static const char *desc[] = {
"[TT]make_edi[tt] generates an essential dynamics (ED) sampling input file to be used with [TT]mdrun[tt]",
"based on eigenvectors of a covariance matrix ([TT]g_covar[tt]) or from a",
- "normal modes anaysis ([TT]g_nmeig[tt]).",
+ "normal modes analysis ([TT]g_nmeig[tt]).",
"ED sampling can be used to manipulate the position along collective coordinates",
"(eigenvectors) of (biological) macromolecules during a simulation. Particularly,",
"it may be used to enhance the sampling efficiency of MD simulations by stimulating",
"[TT]-radcon[tt]: perform acceptance radius contraction along selected eigenvectors",
"towards a target structure specified with [TT]-tar[tt].[PAR]",
"NOTE: each eigenvector can be selected only once. [PAR]",
- "[TT]-outfrq[tt]: frequency (in steps) of writing out projections etc. to [TT].edo[tt] file[PAR]",
+ "[TT]-outfrq[tt]: frequency (in steps) of writing out projections etc. to [TT].xvg[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]",
"before a new cycle is started.[PAR]",
"Note on the parallel implementation: since ED sampling is a 'global' thing",
"(collective coordinates etc.), at least on the 'protein' side, ED sampling",
- "is not very parallel-friendly from an implentation point of view. Because",
+ "is not very parallel-friendly from an implementation point of view. Because",
"parallel ED requires some extra communication, expect the performance to be",
- "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]",
- "[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",
+ "lower as in a free MD simulation, especially on a large number of nodes and/or",
+ "when the ED group contains a lot of atoms. [PAR]",
+ "Please also note that if your ED group contains more than a single protein,",
+ "then the [TT].tpr[tt] file must contain the correct PBC representation of the ED group.",
+ "Take a look on the initial RMSD from the reference structure, which is printed",
+ "out at the start of the simulation; if this is much higher than expected, one",
+ "of the ED molecules might be shifted by a box vector. [PAR]",
+ "All ED-related output of [TT]mdrun[tt] (specify with [TT]-eo[tt]) is written to a [TT].xvg[tt] file",
+ "as a function of time in intervals of OUTFRQ steps.[PAR]",
+ "[BB]Note[bb] that you can impose multiple ED constraints and flooding potentials in",
"a single simulation (on different molecules) if several [TT].edi[tt] files were concatenated",
- "first. The constraints are applied in the order they appear in the [TT].edi[tt] file.) [BR]",
- "[TT]*[tt] RMSD (for atoms involved in fitting prior to calculating the ED constraints)[BR]",
- "* projections of the positions onto selected eigenvectors[BR]",
+ "first. The constraints are applied in the order they appear in the [TT].edi[tt] file. ",
+ "Depending on what was specified in the [TT].edi[tt] input file, the output file contains for each ED dataset[PAR]",
+ "[TT]*[tt] the RMSD of the fitted molecule to the reference structure (for atoms involved in fitting prior to calculating the ED constraints)[BR]",
+ "[TT]*[tt] projections of the positions onto selected eigenvectors[BR]",
"[PAR][PAR]",
"FLOODING:[PAR]",
"with [TT]-flood[tt], you can specify which eigenvectors are used to compute a flooding potential,",
"is kept in that region.",
"[PAR]",
"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.",
+ "It can be changed with [TT]-ori[tt] to an arbitrary position in configuration 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 [GRK]tau[grk] means slow adaption (i.e. growth). ",
{ "-flood", FALSE, etSTR, {&evSelections[2]},
"Indices of eigenvectors for flooding"},
{ "-outfrq", FALSE, etINT, {&edi_params.outfrq},
- "Freqency (in steps) of writing output in [TT].edo[tt] file" },
+ "Freqency (in steps) of writing output in [TT].xvg[tt] file" },
{ "-slope", FALSE, etREAL, { &edi_params.slope},
"Minimal slope in acceptance radius expansion"},
{ "-linstep", FALSE, etSTR, {&evParams[0]},
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff