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

[pascal.baillod at epfl.ch]

Dear David and Yang,

Thank you very much for your indications. I am having some trouble to understand
how the potential energy data structures are defined in the code.

I have defined the routine sum_epotPROT (see copy here below) in tgroup.c and
the index F_EPOTprot, used in this routine and defined in idef.h. Following
David's proposal, I have been trying to get the protein-protein and
protein-solvent energy terms with 

sum_v(grps->estat.nn,grps->estat.ee[egCOULSR][x])

with indexes x = 0, 1 and 2. 

1) There is the following compilation error message, shown for every line of the
subroutine sum_epotPROT with "...->estat.ee[egCOULSR][x]":

tgroup.c(317): error: argument of type "real={float}" is incompatible with
parameter of type "real={float} *"

2) It would help understanding how the epot and estat.ee[egLJ14][x] data
structures are organised. epot is a one dimensional array, what about estat?

3) Am I correct in invoking epot on the left of the "="? Or should I define a
new array? How dose the indexing work?

Thank you very much for any help!

Pascal




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[egCOULSR][0]);
  epot[F_COUL_SR]    += sum_v(grps->estat.nn,grps->estat.ee[egCOULSR][1]);
  epot[F_COUL_SR]    += sum_v(grps->estat.nn,grps->estat.ee[egCOULSR][2]);
  epot[F_LJ] 	      = sum_v(grps->estat.nn,grps->estat.ee[egLJSR][0]);
  epot[F_LJ] 	     += sum_v(grps->estat.nn,grps->estat.ee[egLJSR][1]);
  epot[F_LJ]         += sum_v(grps->estat.nn,grps->estat.ee[egLJSR][2]);
  epot[F_LJ14]        = sum_v(grps->estat.nn,grps->estat.ee[egLJ14][0]);
  epot[F_LJ14]       += sum_v(grps->estat.nn,grps->estat.ee[egLJ14][1]);
  epot[F_LJ14]       += sum_v(grps->estat.nn,grps->estat.ee[egLJ14][2]);
  epot[F_COUL14]      = sum_v(grps->estat.nn,grps->estat.ee[egCOUL14][0]);
  epot[F_COUL14]     += sum_v(grps->estat.nn,grps->estat.ee[egCOUL14][1]);
  epot[F_COUL14]     += sum_v(grps->estat.nn,grps->estat.ee[egCOUL14][2]);
  epot[F_COUL_LR]    += sum_v(grps->estat.nn,grps->estat.ee[egCOULLR][0]);
  epot[F_COUL_LR]    += sum_v(grps->estat.nn,grps->estat.ee[egCOULLR][1]);
  epot[F_COUL_LR]    += sum_v(grps->estat.nn,grps->estat.ee[egCOULLR][2]);
  epot[F_LJ_LR]      += sum_v(grps->estat.nn,grps->estat.ee[egLJLR][0]);
  epot[F_LJ_LR]      += sum_v(grps->estat.nn,grps->estat.ee[egLJLR][1]);
  epot[F_LJ_LR]      += sum_v(grps->estat.nn,grps->estat.ee[egLJLR][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][0]);
  epot[F_BHAM]       += sum_v(grps->estat.nn,grps->estat.ee[egBHAMSR][1]);
  epot[F_BHAM]       += sum_v(grps->estat.nn,grps->estat.ee[egBHAMSR][2]);
  epot[F_BHAM_LR]     = sum_v(grps->estat.nn,grps->estat.ee[egBHAMLR][0]);
  epot[F_BHAM_LR]    += sum_v(grps->estat.nn,grps->estat.ee[egBHAMLR][1]);
  epot[F_BHAM_LR]    += sum_v(grps->estat.nn,grps->estat.ee[egBHAMLR][2]);

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

*******************************************************************************
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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