src/tools/gmx_lie.c

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