{
const char *desc[] = {
"tpbconv can edit run input files in four ways.[PAR]",
- "[BB]1st.[bb] by modifying the number of steps in a run input file",
+ "[BB]1.[bb] by modifying the number of steps in a run input file",
"with options [TT]-extend[tt], [TT]-until[tt] or [TT]-nsteps[tt]",
"(nsteps=-1 means unlimited number of steps)[PAR]",
- "[BB]2nd.[bb] (OBSOLETE) by creating a run input file",
+ "[BB]2.[bb] (OBSOLETE) by creating a run input file",
"for a continuation run when your simulation has crashed due to e.g.",
"a full disk, or by making a continuation run input file.",
"This option is obsolete, since mdrun now writes and reads",
"checkpoint files.",
- "Note that a frame with coordinates and velocities is needed.",
+ "[BB]Note[bb] that a frame with coordinates and velocities is needed.",
"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]3rd.[bb] by creating a tpx file for a subset of your original",
+ "[BB]3.[bb] by creating a tpx file for a subset of your original",
"tpx file, which is useful when you want to remove the solvent from",
"your tpx file, or when you want to make e.g. a pure Ca tpx file.",
- "Note that you may need to use -nsteps -1 (or similar) to get",
+ "Note that you may need to use [TT]-nsteps -1[tt] (or similar) to get",
"this to work.",
"[BB]WARNING: this tpx file is not fully functional[bb].[PAR]",
- "[BB]4th.[bb] by setting the charges of a specified group",
+ "[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."
};
"[TT]-rotate[tt] rotates the coordinates and velocities.",
"[PAR]",
"[TT]-princ[tt] aligns the principal axes of the system along the",
- "coordinate axes, this may allow you to decrease the box volume,",
+ "coordinate axes, with the longest axis aligned with the x axis. ",
+ "This may allow you to decrease the box volume,",
"but beware that molecules can rotate significantly in a nanosecond.",
"[PAR]",
"Scaling is applied before any of the other operations are",
"[TT]-density[tt]). Note that this may be inaccurate in case a gro",
"file is given as input. A special feature of the scaling option, when the",
"factor -1 is given in one dimension, one obtains a mirror image,",
- "mirrored in one of the plains, when one uses -1 in three dimensions",
+ "mirrored in one of the planes. When one uses -1 in three dimensions, ",
"a point-mirror image is obtained.[PAR]",
"Groups are selected after all operations have been applied.[PAR]",
"Periodicity can be removed in a crude manner.",
- "It is important that the box sizes at the bottom of your input file",
+ "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",
"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 -mead a special pdb (pqr) file for the MEAD electrostatics",
+ "With the option [TT]-mead[tt] a special pdb (pqr) 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.",
"The B-factor field is then filled with the Van der Waals radius",
"of the atoms while the occupancy field will hold the charge.",
"[PAR]",
- "The option -grasp is similar, but it puts the charges in the B-factor",
+ "The option [TT]-grasp[tt] is similar, but it puts the charges in the B-factor",
"and the radius in the occupancy.",
"[PAR]",
"Option [TT]-align[tt] allows alignment",
"of the principal axis of a specified group against the given vector, ",
"with an optional center of rotation specified by [TT]-aligncenter[tt].",
"[PAR]",
- "Finally with option [TT]-label[tt] editconf can add a chain identifier",
+ "Finally with option [TT]-label[tt], editconf can add a chain identifier",
"to a pdb file, which can be useful for analysis with e.g. rasmol.",
- "[PAR]",
+ "[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]",
+ "a cubic box with the corners cut off (such as GROMOS), use:[BR]",
"[TT]editconf -f <in> -rotate 0 45 35.264 -bt o -box <veclen> -o <out>[tt][BR]",
"where [TT]veclen[tt] is the size of the cubic box times sqrt(3)/2." };
const char *bugs[] =
"genion replaces solvent molecules by monoatomic ions at",
"the position of the first atoms with the most favorable electrostatic",
"potential or at random. The potential is calculated on all atoms, using",
- "normal GROMACS particle based methods (in contrast to other methods",
+ "normal GROMACS particle-based methods (in contrast to other methods",
"based on solving the Poisson-Boltzmann equation).",
"The potential is recalculated after every ion insertion.",
"If specified in the run input file, a reaction field, shift function",
"in a pdb file (for visualisation using e.g. rasmol).",
"The unit of the potential is 1000 kJ/(mol e), the scaling be changed",
"with the [TT]-scale[tt] option.[PAR]",
- "For larger ions, e.g. sulfate we recommended to use genbox."
+ "For larger ions, e.g. sulfate we recommended using genbox."
};
const char *bugs[] = {
"Calculation of the potential is not reliable, therefore the [TT]-random[tt] option is now turned on by default.",
"in the topology start at 1 and the numbers in the input file for",
"genpr number consecutively from 1, genpr will only produce a useful",
"file for the first molecule.[PAR]",
- "The -of option produces an index file that can be used for",
- "freezing atoms. In this case the input file must be a pdb file.[PAR]",
- "With the [TT]-disre[tt] option half a matrix of distance restraints",
+ "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 pdb 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-alpha atoms in a protein, one can",
"maintain the overall conformation of a protein without tieing it to",
const char *desc[] = {
"g_sham makes multi-dimensional free-energy, enthalpy and entropy plots.",
"g_sham reads one or more xvg files and analyzes data sets.",
- "g_sham basic purpose is plotting Gibbs free energy landscapes",
+ "The basic purpose of g_sham is to plot Gibbs free energy landscapes",
"(option [TT]-ls[tt])",
- "by Bolzmann inverting multi-dimensional histograms (option [TT]-lp[tt])",
+ "by Bolzmann inverting multi-dimensional histograms (option [TT]-lp[tt]),",
"but it can also",
"make enthalpy (option [TT]-lsh[tt]) and entropy (option [TT]-lss[tt])",
"plots. The histograms can be made for any quantities the user supplies.",
"[PAR]",
"Option [TT]-ene[tt] can be used to supply a file with energies.",
"These energies are used as a weighting function in the single",
- "histogram analysis method due to Kumar et. al. When also temperatures",
- "are supplied (as a second column in the file) an experimental",
+ "histogram analysis method by Kumar et. al. When temperatures",
+ "are supplied (as a second column in the file), an experimental",
"weighting scheme is applied. In addition the vales",
"are used for making enthalpy and entropy plots.",
"[PAR]",
- "With option [TT]-dim[tt] dimensions can be gives for distances.",
+ "With option [TT]-dim[tt], dimensions can be gives for distances.",
"When a distance is 2- or 3-dimensional, the circumference or surface",
"sampled by two particles increases with increasing distance.",
"Depending on what one would like to show, one can choose to correct",
"respectively.",
"A value of -1 is used to indicate an angle in degrees between two",
"vectors: a sin(angle) normalization will be applied.",
- "Note that for angles between vectors the inner-product or cosine",
+ "[BB]Note[bb] that for angles between vectors the inner-product or cosine",
"is the natural quantity to use, as it will produce bins of the same",
"volume."
};
"In case of double time frames the one in the later file is used. ",
"By specifying [TT]-settime[tt] you will be asked for the start time ",
"of each file. The input files are taken from the command line, ",
- "such that a command like [TT]trjcat -o fixed.trr *.trr[tt] should do ",
- "the trick. Using [TT]-cat[tt] you can simply paste several files ",
+ "such that a command like [TT]trjcat -f *.trr -o fixed.trr[tt] should do ",
+ "the trick. Using [TT]-cat[tt], you can simply paste several files ",
"together without removal of frames with identical time stamps.[PAR]",
"One important option is inferred when the output file is amongst the",
"input files. In that case that particular file will be appended to",
"If the [TT]-demux[tt] option is given, the N trajectories that are",
"read, are written in another order as specified in the xvg file.",
"The xvg file should contain something like:[PAR]",
- "0 0 1 2 3 4 5[BR]",
- "2 1 0 2 3 5 4[BR]",
+ "[TT]0 0 1 2 3 4 5[BR]",
+ "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",
"([TT]-t0[tt] and [TT]-timestep[tt])[BR]",
"[BB]9.[bb] cut the trajectory in small subtrajectories according",
"to information in an index file. This allows subsequent analysis of",
- "the subtrajectories that could, for example be the result of a",
+ "the subtrajectories that could, for example, be the result of a",
"cluster analysis. Use option [TT]-sub[tt].",
"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]",
"[BB]10.[bb] select frames within a certain range of a quantity given",
"in an [TT].xvg[tt] file.[PAR]",
- "The program [TT]trjcat[tt] can concatenate multiple trajectory files.",
+ "The program [TT]trjcat[tt] is better suited for concatenating multiple trajectory files.",
"[PAR]",
"Currently seven formats are supported for input and output:",
"[TT].xtc[tt], [TT].trr[tt], [TT].trj[tt], [TT].gro[tt], [TT].g96[tt],",
"No checks are performed to ensure integrity",
"of the resulting combined trajectory file.[PAR]",
"Option [TT]-sep[tt] can be used to write every frame to a separate",
- ".gro, .g96 or .pdb file, default all frames all written to one file.",
+ "[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]rasmol -nmrpdb[tt].[PAR]",
"It is possible to select part of your trajectory and write it out",
"We recommend to use the portable [TT].xtc[tt] 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",
- "either for essential dynamics analysis or for whatever.",
+ "either for essential dynamics analysis, etc.",
"The first option is just plain fitting to a reference structure",
- "in the structure file, the second option is a progressive fit",
+ "in the structure file. The second option is a progressive fit",
"in which the first timeframe is fitted to the reference structure ",
"in the structure file to obtain and each subsequent timeframe is ",
"fitted to the previously fitted structure. This way a continuous",
"conformational transitions.[PAR]",
"Option [TT]-pbc[tt] sets the type of periodic boundary condition",
"treatment:[BR]",
- "* [TT]mol[tt] puts the center of mass of molecules in the box.[BR]",
- "* [TT]res[tt] puts the center of mass of residues in the box.[BR]",
- "* [TT]atom[tt] puts all the atoms in the box.[BR]",
- "* [TT]nojump[tt] checks if atoms jump across the box and then puts",
+ "[TT]* mol[tt] puts the center of mass of molecules in the box.[BR]",
+ "[TT]* res[tt] puts the center of mass of residues in the box.[BR]",
+ "[TT]* atom[tt] puts all the atoms in the box.[BR]",
+ "[TT]* nojump[tt] checks if atoms jump across the box and then puts",
"them back. This has the effect that all molecules",
"will remain whole (provided they were whole in the initial",
- "conformation), note that this ensures a continuous trajectory but",
+ "conformation). [BB]Note[bb] that this ensures a continuous trajectory but",
"molecules may diffuse out of the box. The starting configuration",
"for this procedure is taken from the structure file, if one is",
"supplied, otherwise it is the first frame.[BR]",
- "* [TT]cluster[tt] clusters all the atoms in the selected index",
- "such that they are all closest to the center of mass of the cluster",
- "which is iteratively updated. Note that this will only give meaningful",
+ "[TT]* cluster[tt] clusters all the atoms in the selected index",
+ "such that they are all closest to the center of mass of the cluster,",
+ "which is iteratively updated. [BB]Note[bb] that this will only give meaningful",
"results if you in fact have a cluster. Luckily that can be checked",
"afterwards using a trajectory viewer. Note also that if your molecules",
"are broken this will not work either.[BR]",
- "* [TT]whole[tt] only makes broken molecules whole.[PAR]",
+ "[TT]* whole[tt] only makes broken molecules whole.[PAR]",
"Option [TT]-ur[tt] sets the unit cell representation for options",
"[TT]mol[tt], [TT]res[tt] and [TT]atom[tt] of [TT]-pbc[tt].",
"All three options give different results for triclinic boxes and",
"[TT]tric[tt] is the triclinic unit cell.",
"[TT]compact[tt] puts all atoms at the closest distance from the center",
"of the box. This can be useful for visualizing e.g. truncated",
- "octahedrons. The center for options [TT]tric[tt] and [TT]compact[tt]",
+ "octahedra. The center for options [TT]tric[tt] and [TT]compact[tt]",
"is [TT]tric[tt] (see below), unless the option [TT]-boxcenter[tt]",
"is set differently.[PAR]",
"Option [TT]-center[tt] centers the system in the box. The user can",
"[TT]zero[tt]: zero.",
"Use option [TT]-pbc mol[tt] in addition to [TT]-center[tt] when you",
"want all molecules in the box after the centering.[PAR]",
- "With [TT]-dt[tt] it is possible to reduce the number of ",
+ "With [TT]-dt[tt], it is possible to reduce the number of ",
"frames in the output. This option relies on the accuracy of the times",
"in your input trajectory, so if these are inaccurate use the",
"[TT]-timestep[tt] option to modify the time (this can be done",
- "simultaneously). For making smooth movies the program [TT]g_filter[tt]",
+ "simultaneously). For making smooth movies, the program [TT]g_filter[tt]",
"can reduce the number of frames while using low-pass frequency",
"filtering, this reduces aliasing of high frequency motions.[PAR]",
"Using [TT]-trunc[tt] trjconv can truncate [TT].trj[tt] in place, i.e.",
"without copying the file. This is useful when a run has crashed",
- "during disk I/O (one more disk full), or when two contiguous",
- "trajectories must be concatenated without have double frames.[PAR]",
- "[TT]trjcat[tt] is more suitable for concatenating trajectory files.[PAR]",
+ "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.",
"titlefont -> legendfont; titlefont -> (xfont -> yfont -> ytickfont)",
"-> xtickfont, e.g. setting titlefont sets all fonts, setting xfont",
"sets yfont, ytickfont and xtickfont.[PAR]",
- "When no [TT]m2p[tt] file is supplied, many setting are set by",
- "command line options. The most important option is [TT]-size[tt]",
+ "When no [TT]m2p[tt] file is supplied, many settings are taken from",
+ "command line options. The most important option is [TT]-size[tt],",
"which sets the size of the whole matrix in postscript units.",
"This option can be overridden with the [TT]-bx[tt] and [TT]-by[tt]",
"options (and the corresponding parameters in the [TT]m2p[tt] file),",
"which set the size of a single matrix element.[PAR]",
- "With [TT]-f2[tt] a 2nd matrix file can be supplied, both matrix",
+ "With [TT]-f2[tt] a second matrix file can be supplied. Both matrix",
"files will be read simultaneously and the upper left half of the",
"first one ([TT]-f[tt]) is plotted together with the lower right",
"half of the second one ([TT]-f2[tt]). The diagonal will contain",
"If the color coding and legend labels of both matrices are identical,",
"only one legend will be displayed, else two separate legends are",
"displayed.",
- "With [TT]-combine[tt] an alternative operation can be selected",
+ "With [TT]-combine[tt], an alternative operation can be selected",
"to combine the matrices. The output range is automatically set",
"to the actual range of the combined matrix. This can be overridden",
"with [TT]-cmin[tt] and [TT]-cmax[tt].[PAR]",
"[TT]-title[tt] can be set to [TT]none[tt] to suppress the title, or to",
"[TT]ylabel[tt] to show the title in the Y-label position (alongside",
"the Y-axis).[PAR]",
- "With the [TT]-rainbow[tt] option dull grey-scale matrices can be turned",
+ "With the [TT]-rainbow[tt] option, dull grayscale matrices can be turned",
"into attractive color pictures.[PAR]",
"Merged or rainbowed matrices can be written to an XPixelMap file with",
"the [TT]-xpm[tt] option."
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff