"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.
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff