensional histograms (option [TT]-lp[tt]),",
"provided velocities are present in the trajectory file.",
"This implies [TT]-com[tt].[PAR]",
"Options [TT]-cv[tt] and [TT]-cf[tt] write the average velocities",
- "and average forces as temperature factors to a [TT].pdb[tt] file with",
+ "and average forces as temperature factors to a [REF].pdb[ref] file with",
"the average coordinates or the coordinates at [TT]-ctime[tt].",
"The temperature factors are scaled such that the maximum is 10.",
"The scaling can be changed with the option [TT]-scale[tt].",
"desired frame. When averaging over frames you might need to use",
"the [TT]-nojump[tt] option to obtain the correct average coordinates.",
"If you select either of these option the average force and velocity",
- "for each atom are written to an [TT].xvg[tt] file as well",
+ "for each atom are written to an [REF].xvg[ref] file as well",
"(specified with [TT]-av[tt] or [TT]-af[tt]).[PAR]",
"Option [TT]-vd[tt] computes a velocity distribution, i.e. the",
"norm of the vector is plotted. In addition in the same graph",
{ "-ctime", FALSE, etREAL, {&ctime},
"Use frame at this time for x in [TT]-cv[tt] and [TT]-cf[tt] instead of the average x" },
{ "-scale", FALSE, etREAL, {&scale},
- "Scale factor for [TT].pdb[tt] output, 0 is autoscale" }
+ "Scale factor for [REF].pdb[ref] output, 0 is autoscale" }
};
FILE *outx = NULL, *outv = NULL, *outf = NULL, *outb = NULL, *outt = NULL;
FILE *outekt = NULL, *outekr = NULL;
"Obviously the file to append to has to be the one with lowest starting",
"time since one can only append at the end of a file.[PAR]",
"If the [TT]-demux[tt] option is given, the N trajectories that are",
- "read, are written in another order as specified in the [TT].xvg[tt] file.",
- "The [TT].xvg[tt] file should contain something like:[PAR]",
+ "read, are written in another order as specified in the [REF].xvg[ref] file.",
+ "The [REF].xvg[ref] file should contain something like:[PAR]",
"[TT]0 0 1 2 3 4 5[tt][BR]",
"[TT]2 1 0 2 3 5 4[tt][BR]",
"Where the first number is the time, and subsequent numbers point to",
"trajectory indices.",
"The frames corresponding to the numbers present at the first line",
"are collected into the output trajectory. If the number of frames in",
- "the trajectory does not match that in the [TT].xvg[tt] file then the program",
+ "the trajectory does not match that in the [REF].xvg[ref] file then the program",
"tries to be smart. Beware."
};
static gmx_bool bVels = TRUE;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
"This assumes that the entries in the index file are frame numbers and",
"dumps each group in the index file to a separate trajectory file.[BR]",
"* select frames within a certain range of a quantity given",
- "in an [TT].xvg[tt] file.[PAR]",
+ "in an [REF].xvg[ref] file.[PAR]",
"[gmx-trjcat] is better suited for concatenating multiple trajectory files.",
"[PAR]",
"The following formats are supported for input and output:",
- "[TT].xtc[tt], [TT].trr[tt], [TT].gro[tt], [TT].g96[tt]",
- "and [TT].pdb[tt].",
+ "[REF].xtc[ref], [REF].trr[ref], [REF].gro[ref], [TT].g96[tt]",
+ "and [REF].pdb[ref].",
"The file formats are detected from the file extension.",
- "The precision of [TT].xtc[tt] and [TT].gro[tt] output is taken from the",
- "input file for [TT].xtc[tt], [TT].gro[tt] and [TT].pdb[tt],",
+ "The precision of [REF].xtc[ref] and [REF].gro[ref] output is taken from the",
+ "input file for [REF].xtc[ref], [REF].gro[ref] and [REF].pdb[ref],",
"and from the [TT]-ndec[tt] option for other input formats. The precision",
"is always taken from [TT]-ndec[tt], when this option is set.",
- "All other formats have fixed precision. [TT].trr[tt]",
+ "All other formats have fixed precision. [REF].trr[ref]",
"output can be single or double precision, depending on the precision",
"of the [THISMODULE] binary.",
"Note that velocities are only supported in",
- "[TT].trr[tt], [TT].gro[tt] and [TT].g96[tt] files.[PAR]",
+ "[REF].trr[ref], [REF].gro[ref] and [TT].g96[tt] files.[PAR]",
"Option [TT]-sep[tt] can be used to write every frame to a separate",
- "[TT].gro, .g96[tt] or [TT].pdb[tt] file. By default, all frames all written to one file.",
- "[TT].pdb[tt] files with all frames concatenated can be viewed with",
+ "[TT].gro, .g96[tt] or [REF].pdb[ref] file. By default, all frames all written to one file.",
+ "[REF].pdb[ref] files with all frames concatenated can be viewed with",
"[TT]rasmol -nmrpdb[tt].[PAR]",
"It is possible to select part of your trajectory and write it out",
"to a new trajectory file in order to save disk space, e.g. for leaving",
"out the water from a trajectory of a protein in water.",
"[BB]ALWAYS[bb] put the original trajectory on tape!",
- "We recommend to use the portable [TT].xtc[tt] format for your analysis",
+ "We recommend to use the portable [REF].xtc[ref] format for your analysis",
"to save disk space and to have portable files.[PAR]",
"There are two options for fitting the trajectory to a reference",
"can reduce the number of frames while using low-pass frequency",
"filtering, this reduces aliasing of high frequency motions.[PAR]",
- "Using [TT]-trunc[tt] [THISMODULE] can truncate [TT].trr[tt] in place, i.e.",
+ "Using [TT]-trunc[tt] [THISMODULE] can truncate [REF].trr[ref] in place, i.e.",
"without copying the file. This is useful when a run has crashed",
"during disk I/O (i.e. full disk), or when two contiguous",
"trajectories must be concatenated without having double frames.[PAR]",
"Option [TT]-dump[tt] can be used to extract a frame at or near",
"one specific time from your trajectory.[PAR]",
- "Option [TT]-drop[tt] reads an [TT].xvg[tt] file with times and values.",
+ "Option [TT]-drop[tt] reads an [REF].xvg[ref] file with times and values.",
"When options [TT]-dropunder[tt] and/or [TT]-dropover[tt] are set,",
"frames with a value below and above the value of the respective options",
"will not be written."
{ &dropover }, "Drop all frames above this value" },
{ "-conect", FALSE, etBOOL,
{ &bCONECT },
- "Add conect records when writing [TT].pdb[tt] files. Useful "
+ "Add conect records when writing [REF].pdb[ref] files. Useful "
"for visualization of non-standard molecules, e.g. "
"coarse grained ones" }
};
"of the first n waters is made, the ordered trajectory can be used",
"with any Gromacs program to analyze the n closest waters.",
"[PAR]",
- "If the output file is a [TT].pdb[tt] file, the distance to the reference target",
+ "If the output file is a [REF].pdb[ref] file, the distance to the reference target",
"will be stored in the B-factor field in order to color with e.g. Rasmol.",
"[PAR]",
"With option [TT]-nshell[tt] the number of molecules within a shell",
"which setting is fastest. It will also test whether performance can",
"be enhanced by shifting load from the reciprocal to the real space",
"part of the Ewald sum. ",
- "Simply pass your [TT].tpr[tt] file to [THISMODULE] together with other options",
+ "Simply pass your [REF].tpr[ref] file to [THISMODULE] together with other options",
"for [gmx-mdrun] as needed.[PAR]",
"Which executables are used can be set in the environment variables",
"MPIRUN and MDRUN. If these are not present, 'mpirun' and 'mdrun'",
"tests on, or [TT]-ntmpi[tt] for the number of threads. You can also add [TT]-r[tt]",
"to repeat each test several times to get better statistics. [PAR]",
"[THISMODULE] can test various real space / reciprocal space workloads",
- "for you. With [TT]-ntpr[tt] you control how many extra [TT].tpr[tt] files will be",
+ "for you. With [TT]-ntpr[tt] you control how many extra [REF].tpr[ref] files will be",
"written with enlarged cutoffs and smaller Fourier grids respectively.",
"Typically, the first test (number 0) will be with the settings from the input",
- "[TT].tpr[tt] file; the last test (number [TT]ntpr[tt]) will have the Coulomb cutoff",
+ "[REF].tpr[ref] file; the last test (number [TT]ntpr[tt]) will have the Coulomb cutoff",
"specified by [TT]-rmax[tt] with a somewhat smaller PME grid at the same time. ",
"In this last test, the Fourier spacing is multiplied with [TT]rmax[tt]/rcoulomb. ",
- "The remaining [TT].tpr[tt] files will have equally-spaced Coulomb radii (and Fourier "
+ "The remaining [REF].tpr[ref] files will have equally-spaced Coulomb radii (and Fourier "
"spacings) between these extremes. [BB]Note[bb] that you can set [TT]-ntpr[tt] to 1",
"if you just seek the optimal number of PME-only ranks; in that case",
- "your input [TT].tpr[tt] file will remain unchanged.[PAR]",
+ "your input [REF].tpr[ref] file will remain unchanged.[PAR]",
"For the benchmark runs, the default of 1000 time steps should suffice for most",
"MD systems. The dynamic load balancing needs about 100 time steps",
"to adapt to local load imbalances, therefore the time step counters",
{ "-scalevdw", FALSE, etBOOL, {&bScaleRvdw},
"Scale rvdw along with rcoulomb"},
{ "-ntpr", FALSE, etINT, {&ntprs},
- "Number of [TT].tpr[tt] files to benchmark. Create this many files with different rcoulomb scaling factors depending on -rmin and -rmax. "
- "If < 1, automatically choose the number of [TT].tpr[tt] files to test" },
+ "Number of [REF].tpr[ref] files to benchmark. Create this many files with different rcoulomb scaling factors depending on -rmin and -rmax. "
+ "If < 1, automatically choose the number of [REF].tpr[ref] files to test" },
{ "-steps", FALSE, etINT64, {&bench_nsteps},
"Take timings for this many steps in the benchmark runs" },
{ "-resetstep", FALSE, etINT, {&presteps},
"Let dlb equilibrate this many steps before timings are taken (reset cycle counters after this many steps)" },
{ "-nsteps", FALSE, etINT64, {&new_sim_nsteps},
- "If non-negative, perform this many steps in the real run (overwrites nsteps from [TT].tpr[tt], add [TT].cpt[tt] steps)" },
+ "If non-negative, perform this many steps in the real run (overwrites nsteps from [REF].tpr[ref], add [REF].cpt[ref] steps)" },
{ "-launch", FALSE, etBOOL, {&bLaunch},
"Launch the real simulation after optimization" },
{ "-bench", FALSE, etBOOL, {&bBenchmark},
- "Run the benchmarks or just create the input [TT].tpr[tt] files?" },
+ "Run the benchmarks or just create the input [REF].tpr[ref] files?" },
{ "-check", FALSE, etBOOL, {&bCheck},
"Before the benchmark runs, check whether mdrun works in parallel" },
{ "-gpu_id", FALSE, etSTR, {&eligible_gpu_ids},
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
"molecules is calculated. In this case the index group should consist",
"of molecule numbers instead of atom numbers.[PAR]",
"Be sure that your trajectory contains frames with velocity information",
- "(i.e. [TT]nstvout[tt] was set in your original [TT].mdp[tt] file),",
+ "(i.e. [TT]nstvout[tt] was set in your original [REF].mdp[ref] file),",
"and that the time interval between data collection points is",
"much shorter than the time scale of the autocorrelation."
};
"compute a potential of mean force (PMF). [PAR] ",
"At present, three input modes are supported.[BR]",
"[TT]*[tt] With option [TT]-it[tt], the user provides a file which contains the",
- " file names of the umbrella simulation run-input files ([TT].tpr[tt] files),",
+ " file names of the umbrella simulation run-input files ([REF].tpr[ref] files),",
" AND, with option [TT]-ix[tt], a file which contains file names of",
- " the pullx [TT]mdrun[tt] output files. The [TT].tpr[tt] and pullx files must",
- " be in corresponding order, i.e. the first [TT].tpr[tt] created the",
+ " the pullx [TT]mdrun[tt] output files. The [REF].tpr[ref] and pullx files must",
+ " be in corresponding order, i.e. the first [REF].tpr[ref] created the",
" first pullx, etc.[BR]",
"[TT]*[tt] Same as the previous input mode, except that the the user",
" provides the pull force output file names ([TT]pullf.xvg[tt]) with option [TT]-if[tt].",
" From the pull force the position in the umbrella potential is",
" computed. This does not work with tabulated umbrella potentials.[BR]"
- "[TT]*[tt] With option [TT]-ip[tt], the user provides file names of (gzipped) [TT].pdo[tt] files, i.e.",
+ "[TT]*[tt] With option [TT]-ip[tt], the user provides file names of (gzipped) [REF].pdo[ref] files, i.e.",
" the GROMACS 3.3 umbrella output files. If you have some unusual"
- " reaction coordinate you may also generate your own [TT].pdo[tt] files and",
- " feed them with the [TT]-ip[tt] option into to [THISMODULE]. The [TT].pdo[tt] file header",
+ " reaction coordinate you may also generate your own [REF].pdo[ref] files and",
+ " feed them with the [TT]-ip[tt] option into to [THISMODULE]. The [REF].pdo[ref] file header",
" must be similar to the following:[PAR]",
"# UMBRELLA 3.0[BR]",
"# Component selection: 0 0 1[BR]",
"may (of course) differ. Following the header, a time column and ",
"a data column for each pull group follows (i.e. the displacement",
"with respect to the umbrella center). Up to four pull groups are possible ",
- "per [TT].pdo[tt] file at present.[PAR]",
+ "per [REF].pdo[ref] file at present.[PAR]",
"By default, all pull groups found in all pullx/pullf files are used in WHAM. If only ",
"some of the pull groups should be used, a pull group selection file (option [TT]-is[tt]) can ",
"be provided. The selection file must contain one line for each tpr file in tpr-files.dat.",
" [TT]-hist[tt] Histograms output file[BR]",
"Always check whether the histograms sufficiently overlap.[PAR]",
"The umbrella potential is assumed to be harmonic and the force constants are ",
- "read from the [TT].tpr[tt] or [TT].pdo[tt] files. If a non-harmonic umbrella force was applied ",
+ "read from the [REF].tpr[ref] or [REF].pdo[ref] files. If a non-harmonic umbrella force was applied ",
"a tabulated potential can be provided with [TT]-tab[tt].[PAR]",
"WHAM OPTIONS[BR]------------[BR]",
" [TT]-bins[tt] Number of bins used in analysis[BR]",
"less robust) method such as fitting to a double exponential, you can ",
"compute the IACTs with [gmx-analyze] and provide them to [THISMODULE] with the file ",
"[TT]iact-in.dat[tt] (option [TT]-iiact[tt]), which should contain one line per ",
- "input file ([TT].pdo[tt] or pullx/f file) and one column per pull group in the respective file.[PAR]",
+ "input file ([REF].pdo[ref] or pullx/f file) and one column per pull group in the respective file.[PAR]",
"ERROR ANALYSIS[BR]--------------[BR]",
"Statistical errors may be estimated with bootstrap analysis. Use it with care, ",
"otherwise the statistical error may be substantially underestimated. ",
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
const char *desc[] = {
"[THISMODULE] plots a helical wheel representation of your sequence.",
- "The input sequence is in the [TT].dat[tt] file where the first line contains",
+ "The input sequence is in the [REF].dat[ref] file where the first line contains",
"the number of residues and each consecutive line contains a residue "
"name."
};
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{ "-skip", FALSE, etINT, {&skip},
"only write out every nr-th row and column" },
{ "-zeroline", FALSE, etBOOL, {&bZeroLine},
- "insert line in [TT].xpm[tt] matrix where axis label is zero"},
+ "insert line in [REF].xpm[ref] matrix where axis label is zero"},
{ "-legoffset", FALSE, etINT, {&mapoffset},
- "Skip first N colors from [TT].xpm[tt] file for the legend" },
+ "Skip first N colors from [REF].xpm[ref] file for the legend" },
{ "-combine", FALSE, etENUM, {combine}, "Combine two matrices" },
{ "-cmin", FALSE, etREAL, {&cmin}, "Minimum for combination output" },
{ "-cmax", FALSE, etREAL, {&cmax}, "Maximum for combination output" }
/* Set the relative box lengths for preserving the box shape.
* Note that this call can lead to differences in the last bit
- * with respect to using gmx convert-tpr to create a [TT].tpx[tt] file.
+ * with respect to using gmx convert-tpr to create a [REF].tpx[ref] file.
*/
set_box_rel(ir, state);
"#include \"filename\"[BR]",
"#include <filename>[PAR]",
"The functioning of these statements in your topology may be modulated by",
- "using the following two flags in your [TT].mdp[tt] file:[PAR]",
+ "using the following two flags in your [REF].mdp[ref] file:[PAR]",
"[TT]define = -DVARIABLE1 -DVARIABLE2[tt][BR]",
"[TT]include = -I/home/john/doe[tt][BR]",
"For further information a C-programming textbook may help you out.",
"unless the [TT]-time[tt] option is used. Only if this information",
"is absent will the coordinates in the [TT]-c[tt] file be used.",
"Note that these velocities will not be used when [TT]gen_vel = yes[tt]",
- "in your [TT].mdp[tt] file. An energy file can be supplied with",
+ "in your [REF].mdp[ref] file. An energy file can be supplied with",
"[TT]-e[tt] to read Nose-Hoover and/or Parrinello-Rahman coupling",
"variables.[PAR]",
"You then supply the old checkpoint file directly to [gmx-mdrun]",
"with [TT]-cpi[tt]. If you wish to change the ensemble or things",
"like output frequency, then supplying the checkpoint file to",
- "[THISMODULE] with [TT]-t[tt] along with a new [TT].mdp[tt] file",
+ "[THISMODULE] with [TT]-t[tt] along with a new [REF].mdp[ref] file",
"with [TT]-f[tt] is the recommended procedure.[PAR]",
"By default, all bonded interactions which have constant energy due to",
int gmx_pdb2gmx(int argc, char *argv[])
{
const char *desc[] = {
- "[THISMODULE] reads a [TT].pdb[tt] (or [TT].gro[tt]) file, reads",
+ "[THISMODULE] reads a [REF].pdb[ref] (or [REF].gro[ref]) file, reads",
"some database files, adds hydrogens to the molecules and generates",
- "coordinates in GROMACS (GROMOS), or optionally [TT].pdb[tt], format",
+ "coordinates in GROMACS (GROMOS), or optionally [REF].pdb[ref], format",
"and a topology in GROMACS format.",
"These files can subsequently be processed to generate a run input file.",
"[PAR]",
"Check Chapter 5 of the manual for more information about file formats.",
"[PAR]",
- "Note that a [TT].pdb[tt] file is nothing more than a file format, and it",
+ "Note that a [REF].pdb[ref] file is nothing more than a file format, and it",
"need not necessarily contain a protein structure. Every kind of",
"molecule for which there is support in the database can be converted.",
"If there is no support in the database, you can add it yourself.[PAR]",
"This can be turned off (no merging), all non-water chains can be merged into a",
"single molecule, or the selection can be done interactively.[PAR]",
- "[THISMODULE] will also check the occupancy field of the [TT].pdb[tt] file.",
+ "[THISMODULE] will also check the occupancy field of the [REF].pdb[ref] file.",
"If any of the occupancies are not one, indicating that the atom is",
"not resolved well in the structure, a warning message is issued.",
- "When a [TT].pdb[tt] file does not originate from an X-ray structure determination",
+ "When a [REF].pdb[ref] file does not originate from an X-ray structure determination",
"all occupancy fields may be zero. Either way, it is up to the user",
"to verify the correctness of the input data (read the article!).[PAR]",
"from the input and before new hydrogens are added. This means that",
"you should not use [TT]-ignh[tt].[PAR]",
- "The [TT].gro[tt] and [TT].g96[tt] file formats do not support chain",
- "identifiers. Therefore it is useful to enter a [TT].pdb[tt] file name at",
- "the [TT]-o[tt] option when you want to convert a multi-chain [TT].pdb[tt] file.",
+ "The [REF].gro[ref] and [TT].g96[tt] file formats do not support chain",
+ "identifiers. Therefore it is useful to enter a [REF].pdb[ref] file name at",
+ "the [TT]-o[tt] option when you want to convert a multi-chain [REF].pdb[ref] file.",
"[PAR]",
"The option [TT]-vsite[tt] removes hydrogen and fast improper dihedral",
{ "-deuterate", FALSE, etBOOL, {&bDeuterate},
"Change the mass of hydrogens to 2 amu" },
{ "-chargegrp", TRUE, etBOOL, {&bChargeGroups},
- "Use charge groups in the [TT].rtp[tt] file" },
+ "Use charge groups in the [REF].rtp[ref] file" },
{ "-cmap", TRUE, etBOOL, {&bCmap},
- "Use cmap torsions (if enabled in the [TT].rtp[tt] file)" },
+ "Use cmap torsions (if enabled in the [REF].rtp[ref] file)" },
{ "-renum", TRUE, etBOOL, {&bRenumRes},
"Renumber the residues consecutively in the output" },
{ "-rtpres", TRUE, etBOOL, {&bRTPresname},
- "Use [TT].rtp[tt] entry names as residue names" }
+ "Use [REF].rtp[ref] entry names as residue names" }
};
#define NPARGS asize(pa)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
"is specified, the conformation(s) will be read from this file, ",
"which can be either a single conformation or a trajectory.",
"[PAR]",
- "If a [TT].pdb[tt] file is supplied, residue names might not correspond to",
+ "If a [REF].pdb[ref] file is supplied, residue names might not correspond to",
"to the GROMACS naming conventions, in which case these residues will",
"probably not be properly protonated.",
"[PAR]",
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
"[THISMODULE] generates a primitive topology from a coordinate file.",
"The program assumes all hydrogens are present when defining",
"the hybridization from the atom name and the number of bonds.",
- "The program can also make an [TT].rtp[tt] entry, which you can then add",
- "to the [TT].rtp[tt] database.[PAR]",
+ "The program can also make an [REF].rtp[ref] entry, which you can then add",
+ "to the [REF].rtp[ref] database.[PAR]",
"When [TT]-param[tt] is set, equilibrium distances and angles",
"and force constants will be printed in the topology for all",
"interactions. The equilibrium distances and angles are taken",
{ "-pbc", FALSE, etBOOL, {&bPBC},
"Use periodic boundary conditions." },
{ "-pdbq", FALSE, etBOOL, {&bUsePDBcharge},
- "Use the B-factor supplied in a [TT].pdb[tt] file for the atomic charges" },
+ "Use the B-factor supplied in a [REF].pdb[ref] file for the atomic charges" },
{ "-param", FALSE, etBOOL, {&bParam},
"Print parameters in the output" },
{ "-round", FALSE, etBOOL, {&bRound},
const t_sandr sandrTty[] = {
{ "\\*", "*" },
{ "\\=", "=" },
+ { "[REF]", "" },
+ { "[ref]", "" },
{ "[TT]", "" },
{ "[tt]", "" },
{ "[BB]", "" },
replacement = repall(displayName, sandrTty);
break;
case eHelpOutputFormat_Rst:
- replacement = formatString(
- ":doc:`%s <%s>`", repall(displayName, sandrTty).c_str(),
- targetName.c_str());
+ replacement = targetName;
break;
default:
GMX_RELEASE_ASSERT(false, "Output format not implemented for links");
{
result = repall(result, sandrRst);
result = replaceLinks(result);
+ result = replaceAll(result, "[REF]", "");
+ result = replaceAll(result, "[ref]", "");
return wrapper->wrap(result);
}
default:
result.append(":");
for (int i = 0; i < typeHandler.extensionCount(); ++i)
{
- result.append(" ");
+ result.append(" [REF]");
// Skip the dot.
result.append(typeHandler.extension(i) + 1);
+ result.append("[ref]");
}
}
return result;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int gmx_check(int argc, char *argv[])
{
const char *desc[] = {
- "[THISMODULE] reads a trajectory ([TT].tng[tt], [TT].trr[tt] or ",
- "[TT].xtc[tt]), an energy file ([TT].edr[tt])",
- "or an index file ([TT].ndx[tt])",
+ "[THISMODULE] reads a trajectory ([REF].tng[ref], [REF].trr[ref] or ",
+ "[REF].xtc[ref]), an energy file ([REF].edr[ref])",
+ "or an index file ([REF].ndx[ref])",
"and prints out useful information about them.[PAR]",
"Option [TT]-c[tt] checks for presence of coordinates,",
"velocities and box in the file, for close contacts (smaller than",
"no problem). If velocities are present, an estimated temperature",
"will be calculated from them.[PAR]",
"If an index file, is given its contents will be summarized.[PAR]",
- "If both a trajectory and a [TT].tpr[tt] file are given (with [TT]-s1[tt])",
+ "If both a trajectory and a [REF].tpr[ref] file are given (with [TT]-s1[tt])",
"the program will check whether the bond lengths defined in the tpr",
"file are indeed correct in the trajectory. If not you may have",
"non-matching files due to e.g. deshuffling or due to problems with",
"virtual sites. With these flags, [TT]gmx check[tt] provides a quick check for such problems.[PAR]",
- "The program can compare two run input ([TT].tpr[tt])",
+ "The program can compare two run input ([REF].tpr[ref])",
"files",
"when both [TT]-s1[tt] and [TT]-s2[tt] are supplied.",
"Similarly a pair of trajectory files can be compared (using the [TT]-f2[tt]",
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
"When pressure and/or Nose-Hoover temperature coupling is used",
"an energy file can be supplied to get an exact continuation",
"of the original run.[PAR]",
- "[BB]3.[bb] by creating a [TT].tpx[tt] file for a subset of your original",
+ "[BB]3.[bb] by creating a [REF].tpx[ref] file for a subset of your original",
"tpx file, which is useful when you want to remove the solvent from",
- "your [TT].tpx[tt] file, or when you want to make e.g. a pure C[GRK]alpha[grk] [TT].tpx[tt] file.",
+ "your [REF].tpx[ref] file, or when you want to make e.g. a pure C[GRK]alpha[grk] [REF].tpx[ref] file.",
"Note that you may need to use [TT]-nsteps -1[tt] (or similar) to get",
"this to work.",
- "[BB]WARNING: this [TT].tpx[tt] file is not fully functional[bb].[PAR]",
+ "[BB]WARNING: this [REF].tpx[ref] file is not fully functional[bb].[PAR]",
"[BB]4.[bb] by setting the charges of a specified group",
"to zero. This is useful when doing free energy estimates",
"using the LIE (Linear Interaction Energy) method."
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int gmx_dump(int argc, char *argv[])
{
const char *desc[] = {
- "[THISMODULE] reads a run input file ([TT].tpr[tt]),",
- "a trajectory ([TT].trr[tt]/[TT].xtc[tt]/[TT]/tng[tt]), an energy",
- "file ([TT].edr[tt]) or a checkpoint file ([TT].cpt[tt])",
+ "[THISMODULE] reads a run input file ([REF].tpr[ref]),",
+ "a trajectory ([REF].trr[ref]/[REF].xtc[ref]/[TT]/tng[tt]), an energy",
+ "file ([REF].edr[ref]) or a checkpoint file ([REF].cpt[ref])",
"and prints that to standard output in a readable format.",
"This program is essential for checking your run input file in case of",
"problems.[PAR]",
"See Eisenhaber F, Lijnzaad P, Argos P, Sander C, & Scharf M",
"(1995) J. Comput. Chem. 16, 273-284 for the algorithm used.",
"With [TT]-q[tt], the Connolly surface can be generated as well",
- "in a [TT].pdb[tt] file where the nodes are represented as atoms",
+ "in a [REF].pdb[ref] file where the nodes are represented as atoms",
"and the edges connecting the nearest nodes as CONECT records.",
"[TT]-odg[tt] allows for estimation of solvation free energies",
"from per-atom solvation energies per exposed surface area.[PAR]",
"The average and standard deviation of the area over the trajectory",
"can be calculated per residue and atom (options [TT]-or[tt] and",
"[TT]-oa[tt]).[PAR]",
- //"In combination with the latter option an [TT].itp[tt] file can be",
+ //"In combination with the latter option an [REF].itp[ref] file can be",
//"generated (option [TT]-i[tt])",
//"which can be used to restrain surface atoms.[PAR]",
//options->addOption(DoubleOption("minarea").store(&minarea_)
// .description("The minimum area (nm^2) to count an atom as a surface atom when writing a position restraint file (see help)"));
options->addOption(BooleanOption("prot").store(&bIncludeSolute_)
- .description("Output the protein to the Connolly [TT].pdb[tt] file too"));
+ .description("Output the protein to the Connolly [REF].pdb[ref] file too"));
options->addOption(DoubleOption("dgs").store(&dgsDefault_)
.description("Default value for solvation free energy per area (kJ/mol/nm^2)"));
"should look there for practical advice on using many of the options",
"available in mdrun.[PAR]",
"ED (essential dynamics) sampling and/or additional flooding potentials",
- "are switched on by using the [TT]-ei[tt] flag followed by an [TT].edi[tt]",
- "file. The [TT].edi[tt] file can be produced with the [TT]make_edi[tt] tool",
+ "are switched on by using the [TT]-ei[tt] flag followed by an [REF].edi[ref]",
+ "file. The [REF].edi[ref] file can be produced with the [TT]make_edi[tt] tool",
"or by using options in the essdyn menu of the WHAT IF program.",
- "[TT]mdrun[tt] produces a [TT].xvg[tt] output file that",
+ "[TT]mdrun[tt] produces a [REF].xvg[ref] output file that",
"contains projections of positions, velocities and forces onto selected",
"eigenvectors.[PAR]",
"When user-defined potential functions have been selected in the",
- "[TT].mdp[tt] file the [TT]-table[tt] option is used to pass [TT]mdrun[tt]",
+ "[REF].mdp[ref] file the [TT]-table[tt] option is used to pass [TT]mdrun[tt]",
"a formatted table with potential functions. The file is read from",
"either the current directory or from the [TT]GMXLIB[tt] directory.",
"A number of pre-formatted tables are presented in the [TT]GMXLIB[tt] dir,",
"and finally the table number of the interaction type.[PAR]",
"The options [TT]-px[tt] and [TT]-pf[tt] are used for writing pull COM",
"coordinates and forces when pulling is selected",
- "in the [TT].mdp[tt] file.[PAR]",
+ "in the [REF].mdp[ref] file.[PAR]",
"Finally some experimental algorithms can be tested when the",
"appropriate options have been given. Currently under",
"investigation are: polarizability.",
"A simulation can be continued by reading the full state from file",
"with option [TT]-cpi[tt]. This option is intelligent in the way that",
"if no checkpoint file is found, Gromacs just assumes a normal run and",
- "starts from the first step of the [TT].tpr[tt] file. By default the output",
+ "starts from the first step of the [REF].tpr[ref] file. By default the output",
"will be appending to the existing output files. The checkpoint file",
"contains checksums of all output files, such that you will never",
"loose data when some output files are modified, corrupt or removed.",
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff