{ "[BR]", "\\\\" },
{ "%", "\\%" },
{ "&", "\\&" },
+ /* The next couple of lines allow true Greek symbols to be written to the
+ manual, which makes it look pretty */
+ { "[GRK]", "$\\" },
+ { "[grk]", "$" },
/* The next two lines used to substitute "|" and "||" to "or", but only
* g_angle used that functionality, so that was changed to a textual
* "or" there, so that other places could use those symbols to indicate
{ "[IT]", "" },
{ "[it]", "" },
{ "[PAR]","\n\n" },
- { "[BR]", "\n"}
+ { "[BR]", "\n"},
+ { "[GRK]", "" },
+ { "[grk]", "" }
};
#define NSRTTY asize(sandrTty)
{ "[IT]", "<it>" },
{ "[it]", "</it>" },
{ "[PAR]","<p>" },
- { "[BR]", "<br>" }
+ { "[BR]", "<br>" },
+ { "[GRK]", "&" },
+ { "[grk]", ";" }
};
#define NSRHTML asize(sandrHTML)
"[TT]g_protonate[tt] 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",
+ "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",
"G53a5 GROMOS96 53a5 Forcefield (official distribution)[PAR]",
"oplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)[PAR]",
"The corresponding data files can be found in the library directory",
- "with name atomname2type.n2t. Check chapter 5 of the manual for more",
- "information about file formats. By default the forcefield selection",
+ "with name [TT]atomname2type.n2t[tt]. Check Chapter 5 of the manual for more",
+ "information about file formats. By default, the force field selection",
"is interactive, but you can use the [TT]-ff[tt] option to specify",
"one of the short names above on the command line instead. In that",
- "case [TT]pdb2gmx[tt] just looks for the corresponding file.[PAR]",
+ "case [TT]g_x2top[tt] just looks for the corresponding file.[PAR]",
};
const char *bugs[] = {
"The atom type selection is primitive. Virtually no chemical knowledge is used",
"Periodic boundary conditions screw up the bonding",
"No improper dihedrals are generated",
- "The atoms to atomtype translation table is incomplete (atomname2type.n2t files in the data directory). Please extend it and send the results back to the GROMACS crew."
+ "The atoms to atomtype translation table is incomplete ([TT]atomname2type.n2t[tt] file in the data directory). Please extend it and send the results back to the GROMACS crew."
};
FILE *fp;
t_params plist[F_NRE];
"only the atom types are used for generating interaction parameters.[PAR]",
"[TT]grompp[tt] uses a built-in preprocessor to resolve includes, macros, ",
- "etc. The preprocessor supports the following keywords:[BR]",
+ "etc. The preprocessor supports the following keywords:[PAR]",
"#ifdef VARIABLE[BR]",
"#ifndef VARIABLE[BR]",
"#else[BR]",
"#define VARIABLE[BR]",
"#undef VARIABLE[BR]"
"#include \"filename\"[BR]",
- "#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:[BR]",
- "define = -DVARIABLE1 -DVARIABLE2[BR]",
- "include = -I/home/john/doe[BR]",
+ "using the following two flags in your [TT].mdp[tt] file:[PAR]",
+ "[TT]define = -DVARIABLE1 -DVARIABLE2[BR]",
+ "include = -I/home/john/doe[tt][BR]",
"For further information a C-programming textbook may help you out.",
"Specifying the [TT]-pp[tt] flag will get the pre-processed",
"topology file written out so that you can verify its contents.[PAR]",
-
- "If your system does not have a c-preprocessor, you can still",
- "use [TT]grompp[tt], but you do not have access to the features ",
- "from the cpp. Command line options to the c-preprocessor can be given",
- "in the [TT].mdp[tt] file. See your local manual (man cpp).[PAR]",
+
+ /* cpp has been unnecessary for some time, hasn't it?
+ "If your system does not have a C-preprocessor, you can still",
+ "use [TT]grompp[tt], but you do not have access to the features ",
+ "from the cpp. Command line options to the C-preprocessor can be given",
+ "in the [TT].mdp[tt] file. See your local manual (man cpp).[PAR]",
+ */
"When using position restraints a file with restraint coordinates",
"can be supplied with [TT]-r[tt], otherwise restraining will be done",
"[TT]-e[tt] to read Nose-Hoover and/or Parrinello-Rahman coupling",
"variables.[PAR]",
- "[TT]grompp[tt] can be used to restart simulations preserving",
- "continuity by supplying just a checkpoint file with [TT]-t[tt].",
+ "[TT]grompp[tt] can be used to restart simulations (preserving",
+ "continuity) by supplying just a checkpoint file with [TT]-t[tt].",
"However, for simply changing the number of run steps to extend",
"a run, using [TT]tpbconv[tt] is more convenient than [TT]grompp[tt].",
"You then supply the old checkpoint file directly to [TT]mdrun[tt]",
"of virtual site constructions will be removed. If any constraints remain",
"which involve virtual sites, a fatal error will result.[PAR]"
- "To verify your run input file, please make notice of all warnings",
+ "To verify your run input file, please take note of all warnings",
"on the screen, and correct where necessary. Do also look at the contents",
- "of the [TT]mdout.mdp[tt] file, this contains comment lines, as well as",
- "the input that [TT]grompp[tt] has read. If in doubt you can start grompp",
+ "of the [TT]mdout.mdp[tt] file; this contains comment lines, as well as",
+ "the input that [TT]grompp[tt] has read. If in doubt, you can start [TT]grompp[tt]",
"with the [TT]-debug[tt] option which will give you more information",
"in a file called [TT]grompp.log[tt] (along with real debug info). You",
"can see the contents of the run input file with the [TT]gmxdump[tt]",
"(the simulation will run correctly also when this is not the case).",
"[PAR]",
"This section lists all options that affect the domain decomposition.",
- "[BR]",
+ "[PAR]",
"Option [TT]-rdd[tt] can be used to set the required maximum distance",
"for inter charge-group bonded interactions.",
"Communication for two-body bonded interactions below the non-bonded",
"By default [TT]-rdd[tt] is determined by [TT]mdrun[tt] based on",
"the initial coordinates. The chosen value will be a balance",
"between interaction range and communication cost.",
- "[BR]",
+ "[PAR]",
"When inter charge-group bonded interactions are beyond",
"the bonded cut-off distance, [TT]mdrun[tt] terminates with an error message.",
"For pair interactions and tabulated bonds",
"that do not generate exclusions, this check can be turned off",
"with the option [TT]-noddcheck[tt].",
- "[BR]",
+ "[PAR]",
"When constraints are present, option [TT]-rcon[tt] influences",
"the cell size limit as well.",
"Atoms connected by NC constraints, where NC is the LINCS order plus 1,",
"By default [TT]mdrun[tt] estimates the minimum cell size required for P-LINCS",
"in a conservative fashion. For high parallelization it can be useful",
"to set the distance required for P-LINCS with the option [TT]-rcon[tt].",
- "[BR]",
+ "[PAR]",
"The [TT]-dds[tt] option sets the minimum allowed x, y and/or z scaling",
"of the cells with dynamic load balancing. [TT]mdrun[tt] will ensure that",
"the cells can scale down by at least this factor. This option is used",
"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]",
"a formatted table with potential functions. The file is read from",
- "either the current directory or from the GMXLIB directory.",
- "A number of pre-formatted tables are presented in the GMXLIB dir,",
- "for 6-8, 6-9, 6-10, 6-11, 6-12 Lennard Jones potentials with",
+ "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,",
+ "for 6-8, 6-9, 6-10, 6-11, 6-12 Lennard-Jones potentials with",
"normal Coulomb.",
- "When pair interactions are present a separate table for pair interaction",
+ "When pair interactions are present, a separate table for pair interaction",
"functions is read using the [TT]-tablep[tt] option.[PAR]",
"When tabulated bonded functions are present in the topology,",
"interaction functions are read using the [TT]-tableb[tt] option.",
"For each different tabulated interaction type the table file name is",
"modified in a different way: before the file extension an underscore is",
- "appended, then a b for bonds, an a for angles or a d for dihedrals",
+ "appended, then a 'b' for bonds, an 'a' for angles or a 'd' for dihedrals",
"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",
"is performed after every exchange.[PAR]",
"Finally some experimental algorithms can be tested when the",
"appropriate options have been given. Currently under",
- "investigation are: polarizability, and X-Ray bombardments.",
+ "investigation are: polarizability and X-ray bombardments.",
"[PAR]",
"The option [TT]-pforce[tt] is useful when you suspect a simulation",
"crashes due to too large forces. With this option coordinates and",
"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.",
- "There are three scenarios with [TT]-cpi[tt]:[BR]",
- "* no files with matching names are present: new output files are written[BR]",
- "* all files are present with names and checksums matching those stored",
- "in the checkpoint file: files are appended[BR]",
- "* otherwise no files are modified and a fatal error is generated[BR]",
+ "There are three scenarios with [TT]-cpi[tt]:[PAR]",
+ "[TT]*[tt] no files with matching names are present: new output files are written[PAR]",
+ "[TT]*[tt] all files are present with names and checksums matching those stored",
+ "in the checkpoint file: files are appended[PAR]",
+ "[TT]*[tt] otherwise no files are modified and a fatal error is generated[PAR]",
"With [TT]-noappend[tt] new output files are opened and the simulation",
"part number is added to all output file names.",
"Note that in all cases the checkpoint file itself is not renamed",
const char *desc[] = {
"This program reads a [TT].pdb[tt] (or [TT].gro[tt]) file, reads",
"some database files, adds hydrogens to the molecules and generates",
- "coordinates in Gromacs (Gromos), or optionally [TT].pdb[tt], format",
- "and a topology in Gromacs format.",
+ "coordinates in GROMACS (GROMOS), or optionally [TT].pdb[tt], format",
+ "and a topology in GROMACS format.",
"These files can subsequently be processed to generate a run input file.",
"[PAR]",
"[TT]pdb2gmx[tt] will search for force fields by looking for",
"you will need to modify [TT]residuetypes.dat[tt] in the library directory",
"or copy the whole library directory to a local directory and set",
"the environment variable [TT]GMXLIB[tt] to the name of that directory.",
- "Check chapter 5 of the manual for more information about file formats.",
+ "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",
"if you want a disulfide bridge or distance restraints between",
"two protein chains or if you have a HEME group bound to a protein.",
"In such cases multiple chains should be contained in a single",
- "[TT]molecule_type[tt] definition.",
+ "[TT]moleculetype[tt] definition.",
"To handle this, [TT]pdb2gmx[tt] has an option [TT]-chainsep[tt] so you can",
"choose whether a new chain should start when we find a TER record,",
"when the chain id changes, combinations of either or both of these",
"[TT]pdb2gmx[tt] will also check the occupancy field of the [TT].pdb[tt] 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 [TT].pdb[tt] 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]",
- "During processing the atoms will be reordered according to Gromacs",
+ "During processing the atoms will be reordered according to GROMACS",
"conventions. With [TT]-n[tt] an index file can be generated that",
"contains one group reordered in the same way. This allows you to",
- "convert a Gromos trajectory and coordinate file to Gromos. There is",
+ "convert a GROMOS trajectory and coordinate file to GROMOS. There is",
"one limitation: reordering is done after the hydrogens are stripped",
"from the input and before new hydrogens are added. This means that",
"you should not use [TT]-ignh[tt].[PAR]",
"position relative to neighboring atoms. Additionally, all atoms in the",
"aromatic rings of the standard amino acids (i.e. PHE, TRP, TYR and HIS)",
"can be converted into virtual sites, eliminating the fast improper dihedral",
- "fluctuations in these rings. Note that in this case all other hydrogen",
+ "fluctuations in these rings. [BB]Note[bb] that in this case all other hydrogen",
"atoms are also converted to virtual sites. The mass of all atoms that are",
"converted into virtual sites, is added to the heavy atoms.[PAR]",
"Also slowing down of dihedral motion can be done with [TT]-heavyh[tt]",
{ "-ter", FALSE, etBOOL, {&bTerMan},
"Interactive termini selection, iso charged" },
{ "-lys", FALSE, etBOOL, {&bLysMan},
- "Interactive Lysine selection, iso charged" },
+ "Interactive lysine selection, iso charged" },
{ "-arg", FALSE, etBOOL, {&bArgMan},
- "Interactive Arganine selection, iso charged" },
+ "Interactive arginine selection, iso charged" },
{ "-asp", FALSE, etBOOL, {&bAspMan},
- "Interactive Aspartic Acid selection, iso charged" },
+ "Interactive aspartic Acid selection, iso charged" },
{ "-glu", FALSE, etBOOL, {&bGluMan},
- "Interactive Glutamic Acid selection, iso charged" },
+ "Interactive glutamic Acid selection, iso charged" },
{ "-gln", FALSE, etBOOL, {&bGlnMan},
- "Interactive Glutamine selection, iso neutral" },
+ "Interactive glutamine selection, iso neutral" },
{ "-his", FALSE, etBOOL, {&bHisMan},
- "Interactive Histidine selection, iso checking H-bonds" },
+ "Interactive histidine selection, iso checking H-bonds" },
{ "-angle", FALSE, etREAL, {&angle},
"Minimum hydrogen-donor-acceptor angle for a H-bond (degrees)" },
{ "-dist", FALSE, etREAL, {&distance},
"Maximum donor-acceptor distance for a H-bond (nm)" },
{ "-una", FALSE, etBOOL, {&bUnA},
- "Select aromatic rings with united CH atoms on Phenylalanine, "
- "Tryptophane and Tyrosine" },
+ "Select aromatic rings with united CH atoms on phenylalanine, "
+ "tryptophane and tyrosine" },
{ "-sort", FALSE, etBOOL, {&bSort},
"HIDDENSort the residues according to database, turning this off is dangerous as charge groups might be broken in parts" },
{ "-ignh", FALSE, etBOOL, {&bRemoveH},
"of the original run.[PAR]",
"[BB]3.[bb] by creating a [TT].tpx[tt] 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 Ca [TT].tpx[tt] file.",
+ "your [TT].tpx[tt] file, or when you want to make e.g. a pure C[GRK]alpha[grk] [TT].tpx[tt] 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]",
int main(int argc, char *argv[])
{
const char *desc[] = {
- "[TT]ngmx[tt] is the Gromacs trajectory viewer. This program reads a",
+ "[TT]ngmx[tt] is the GROMACS trajectory viewer. This program reads a",
"trajectory file, a run input file and an index file and plots a",
"3D structure of your molecule on your standard X Window",
"screen. No need for a high end graphics workstation, it even",
"runs on MIT-X (real X), open windows and motif,",
"user friendly menus, option to remove periodicity, option to",
"show computational box.[PAR]",
- "Some of the more common X command line options can be used:[BR]",
- "[TT]-bg[tt], [TT]-fg[tt] change colors, [TT]-font[tt] fontname, changes the font."
+ "Some of the more common X command line options can be used: ",
+ "[TT]-bg[tt], [TT]-fg[tt] change colors, [TT]-font fontname[tt] changes the font."
};
const char *bugs[] = {
"Balls option does not work",
"reads a trajectory file and computes the secondary structure for",
"each time frame ",
"calling the dssp program. If you do not have the dssp program,",
- "get it. [TT]do_dssp[tt] assumes that the dssp executable is",
- "/usr/local/bin/dssp. If this is not the case, then you should",
+ "get it from http://swift.cmbi.ru.nl/gv/dssp. [TT]do_dssp[tt] assumes ",
+ "that the dssp executable is located in ",
+ "[TT]/usr/local/bin/dssp[tt]. If this is not the case, then you should",
"set an environment variable [TT]DSSP[tt] pointing to the dssp",
"executable, e.g.: [PAR]",
"[TT]setenv DSSP /opt/dssp/bin/dssp[tt][PAR]",
int main(int argc,char *argv[])
{
const char *desc[] = {
- "[TT]g_sigeps[tt] is a simple utility that converts c6/c12 or c6/cn combinations",
- "to sigma and epsilon, or vice versa. It can also plot the potential",
- "in file. In addition it makes an approximation of a Buckingham potential",
- "to a Lennard Jones potential."
+ "[TT]g_sigeps[tt] is a simple utility that converts C6/C12 or C6/Cn combinations",
+ "to [GRK]sigma[grk] and [GRK]epsilon[grk], or vice versa. It can also plot the potential",
+ "in file. In addition, it makes an approximation of a Buckingham potential",
+ "to a Lennard-Jones potential."
};
static real c6=1.0e-3,cn=1.0e-6,qi=0,qj=0,sig=0.3,eps=1,sigfac=0.7;
static real Abh=1e5,Bbh=32,Cbh=1e-3;
"can use [TT]rasmol -nmrpdb[tt] to view such a [TT].pdb[tt] file).[PAR]",
" Overlap calculations between covariance analysis:[BR]",
- " NOTE: the analysis should use the same fitting structure[PAR]",
+ " [BB]Note:[bb] the analysis should use the same fitting structure[PAR]",
"[TT]-over[tt]: calculate the subspace overlap of the eigenvectors in",
"file [TT]-v2[tt] with eigenvectors [TT]-first[tt] to [TT]-last[tt]",
int gmx_analyze(int argc,char *argv[])
{
static const char *desc[] = {
- "[TT]g_analyze[tt] reads an ascii file and analyzes data sets.",
+ "[TT]g_analyze[tt] reads an ASCII file and analyzes data sets.",
"A line in the input file may start with a time",
- "(see option [TT]-time[tt]) and any number of y values may follow.",
+ "(see option [TT]-time[tt]) and any number of [IT]y[it]-values may follow.",
"Multiple sets can also be",
- "read when they are separated by & (option [TT]-n[tt]),",
- "in this case only one y value is read from each line.",
+ "read when they are separated by & (option [TT]-n[tt]);",
+ "in this case only one [IT]y[it]-value is read from each line.",
"All lines starting with # and @ are skipped.",
"All analyses can also be done for the derivative of a set",
"(option [TT]-d[tt]).[PAR]",
- "All options, except for [TT]-av[tt] and [TT]-power[tt] assume that the",
+ "All options, except for [TT]-av[tt] and [TT]-power[tt], assume that the",
"points are equidistant in time.[PAR]",
"[TT]g_analyze[tt] always shows the average and standard deviation of each",
- "set. For each set it also shows the relative deviation of the third",
+ "set, as well as the relative deviation of the third",
"and fourth cumulant from those of a Gaussian distribution with the same",
"standard deviation.[PAR]",
"Option [TT]-cc[tt] plots the resemblance of set i with a cosine of",
"i/2 periods. The formula is:[BR]"
- "2 (int0-T y(t) cos(i pi t) dt)^2 / int0-T y(t) y(t) dt[BR]",
+ "2 (int0-T y(t) cos(i [GRK]pi[grk] t) dt)^2 / int0-T y(t) y(t) dt[BR]",
"This is useful for principal components obtained from covariance",
"analysis, since the principal components of random diffusion are",
"pure cosines.[PAR]",
"Also an analytical block average curve is plotted, assuming",
"that the autocorrelation is a sum of two exponentials.",
"The analytical curve for the block average is:[BR]",
- "f(t) = sigma sqrt(2/T ( a (tau1 ((exp(-t/tau1) - 1) tau1/t + 1)) +[BR]",
- " (1-a) (tau2 ((exp(-t/tau2) - 1) tau2/t + 1)))),[BR]"
+ "f(t) = [GRK]sigma[grk][TT]*[tt]sqrt(2/T ( [GRK]alpha[grk] ([GRK]tau[grk]1 ((exp(-t/[GRK]tau[grk]1) - 1) [GRK]tau[grk]1/t + 1)) +[BR]",
+ " (1-[GRK]alpha[grk]) ([GRK]tau[grk]2 ((exp(-t/[GRK]tau[grk]2) - 1) [GRK]tau[grk]2/t + 1)))),[BR]"
"where T is the total time.",
- "a, tau1 and tau2 are obtained by fitting f^2(t) to error^2.",
+ "[GRK]alpha[grk], [GRK]tau[grk]1 and [GRK]tau[grk]2 are obtained by fitting f^2(t) to error^2.",
"When the actual block average is very close to the analytical curve,",
- "the error is sigma*sqrt(2/T (a tau1 + (1-a) tau2)).",
+ "the error is [GRK]sigma[grk][TT]*[tt]sqrt(2/T (a [GRK]tau[grk]1 + (1-a) [GRK]tau[grk]2)).",
"The complete derivation is given in",
"B. Hess, J. Chem. Phys. 116:209-217, 2002.[PAR]",
"Option [TT]-filter[tt] prints the RMS high-frequency fluctuation",
"of each set and over all sets with respect to a filtered average.",
- "The filter is proportional to cos(pi t/len) where t goes from -len/2",
+ "The filter is proportional to cos([GRK]pi[grk] t/len) where t goes from -len/2",
"to len/2. len is supplied with the option [TT]-filter[tt].",
"This filter reduces oscillations with period len/2 and len by a factor",
"of 0.79 and 0.33 respectively.[PAR]",
"Option [TT]-power[tt] fits the data to b t^a, which is accomplished",
"by fitting to a t + b on log-log scale. All points after the first",
- "zero or negative value are ignored.[PAR]"
+ "zero or with a negative value are ignored.[PAR]"
"Option [TT]-luzar[tt] performs a Luzar & Chandler kinetics analysis",
"on output from [TT]g_hbond[tt]. The input file can be taken directly",
{ "-xydy", FALSE, etBOOL, {&bXYdy},
"Interpret second data set as error in the y values for integrating" },
{ "-regression",FALSE,etBOOL,{&bRegression},
- "Perform a linear regression analysis on the data. If [TT]-xydy[tt] is set a second set will be interpreted as the error bar in the Y value. Otherwise, if multiple data sets are present a multilinear regression will be performed yielding the constant A that minimize chi^2 = (y - A0 x0 - A1 x1 - ... - AN xN)^2 where now Y is the first data set in the input file and xi the others. Do read the information at the option [TT]-time[tt]." },
+ "Perform a linear regression analysis on the data. If [TT]-xydy[tt] is set a second set will be interpreted as the error bar in the Y value. Otherwise, if multiple data sets are present a multilinear regression will be performed yielding the constant A that minimize [GRK]chi[grk]^2 = (y - A0 x0 - A1 x1 - ... - AN xN)^2 where now Y is the first data set in the input file and xi the others. Do read the information at the option [TT]-time[tt]." },
{ "-luzar", FALSE, etBOOL, {&bLuzar},
"Do a Luzar and Chandler analysis on a correlation function and related as produced by [TT]g_hbond[tt]. When in addition the [TT]-xydy[tt] flag is given the second and fourth column will be interpreted as errors in c(t) and n(t)." },
{ "-temp", FALSE, etREAL, {&temp},
{ "-fitend", FALSE, etREAL, {&fit_end},
"Time (ps) where to stop fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation. Only with [TT]-gem[tt]" },
{ "-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/tau)" },
+ "If >= 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(-x/[GRK]tau[grk])" },
{ "-nbmin", FALSE, etINT, {&nb_min},
"HIDDENMinimum number of blocks for block averaging" },
{ "-resol", FALSE, etINT, {&resol},
"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",
+ "controlled by a parameter, [GRK]lambda[grk] (see the [TT].mdp[tt] 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",
+ "vice versa. If the Hamiltonian does not depend linearly on [GRK]lambda[grk]",
"(in which case we can extrapolate the derivative of the Hamiltonian",
- "with respect to lambda, as is the default when [TT]free_energy[tt] is on),",
+ "with respect to [GRK]lambda[grk], 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 [TT]foreign_lambda[tt].[PAR]",
+ "the [TT].mdp[tt] option [TT]foreign_lambda[tt].[PAR]",
- "Input option [TT]-f[tt] expects multiple dhdl files. ",
+ "Input option [TT]-f[tt] expects multiple [TT]dhdl.xvg[tt] files. ",
"Two types of input files are supported:[BR]",
- "[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",
+ "[TT]*[tt] Files with only one [IT]y[it]-value, for such files it is assumed ",
+ " that the [IT]y[it]-value is dH/d[GRK]lambda[grk] and that the Hamiltonian depends ",
+ " linearly on [GRK]lambda[grk]. The [GRK]lambda[grk] value of the simulation is inferred ",
+ " from the subtitle (if present), otherwise from a number in the",
" subdirectory in the file name.",
"[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 lambdas from the legend ",
+ "[TT]*[tt] Files with more than one [IT]y[it]-value. The files should have columns ",
+ " with dH/d[GRK]lambda[grk] and [GRK]Delta[grk][GRK]lambda[grk]. The [GRK]lambda[grk] values are inferred ",
+ " from the legends: [GRK]lambda[grk] of the simulation from the legend of dH/d[GRK]lambda[grk] ",
+ " and the foreign [GRK]lambda[grk] values from the legends of Delta H.[PAR]",
+ "The [GRK]lambda[grk] of the simulation is parsed from [TT]dhdl.xvg[tt] file's legend ",
+ "containing the string 'dH', the foreign [GRK]lambda[grk] values 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. ",
+ "The input option [TT]-g[tt] expects multiple [TT].edr[tt] 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 [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]"
+ "[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 [TT]dh_hist_spacing[tt]).",
+ "The temperature and [GRK]lambda[grk] values are automatically deduced from",
+ "the [TT]ener.edr[tt] file.[PAR]"
"The free energy estimates are determined using BAR with bisection, ",
- "the precision of the output is set with [TT]-prec[tt]. ",
+ "with the precision of the output set with [TT]-prec[tt]. ",
"An error estimate taking into account time correlations ",
"is made by splitting the data into blocks and determining ",
"the free energy differences over those blocks and assuming ",
"the blocks are independent. ",
"The final error estimate is determined from the average variance ",
- "over 5 blocks. A range of blocks numbers for error estimation can ",
+ "over 5 blocks. A range of block numbers for error estimation can ",
"be provided with the options [TT]-nbmin[tt] and [TT]-nbmax[tt].[PAR]",
"[TT]g_bar[tt] tries to aggregate samples with the same 'native' and 'foreign'",
- "lambda values, but always assumes independent samples: note that",
+ "[GRK]lambda[grk] values, but always assumes independent samples. [BB]Note[bb] that",
"when aggregating energy differences/derivatives with different",
- "sampling intervals, this is almost certainly not correct: usually",
+ "sampling intervals, this is almost certainly not correct. Usually",
"subsequent energies are correlated and different time intervals mean",
"different degrees of correlation between samples.[PAR]",
"difference estimates and phase space overlap measures in units of ",
"kT (together with their computed error estimate). The printed ",
"values are:[BR]",
- "[TT]*[tt] lam_A: the lambda values for point A.[BR]",
- "[TT]*[tt] lam_B: the lambda values for point B.[BR]",
+ "[TT]*[tt] lam_A: the [GRK]lambda[grk] values for point A.[BR]",
+ "[TT]*[tt] lam_B: the [GRK]lambda[grk] 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]",
"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",
- "to the axis numbers. When viewing this file with [TT]rasmol[tt], use the",
+ "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."
};
{ "-na", FALSE, etINT, {&n},
"Number of axes" },
{ "-z", FALSE, etBOOL, {&bZ},
- "Use the Z-axis as reference iso the average axis" }
+ "Use the [IT]z[it]-axis as reference instead of the average axis" }
};
FILE *out,*flen,*fdist,*fz,*ftilt,*ftiltr,*ftiltl;
FILE *fkink=NULL,*fkinkr=NULL,*fkinkl=NULL;
int gmx_chi(int argc,char *argv[])
{
const char *desc[] = {
- "[TT]g_chi[tt] computes phi, psi, omega and chi dihedrals for all your ",
+ "[TT]g_chi[tt] computes [GRK]phi[grk], [GRK]psi[grk], [GRK]omega[grk], and [GRK]chi[grk] dihedrals for all your ",
"amino acid backbone and sidechains.",
"It can compute dihedral angle as a function of time, and as",
"histogram distributions.",
"The distributions [TT](histo-(dihedral)(RESIDUE).xvg[tt]) are cumulative over all residues of each type.[PAR]",
"If option [TT]-corr[tt] is given, the program will",
"calculate dihedral autocorrelation functions. The function used",
- "is C(t) = < cos(chi(tau)) cos(chi(tau+t)) >. The use of cosines",
+ "is C(t) = < cos([GRK]chi[grk]([GRK]tau[grk])) cos([GRK]chi[grk]([GRK]tau[grk]+t)) >. The use of cosines",
"rather than angles themselves, resolves the problem of periodicity.",
"(Van der Spoel & Berendsen (1997), Biophys. J. 72, 2032-2041).",
"Separate files for each dihedral of each residue",
"These can be in radians or degrees.[PAR]",
"A log file (argument [TT]-g[tt]) is also written. This contains [BR]",
"(a) information about the number of residues of each type.[BR]",
- "(b) The NMR 3J coupling constants from the Karplus equation.[BR]",
+ "(b) The NMR ^3J coupling constants from the Karplus equation.[BR]",
"(c) a table for each residue of the number of transitions between ",
- "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 ",
+ "rotamers per nanosecond, and the order parameter S^2 of each dihedral.[BR]",
+ "(d) a table for each residue of the rotamer occupancy.[PAR]",
+ "All rotamers are taken as 3-fold, except for [GRK]omega[grk] and [GRK]chi[grk] dihedrals",
+ "to planar groups (i.e. [GRK]chi[grk]2 of aromatics, Asp and Asn; [GRK]chi[grk]3 of Glu",
+ "and Gln; and [GRK]chi[grk]4 of Arg), which are 2-fold. \"rotamer 0\" means ",
"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 S2 order parameters are also output to an [TT].xvg[tt] file",
+ "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 S2 values as B-factor (argument [TT]-p[tt]). ",
+ "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]), ",
+ "(argument [TT]-rt[tt]), and the ^3J couplings (argument [TT]-jc[tt]), ",
"can also be written to [TT].xvg[tt] files.[PAR]",
- "If [TT]-chi_prod[tt] is set (and maxchi > 0), cumulative rotamers, e.g.",
- "1+9(chi1-1)+3(chi2-1)+(chi3-1) (if the residue has three 3-fold ",
- "dihedrals and maxchi >= 3)",
+ "If [TT]-chi_prod[tt] is set (and [TT]-maxchi[tt] > 0), cumulative rotamers, e.g.",
+ "1+9([GRK]chi[grk]1-1)+3([GRK]chi[grk]2-1)+([GRK]chi[grk]3-1) (if the residue has three 3-fold ",
+ "dihedrals and [TT]-maxchi[tt] >= 3)",
"are calculated. As before, if any dihedral is not in the core region,",
"the rotamer is taken to be 0. The occupancies of these cumulative ",
"rotamers (starting with rotamer 0) are written to the file",
"are written to [TT]chiproduct(RESIDUE)(nresnr).xvg[tt] ",
"and their occupancies to [TT]histo-chiproduct(RESIDUE)(nresnr).xvg[tt].[PAR]",
- "The option [TT]-r[tt] generates a contour plot of the average omega angle",
- "as a function of the phi and psi angles, that is, in a Ramachandran plot",
- "the average omega angle is plotted using color coding.",
+ "The option [TT]-r[tt] generates a contour plot of the average [GRK]omega[grk] angle",
+ "as a function of the [GRK]phi[grk] and [GRK]psi[grk] angles, that is, in a Ramachandran plot",
+ "the average [GRK]omega[grk] angle is plotted using color coding.",
};
const char *bugs[] = {
"Produces MANY output files (up to about 4 times the number of residues in the protein, twice that if autocorrelation functions are calculated). Typically several hundred files are output.",
- "Phi and psi dihedrals are calculated in a non-standard way, using H-N-CA-C for phi instead of C(-)-N-CA-C, and N-CA-C-O for psi instead of N-CA-C-N(+). This causes (usually small) discrepancies with the output of other tools like [TT]g_rama[tt].",
+ "[GRK]phi[grk] and [GRK]psi[grk] dihedrals are calculated in a non-standard way, using H-N-CA-C for [GRK]phi[grk] instead of C(-)-N-CA-C, and N-CA-C-O for [GRK]psi[grk] instead of N-CA-C-N(+). This causes (usually small) discrepancies with the output of other tools like [TT]g_rama[tt].",
"[TT]-r0[tt] option does not work properly",
- "Rotamers with multiplicity 2 are printed in chi.log as if they had multiplicity 3, with the 3rd (g(+)) always having probability 0"
+ "Rotamers with multiplicity 2 are printed in [TT]chi.log[tt] as if they had multiplicity 3, with the 3rd (g(+)) always having probability 0"
};
/* defaults */
{ "-r0", FALSE, etINT, {&r0},
"starting residue" },
{ "-phi", FALSE, etBOOL, {&bPhi},
- "Output for Phi dihedral angles" },
+ "Output for [GRK]phi[grk] dihedral angles" },
{ "-psi", FALSE, etBOOL, {&bPsi},
- "Output for Psi dihedral angles" },
+ "Output for [GRK]psi[grk] dihedral angles" },
{ "-omega",FALSE, etBOOL, {&bOmega},
- "Output for Omega dihedrals (peptide bonds)" },
+ "Output for [GRK]omega[grk] dihedrals (peptide bonds)" },
{ "-rama", FALSE, etBOOL, {&bRama},
- "Generate Phi/Psi and Chi1/Chi2 ramachandran plots" },
+ "Generate [GRK]phi[grk]/[GRK]psi[grk] and [GRK]chi[grk]1/[GRK]chi[grk]2 Ramachandran plots" },
{ "-viol", FALSE, etBOOL, {&bViol},
"Write a file that gives 0 or 1 for violated Ramachandran angles" },
{ "-periodic", FALSE, etBOOL, {&bPBC},
{ "-rad", FALSE, etBOOL, {&bRAD},
"in angle vs time files, use radians rather than degrees."},
{ "-shift", FALSE, etBOOL, {&bShift},
- "Compute chemical shifts from Phi/Psi angles" },
+ "Compute chemical shifts from [GRK]phi[grk]/[GRK]psi[grk] angles" },
{ "-binwidth", FALSE, etINT, {&ndeg},
"bin width for histograms (degrees)" },
{ "-core_rotamer", FALSE, etREAL, {&core_frac},
"only the central [TT]-core_rotamer[tt]*(360/multiplicity) belongs to each rotamer (the rest is assigned to rotamer 0)" },
{ "-maxchi", FALSE, etENUM, {maxchistr},
- "calculate first ndih Chi dihedrals" },
+ "calculate first ndih [GRK]chi[grk] dihedrals" },
{ "-normhisto", FALSE, etBOOL, {&bNormHisto},
"Normalize histograms" },
{ "-ramomega",FALSE,etBOOL, {&bRamOmega},
{ "-nojump", FALSE, etBOOL, {&bNoJump},
"Removes jumps of atoms across the box."},
{ "-eps", FALSE, etREAL, {&eps_rf},
- "Dielectric constant of the surrounding medium. eps=0.0 corresponds to eps=infinity (thinfoil boundary conditions)."},
+ "Dielectric constant of the surrounding medium. eps=0.0 corresponds to eps=infinity (tin-foil boundary conditions)."},
{ "-bfit", FALSE, etREAL, {&bfit},
"Begin of the fit of the straight line to the MSD of the translational fraction of the dipole moment."},
{ "-efit", FALSE, etREAL, {&efit},
const char *desc[] = {
- "This is a tool for calculating the current autocorrelation function, the correlation",
+ "[TT]g_current[tt] is a tool for calculating the current autocorrelation function, the correlation",
"of the rotational and translational dipole moment of the system, and the resulting static",
- "dielectric constant. To obtain a reasonable result the index group has to be neutral.",
- "Furthermore the routine is capable of extracting the static conductivity from the current ",
- "autocorrelation function, if velocities are given. Additionally an Einstein-Helfand fit also",
- "allows to get the static conductivity."
+ "dielectric constant. To obtain a reasonable result, the index group has to be neutral.",
+ "Furthermore, the routine is capable of extracting the static conductivity from the current ",
+ "autocorrelation function, if velocities are given. Additionally, an Einstein-Helfand fit ",
+ "can be used to obtain the static conductivity."
"[PAR]",
"The flag [TT]-caf[tt] is for the output of the current autocorrelation function and [TT]-mc[tt] writes the",
"correlation of the rotational and translational part of the dipole moment in the corresponding",
- "file. However this option is only available for trajectories containing velocities.",
+ "file. However, this option is only available for trajectories containing velocities.",
"Options [TT]-sh[tt] and [TT]-tr[tt] are responsible for the averaging and integration of the",
"autocorrelation functions. Since averaging proceeds by shifting the starting point",
"through the trajectory, the shift can be modified with [TT]-sh[tt] to enable the choice of uncorrelated",
"tin-foil boundary conditions).",
"[PAR]",
"[TT]-[no]nojump[tt] unfolds the coordinates to allow free diffusion. This is required to get a continuous",
- "translational dipole moment, required for the Einstein-Helfand fit. The resuls from the fit allow to",
- "determine the dielectric constant for system of charged molecules. However it is also possible to extract",
+ "translational dipole moment, required for the Einstein-Helfand fit. The results from the fit allow",
+ "the determination of the dielectric constant for system of charged molecules. However, it is also possible to extract",
"the dielectric constant from the fluctuations of the total dipole moment in folded coordinates. But this",
- "options has to be used with care, since only very short time spans fulfill the approximation, that the density",
+ "option has to be used with care, since only very short time spans fulfill the approximation that the density",
"of the molecules is approximately constant and the averages are already converged. To be on the safe side,",
"the dielectric constant should be calculated with the help of the Einstein-Helfand method for",
"the translational part of the dielectric constant."
{ "-fft", FALSE, etBOOL, {&bFour},
"use fast fourier transform for correlation function" },
{ "-x1", FALSE, etBOOL, {&bX},
- "use first column as X axis rather than first data set" },
+ "use first column as [IT]x[it]-axis rather than first data set" },
{ "-eint", FALSE, etREAL, {&tendInt},
- "Time were to end the integration of the data and start to use the fit"},
+ "Time to end the integration of the data and start to use the fit"},
{ "-bfit", FALSE, etREAL, {&tbegin},
"Begin time of fit" },
{ "-efit", FALSE, etREAL, {&tend},
{ "-A", FALSE, etREAL, {&A},
"Start value for fit parameter A" },
{ "-tau1", FALSE, etREAL, {&tau1},
- "Start value for fit parameter tau1" },
+ "Start value for fit parameter [GRK]tau[grk]1" },
{ "-tau2", FALSE, etREAL, {&tau2},
- "Start value for fit parameter tau2" },
+ "Start value for fit parameter [GRK]tau[grk]2" },
{ "-eps0", FALSE, etREAL, {&eps0},
- "Epsilon 0 of your liquid" },
+ "[GRK]epsilon[grk]0 of your liquid" },
{ "-epsRF", FALSE, etREAL, {&epsRF},
- "Epsilon of the reaction field used in your simulation. A value of 0 means infinity." },
+ "[GRK]epsilon[grk] of the reaction field used in your simulation. A value of 0 means infinity." },
{ "-fix", FALSE, etINT, {&fix},
"Fix parameters at their start values, A (2), tau1 (1), or tau2 (4)" },
{ "-ffn", FALSE, etENUM, {s_ffn},
const char *desc[] = {
"[TT]g_dipoles[tt] computes the total dipole plus fluctuations of a simulation",
"system. From this you can compute e.g. the dielectric constant for",
- "low dielectric media.",
+ "low-dielectric media.",
"For molecules with a net charge, the net charge is subtracted at",
"center of mass of the molecule.[PAR]",
"The file [TT]Mtot.xvg[tt] contains the total dipole moment of a frame, the",
"simulation.",
"The file [TT]dipdist.xvg[tt] contains the distribution of dipole moments during",
"the simulation",
- "The mu_max is used as the highest value in the distribution graph.[PAR]",
- "Furthermore the dipole autocorrelation function will be computed when",
+ "The value of [TT]-mumax[tt] is used as the highest value in the distribution graph.[PAR]",
+ "Furthermore, the dipole autocorrelation function will be computed when",
"option [TT]-corr[tt] is used. The output file name is given with the [TT]-c[tt]",
"option.",
"The correlation functions can be averaged over all molecules",
"Option [TT]-g[tt] produces a plot of the distance dependent Kirkwood",
"G-factor, as well as the average cosine of the angle between the dipoles",
"as a function of the distance. The plot also includes gOO and hOO",
- "according to Nymand & Linse, JCP 112 (2000) pp 6386-6395. In the same plot",
+ "according to Nymand & Linse, J. Chem. Phys. 112 (2000) pp 6386-6395. In the same plot, ",
"we also include the energy per scale computed by taking the inner product of",
"the dipoles divided by the distance to the third power.[PAR]",
"[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",
- "frames will be used. Further the dielectric constant will be calculated",
- "using an epsilonRF of infinity (default), temperature of 300 K (default) and",
+ "frames will be used. Further, the dielectric constant will be calculated",
+ "using an [GRK]epsilon[grk]RF of infinity (default), temperature of 300 K (default) and",
"an average dipole moment of the molecule of 2.273 (SPC). For the",
"distribution function a maximum of 5.0 will be used."
};
{ "-corr", FALSE, etENUM, {corrtype},
"Correlation function to calculate" },
{ "-pairs", FALSE, etBOOL, {&bPairs},
- "Calculate |cos theta| between all pairs of molecules. May be slow" },
+ "Calculate |cos [GRK]theta[grk]| between all pairs of molecules. May be slow" },
{ "-ncos", FALSE, etINT, {&ncos},
"Must be 1 or 2. Determines whether the <cos> is computed between all molecules in one group, or between molecules in two different groups. This turns on the [TT]-gkr[tt] flag." },
{ "-axis", FALSE, etSTR, {&axtitle},
{ "-gkratom2", FALSE, etINT, {&nFB},
"Same as previous option in case ncos = 2, i.e. dipole interaction between two groups of molecules" },
{ "-rcmax", FALSE, etREAL, {&rcmax},
- "Maximum distance to use in the dipole orientation distribution (with ncos == 2). If zero, a criterium based on the box length will be used." },
+ "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." },
{ "-nlevels", FALSE, etINT, {&nlevels},
"Number of colors in the cmap output" },
{ "-ndegrees", FALSE, etINT, {&ndegrees},
- "Number of divisions on the y-axis in the camp output (for 180 degrees)" }
+ "Number of divisions on the [IT]y[it]-axis in the cmap output (for 180 degrees)" }
};
int *gnx;
int nFF[2];
const char *desc[] = {
"[TT]g_dist[tt] can calculate the distance between the centers of mass of two",
"groups of atoms as a function of time. The total distance and its",
- "x, y and z components are plotted.[PAR]",
+ "[IT]x[it]-, [IT]y[it]-, and [IT]z[it]-components are plotted.[PAR]",
"Or when [TT]-dist[tt] is set, print all the atoms in group 2 that are",
"closer than a certain distance to the center of mass of group 1.[PAR]",
"With options [TT]-lt[tt] and [TT]-dist[tt] the number of contacts",
"(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",
+ "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)",
"and the angle of rotation (also as command line arguments). If the angle",
{ "-maxangle", FALSE, etREAL, {&maxangle},
"DymDom dtermined angle of rotation about rotation vector" },
{ "-trans", FALSE, etREAL, {&trans0},
- "Translation (Aangstroem) along rotation vector (see DynDom info file)" },
+ "Translation (Angstrom) along rotation vector (see DynDom info file)" },
{ "-head", FALSE, etRVEC, {head},
"First atom of the arrow vector" },
{ "-tail", FALSE, etRVEC, {tail},
"The last two are special cases of a triclinic box.",
"The length of the three box vectors of the truncated octahedron is the",
"shortest distance between two opposite hexagons.",
- "The volume of a dodecahedron is 0.71 and that of a truncated octahedron",
- "is 0.77 of that of a cubic box with the same periodic image distance.",
+ "Relative to a cubic box with some periodic image distance, the volume of a ",
+ "dodecahedron with this same periodic distance is 0.71 times that of the cube, ",
+ "and that of a truncated octahedron is 0.77 times.",
"[PAR]",
"Option [TT]-box[tt] requires only",
- "one value for a cubic box, dodecahedron and a truncated octahedron.",
+ "one value for a cubic, rhombic dodecahedral, or truncated octahedral box.",
"[PAR]",
- "With [TT]-d[tt] and a [TT]triclinic[tt] box the size of the system in the x, y",
- "and z directions is used. With [TT]-d[tt] and [TT]cubic[tt],",
+ "With [TT]-d[tt] and a [TT]triclinic[tt] box the size of the system in the [IT]x[it]-, [IT]y[it]-,",
+ "and [IT]z[it]-directions is used. With [TT]-d[tt] and [TT]cubic[tt],",
"[TT]dodecahedron[tt] or [TT]octahedron[tt] boxes, the dimensions are set",
"to the diameter of the system (largest distance between atoms) plus twice",
"the specified distance.",
"[PAR]",
"Option [TT]-angles[tt] is only meaningful with option [TT]-box[tt] and",
- "a triclinic box and can not be used with option [TT]-d[tt].",
+ "a triclinic box and cannot be used with option [TT]-d[tt].",
"[PAR]",
"When [TT]-n[tt] or [TT]-ndef[tt] is set, a group",
"can be selected for calculating the size and the geometric center,",
"[TT]-rotate[tt] rotates the coordinates and velocities.",
"[PAR]",
"[TT]-princ[tt] aligns the principal axes of the system along the",
- "coordinate axes, with the longest axis aligned with the x axis. ",
+ "coordinate axes, with the longest axis aligned with the [IT]x[it]-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",
"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 gro",
- "file is given as input. A special feature of the scaling option, when the",
+ "[TT]-density[tt]). Note that this may be inaccurate in case a [TT].gro[tt]",
+ "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, ",
"a point-mirror image is obtained.[PAR]",
"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], [TT]editconf[tt] can add a chain identifier",
- "to a [TT].pdb[tt] file, which can be useful for analysis with e.g. rasmol.",
+ "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.",
"[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]",
const char *desc[] = {
"With [IT]multiple files[it] specified for the [TT]-f[tt] option:[BR]",
"Concatenates several energy files in sorted order.",
- "In case of double time frames the one",
+ "In the 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 the command [TT]eneconv -o fixed.edr *.edr[tt] should do",
+ "such that the command [TT]eneconv -f *.edr -o fixed.edr[tt] should do",
"the trick. [PAR]",
"With [IT]one file[it] specified for [TT]-f[tt]:[BR]",
"Reads one energy file and writes another, applying the [TT]-dt[tt],",
"line a group of atoms to be used. For these groups matrix of",
"interaction energies will be extracted from the energy file",
"by looking for energy groups with names corresponding to pairs",
- "of groups of atoms. E.g. if your [TT]-groups[tt] file contains:[BR]",
+ "of groups of atoms, e.g. if your [TT]-groups[tt] file contains:[BR]",
"[TT]2[tt][BR]",
"[TT]Protein[tt][BR]",
"[TT]SOL[tt][BR]",
"data from an energy file. The user is prompted to interactively",
"select the energy terms she wants.[PAR]",
- "Average, RMSD and drift are calculated with full precision from the",
+ "Average, RMSD, and drift are calculated with full precision from the",
"simulation (see printed manual). Drift is calculated by performing",
"a least-squares fit of the data to a straight line. The reported total drift",
"is the difference of the fit at the first and last point.",
"An error estimate of the average is given based on a block averages",
- "over 5 blocks using the full precision averages. The error estimate",
+ "over 5 blocks using the full-precision averages. The error estimate",
"can be performed over multiple block lengths with the options",
"[TT]-nbmin[tt] and [TT]-nbmax[tt].",
- "Note that in most cases the energy files contains averages over all",
+ "[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 [TT]g_energy[tt] statistics output more accurate",
"than the [TT].xvg[tt] output. When exact averages are not present in the energy",
- "file the statistics mentioned above are simply over the single, per-frame",
+ "file, the statistics mentioned above are simply over the single, per-frame",
"energy values.[PAR]",
"The term fluctuation gives the RMSD around the least-squares fit.[PAR]",
"With [TT]-fee[tt] an estimate is calculated for the free-energy",
"difference with an ideal gas state: [BR]",
- " Delta A = A(N,V,T) - A_idgas(N,V,T) = kT ln < e^(Upot/kT) >[BR]",
- " Delta G = G(N,p,T) - G_idgas(N,p,T) = kT ln < e^(Upot/kT) >[BR]",
+ " [GRK]Delta[grk] A = A(N,V,T) - A_idgas(N,V,T) = kT ln < e^(Upot/kT) >[BR]",
+ " [GRK]Delta[grk] G = G(N,p,T) - G_idgas(N,p,T) = kT ln < e^(Upot/kT) >[BR]",
"where k is Boltzmann's constant, T is set by [TT]-fetemp[tt] and",
"the average is over the ensemble (or time in a trajectory).",
"Note that this is in principle",
"only correct when averaging over the whole (Boltzmann) ensemble",
"and using the potential energy. This also allows for an entropy",
"estimate using:[BR]",
- " Delta S(N,V,T) = S(N,V,T) - S_idgas(N,V,T) = (<Upot> - Delta A)/T[BR]",
- " Delta S(N,p,T) = S(N,p,T) - S_idgas(N,p,T) = (<Upot> + pV - Delta G)/T",
+ " [GRK]Delta[grk] S(N,V,T) = S(N,V,T) - S_idgas(N,V,T) = (<Upot> - [GRK]Delta[grk] A)/T[BR]",
+ " [GRK]Delta[grk] S(N,p,T) = S(N,p,T) - S_idgas(N,p,T) = (<Upot> + pV - [GRK]Delta[grk] G)/T",
"[PAR]",
"When a second energy file is specified ([TT]-f2[tt]), a free energy",
"difference is calculated dF = -kT ln < e ^ -(EB-EA)/kT >A ,",
"where EA and EB are the energies from the first and second energy",
- "files, and the average is over the ensemble A. [BB]NOTE[bb] that",
+ "files, and the average is over the ensemble A. [BB]Note[bb] that",
"the energies must both be calculated from the same trajectory."
};
{
const char *desc[] = {
"[TT]g_filter[tt] performs frequency filtering on a trajectory.",
- "The filter shape is cos(pi t/A) + 1 from -A to +A, where A is given",
+ "The filter shape is cos([GRK]pi[grk] t/A) + 1 from -A to +A, where A is given",
"by the option [TT]-nf[tt] times the time step in the input trajectory.",
"This filter reduces fluctuations with period A by 85%, with period",
"2*A by 50% and with period 3*A by 17% for low-pass filtering.",
"Both a low-pass and high-pass filtered trajectory can be written.[PAR]",
"Option [TT]-ol[tt] writes a low-pass filtered trajectory.",
- "A frame is written every [TT]nf[tt] input frames.",
+ "A frame is written every [TT]-nf[tt] input frames.",
"This ratio of filter length and output interval ensures a good",
"suppression of aliasing of high-frequency motion, which is useful for",
"making smooth movies. Also averages of properties which are linear",
"The program iterates until [TT]nmol[tt] molecules",
"have been inserted in the box. To test whether an insertion is ",
"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 ",
+ "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 [TT]-try[tt] if you have several small holes to fill.[PAR]",
const char *desc[] = {
"[TT]genconf[tt] multiplies a given coordinate file by simply stacking them",
"on top of each other, like a small child playing with wooden blocks.",
- "The program makes a grid of [IT]user defined[it]",
+ "The program makes a grid of [IT]user-defined[it]",
"proportions ([TT]-nbox[tt]), ",
"and interspaces the grid point with an extra space [TT]-dist[tt].[PAR]",
"When option [TT]-rot[tt] is used the program does not check for overlap",
"between molecules on grid points. It is recommended to make the box in",
"the input file at least as big as the coordinates + ",
- "Van der Waals radius.[PAR]",
+ "van der Waals radius.[PAR]",
"If the optional trajectory file is given, conformations are not",
"generated, but read from this file and translated appropriately to",
"build the grid."
"[PAR]Ions which can have multiple charge states get the multiplicity",
"added, without sign, for the uncommon states only.[PAR]",
"With the option [TT]-pot[tt] the potential can be written as B-factors",
- "in a [TT].pdb[tt] file (for visualisation using e.g. rasmol).",
+ "in a [TT].pdb[tt] 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 using [TT]genbox[tt]."
const char *desc[] = {
"[TT]genrestr[tt] produces an include file for a topology containing",
"a list of atom numbers and three force constants for the",
- "X, Y and Z direction. A single isotropic force constant may",
+ "[IT]x[it]-, [IT]y[it]-, and [IT]z[it]-direction. A single isotropic force constant may",
"be given on the command line instead of three components.[PAR]",
"WARNING: position restraints only work for the one molecule at a time.",
"Position restraints are interactions within molecules, therefore",
"freezing atoms. In this case, the input file must be a [TT].pdb[tt] 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",
+ "one typically would apply to C[GRK]alpha[grk] atoms in a protein, one can",
"maintain the overall conformation of a protein without tieing it to",
"a specific position (as with position restraints)."
};
t_pargs pa[] = {
{ "-fc", FALSE, etRVEC, {fc},
- "force constants (kJ mol-1 nm-2)" },
+ "force constants (kJ/mol nm^2)" },
{ "-freeze", FALSE, etREAL, {&freeze_level},
"if the [TT]-of[tt] option or this one is given an index file will be written containing atom numbers of all atoms that have a B-factor less than the level given here" },
{ "-disre", FALSE, etBOOL, {&bDisre},
{
const char *desc[] = {
"[TT]g_gyrate[tt] computes the radius of gyration of a group of atoms",
- "and the radii of gyration about the x, y and z axes,",
+ "and the radii of gyration about the [IT]x[it]-, [IT]y[it]- and [IT]z[it]-axes,",
"as a function of time. The atoms are explicitly mass weighted.[PAR]",
"With the [TT]-nmol[tt] option the radius of gyration will be calculated",
"for multiple molecules by splitting the analysis group in equally",
"sized parts.[PAR]",
- "With the option [TT]-nz[tt] 2D radii of gyration in the x-y plane",
- "of slices along the z-axis are calculated."
+ "With the option [TT]-nz[tt] 2D radii of gyration in the [IT]x-y[it] plane",
+ "of slices along the [IT]z[it]-axis are calculated."
};
static int nmol=1,nz=0;
static gmx_bool bQ=FALSE,bRot=FALSE,bMOI=FALSE;
{ "-temp", FALSE, etREAL, {&temp},
"Temperature (K) for computing the Gibbs energy corresponding to HB breaking and reforming" },
{ "-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/tau)" },
+ "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" },
{ "-max_hb",FALSE, etREAL, {&maxnhb},
{ "-geminate", FALSE, etENUM, {gemType},
"Use reversible geminate recombination for the kinetics/thermodynamics calclations. See Markovitch et al., J. Chem. Phys 129, 084505 (2008) for details."},
{ "-diff", FALSE, etREAL, {&D},
- "Dffusion coefficient to use in the rev. gem. recomb. kinetic model. If non-positive, then it will be fitted to the ACF along with ka and kd."},
+ "Dffusion coefficient to use in the reversible geminate recombination kinetic model. If negative, then it will be fitted to the ACF along with ka and kd."},
#ifdef HAVE_OPENMP
{ "-nthreads", FALSE, etINT, {&nThreads},
"Number of threads used for the parallel loop over autocorrelations. nThreads <= 0 means maximum number of threads. Requires linking with OpenMP. The number of threads is limited by the number of processors (before OpenMP v.3 ) or environment variable OMP_THREAD_LIMIT (OpenMP v.3)"},
const char *desc[] = {
"[TT]g_helix[tt] computes all kinds of helix properties. First, the peptide",
"is checked to find the longest helical part, as determined by",
- "hydrogen bonds and Phi/Psi angles.",
+ "hydrogen bonds and [GRK]phi[grk]/[GRK]psi[grk] angles.",
"That bit is fitted",
- "to an ideal helix around the Z-axis and centered around the origin.",
+ "to an ideal helix around the [IT]z[it]-axis and centered around the origin.",
"Then the following properties are computed:[PAR]",
"[BB]1.[bb] Helix radius (file [TT]radius.xvg[tt]). This is merely the",
- "RMS deviation in two dimensions for all C-alpha atoms.",
+ "RMS deviation in two dimensions for all C[GRK]alpha[grk] atoms.",
"it is calced as sqrt((SUM i(x^2(i)+y^2(i)))/N), where N is the number",
"of backbone atoms. For an ideal helix the radius is 0.23 nm[BR]",
"[BB]2.[bb] Twist (file [TT]twist.xvg[tt]). The average helical angle per",
- "residue is calculated. For alpha helix it is 100 degrees,",
- "for 3-10 helices it will be smaller,",
+ "residue is calculated. For an [GRK]alpha[grk]-helix it is 100 degrees,",
+ "for 3-10 helices it will be smaller, and ",
"for 5-helices it will be larger.[BR]",
"[BB]3.[bb] Rise per residue (file [TT]rise.xvg[tt]). The helical rise per",
- "residue is plotted as the difference in Z-coordinate between Ca",
- "atoms. For an ideal helix this is 0.15 nm[BR]",
+ "residue is plotted as the difference in [IT]z[it]-coordinate between C[GRK]alpha[grk]",
+ "atoms. For an ideal helix, this is 0.15 nm[BR]",
"[BB]4.[bb] Total helix length (file [TT]len-ahx.xvg[tt]). The total length",
"of the",
"helix in nm. This is simply the average rise (see above) times the",
"[BB]5.[bb] Number of helical residues (file [TT]n-ahx.xvg[tt]). The title says",
"it all.[BR]",
"[BB]6.[bb] Helix dipole, backbone only (file [TT]dip-ahx.xvg[tt]).[BR]",
- "[BB]7.[bb] RMS deviation from ideal helix, calculated for the C-alpha",
+ "[BB]7.[bb] RMS deviation from ideal helix, calculated for the C[GRK]alpha[grk]",
"atoms only (file [TT]rms-ahx.xvg[tt]).[BR]",
- "[BB]8.[bb] Average C-alpha - C-alpha dihedral angle (file [TT]phi-ahx.xvg[tt]).[BR]",
- "[BB]9.[bb] Average Phi and Psi angles (file [TT]phipsi.xvg[tt]).[BR]",
+ "[BB]8.[bb] Average C[GRK]alpha[grk] - C[GRK]alpha[grk] dihedral angle (file [TT]phi-ahx.xvg[tt]).[BR]",
+ "[BB]9.[bb] Average [GRK]phi[grk] and [GRK]psi[grk] angles (file [TT]phipsi.xvg[tt]).[BR]",
"[BB]10.[bb] Ellipticity at 222 nm according to Hirst and Brooks.",
"[PAR]"
};
const char *desc[] = {
"[TT]g_helixorient[tt] calculates the coordinates and direction of the average",
"axis inside an alpha helix, and the direction/vectors of both the",
- "alpha carbon and (optionally) a sidechain atom relative to the axis.[PAR]",
- "As input, you need to specify an index group with alpha carbon atoms",
- "corresponding to an alpha helix of continuous residues. Sidechain",
+ "C[GRK]alpha[grk] and (optionally) a sidechain atom relative to the axis.[PAR]",
+ "As input, you need to specify an index group with C[GRK]alpha[grk] atoms",
+ "corresponding to an [GRK]alpha[grk]-helix of continuous residues. Sidechain",
"directions require a second index group of the same size, containing",
"the heavy atom in each residue that should represent the sidechain.[PAR]",
- "Note that this program does not do any fitting of structures.[PAR]",
- "We need four C-alpha coordinates to define the local direction of the helix",
+ "[BB]Note[bb] that this program does not do any fitting of structures.[PAR]",
+ "We need four C[GRK]alpha[grk] coordinates to define the local direction of the helix",
"axis.[PAR]",
"The tilt/rotation is calculated from Euler rotations, where we define",
- "the helix axis as the local X axis, the residues/CA-vector as Y, and the",
- "Z axis from their cross product. We use the Euler Y-Z-X rotation, meaning",
+ "the helix axis as the local [IT]x[it]-axis, the residues/C[GRK]alpha[grk] vector as [IT]y[it], and the",
+ "[IT]z[it]-axis from their cross product. We use the Euler Y-Z-X rotation, meaning",
"we first tilt the helix axis (1) around and (2) orthogonal to the residues",
"vector, and finally apply the (3) rotation around it. For debugging or other",
"purposes, we also write out the actual Euler rotation angles as [TT]theta[1-3].xvg[tt]"
{ "-ucut", FALSE, etREAL, {&ucut},
"Cut-off (max) value for regarding a structure as intermediate (if not folded)" },
{ "-euf", FALSE, etREAL, {&Euf},
- "Initial guess for energy of activation for folding (kJ/mole)" },
+ "Initial guess for energy of activation for folding (kJ/mol)" },
{ "-efu", FALSE, etREAL, {&Efu},
- "Initial guess for energy of activation for unfolding (kJ/mole)" },
+ "Initial guess for energy of activation for unfolding (kJ/mol)" },
{ "-ei", FALSE, etREAL, {&Ei},
- "Initial guess for energy of activation for intermediates (kJ/mole)" },
+ "Initial guess for energy of activation for intermediates (kJ/mol)" },
{ "-maxiter", FALSE, etINT, {&maxiter},
"Max number of iterations" },
{ "-back", FALSE, etBOOL, {&bBack},
{ "-split", FALSE, etBOOL,{&bSplit},
"Estimate error by splitting the number of replicas in two and refitting" },
{ "-sum", FALSE, etBOOL,{&bSum},
- "Average folding before computing chi^2" },
+ "Average folding before computing [GRK]chi[grk]^2" },
{ "-discrete", FALSE, etBOOL, {&bDiscrete},
- "Use a discrete folding criterium (F <-> U) or a continuous one" },
+ "Use a discrete folding criterion (F <-> U) or a continuous one" },
{ "-mult", FALSE, etINT, {&nmult},
"Factor to multiply the data with before discretization" }
};
{
const char *desc[] = {
"[TT]g_membed[tt] embeds a membrane protein into an equilibrated lipid bilayer at the position",
- "and orientation specified by the user.\n",
- "\n",
- "SHORT MANUAL\n------------\n",
+ "and orientation specified by the user.[PAR]",
+ "SHORT MANUAL[BR]------------[BR]",
"The user should merge the structure files of the protein and membrane (+solvent), creating a",
"single structure file with the protein overlapping the membrane at the desired position and",
- "orientation. Box size should be taken from the membrane structure file. The corresponding topology",
+ "orientation. The box size is taken from the membrane structure file. The corresponding topology",
"files should also be merged. Consecutively, create a [TT].tpr[tt] file (input for [TT]g_membed[tt]) from these files,"
- "with the following options included in the [TT].mdp[tt] file.\n",
+ "with the following options included in the [TT].mdp[tt] file.[BR]",
" - [TT]integrator = md[tt][BR]",
" - [TT]energygrp = Protein[tt] (or other group that you want to insert)[BR]",
" - [TT]freezegrps = Protein[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",
- "For a more extensive manual see Wolf et al, J Comp Chem 31 (2010) 2169-2174, Appendix.\n",
- "\n",
- "SHORT METHOD DESCRIPTION\n",
- "------------------------\n",
+ "solvent molecules will be updated to match the new structure file.[BR]",
+ "For a more extensive manual see Wolf et al, J Comp Chem 31 (2010) 2169-2174, Appendix.[PAR]",
+ "SHORT METHOD DESCRIPTION[BR]",
+ "------------------------[BR]",
"1. The protein is resized around its center of mass by a factor [TT]-xy[tt] in the xy-plane",
- "(the membrane plane) and a factor [TT]-z[tt] in the z-direction (if the size of the",
+ "(the membrane plane) and a factor [TT]-z[tt] in the [IT]z[it]-direction (if the size of the",
"protein in the z-direction is the same or smaller than the width of the membrane, a",
- "[TT]-z[tt] value larger than 1 can prevent that the protein will be enveloped by the lipids).\n",
+ "[TT]-z[tt] value larger than 1 can prevent that the protein will be enveloped by the lipids).[BR]",
"2. All lipid and solvent molecules overlapping with the resized protein are removed. All",
"intraprotein interactions are turned off to prevent numerical issues for small values of [TT]-xy[tt]",
- " or [TT]-z[tt]\n",
- "3. One md step is performed.\n",
+ " or [TT]-z[tt][BR]",
+ "3. One md step is performed.[BR]",
"4. The resize factor ([TT]-xy[tt] or [TT]-z[tt]) is incremented by a small amount ((1-xy)/nxy or (1-z)/nz) and the",
"protein is resized again around its center of mass. The resize factor for the xy-plane",
"is incremented first. The resize factor for the z-direction is not changed until the [TT]-xy[tt] factor",
- "is 1 (thus after [TT]-nxy[tt] iterations).\n",
- "5. Repeat step 3 and 4 until the protein reaches its original size ([TT]-nxy[tt] + [TT]-nz[tt] iterations).\n",
- "For a more extensive method description see Wolf et al, J Comp Chem, 31 (2010) 2169-2174.\n",
- "\n",
- "NOTE\n----\n",
- " - Protein can be any molecule you want to insert in the membrane.\n",
+ "is 1 (thus after [TT]-nxy[tt] iterations).[BR]",
+ "5. Repeat step 3 and 4 until the protein reaches its original size ([TT]-nxy[tt] + [TT]-nz[tt] iterations).[BR]",
+ "For a more extensive method description see Wolf et al, J Comp Chem, 31 (2010) 2169-2174.[PAR]",
+ "NOTE[BR]----[BR]",
+ " - Protein can be any molecule you want to insert in the membrane.[BR]",
" - It is recommended to perform a short equilibration run after the embedding",
"(see Wolf et al, J Comp Chem 31 (2010) 2169-2174), to re-equilibrate the membrane. Clearly",
- "protein equilibration might require longer.\n",
- "\n"
+ "protein equilibration might require longer.[PAR]"
};
t_commrec *cr;
t_filenm fnm[] = {
"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",
- "on the path from input structure x1 to x2. In general the coordinates",
+ "If you specify [TT]-first[tt] < 0 or [TT]-last[tt] > 1 extrapolation will be",
+ "on the path from input structure x1 to x2. In general, the coordinates",
"of the intermediate x(i) out of N total intermidates correspond to:[PAR]",
"x(i) = x1 + (first+(i/(N-1))*(last-first))*(x2-x1)[PAR]",
"Finally the RMSD with respect to both input structures can be computed",
- "if explicitly selected ([TT]-or[tt] option). In that case an index file may be",
- "read to select what group RMS is computed from."
+ "if explicitly selected ([TT]-or[tt] option). In that case, an index file may be",
+ "read to select the group from which the RMS is computed."
};
t_filenm fnm[] = {
{ efSTX, "-f1", "conf1", ffREAD },
"output. In this case, they will no longer be exactly orthogonal in the",
"standard Cartesian norm, but in the mass-weighted norm they would be.[PAR]",
"This program can be optionally used to compute quantum corrections to heat capacity",
- "and enthalpy by providing an extra file argument -qcorr. See gromacs",
- "manual chapter 1 for details. The result includes subtracting a harmonic",
+ "and enthalpy by providing an extra file argument [TT]-qcorr[tt]. See the GROMACS",
+ "manual, Chapter 1, for details. The result includes subtracting a harmonic",
"degree of freedom at the given temperature.",
"The total correction is printed on the terminal screen.",
"The recommended way of getting the corrections out is:[PAR]",
"[TT]g_nmeig -s topol.tpr -f nm.mtx -first 7 -last 10000 -T 300 -qc [-constr][tt][PAR]",
"The [TT]-constr[tt] option should be used when bond constraints were used during the",
- "simulation [BB]for all the covalent bonds[bb]. If this is not the case",
- "you need to analyse the [TT]quant_corr.xvg[tt] file yourself.[PAR]",
+ "simulation [BB]for all the covalent bonds[bb]. If this is not the case, ",
+ "you need to analyze the [TT]quant_corr.xvg[tt] file yourself.[PAR]",
"To make things more flexible, the program can also take virtual sites into account",
"when computing quantum corrections. When selecting [TT]-constr[tt] and",
"[TT]-qc[tt], the [TT]-begin[tt] and [TT]-end[tt] options will be set automatically as well.",
{ "-d", FALSE, etENUM, {normal_axis},
"Direction of the normal on the membrane" },
{ "-sl", FALSE, etINT, {&nslices},
- "Calculate order parameter as function of boxlength, dividing the box"
+ "Calculate order parameter as function of box length, dividing the box"
" in #nr slices." },
{ "-szonly", FALSE, etBOOL,{&bSzonly},
"Only give Sz element of order tensor. (axis can be specified with [TT]-d[tt])" },
int gmx_rama(int argc,char *argv[])
{
const char *desc[] = {
- "[TT]g_rama[tt] selects the Phi/Psi dihedral combinations from your topology file",
+ "[TT]g_rama[tt] selects the [GRK]phi[grk]/[GRK]psi[grk] dihedral combinations from your topology file",
"and computes these as a function of time.",
"Using simple Unix tools such as [IT]grep[it] you can select out",
"specific residues."
"The normal method is around a (set of) particle(s), the other methods",
"are around the center of mass of a set of particles ([TT]-com[tt])",
"or to the closest particle in a set ([TT]-surf[tt]).",
- "With all methods rdf's can also be calculated around axes parallel",
- "to the z-axis with option [TT]-xy[tt].",
+ "With all methods, the RDF can also be calculated around axes parallel",
+ "to the [IT]z[it]-axis with option [TT]-xy[tt].",
"With option [TT]-surf[tt] normalization can not be used.[PAR]",
- "The option [TT]-rdf[tt] sets the type of rdf to be computed.",
+ "The option [TT]-rdf[tt] sets the type of RDF to be computed.",
"Default is for atoms or particles, but one can also select center",
- "of mass or geometry of molecules or residues. In all cases only",
+ "of mass or geometry of molecules or residues. In all cases, only",
"the atoms in the index groups are taken into account.",
- "For molecules and/or the center of mass option a run input file",
+ "For molecules and/or the center of mass option, a run input file",
"is required.",
- "Other weighting than COM or COG can currently only be achieved",
+ "Weighting other than COM or COG can currently only be achieved",
"by providing a run input file with different masses.",
"Options [TT]-com[tt] and [TT]-surf[tt] also work in conjunction",
"with [TT]-rdf[tt].[PAR]",
"If a run input file is supplied ([TT]-s[tt]) and [TT]-rdf[tt] is set",
"to [TT]atom[tt], exclusions defined",
- "in that file are taken into account when calculating the rdf.",
+ "in that file are taken into account when calculating the RDF.",
"The option [TT]-cut[tt] is meant as an alternative way to avoid",
- "intramolecular peaks in the rdf plot.",
+ "intramolecular peaks in the RDF plot.",
"It is however better to supply a run input file with a higher number of",
- "exclusions. For eg. benzene a topology with nrexcl set to 5",
- "would eliminate all intramolecular contributions to the rdf.",
+ "exclusions. For e.g. benzene a topology, setting nrexcl to 5",
+ "would eliminate all intramolecular contributions to the RDF.",
"Note that all atoms in the selected groups are used, also the ones",
"that don't have Lennard-Jones interactions.[PAR]",
- "Option [TT]-cn[tt] produces the cumulative number rdf,",
+ "Option [TT]-cn[tt] produces the cumulative number RDF,",
"i.e. the average number of particles within a distance r.[PAR]",
"To bridge the gap between theory and experiment structure factors can",
"be computed (option [TT]-sq[tt]). The algorithm uses FFT, the grid",
*desc[] =
{
"[TT]g_rms[tt] compares two structures by computing the root mean square",
- "deviation (RMSD), the size-independent 'rho' similarity parameter",
- "(rho) or the scaled rho (rhosc), ",
- "see Maiorov & Crippen, PROTEINS [BB]22[bb], 273 (1995).",
+ "deviation (RMSD), the size-independent [GRK]rho[grk] similarity parameter",
+ "([TT]rho[tt]) or the scaled [GRK]rho[grk] ([TT]rhosc[tt]), ",
+ "see Maiorov & Crippen, Proteins [BB]22[bb], 273 (1995).",
"This is selected by [TT]-what[tt].[PAR]"
- "Each structure from a trajectory ([TT]-f[tt]) is compared to a",
+ "Each structure from a trajectory ([TT]-f[tt]) is compared to a",
"reference structure. The reference structure",
"is taken from the structure file ([TT]-s[tt]).[PAR]",
"With option [TT]-mir[tt] also a comparison with the mirror image of",
"the reference structure is calculated.",
"This is useful as a reference for 'significant' values, see",
- "Maiorov & Crippen, PROTEINS [BB]22[bb], 273 (1995).[PAR]",
+ "Maiorov & Crippen, Proteins [BB]22[bb], 273 (1995).[PAR]",
"Option [TT]-prev[tt] produces the comparison with a previous frame",
"the specified number of frames ago.[PAR]",
"determining the orientation of a molecule",
"at an interface, possibly on a trajectory produced with",
"[TT]trjconv -fit rotxy+transxy[tt] to remove the rotation",
- "in the xy-plane.",
+ "in the [IT]x-y[it] plane.",
"[PAR]",
"Option [TT]-ref[tt] determines a reference structure for fitting,",
"instead of using the structure from [TT]-s[tt]. The structure with",
"the lowest sum of RMSD's to all other structures is used.",
"Since the computational cost of this procedure grows with",
"the square of the number of frames, the [TT]-skip[tt] option",
- "can be useful. A full fit or only a fit in the x/y plane can",
+ "can be useful. A full fit or only a fit in the [IT]x-y[it] plane can",
"be performed.",
"[PAR]",
- "Option [TT]-fitxy[tt] fits in the x/y plane before determining",
+ "Option [TT]-fitxy[tt] fits in the [IT]x-y[it] plane before determining",
"the rotation matrix."
};
const char *reffit[] =
const char *desc[] = {
"[TT]g_saltbr[tt] plots the distance between all combination of charged groups",
"as a function of time. The groups are combined in different ways.",
- "A minimum distance can be given, (ie. a cut-off), then groups",
- "that are never closer than that distance will not be plotted.[BR]",
+ "A minimum distance can be given (i.e. a cut-off), such that groups",
+ "that are never closer than that distance will not be plotted.[PAR]",
"Output will be in a number of fixed filenames, [TT]min-min.xvg[tt], [TT]plus-min.xvg[tt]",
- "and [TT]plus-plus.xvg[tt], or files for every individual ion-pair if the [TT]-sep[tt]",
- "option is selected. In this case files are named as [TT]sb-ResnameResnr-Atomnr[tt].",
- "There may be many such files."
+ "and [TT]plus-plus.xvg[tt], or files for every individual ion pair if the [TT]-sep[tt]",
+ "option is selected. In this case, files are named as [TT]sb-(Resname)(Resnr)-(Atomnr)[tt].",
+ "There may be [BB]many[bb] such files."
};
static gmx_bool bSep=FALSE;
static real truncate=1000.0;
{
const char *desc[] = {
"[TT]g_sas[tt] computes hydrophobic, hydrophilic and total solvent accessible surface area.",
- "As a side effect the Connolly surface can be generated as well in",
+ "As a side effect, the Connolly surface can be generated as well in",
"a [TT].pdb[tt] file where the nodes are represented as atoms and the vertices",
"connecting the nearest nodes as CONECT records.",
"The program will ask for a group for the surface calculation",
"The output group can be the whole or part of the calculation group.",
"The average and standard deviation of the area over the trajectory can be plotted",
"per residue and atom as well (options [TT]-or[tt] and [TT]-oa[tt]).",
- "In combination with the latter option an [TT]itp[tt] file can be",
+ "In combination with the latter option an [TT].itp[tt] file can be",
"generated (option [TT]-i[tt])",
"which can be used to restrain surface atoms.[PAR]",
"By default, periodic boundary conditions are taken into account,",
"Please consider whether the normal probe radius is appropriate",
"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",
+ "approximate. For example, in ice Ih, one can easily fit water molecules in the",
"pores which would yield a volume that is too low, and surface area and density",
"that are both too high."
};
{ "-pbc", FALSE, etBOOL, {&bPBC},
"Take periodicity into account" },
{ "-prot", FALSE, etBOOL, {&bSave},
- "Output the protein to the connelly [TT].pdb[tt] file too" },
+ "Output the protein to the Connelly [TT].pdb[tt] file too" },
{ "-dgs", FALSE, etREAL, {&dgs_default},
- "default value for solvation free energy per area (kJ/mol/nm^2)" }
+ "Default value for solvation free energy per area (kJ/mol/nm^2)" }
};
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
"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 ",
+ "given. Giving, for instance, 5 6 will rotate the vector 5-6 with ",
"180 degrees compared to giving 6 5. [PAR]If three atoms are given, ",
"the normal on the plane spanned by those three atoms will be",
"calculated, using the formula P1P2 x P1P3.",
{ "-one", FALSE, etBOOL, {&bOne},
"Only one group compute angle between vector at time zero and time t"},
{ "-z", FALSE, etBOOL, {&bZ},
- "Use the Z-axis as reference" }
+ "Use the [IT]z[it]-axis as reference" }
};
#define NPA asize(pa)
"make enthalpy (option [TT]-lsh[tt]) and entropy (option [TT]-lss[tt])",
"plots. The histograms can be made for any quantities the user supplies.",
"A line in the input file may start with a time",
- "(see option [TT]-time[tt]) and any number of y values may follow.",
+ "(see option [TT]-time[tt]) and any number of [IT]y[it]-values may follow.",
"Multiple sets can also be",
"read when they are separated by & (option [TT]-n[tt]),",
- "in this case only one y value is read from each line.",
+ "in this case only one [IT]y[it]-value is read from each line.",
"All lines starting with # and @ are skipped.",
"[PAR]",
"Option [TT]-ge[tt] can be used to supply a file with free energies",
"[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 by Kumar et. al. When temperatures",
+ "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.",
"sampled by two particles increases with increasing distance.",
"Depending on what one would like to show, one can choose to correct",
"the histogram and free-energy for this volume effect.",
- "The probability is normalized by r and r^2 for a dimension of 2 and 3",
+ "The probability is normalized by r and r^2 for dimensions of 2 and 3, ",
"respectively.",
"A value of -1 is used to indicate an angle in degrees between two",
"vectors: a sin(angle) normalization will be applied.",
const char *desc[] = {
"[TT]g_sorient[tt] analyzes solvent orientation around solutes.",
"It calculates two angles between the vector from one or more",
- "reference positions to the first atom of each solvent molecule:[BR]",
- "theta1: the angle with the vector from the first atom of the solvent",
+ "reference positions to the first atom of each solvent molecule:[PAR]",
+ "[GRK]theta[grk]1: the angle with the vector from the first atom of the solvent",
"molecule to the midpoint between atoms 2 and 3.[BR]",
- "theta2: the angle with the normal of the solvent plane, defined by the",
- "same three atoms, or when the option [TT]-v23[tt] is set",
- "the angle with the vector between atoms 2 and 3.[BR]",
+ "[GRK]theta[grk]2: the angle with the normal of the solvent plane, defined by the",
+ "same three atoms, or, when the option [TT]-v23[tt] is set, ",
+ "the angle with the vector between atoms 2 and 3.[PAR]",
"The reference can be a set of atoms or",
"the center of mass of a set of atoms. The group of solvent atoms should",
"consist of 3 atoms per solvent molecule.",
"Only solvent molecules between [TT]-rmin[tt] and [TT]-rmax[tt] are",
"considered for [TT]-o[tt] and [TT]-no[tt] each frame.[PAR]",
- "[TT]-o[tt]: distribtion of cos(theta1) for rmin<=r<=rmax.[PAR]",
- "[TT]-no[tt]: distribution of cos(theta2) for rmin<=r<=rmax.[PAR]",
- "[TT]-ro[tt]: <cos(theta1)> and <3cos^2(theta2)-1> as a function of the",
+ "[TT]-o[tt]: distribtion of cos([GRK]theta[grk]1) for rmin<=r<=rmax.[PAR]",
+ "[TT]-no[tt]: distribution of cos([GRK]theta[grk]2) for rmin<=r<=rmax.[PAR]",
+ "[TT]-ro[tt]: <cos([GRK]theta[grk]1)> and <3cos^2([GRK]theta[grk]2)-1> as a function of the",
"distance.[PAR]",
"[TT]-co[tt]: the sum over all solvent molecules within distance r",
- "of cos(theta1) and 3cos^2(theta2)-1 as a function of r.[PAR]",
+ "of cos([GRK]theta[grk]1) and 3cos^2([GRK]theta[grk]2)-1 as a function of r.[PAR]",
"[TT]-rc[tt]: the distribution of the solvent molecules as a function of r"
};
"[TT]g_spatial[tt] 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). ",
- "For a system of 32K atoms and a 50ns trajectory, the SDF can be generated ",
+ "For a system of 32,000 atoms and a 50 ns trajectory, the SDF can be generated ",
"in about 30 minutes, with most of the time dedicated to the two runs through ",
"[TT]trjconv[tt] that are required to center everything properly. ",
"This also takes a whole bunch of space (3 copies of the [TT].xtc[tt] file). ",
"Still, the pictures are pretty and very informative when the fitted selection is properly made. ",
- "3-4 atoms in a widely mobile group like a free amino acid in solution works ",
+ "3-4 atoms in a widely mobile group (like a free amino acid in solution) works ",
"well, or select the protein backbone in a stable folded structure to get the SDF ",
"of solvent and look at the time-averaged solvation shell. ",
- "It is also possible using this program to generate the SDF based on some arbitrarty ",
+ "It is also possible using this program to generate the SDF based on some arbitrary ",
"Cartesian coordinate. To do that, simply omit the preliminary [TT]trjconv[tt] steps. \n",
"USAGE: \n",
"1. Use [TT]make_ndx[tt] to create a group containing the atoms around which you want the SDF \n",
"2. [TT]trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none[tt] \n",
"3. [TT]trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans[tt] \n",
"4. run [TT]g_spatial[tt] on the [TT].xtc[tt] output of step #3. \n",
- "5. Load grid.cube into VMD and view as an isosurface. \n",
- "*** Systems such as micelles will require [TT]trjconv -pbc cluster[tt] between steps 1 and 2\n",
- "WARNINGS: \n",
+ "5. Load [TT]grid.cube[tt] into VMD and view as an isosurface. \n",
+ "[BB]Note[bb] that systems such as micelles will require [TT]trjconv -pbc cluster[tt] between steps 1 and 2\n",
+ "WARNINGS:[BR]",
"The SDF will be generated for a cube that contains all bins that have some non-zero occupancy. ",
"However, the preparatory [TT]-fit rot+trans[tt] option to [TT]trjconv[tt] 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",
+ "BUGS:[BR]",
"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 [TT]-nab[tt] ",
+ "and the program is halted prior to the fault while displaying a warning message suggesting the use of the [TT]-nab[tt] (Number of Additional Bins)",
"option. However, the program does not detect all such events. If you encounter a segmentation fault, run it again ",
"with an increased [TT]-nab[tt] value. \n",
- "RISKY OPTIONS: \n",
+ "RISKY OPTIONS:[BR]",
"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 [TT]trjconv[tt]. ",
"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"
+ "memory is allocated for cube bins based on the initial coordinates and the [TT]-nab[tt] ",
+ "option value. \n"
};
static gmx_bool bPBC=FALSE;
"the inner product of the distance vector",
"and the dipole of the solvent molecule is determined.",
"For solvent molecules with net charge (ions), the net charge of the ion",
- "is subtracted evenly at all atoms in the selection of each ion.",
+ "is subtracted evenly from all atoms in the selection of each ion.",
"The average of these dipole components is printed.",
"The same is done for the polarization, where the average dipole is",
"subtracted from the instantaneous dipole. The magnitude of the average",
{
const char *desc[] = {
"[TT]g_tcaf[tt] computes tranverse current autocorrelations.",
- "These are used to estimate the shear viscosity eta.",
+ "These are used to estimate the shear viscosity, [GRK]eta[grk].",
"For details see: Palmer, JCP 49 (1994) pp 359-366.[PAR]",
"Transverse currents are calculated using the",
- "k-vectors (1,0,0) and (2,0,0) each also in the y- and z-direction,",
+ "k-vectors (1,0,0) and (2,0,0) each also in the [IT]y[it]- and [IT]z[it]-direction,",
"(1,1,0) and (1,-1,0) each also in the 2 other planes (these vectors",
"are not independent) and (1,1,1) and the 3 other box diagonals (also",
"not independent). For each k-vector the sine and cosine are used, in",
"combination with the velocity in 2 perpendicular directions. This gives",
"a total of 16*2*2=64 transverse currents. One autocorrelation is",
- "calculated fitted for each k-vector, which gives 16 tcaf's. Each of",
- "these tcaf's is fitted to f(t) = exp(-v)(cosh(Wv) + 1/W sinh(Wv)),",
- "v = -t/(2 tau), W = sqrt(1 - 4 tau eta/rho k^2), which gives 16 tau's",
- "and eta's. The fit weights decay with time as exp(-t/wt), the tcaf and",
+ "calculated fitted for each k-vector, which gives 16 TCAF's. Each of",
+ "these TCAF's is fitted to f(t) = exp(-v)(cosh(Wv) + 1/W sinh(Wv)),",
+ "v = -t/(2 [GRK]tau[grk]), W = sqrt(1 - 4 [GRK]tau[grk] [GRK]eta[grk]/[GRK]rho[grk] k^2), which gives 16 values of [GRK]tau[grk]",
+ "and [GRK]eta[grk]. The fit weights decay with time as exp(-t/wt), and the TCAF and",
"fit are calculated up to time 5*wt.",
- "The eta's should be fitted to 1 - a eta(k) k^2, from which",
+ "The [GRK]eta[grk] values should be fitted to 1 - a [GRK]eta[grk](k) k^2, from which",
"one can estimate the shear viscosity at k=0.[PAR]",
"When the box is cubic, one can use the option [TT]-oc[tt], which",
- "averages the tcaf's over all k-vectors with the same length.",
+ "averages the TCAF's over all k-vectors with the same length.",
"This results in more accurate tcaf's.",
- "Both the cubic tcaf's and fits are written to [TT]-oc[tt]",
- "The cubic eta estimates are also written to [TT]-ov[tt].[PAR]",
- "With option [TT]-mol[tt] the transverse current is determined of",
- "molecules instead of atoms. In this case the index group should",
+ "Both the cubic TCAF's and fits are written to [TT]-oc[tt]",
+ "The cubic [GRK]eta[grk] estimates are also written to [TT]-ov[tt].[PAR]",
+ "With option [TT]-mol[tt], the transverse current is determined of",
+ "molecules instead of atoms. In this case, the index group should",
"consist of molecule numbers instead of atom numbers.[PAR]",
"The k-dependent viscosities in the [TT]-ov[tt] file should be",
- "fitted to eta(k) = eta0 (1 - a k^2) to obtain the viscosity at",
+ "fitted to [GRK]eta[grk](k) = [GRK]eta[grk]0 (1 - a k^2) to obtain the viscosity at",
"infinite wavelength.[PAR]",
- "NOTE: make sure you write coordinates and velocities often enough.",
+ "[BB]Note:[bb] make sure you write coordinates and velocities often enough.",
"The initial, non-exponential, part of the autocorrelation function",
"is very important for obtaining a good fit."
};
{ "-dt", FALSE, etTIME,
{ &dt }, "Only write frame when t MOD dt = first time (%t)" },
{ "-prec", FALSE, etINT,
- { &prec }, "Precision for .xtc and .gro writing in number of decimal places" },
+ { &prec }, "Precision for [TT].xtc[tt] and [TT].gro[tt] writing in number of decimal places" },
{ "-vel", FALSE, etBOOL,
{ &bVels }, "Read and write velocities if possible" },
{ "-settime", FALSE, etBOOL,
{ "-sort", FALSE, etBOOL,
{ &bSort }, "Sort trajectory files (not frames)" },
{ "-keeplast", FALSE, etBOOL,
- { &bKeepLast }, "keep overlapping frames at end of trajectory" },
+ { &bKeepLast }, "Keep overlapping frames at end of trajectory" },
{ "-overwrite", FALSE, etBOOL,
- { &bOverwrite }, "overwrite overlapping frames during appending" },
+ { &bOverwrite }, "Overwrite overlapping frames during appending" },
{ "-cat", FALSE, etBOOL,
- { &bCat }, "do not discard double time frames" } };
+ { &bCat }, "Do not discard double time frames" } };
#define npargs asize(pa)
int ftpin, i, frame, frame_out, step = 0, trjout = 0;
t_trxstatus *status;
"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",
- "will be stored in the B-factor field in order to color with e.g. rasmol.",
+ "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",
"of radius [TT]-r[tt] around the reference group are printed."
"MPIRUN and MDRUN. If these are not present, 'mpirun' and 'mdrun'",
"will be used as defaults. Note that for certain MPI frameworks you",
"need to provide a machine- or hostfile. This can also be passed",
- "via the MPIRUN variable, e.g.",
+ "via the MPIRUN variable, e.g.[PAR]",
"[TT]export MPIRUN=\"/usr/local/mpirun -machinefile hosts\"[tt][PAR]",
"Please call [TT]g_tune_pme[tt] with the normal options you would pass to",
"[TT]mdrun[tt] and add [TT]-np[tt] for the number of processors to perform the",
"[TT]g_tune_pme[tt] 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",
"written with enlarged cutoffs and smaller fourier grids respectively.",
- "Typically, the first test (No. 0) will be with the settings from the input",
- "[TT].tpr[tt] file; the last test (No. [TT]ntpr[tt]) will have cutoffs multiplied",
+ "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 cutoffs multiplied",
"by (and at the same time fourier grid dimensions divided by) the scaling",
- "factor [TT]-fac[tt] (default 1.2). The remaining [TT].tpr[tt] files will have about equally",
- "spaced values inbetween these extremes. Note that you can set [TT]-ntpr[tt] to 1",
+ "factor [TT]-fac[tt] (default 1.2). The remaining [TT].tpr[tt] files will have about ",
+ "equally-spaced values in between these extremes. [BB]Note[bb] that you can set [TT]-ntpr[tt] to 1",
"if you just want to find the optimal number of PME-only nodes; in that case",
"your input [TT].tpr[tt] file will remain unchanged.[PAR]",
"For the benchmark runs, the default of 1000 time steps should suffice for most",
"are by default reset after 100 steps. For large systems",
"(>1M atoms) you may have to set [TT]-resetstep[tt] to a higher value.",
"From the 'DD' load imbalance entries in the md.log output file you",
- "can tell after how many steps the load is sufficiently balanced.[PAR]"
- "Example call: [TT]g_tune_pme -np 64 -s protein.tpr -launch[tt][PAR]",
+ "can tell after how many steps the load is sufficiently balanced. Example call:[PAR]"
+ "[TT]g_tune_pme -np 64 -s protein.tpr -launch[tt][PAR]",
"After calling [TT]mdrun[tt] several times, detailed performance information",
- "is available in the output file perf.out. ",
- "Note that during the benchmarks a couple of temporary files are written",
+ "is available in the output file [TT]perf.out.[tt] ",
+ "[BB]Note[bb] that during the benchmarks, a couple of temporary files are written",
"(options [TT]-b[tt]*), these will be automatically deleted after each test.[PAR]",
"If you want the simulation to be started automatically with the",
"optimized parameters, use the command line option [TT]-launch[tt].[PAR]",
{ "-np", FALSE, etINT, {&nnodes},
"Number of nodes to run the tests on (must be > 2 for separate PME nodes)" },
{ "-npstring", FALSE, etENUM, {procstring},
- "Specify the number of processors to $MPIRUN using this string"},
+ "Specify the number of processors to [TT]$MPIRUN[tt] using this string"},
{ "-passall", FALSE, etBOOL, {&bPassAll},
- "HIDDENPut arguments unknown to [TT]mdrun[tt] at the end of the command line. Can e.g. be used for debugging purposes. "},
+ "HIDDENPut arguments unknown to [TT]mdrun[tt] at the end of the command line. Can be used for debugging purposes. "},
{ "-nt", FALSE, etINT, {&nthreads},
"Number of threads to run the tests on (turns MPI & mpirun off)"},
{ "-r", FALSE, etINT, {&repeats},
{ "-downfac", FALSE, etREAL, {&downfac},
"Lower limit for rcoulomb scaling factor" },
{ "-ntpr", FALSE, etINT, {&ntprs},
- "Number of [TT].tpr[tt] files to benchmark. Create these many files with scaling factors ranging from 1.0 to fac. If < 1, automatically choose the number of [TT].tpr[tt] files to test" },
+ "Number of [TT].tpr[tt] files to benchmark. Create this many files with scaling factors ranging from 1.0 to fac. If < 1, automatically choose the number of [TT].tpr[tt] files to test" },
{ "-four", FALSE, etREAL, {&fs},
"Use this fourierspacing value instead of the grid found in the [TT].tpr[tt] input file. (Spacing applies to a scaling factor of 1.0 if multiple [TT].tpr[tt] files are written)" },
{ "-steps", FALSE, etGMX_LARGE_INT, {&bench_nsteps},
- "Take timings for these many steps in the benchmark runs" },
+ "Take timings for this many steps in the benchmark runs" },
{ "-resetstep",FALSE, etINT, {&presteps},
- "Let dlb equilibrate these many steps before timings are taken (reset cycle counters after these many steps)" },
+ "Let dlb equilibrate this many steps before timings are taken (reset cycle counters after this many steps)" },
{ "-simsteps", FALSE, etGMX_LARGE_INT, {&new_sim_nsteps},
- "If non-negative, perform these many steps in the real run (overwrite nsteps from [TT].tpr[tt], add [TT].cpt[tt] steps)" },
+ "If non-negative, perform this many steps in the real run (overwrites nsteps from [TT].tpr[tt], add [TT].cpt[tt] steps)" },
{ "-launch", FALSE, etBOOL, {&bLaunch},
"Lauch the real simulation after optimization" },
/******************/
{ "-rerunvsite", FALSE, etBOOL, {&bRerunVSite},
"HIDDENRecalculate virtual site coordinates with [TT]-rerun[tt]" },
{ "-ionize", FALSE, etBOOL, {&bIonize},
- "Do a simulation including the effect of an X-Ray bombardment on your system" },
+ "Do a simulation including the effect of an X-ray bombardment on your system" },
{ "-confout", FALSE, etBOOL, {&bConfout},
"HIDDENWrite the last configuration with [TT]-c[tt] and force checkpointing at the last step" },
{ "-stepout", FALSE, etINT, {&nstepout},
"which may be useful for, e.g. membranes.[PAR]",
"AUTOCORRELATIONS[BR]----------------[BR]",
"With [TT]-ac[tt], [TT]g_wham[tt] estimates the integrated autocorrelation ",
- "time (IACT) tau for each umbrella window and weights the respective ",
- "window with 1/[1+2*tau/dt]. The IACTs are written ",
+ "time (IACT) [GRK]tau[grk] for each umbrella window and weights the respective ",
+ "window with 1/[1+2*[GRK]tau[grk]/dt]. The IACTs are written ",
"to the file defined with [TT]-oiact[tt]. In verbose mode, all ",
"autocorrelation functions (ACFs) are written to [TT]hist_autocorr.xvg[tt]. ",
"Because the IACTs can be severely underestimated in case of limited ",
"sampling, option [TT]-acsig[tt] allows to smooth the IACTs along the ",
- "reaction coordinate with a Gaussian (sigma provided with [TT]-acsig[tt], ",
+ "reaction coordinate with a Gaussian ([GRK]sigma[grk] provided with [TT]-acsig[tt], ",
"see output in [TT]iact.xvg[tt]). Note that the IACTs are estimated by simple ",
"integration of the ACFs while the ACFs are larger 0.05.",
"If you prefer to compute the IACTs by a more sophisticated (but possibly ",
{ "-max", FALSE, etREAL, {&opt.max},
"Maximum coordinate in profile"},
{ "-auto", FALSE, etBOOL, {&opt.bAuto},
- "determine min and max automatically"},
+ "Determine min and max automatically"},
{ "-bins",FALSE, etINT, {&opt.bins},
"Number of bins in profile"},
{ "-temp", FALSE, etREAL, {&opt.Temperature},
{ "-tol", FALSE, etREAL, {&opt.Tolerance},
"Tolerance"},
{ "-v", FALSE, etBOOL, {&opt.verbose},
- "verbose mode"},
+ "Verbose mode"},
{ "-b", FALSE, etREAL, {&opt.tmin},
- "first time to analyse (ps)"},
+ "First time to analyse (ps)"},
{ "-e", FALSE, etREAL, {&opt.tmax},
- "last time to analyse (ps)"},
+ "Last time to analyse (ps)"},
{ "-dt", FALSE, etREAL, {&opt.dt},
"Analyse only every dt ps"},
{ "-histonly", FALSE, etBOOL, {&opt.bHistOnly},
{ "-log", FALSE, etBOOL, {&opt.bLog},
"Calculate the log of the profile before printing"},
{ "-unit", FALSE, etENUM, {en_unit},
- "energy unit in case of log output" },
+ "Energy unit in case of log output" },
{ "-zprof0", FALSE, etREAL, {&opt.zProf0},
"Define profile to 0.0 at this position (with [TT]-log[tt])"},
{ "-cycl", FALSE, etBOOL, {&opt.bCycl},
"Create cyclic/periodic profile. Assumes min and max are the same point."},
{ "-sym", FALSE, etBOOL, {&opt.bSym},
- "symmetrize profile around z=0"},
+ "Symmetrize profile around z=0"},
{ "-hist-eq", FALSE, etBOOL, {&opt.bHistEq},
"HIDDENEnforce equal weight for all histograms. (Non-Weighed-HAM)"},
{ "-ac", FALSE, etBOOL, {&opt.bCalcTauInt},
- "calculate integrated autocorrelation times and use in wham"},
+ "Calculate integrated autocorrelation times and use in wham"},
{ "-acsig", FALSE, etREAL, {&opt.sigSmoothIact},
- "Smooth autocorrelation times along reaction coordinate with Gaussian of this sigma"},
+ "Smooth autocorrelation times along reaction coordinate with Gaussian of this [GRK]sigma[grk]"},
{ "-ac-trestart", FALSE, etREAL, {&opt.acTrestart},
"When computing autocorrelation functions, restart computing every .. (ps)"},
{ "-acred", FALSE, etBOOL, {&opt.bAllowReduceIact},
{ "-nBootstrap", FALSE, etINT, {&opt.nBootStrap},
"nr of bootstraps to estimate statistical uncertainty (e.g., 200)" },
{ "-bs-method", FALSE, etENUM, {en_bsMethod},
- "bootstrap method" },
+ "Bootstrap method" },
{ "-bs-tau", FALSE, etREAL, {&opt.tauBootStrap},
"Autocorrelation time (ACT) assumed for all histograms. Use option [TT]-ac[tt] if ACT is unknown."},
{ "-bs-seed", FALSE, etINT, {&opt.bsSeed},
- "seed for bootstrapping. (-1 = use time)"},
+ "Seed for bootstrapping. (-1 = use time)"},
{ "-histbs-block", FALSE, etINT, {&opt.histBootStrapBlockLength},
- "when mixing histograms only mix within blocks of [TT]-histbs-block[tt]."},
+ "When mixing histograms only mix within blocks of [TT]-histbs-block[tt]."},
{ "-vbs", FALSE, etBOOL, {&opt.bs_verbose},
- "verbose bootstrapping. Print the CDFs and a histogram file for each bootstrap."},
+ "Verbose bootstrapping. Print the CDFs and a histogram file for each bootstrap."},
{ "-stepout", FALSE, etINT, {&opt.stepchange},
"HIDDENWrite maximum change every ... (set to 1 with [TT]-v[tt])"},
{ "-updateContr", FALSE, etINT, {&opt.stepUpdateContrib},
const char *desc[] = {
"[TT]g_wheel[tt] plots a helical wheel representation of your sequence.",
"The input sequence is in the [TT].dat[tt] file where the first line contains",
- "the number of residues and each consecutive line contains a residue"
+ "the number of residues and each consecutive line contains a residue "
"name."
};
output_env_t oenv;
"in the correct matrix format.",
"Matrix data may be generated by programs such as [TT]do_dssp[tt], [TT]g_rms[tt] or",
"[TT]g_mdmat[tt].[PAR]",
- "Parameters are set in the [TT]m2p[tt] file optionally supplied with",
- "[TT]-di[tt]. Reasonable defaults are provided. Settings for the y-axis",
- "default to those for the x-axis. Font names have a defaulting hierarchy:",
+ "Parameters are set in the [TT].m2p[tt] file optionally supplied with",
+ "[TT]-di[tt]. Reasonable defaults are provided. Settings for the [IT]y[it]-axis",
+ "default to those for the [IT]x[it]-axis. Font names have a defaulting hierarchy:",
"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 settings are taken from",
+ "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),",
+ "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 second matrix file can be supplied. Both matrix",
"files will be read simultaneously and the upper left half of the",
"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]",
+ "the [IT]y[it]-axis).[PAR]",
"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",
"J. Biomol. Struct. Dyn. 13 : 741-751 (1996)[BR]",
"B.L. de Groot, A.Amadei, R.M. Scheek, N.A.J. van Nuland and H.J.C. Berendsen; ",
"An extended sampling of the configurational space of HPr from E. coli",
- "PROTEINS: Struct. Funct. Gen. 26: 314-322 (1996)",
+ "Proteins: Struct. Funct. Gen. 26: 314-322 (1996)",
"[PAR]You will be prompted for one or more index groups that correspond to the eigenvectors,",
"reference structure, target positions, etc.[PAR]",
"[TT]-radfix[tt]: perform fixed-step radius expansion along selected eigenvectors.[PAR]",
"[TT]-radacc[tt]: perform acceptance radius expansion along selected eigenvectors.",
"(steps in the desired direction will be accepted, others will be rejected).",
- "Note: by default the starting MD structure will be taken as origin of the first",
+ "[BB]Note:[bb] by default the starting MD structure will be taken as origin of the first",
"expansion cycle for radius expansion. If [TT]-ori[tt] is specified, you will be able",
"to read in a structure file that defines an external origin.[PAR]",
"[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 .edo file[PAR]",
+ "[TT]-outfrq[tt]: frequency (in steps) of writing out projections etc. to [TT].edo[tt] 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 nodes. [PAR]",
"All output of [TT]mdrun[tt] (specify with [TT]-eo[tt]) is written to a .edo file. In the output",
"file, per OUTFRQ step the following information is present: [PAR]",
- "* the step number[BR]",
- "* the number of the ED dataset. (Note that you can impose multiple ED constraints in",
- "a single simulation - on different molecules e.g. - if several .edi files were concatenated",
- "first. The constraints are applied in the order they appear in the .edi file.) [BR]",
- "* RMSD (for atoms involved in fitting prior to calculating the ED constraints)[BR]",
+ "[TT]*[tt] the step number[BR]",
+ "[TT]*[tt] the number of the ED dataset. ([BB]Note[bb] that you can impose multiple ED constraints 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.) [BR]",
+ "[TT]*[tt] RMSD (for atoms involved in fitting prior to calculating the ED constraints)[BR]",
"* projections of the positions onto selected eigenvectors[BR]",
"[PAR][PAR]",
"FLOODING:[PAR]",
- "with -flood you can specify which eigenvectors are used to compute a flooding potential,",
+ "with [TT]-flood[tt], you can specify which eigenvectors are used to compute a flooding potential,",
"which will lead to extra forces expelling the structure out of the region described",
"by the covariance matrix. If you switch -restrain the potential is inverted and the structure",
"is kept in that region.",
"[PAR]",
- "The origin is normally the average structure stored in the eigvec.trr file.",
- "It can be changed with -ori to an arbitrary position in configurational space.",
- "With -tau, -deltaF0 and -Eflnull you control the flooding behaviour.",
+ "The origin is normally the average structure stored in the [TT]eigvec.trr[tt] file.",
+ "It can be changed with [TT]-ori[tt] to an arbitrary position in configurational space.",
+ "With [TT]-tau[tt], [TT]-deltaF0[tt], and [TT]-Eflnull[tt] you control the flooding behaviour.",
"Efl is the flooding strength, it is updated according to the rule of adaptive flooding.",
- "Tau is the time constant of adaptive flooding, high tau means slow adaption (i.e. growth). ",
+ "Tau is the time constant of adaptive flooding, high [GRK]tau[grk] means slow adaption (i.e. growth). ",
"DeltaF0 is the flooding strength you want to reach after tau ps of simulation.",
- "To use constant Efl set -tau to zero.",
+ "To use constant Efl set [TT]-tau[tt] to zero.",
"[PAR]",
- "-alpha is a fudge parameter to control the width of the flooding potential. A value of 2 has been found",
+ "[TT]-alpha[tt] is a fudge parameter to control the width of the flooding potential. A value of 2 has been found",
"to give good results for most standard cases in flooding of proteins.",
- "Alpha basically accounts for incomplete sampling, if you sampled further the width of the ensemble would",
- "increase, this is mimicked by alpha>1.",
- "For restraining alpha<1 can give you smaller width in the restraining potential.",
+ "[GRK]alpha[grk] basically accounts for incomplete sampling, if you sampled further the width of the ensemble would",
+ "increase, this is mimicked by [GRK]alpha[grk] > 1.",
+ "For restraining, [GRK]alpha[grk] < 1 can give you smaller width in the restraining potential.",
"[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 .edi file under DELTA_F0 and EFL_NULL."
+ "the output file and manually put them into the [TT].edi[tt] file under DELTA_F0 and EFL_NULL."
};
/* Save all the params in this struct and then save it in an edi file.
"All these programs can generate default index groups. You ONLY",
"have to use [TT]make_ndx[tt] when you need SPECIAL index groups.",
"There is a default index group for the whole system, 9 default",
- "index groups are generated for proteins, a default index group",
+ "index groups for proteins, and a default index group",
"is generated for every other residue name.[PAR]",
"When no index file is supplied, also [TT]make_ndx[tt] will generate the",
"default groups.",
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff