"[THISMODULE] is an analysis program that implements the Weighted",
"Histogram Analysis Method (WHAM). It is intended to analyze",
"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",
- " file names of the umbrella simulation run-input files ([REF].tpr[ref] files),",
- " AND, with option [TT]-ix[tt], a file which contains file names of",
- " the pullx [TT]mdrun[tt] output files. The [REF].tpr[ref] and pullx files must",
- " be in corresponding order, i.e. the first [REF].tpr[ref] created the",
- " first pullx, etc.[BR]",
- "[TT]*[tt] Same as the previous input mode, except that the the user",
- " provides the pull force output file names ([TT]pullf.xvg[tt]) with option [TT]-if[tt].",
- " From the pull force the position in the umbrella potential is",
- " computed. This does not work with tabulated umbrella potentials.[BR]"
- "[TT]*[tt] With option [TT]-ip[tt], the user provides file names of (gzipped) [REF].pdo[ref] files, i.e.",
- " the GROMACS 3.3 umbrella output files. If you have some unusual"
- " reaction coordinate you may also generate your own [REF].pdo[ref] files and",
- " feed them with the [TT]-ip[tt] option into to [THISMODULE]. The [REF].pdo[ref] file header",
- " must be similar to the following::",
+ "compute a potential of mean force (PMF).",
"",
- " # UMBRELLA 3.0",
- " # Component selection: 0 0 1",
- " # nSkip 1",
- " # Ref. Group 'TestAtom'",
- " # Nr. of pull groups 2",
- " # Group 1 'GR1' Umb. Pos. 5.0 Umb. Cons. 1000.0",
- " # Group 2 'GR2' Umb. Pos. 2.0 Umb. Cons. 500.0",
- " #####",
+ "At present, three input modes are supported.",
+ "",
+ " * With option [TT]-it[tt], the user provides a file which contains the",
+ " file names of the umbrella simulation run-input files ([REF].tpr[ref] files),",
+ " AND, with option [TT]-ix[tt], a file which contains file names of",
+ " the pullx [TT]mdrun[tt] output files. The [REF].tpr[ref] and pullx files must",
+ " be in corresponding order, i.e. the first [REF].tpr[ref] created the",
+ " first pullx, etc.",
+ " * Same as the previous input mode, except that the the user",
+ " provides the pull force output file names ([TT]pullf.xvg[tt]) with option [TT]-if[tt].",
+ " From the pull force the position in the umbrella potential is",
+ " computed. This does not work with tabulated umbrella potentials.",
+ " * With option [TT]-ip[tt], the user provides file names of (gzipped) [REF].pdo[ref] files, i.e.",
+ " the GROMACS 3.3 umbrella output files. If you have some unusual"
+ " reaction coordinate you may also generate your own [REF].pdo[ref] files and",
+ " feed them with the [TT]-ip[tt] option into to [THISMODULE]. The [REF].pdo[ref] file header",
+ " must be similar to the following::",
+ "",
+ " # UMBRELLA 3.0",
+ " # Component selection: 0 0 1",
+ " # nSkip 1",
+ " # Ref. Group 'TestAtom'",
+ " # Nr. of pull groups 2",
+ " # Group 1 'GR1' Umb. Pos. 5.0 Umb. Cons. 1000.0",
+ " # Group 2 'GR2' Umb. Pos. 2.0 Umb. Cons. 500.0",
+ " #####",
+ "",
+ " The number of pull groups, umbrella positions, force constants, and names ",
+ " may (of course) differ. Following the header, a time column and ",
+ " a data column for each pull group follows (i.e. the displacement",
+ " with respect to the umbrella center). Up to four pull groups are possible ",
+ " per [REF].pdo[ref] file at present.",
"",
- "The number of pull groups, umbrella positions, force constants, and names ",
- "may (of course) differ. Following the header, a time column and ",
- "a data column for each pull group follows (i.e. the displacement",
- "with respect to the umbrella center). Up to four pull groups are possible ",
- "per [REF].pdo[ref] file at present.[PAR]",
"By default, all pull groups found in all pullx/pullf files are used in WHAM. If only ",
"some of the pull groups should be used, a pull group selection file (option [TT]-is[tt]) can ",
"be provided. The selection file must contain one line for each tpr file in tpr-files.dat.",
" 1 1 0 0",
" 1 1 0 0",
"",
- "By default, the output files are[BR]",
- " [TT]-o[tt] PMF output file[BR]",
- " [TT]-hist[tt] Histograms output file[BR]",
+ "By default, the output files are",
+ "",
+ " * [TT]-o[tt] PMF output file",
+ " * [TT]-hist[tt] Histograms output file",
+ "",
"Always check whether the histograms sufficiently overlap.[PAR]",
"The umbrella potential is assumed to be harmonic and the force constants are ",
"read from the [REF].tpr[ref] or [REF].pdo[ref] files. If a non-harmonic umbrella force was applied ",
"a tabulated potential can be provided with [TT]-tab[tt].[PAR]",
"WHAM OPTIONS[BR]------------[BR]",
- " [TT]-bins[tt] Number of bins used in analysis[BR]",
- " [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]",
+ "",
+ " * [TT]-bins[tt] Number of bins used in analysis",
+ " * [TT]-temp[tt] Temperature in the simulations",
+ " * [TT]-tol[tt] Stop iteration if profile (probability) changed less than tolerance",
+ " * [TT]-auto[tt] Automatic determination of boundaries",
+ " * [TT]-min,-max[tt] Boundaries of the profile",
+ "",
"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 ",
"Statistical errors may be estimated with bootstrap analysis. Use it with care, ",
"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) 6: 3713-3720.[BR]",
+ "Hub, de Groot and Van der Spoel, JCTC (2010) 6: 3713-3720.",
"[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",
- "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]",
- "(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].[PAR]"
- "Bootstrapping output:[BR]",
- " [TT]-bsres[tt] Average profile and standard deviations[BR]",
- " [TT]-bsprof[tt] All bootstrapping profiles[BR]",
+ "selected with [TT]-bs-method[tt].",
+ "",
+ " * [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.",
+ " * [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.",
+ " * [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.",
+ " * [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].",
+ "",
+ "Bootstrapping output:",
+ "",
+ " * [TT]-bsres[tt] Average profile and standard deviations",
+ " * [TT]-bsprof[tt] All bootstrapping profiles",
+ "",
"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."
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff