src/tools/gmx_lie.c

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  38 #ifdef HAVE_CONFIG_H
  39 #include <config.h>
  40 #endif
  41
  42 #include <stdio.h>
  43 #include <stdlib.h>
  44 #include <math.h>
  45 #include <string.h>
  46
  47 #include "statutil.h"
  48 #include "sysstuff.h"
  49 #include "typedefs.h"
  50 #include "smalloc.h"
  51 #include "macros.h"
  52 #include "gmx_fatal.h"
  53 #include "vec.h"
  54 #include "copyrite.h"
  55 #include "futil.h"
  56 #include "statutil.h"
  57 #include "txtdump.h"
  58 #include "enxio.h"
  59 #include "gstat.h"
  60 #include "xvgr.h"
  61 #include "gmx_ana.h"
  62
  63
  64 typedef struct {
  65     int  nlj, nqq;
  66     int *lj;
  67     int *qq;
  68 } t_liedata;
  69
  70 static t_liedata *analyze_names(int nre, gmx_enxnm_t *names, const char *ligand)
  71 {
  72     int        i;
  73     t_liedata *ld;
  74     char       self[256];
  75
  76     /* Skip until we come to pressure */
  77     for (i = 0; (i < F_NRE); i++)
  78     {
  79         if (strcmp(names[i].name, interaction_function[F_PRES].longname) == 0)
  80         {
  81             break;
  82         }
  83     }
  84
  85     /* Now real analysis: find components of energies */
  86     sprintf(self, "%s-%s", ligand, ligand);
  87     snew(ld, 1);
  88     for (; (i < nre); i++)
  89     {
  90         if ((strstr(names[i].name, ligand) != NULL) &&
  91             (strstr(names[i].name, self) == NULL))
  92         {
  93             if (strstr(names[i].name, "LJ") != NULL)
  94             {
  95                 ld->nlj++;
  96                 srenew(ld->lj, ld->nlj);
  97                 ld->lj[ld->nlj-1] = i;
  98             }
  99             else if (strstr(names[i].name, "Coul") != NULL)
 100             {
 101                 ld->nqq++;
 102                 srenew(ld->qq, ld->nqq);
 103                 ld->qq[ld->nqq-1] = i;
 104             }
 105         }
 106     }
 107     printf("Using the following energy terms:\n");
 108     printf("LJ:  ");
 109     for (i = 0; (i < ld->nlj); i++)
 110     {
 111         printf("  %12s", names[ld->lj[i]].name);
 112     }
 113     printf("\nCoul:");
 114     for (i = 0; (i < ld->nqq); i++)
 115     {
 116         printf("  %12s", names[ld->qq[i]].name);
 117     }
 118     printf("\n");
 119
 120     return ld;
 121 }
 122
 123 real calc_lie(t_liedata *ld, t_energy ee[], real lie_lj, real lie_qq,
 124               real fac_lj, real fac_qq)
 125 {
 126     int  i;
 127     real lj_tot, qq_tot;
 128
 129     lj_tot = 0;
 130     for (i = 0; (i < ld->nlj); i++)
 131     {
 132         lj_tot += ee[ld->lj[i]].e;
 133     }
 134     qq_tot = 0;
 135     for (i = 0; (i < ld->nqq); i++)
 136     {
 137         qq_tot += ee[ld->qq[i]].e;
 138     }
 139
 140     /* And now the great LIE formula: */
 141     return fac_lj*(lj_tot-lie_lj)+fac_qq*(qq_tot-lie_qq);
 142 }
 143
 144 int gmx_lie(int argc, char *argv[])
 145 {
 146     const char        *desc[] = {
 147         "[TT]g_lie[tt] computes a free energy estimate based on an energy analysis",
 148         "from nonbonded energies. One needs an energy file with the following components:",
 149         "Coul-(A-B) LJ-SR (A-B) etc.[PAR]",
 150         "To utilize [TT]g_lie[tt] correctly, two simulations are required: one with the",
 151         "molecule of interest bound to its receptor and one with the molecule in water.",
 152         "Both need to utilize [TT]energygrps[tt] such that Coul-SR(A-B), LJ-SR(A-B), etc. terms",
 153         "are written to the [TT].edr[tt] file. Values from the molecule-in-water simulation",
 154         "are necessary for supplying suitable values for -Elj and -Eqq."
 155     };
 156     static real        lie_lj = 0, lie_qq = 0, fac_lj = 0.181, fac_qq = 0.5;
 157     static const char *ligand = "none";
 158     t_pargs            pa[]   = {
 159         { "-Elj",  FALSE, etREAL, {&lie_lj},
 160           "Lennard-Jones interaction between ligand and solvent" },
 161         { "-Eqq",  FALSE, etREAL, {&lie_qq},
 162           "Coulomb interaction between ligand and solvent" },
 163         { "-Clj",  FALSE, etREAL, {&fac_lj},
 164           "Factor in the LIE equation for Lennard-Jones component of energy" },
 165         { "-Cqq",  FALSE, etREAL, {&fac_qq},
 166           "Factor in the LIE equation for Coulomb component of energy" },
 167         { "-ligand",  FALSE, etSTR, {&ligand},
 168           "Name of the ligand in the energy file" }
 169     };
 170 #define NPA asize(pa)
 171
 172     FILE         *out;
 173     int           nre, nframes = 0, ct = 0;
 174     ener_file_t   fp;
 175     gmx_bool      bCont;
 176     t_liedata    *ld;
 177     gmx_enxnm_t  *enm = NULL;
 178     t_enxframe   *fr;
 179     real          lie;
 180     double        lieaver = 0, lieav2 = 0;
 181     output_env_t  oenv;
 182
 183     t_filenm      fnm[] = {
 184         { efEDR, "-f",    "ener",     ffREAD   },
 185         { efXVG, "-o",    "lie",      ffWRITE  }
 186     };
 187 #define NFILE asize(fnm)
 188
 189     CopyRight(stderr, argv[0]);
 190     parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
 191                       NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv);
 192
 193     fp = open_enx(ftp2fn(efEDR, NFILE, fnm), "r");
 194     do_enxnms(fp, &nre, &enm);
 195
 196     ld = analyze_names(nre, enm, ligand);
 197     snew(fr, 1);
 198
 199     out = xvgropen(ftp2fn(efXVG, NFILE, fnm), "LIE free energy estimate",
 200                    "Time (ps)", "DGbind (kJ/mol)", oenv);
 201     while (do_enx(fp, fr))
 202     {
 203         ct = check_times(fr->t);
 204         if (ct == 0)
 205         {
 206             lie      = calc_lie(ld, fr->ener, lie_lj, lie_qq, fac_lj, fac_qq);
 207             lieaver += lie;
 208             lieav2  += lie*lie;
 209             nframes++;
 210             fprintf(out, "%10g  %10g\n", fr->t, lie);
 211         }
 212     }
 213     close_enx(fp);
 214     ffclose(out);
 215     fprintf(stderr, "\n");
 216
 217     if (nframes > 0)
 218     {
 219         printf("DGbind = %.3f (%.3f)\n", lieaver/nframes,
 220                sqrt(lieav2/nframes-sqr(lieaver/nframes)));
 221     }
 222
 223     do_view(oenv, ftp2fn(efXVG, NFILE, fnm), "-nxy");
 224
 225     thanx(stderr);
 226
 227     return 0;
 228 }