/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, 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.
+ *
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*
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+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+#include <math.h>
#include <stdio.h>
#include <stdlib.h>
-#include <math.h>
#include <string.h>
-#include "statutil.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "smalloc.h"
-#include "macros.h"
-#include "gmx_fatal.h"
-#include "vec.h"
-#include "copyrite.h"
-#include "futil.h"
-#include "statutil.h"
-#include "txtdump.h"
-#include "enxio.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/fileio/enxio.h"
#include "gstat.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/viewit.h"
#include "gmx_ana.h"
-
+#include "gromacs/fileio/trxio.h"
typedef struct {
int nlj, nqq;
int gmx_lie(int argc, char *argv[])
{
const char *desc[] = {
- "[TT]g_lie[tt] computes a free energy estimate based on an energy analysis",
- "from. One needs an energy file with the following components:",
- "Coul (A-B) LJ-SR (A-B) etc."
+ "[THISMODULE] computes a free energy estimate based on an energy analysis",
+ "from nonbonded energies. One needs an energy file with the following components:",
+ "Coul-(A-B) LJ-SR (A-B) etc.[PAR]",
+ "To utilize [TT]g_lie[tt] correctly, two simulations are required: one with the",
+ "molecule of interest bound to its receptor and one with the molecule in water.",
+ "Both need to utilize [TT]energygrps[tt] such that Coul-SR(A-B), LJ-SR(A-B), etc. terms",
+ "are written to the [TT].edr[tt] file. Values from the molecule-in-water simulation",
+ "are necessary for supplying suitable values for -Elj and -Eqq."
};
static real lie_lj = 0, lie_qq = 0, fac_lj = 0.181, fac_qq = 0.5;
static const char *ligand = "none";
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
- NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
+ NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
fp = open_enx(ftp2fn(efEDR, NFILE, fnm), "r");
do_enxnms(fp, &nre, &enm);
ld = analyze_names(nre, enm, ligand);
snew(fr, 1);
+
out = xvgropen(ftp2fn(efXVG, NFILE, fnm), "LIE free energy estimate",
"Time (ps)", "DGbind (kJ/mol)", oenv);
while (do_enx(fp, fr))
}
}
close_enx(fp);
- ffclose(out);
+ gmx_ffclose(out);
fprintf(stderr, "\n");
if (nframes > 0)
do_view(oenv, ftp2fn(efXVG, NFILE, fnm), "-nxy");
- thanx(stderr);
-
return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff