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

[David van der Spoel]

pascal.baillod at epfl.ch wrote:
> Hello,
> 
> I thank you very much for your reply, David and Yang! May I ask you some more
> details?
> 
> 
> 
>>Add one more item after F_NRE
>>This is one trick so that you just need to change the memory allocation
>>in md.c to snew(ener,F_NRE+x); x is 1 for this case. If you put new 
>>energy part before F_NRE
> 
> 
> 2) ..would this new energy part be F-EPOTprot (as re-used in my new routine
> sum_epotPROT below)? Should I first define it, as you suggest, in idef.h, as:
> 
> typedef atom_id t_iatom;
> 
> /* this MUST correspond to the 
>    t_interaction_function[F_NRE] in gmxlib/ifunc.c */
> enum {
>   F_BONDS,
> /*  ......... a list of other contributrions*/
>   F_DVDL,
>   F_DVDLKIN,
>   F_NRE,             /* This number is for the total number of energies	*/
>   F-EPOTprot         /* MY NEW CONTRIBUTION, after F_NRE */

Put it before F_NRE.

> };
> 
> 
> 3) Are the indexes in my proposed routine sum_epotPROT (copied here below)
> correct? Is the final summing loop still correct?
> 
> 4) Finally, do you know how I could include any missing PME terms? David was
> mentioning some,  contained in another file and from which I should also derive
> a protein specific contribution..
> 
> 5) Are there any workshops on the gromacs code and development issues, or any
> other way or reference to get familiar with the routines, data structures and
> variables?
> 
> Thank you very much for your help!
> 
> Regards,
> 
> Pascal
> 
> 
> 
> ---------- my adapted routine sum_epotPROT (added to tgroup.c) -----------
> 
> 
> void sum_epotPROT(t_grpopts *opts,t_groups *grps,real epot[])
> {
>   int i;
> 
>   /* Accumulate energies */
>   epot[F_COUL_SR][0]  = sum_v(grps->estat.nn,grps->estat.ee[egCOULSR][0]);
>   epot[F_COUL_SR][1]  = sum_v(grps->estat.nn,grps->estat.ee[egCOULSR][1]);
>   epot[F_COUL_SR][2]  = sum_v(grps->estat.nn,grps->estat.ee[egCOULSR][2]);

Epot is a one dimensional array

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