src/gromacs/gmxana/gmx_lie.cpp

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