/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* on the code from g_anaeig. You can reach him as olange@gwdg.de. He
* probably also holds copyright to the following code.
*/
-#include "config.h"
+#include "gmxpre.h"
+#include <ctype.h>
#include <math.h>
#include <stdlib.h>
-#include <ctype.h>
#include <string.h>
-#include "gromacs/legacyheaders/readinp.h"
+
#include "gromacs/commandline/pargs.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/eigio.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/readinp.h"
#include "gromacs/legacyheaders/txtdump.h"
-#include "eigio.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
#include "gromacs/topology/index.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
typedef struct
{
"to keep the position along a certain (set of) coordinate(s) fixed ([TT]-linfix[tt]),",
"or to only monitor the projections of the positions onto",
"these coordinates ([TT]-mon[tt]).[PAR]",
- "References:[BR]",
+ "References:[PAR]",
"A. Amadei, A.B.M. Linssen, B.L. de Groot, D.M.F. van Aalten and ",
"H.J.C. Berendsen; An efficient method for sampling the essential subspace ",
- "of proteins., J. Biomol. Struct. Dyn. 13:615-626 (1996)[BR]",
+ "of proteins., J. Biomol. Struct. Dyn. 13:615-626 (1996)[PAR]",
"B.L. de Groot, A. Amadei, D.M.F. van Aalten and H.J.C. Berendsen; ",
"Towards an exhaustive sampling of the configurational spaces of the ",
"two forms of the peptide hormone guanylin,",
- "J. Biomol. Struct. Dyn. 13 : 741-751 (1996)[BR]",
+ "J. Biomol. Struct. Dyn. 13 : 741-751 (1996)[PAR]",
"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)",
"[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].xvg[tt] file[PAR]",
+ "[TT]-outfrq[tt]: frequency (in steps) of writing out projections etc. to [REF].xvg[ref] 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 ranks 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.",
+ "then the [REF].tpr[ref] 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",
+ "All ED-related output of [TT]mdrun[tt] (specify with [TT]-eo[tt]) is written to a [REF].xvg[ref] 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. ",
- "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]",
+ "a single simulation (on different molecules) if several [REF].edi[ref] files were concatenated",
+ "first. The constraints are applied in the order they appear in the [REF].edi[ref] file. ",
+ "Depending on what was specified in the [REF].edi[ref] input file, the output file contains for each ED dataset",
+ "",
+ " * the RMSD of the fitted molecule to the reference structure (for atoms involved in fitting prior to calculating the ED constraints)",
+ " * projections of the positions onto selected eigenvectors",
+ "",
"FLOODING:[PAR]",
"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",
"[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 [TT].edi[tt] file under DELTA_F0 and EFL_NULL."
+ "the output file and manually put them into the [REF].edi[ref] file under DELTA_F0 and EFL_NULL."
};
/* Save all the params in this struct and then save it in an edi file.
{ "-flood", FALSE, etSTR, {&evSelections[2]},
"Indices of eigenvectors for flooding"},
{ "-outfrq", FALSE, etINT, {&edi_params.outfrq},
- "Freqency (in steps) of writing output in [TT].xvg[tt] file" },
+ "Freqency (in steps) of writing output in [REF].xvg[ref] 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