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