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

[David van der Spoel]

pascal.baillod at epfl.ch wrote:
> 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]

the array above is two-dimensional (check the sum_v routine).

> 
> ...to 0, 1 and 2.
> 
> But I cannot, I suppose, simply replace the original indexes egCOULSR, egLJSR,
> egLJ14 by 0, 1 and 2?
you need to sum the subset of all of these, e.g. 
grps->estat.ee[egCOULSR][0] etc.

you will also have to treat PME in some way, which really is quite 
complicated.

>
-- 
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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