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

[David van der Spoel]

pascal.baillod at epfl.ch wrote:
> Hello 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.) 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];
> }

This is turning into a developer thread...
The sum_v routine justs sums the contents of NN entries in the 
grps->estat.ee[i]. In your case you want entry [0] (protein-protein) and 
[1] and [2] protein-sol and sol-protein respectively and sum them. You 
probably want 0.5 times the protein-sol energy.


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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