[gmx-developers] Computing prot pot ener in the gmx code

[pascal.baillod at epfl.ch]

Hi!

I am trying to get protein potential energies in order to carry out REMD 
simulations in function of the potential energy of a solute and not of the
entire system. I checked the tgroup.c file and found the following:


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

  /* Accumulate energies */
  epot[F_COUL_SR]  = sum_v(grps->estat.nn,grps->estat.ee[egCOULSR]);
  epot[F_LJ]       = sum_v(grps->estat.nn,grps->estat.ee[egLJSR]);
  epot[F_LJ14]     = sum_v(grps->estat.nn,grps->estat.ee[egLJ14]);
  epot[F_COUL14]   = sum_v(grps->estat.nn,grps->estat.ee[egCOUL14]);
  epot[F_COUL_LR] += sum_v(grps->estat.nn,grps->estat.ee[egCOULLR]);
  epot[F_LJ_LR]   += sum_v(grps->estat.nn,grps->estat.ee[egLJLR]);
/* 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];
}

Could the potential energy of the protein be obtained with a new routine, that
would look like

void sum_epotPROT(t_grpopts *opts,t_groups *grps,real epot[])
{
(same as routine sum_epot above)
}

...in which I have been told I would have to change the indexes X of

grps->estat.nn,grps->estat.ee[X]

...to 0, 1 and 2.

But I cannot, I suppose, simply replace the original indexes egCOULSR, egLJSR,
egLJ14 by 0, 1 and 2?

Thank you very much for any help!

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
Room BCH 4121, Avenue Forel,	                        http://lcbcpc21.epfl.ch
CH-1015 Lausanne	
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