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

[David van der Spoel]

pascal.baillod at epfl.ch wrote:
> 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:
The energies are stored partly in the first and partly in the second 
entry (it's a matrix really).
The half is for other reasons.
> 
> 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
> 
> 
> 
> *******************************************************************************
> Pascal Baillod (PhD student) 
> *******************************************************************************
> 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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-- 
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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