"output files generated by umbrella sampling simulations to ",
"compute a potential of mean force (PMF). [PAR] ",
"At present, three input modes are supported.[BR]",
- "[TT]*[tt] With option [TT]-it[tt], the user provides a file which contains the[BR]",
- " file names of the umbrella simulation run-input files (tpr files),[BR]",
- " AND, with option [TT]-ix[tt], a file which contains file names of [BR]",
- " the pullx mdrun output files. The tpr and pullx files must [BR]",
- " be in corresponding order, i.e. the first tpr created the [BR]",
- " first pullx, etc.[BR]",
- "[TT]*[tt] Same as the previous input mode, except that the the user [BR]",
- " provides the pull force output file names (pullf.xvg) with option [TT]-if[tt].[BR]",
- " From the pull force the position in the umbrella potential is [BR]",
- " computed. This does not work with tabulated umbrella potentials.[BR]"
- "[TT]*[tt] With option [TT]-ip[tt], the user provides file names of (gzipped) pdo files, i.e.[BR]",
- " the gromacs 3.3 umbrella output files. If you have some unusual[BR]"
- " reaction coordinate you may also generate your own pdo files and [BR]",
- " feed them with the [TT]-ip[tt] option into to g_wham. The pdo file header [BR]",
- " must be similar to the following:[BR]",
+ "[TT]*[tt] With option [TT]-it[tt], the user provides a file which contains the",
+ " file names of the umbrella simulation run-input files (tpr files),",
+ " AND, with option [TT]-ix[tt], a file which contains file names of",
+ " the pullx mdrun output files. The tpr and pullx files must",
+ " be in corresponding order, i.e. the first tpr created the",
+ " first pullx, etc.[BR]",
+ "[TT]*[tt] Same as the previous input mode, except that the the user",
+ " provides the pull force output file names (pullf.xvg) with option [TT]-if[tt].",
+ " From the pull force the position in the umbrella potential is",
+ " computed. This does not work with tabulated umbrella potentials.[BR]"
+ "[TT]*[tt] With option [TT]-ip[tt], the user provides file names of (gzipped) pdo files, i.e.",
+ " the GROMACS 3.3 umbrella output files. If you have some unusual"
+ " reaction coordinate you may also generate your own pdo files and",
+ " feed them with the [TT]-ip[tt] option into to g_wham. The pdo file header",
+ " must be similar to the following:[PAR]",
"[TT]# UMBRELLA 3.0[BR]",
"# Component selection: 0 0 1[BR]",
"# nSkip 1[BR]",
"# Nr. of pull groups 2[BR]",
"# Group 1 'GR1' Umb. Pos. 5.0 Umb. Cons. 1000.0[BR]",
"# Group 2 'GR2' Umb. Pos. 2.0 Umb. Cons. 500.0[BR]",
- "#####[tt][BR]",
- "Nr of pull groups, umbrella positions, force constants, and names ",
+ "#####[tt][PAR]",
+ "The number of pull groups, umbrella positions, force constants, and names ",
"may (of course) differ. Following the header, a time column and ",
- "a data columns for each pull group follows (i.e. the displacement",
+ "a data column for each pull group follows (i.e. the displacement",
"with respect to the umbrella center). Up to four pull groups are possible ",
"per pdo file at present.[PAR]",
"By default, the output files are[BR]",
" [TT]-o[tt] PMF output file[BR]",
- " [TT]-hist[tt] histograms output file[BR]",
- "Always check whether the histograms sufficiently overlap![PAR]",
+ " [TT]-hist[tt] Histograms output file[BR]",
+ "Always check whether the histograms sufficiently overlap.[PAR]",
"The umbrella potential is assumed to be harmonic and the force constants are ",
"read from the tpr or pdo files. If a non-harmonic umbrella force was applied ",
"a tabulated potential can be provided with [TT]-tab[tt].[PAR]",
"WHAM OPTIONS[BR]------------[BR]",
- " [TT]-bins[tt] Nr of bins used in analysis[BR]",
+ " [TT]-bins[tt] Number of bins used in analysis[BR]",
" [TT]-temp[tt] Temperature in the simulations[BR]",
" [TT]-tol[tt] Stop iteration if profile (probability) changed less than tolerance[BR]",
" [TT]-auto[tt] Automatic determination of boundaries[BR]",
" [TT]-min,-max[tt] Boundaries of the profile [BR]",
- "The data points which are used ",
- "to compute the profile can be restricted with options [TT]-b[tt], [TT]-e[tt], and [TT]-dt[tt]. ",
- "Play particularly with [TT]-b[tt] to ensure sufficient equilibration in each ",
- "umbrella window![PAR]",
- "With [TT]-log[tt] (default) the profile is written in energy units, otherwise ([TT]-nolog[tt]) as ",
- "probability. The unit can be specified with [TT]-unit[tt]. With energy output, ",
- "the energy in the first bin is defined to be zero. If you want the free energy at a different ",
- "position to be zero, choose with [TT]-zprof0[tt] (useful with bootstrapping, see below).[PAR]",
- "For cyclic (or periodic) reaction coordinates (dihedral angle, channel PMF",
+ "The data points that are used to compute the profile",
+ "can be restricted with options [TT]-b[tt], [TT]-e[tt], and [TT]-dt[tt]. ",
+ "Adjust [TT]-b[tt] to ensure sufficient equilibration in each ",
+ "umbrella window.[PAR]",
+ "With [TT]-log[tt] (default) the profile is written in energy units, otherwise ",
+ "(with [TT]-nolog[tt]) as probability. The unit can be specified with [TT]-unit[tt]. ",
+ "With energy output, the energy in the first bin is defined to be zero. ",
+ "If you want the free energy at a different ",
+ "position to be zero, set [TT]-zprof0[tt] (useful with bootstrapping, see below).[PAR]",
+ "For cyclic or periodic reaction coordinates (dihedral angle, channel PMF",
"without osmotic gradient), the option [TT]-cycl[tt] is useful. g_wham will make use of the ",
"periodicity of the system and generate a periodic PMF. The first and the last bin of the",
- "reaction coordinate will assumed be be neighbors[PAR]",
- "Option [TT]-sym[tt] symmetrizes the profile around z=0 before output (useful for membrane etc.)[PAR]",
+ "reaction coordinate will assumed be be neighbors.[PAR]",
+ "Option [TT]-sym[tt] symmetrizes the profile around z=0 before output, ",
+ "which may be useful for, e.g. membranes.[PAR]",
"AUTOCORRELATIONS[BR]----------------[BR]",
- "With [TT]-ac[tt], g_wham 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 ",
- "to the file defined with [TT]-oiact[tt]. In verbose mode, all autocorrelation functions (ACFs) are",
- "written to hist_autocorr.xvg. 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], see output in iact.xvg). 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 less robust) method ",
- "such as fitting to a double exponential, you can compute the IACTs with g_analyze and provide",
- "them to g_wham with the file iact-in.dat (option [TT]-iiact[tt]). iact-in.dat should contain ",
- "one line per input file (pdo or pullx/f file) and one column per pull group in the respective file.[PAR]"
+ "With [TT]-ac[tt], g_wham 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 ",
+ "to the file defined with [TT]-oiact[tt]. In verbose mode, all ",
+ "autocorrelation functions (ACFs) are written to hist_autocorr.xvg. ",
+ "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], ",
+ "see output in iact.xvg). 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 ",
+ "less robust) method such as fitting to a double exponential, you can ",
+ "compute the IACTs with g_analyze and provide them to g_wham with the file ",
+ "iact-in.dat (option [TT]-iiact[tt]), which should contain one line per ",
+ "input file (pdo or pullx/f file) and one column per pull group in the respective file.[PAR]",
"ERROR ANALYSIS[BR]--------------[BR]",
"Statistical errors may be estimated with bootstrap analysis. Use it with care, ",
- "otherwise the statistical error may be substantially underestimated !![BR]",
+ "otherwise the statistical error may be substantially underestimated. ",
"More background and examples for the bootstrap technique can be found in ",
- "Hub, de Groot and Van der Spoel, JCTC (2010)[BR]",
- "-nBootstrap defines the nr of bootstraps (use, e.g., 100). Four bootstrapping methods are supported and ",
+ "Hub, de Groot and Van der Spoel, JCTC (2010) 6: 3713-3720.[BR]",
+ "[TT]-nBootstrap[tt] defines the number of bootstraps (use, e.g., 100). ",
+ "Four bootstrapping methods are supported and ",
"selected with [TT]-bs-method[tt].[BR]",
- " (1) [TT]b-hist[tt] Default: complete histograms are considered as independent data points, and ",
- " the bootstrap is carried out by assigning random weights to the histograms (\"Bayesian bootstrap\").",
- " Note that each point along the reaction coordinate",
+ " (1) [TT]b-hist[tt] Default: complete histograms are considered as independent ",
+ "data points, and the bootstrap is carried out by assigning random weights to the ",
+ "histograms (\"Bayesian bootstrap\"). Note that each point along the reaction coordinate",
"must be covered by multiple independent histograms (e.g. 10 histograms), otherwise the ",
- "statistical error is underestimated![BR]",
- " (2) [TT]hist[tt] Complete histograms are considered as independent data points. For each",
- "bootstrap, N histograms are randomly chosen from the N given histograms (allowing duplication, i.e. ",
- "sampling with replacement).",
- "To avoid gaps without data along the reaction coordinate blocks of histograms ([TT]-histbs-block[tt])",
- "may be defined. In that case, the given histograms are divided into blocks and ",
- "only histograms within each block are mixed. Note that the histograms",
- "within each block must be representative for all possible histograms, otherwise the",
- "statistical error is underestimated![BR]",
+ "statistical error is underestimated.[BR]",
+ " (2) [TT]hist[tt] Complete histograms are considered as independent data points. ",
+ "For each bootstrap, N histograms are randomly chosen from the N given histograms ",
+ "(allowing duplication, i.e. sampling with replacement).",
+ "To avoid gaps without data along the reaction coordinate blocks of histograms ",
+ "([TT]-histbs-block[tt]) may be defined. In that case, the given histograms are ",
+ "divided into blocks and only histograms within each block are mixed. Note that ",
+ "the histograms within each block must be representative for all possible histograms, ",
+ "otherwise the statistical error is underestimated.[BR]",
" (3) [TT]traj[tt] The given histograms are used to generate new random trajectories,",
"such that the generated data points are distributed according the given histograms ",
- "and properly autocorrelated. The ",
- "autocorrelation time (ACT) for each window must be known, so use [TT]-ac[tt] or provide the ACT",
- "with [TT]-iiact[tt]. If the ACT of all windows are identical (and known), you can also ",
- "provide them with [TT]-bs-tau[tt]. Note that this method may severely underestimate the error ",
- "in case of limited sampling, that is if individual histograms do not represent the complete",
- "phase space at the respective positions.[BR]",
- " (4) [TT]traj-gauss[tt] The same as Method [TT]traj[tt], but the trajectories are not bootstrapped ",
- "from the umbrella histograms but from Gaussians with the average and width of the umbrella ",
- "histograms. That method yields similar error estimates like method [TT]traj[tt].[BR]"
+ "and properly autocorrelated. The autocorrelation time (ACT) for each window must be ",
+ "known, so use [TT]-ac[tt] or provide the ACT with [TT]-iiact[tt]. If the ACT of all ",
+ "windows are identical (and known), you can also provide them with [TT]-bs-tau[tt]. ",
+ "Note that this method may severely underestimate the error in case of limited sampling, ",
+ "that is if individual histograms do not represent the complete phase space at ",
+ "the respective positions.[BR]",
+ " (4) [TT]traj-gauss[tt] The same as method [TT]traj[tt], but the trajectories are ",
+ "not bootstrapped from the umbrella histograms but from Gaussians with the average ",
+ "and width of the umbrella histograms. That method yields similar error estimates ",
+ "like method [TT]traj[tt].[PAR]"
"Bootstrapping output:[BR]",
" [TT]-bsres[tt] Average profile and standard deviations[BR]",
" [TT]-bsprof[tt] All bootstrapping profiles[BR]",
- "With [TT]-vbs[tt] (verbose bootstrapping), the histograms of each bootstrap are written, and, ",
- "with bootstrap method [TT]traj[tt], the cumulative distribution functions of the histograms.",
+ "With [TT]-vbs[tt] (verbose bootstrapping), the histograms of each bootstrap are written, ",
+ "and, with bootstrap method [TT]traj[tt], the cumulative distribution functions of ",
+ "the histograms."
};
const char *en_unit[]={NULL,"kJ","kCal","kT",NULL};
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff