[gmx-users] Re: Computing prot pot ener in the gmx code

[pascal.baillod at epfl.ch]

Thank you very much, David!

Thanks for your indications concerning the summing of potential energy terms in
gromacs. (For reminder, I am trying to get them in order to carry out REMD
simulations in function of the potential energy of a solute and not of the
entire system.)

If I understood you well, I could, in the file tgroup.c, create a new routine
sum_epotPROT, that would be exactly like the routine sum_epot of the same file,
safe for the indexes of grps->estat.ee[i]. The new routine would look like:

void sum_epotPROT(t_grpopts *opts,t_groups *grps,real epot[])
{
  int i;

  /* Accumulate energies */
  epot[F_COUL_SR]  = sum_v(grps->estat.nn,grps->estat.ee[0]);
  epot[F_LJ]       = sum_v(grps->estat.nn,grps->estat.ee[1]);
  epot[F_LJ14]     = sum_v(grps->estat.nn,grps->estat.ee[2]);
/* lattice part of LR doesnt belong to any group
 * and has been added earlier
 */
  epot[F_BHAM]     = sum_v(grps->estat.nn,grps->estat.ee[egBHAMSR]);
  epot[F_BHAM_LR]  = sum_v(grps->estat.nn,grps->estat.ee[egBHAMLR]);

  epot[F_EPOT] = 0;
  for(i=0; (i<F_EPOT); i++)
    if (i != F_DISRESVIOL && i != F_ORIRESDEV && i != F_DIHRESVIOL)
      epot[F_EPOT] += epot[i];
}


The prot-solvent terms are not quite clear to me. You say index i stands for
i=1: Prot-solvent
i=2: Solvent-protein

What exactly is the difference between these 2? Would you scale it down in order
not to have it twice with:

epot[F_LJ]       = sum_v(grps->estat.nn,grps->estat.ee[1]*0.5);
epot[F_LJ14]     = sum_v(grps->estat.nn,grps->estat.ee[2]*0.5);

..in the new routine sum_epotPROT?

Thank you very much for your help!

ps. I'll post further email on this issue on the developers mailing list.

Pascal



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Pascal Baillod (PhD student) 
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Swiss Federal Institute of Technology EPFL	        Tel: +41-(0)21-693-0322
Institute of Chemical Sciences and Engineering ,	Fax: +41-(0)21-693-0320
Laboratory of Computational Chemistry and Biochemistry	pascal.baillod at epfl.ch
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