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

[Yang Ye]

pascal.baillod at epfl.ch wrote:
> Hello,
>
> Thank you very much for theses indications, David! The compilation of mdrun with
> my new sum_epotPROT routine (copy below) works fine, but when I try to run it (2
> cpus, 2 PT replicas, runs fine with normal code), I get the following error message:
>
>
> Reading file md1.tpr, VERSION 3.3 (single precision)
> -------------------------------------------------------
> Program mdrun_mpi, VERSION 3.3
> Source code file: smalloc.c, line: 113
>  
> Fatal error:
> calloc for ir->opts.nrdf (nelem=-1079115263, elsize=4, file tpxio.c, line 487)
>
> tpxio.c line 487 looks like: 
> snew(ir->opts.nrdf,   ir->opts.ngtc);
>
> Here below, I send a copy of the 3 changes I put in the code, 2 of which are
> supposed to settle memory allocation problems:
>
> 1) idef.h -----------------------------------------
>
> typedef atom_id t_iatom;
>
> /* this MUST correspond to the 
>    t_interaction_function[F_NRE] in gmxlib/ifunc.c */
> enum {
>   F_BONDS,
>   F_G96BONDS,
>   /* a number of other contributions */
>   F_EPOTprot,     /* the index of my new prot ener term	*/
>   F_NRE           /* This number is for the total number of energies	*/
> };
> 2) md.c ---------------------------------------------
>
>   /* Initiate everything (snew sets to zero!) */
>   snew(ener,F_NRE+1);
>
> ... with the idea that F_NRE+1 should account for memory allocation for my new
> prot energy term.
>   
If you have placed F_EPOTprot before F_NRE, you shall not use +1. Your 
error was my error. So try place  F_EPOTprot after F_NRE and use +1. You 
shall get it.
> 3) tgroup.c ----------------------------------------------
>
>
> void sum_epotPROT(t_grpopts *opts,t_groups *grps,real epot[])
> {
>   int i;
>
>   /* Accumulate energies */
>   epot[F_COUL_SR]  = grps->estat.ee[egCOULSR][0] +
> 0.5*(grps->estat.ee[egCOULSR][1] + grps->estat.ee[egCOULSR][2]);
>   epot[F_LJ]       = grps->estat.ee[egLJSR][0] + 0.5*(grps->estat.ee[egLJSR][1]
> + grps->estat.ee[egLJSR][2]);
>   epot[F_LJ14]     = grps->estat.ee[egLJ14][0] + 0.5*(grps->estat.ee[egLJ14][1]
> + grps->estat.ee[egLJ14][2]);
>   epot[F_COUL14]   = grps->estat.ee[egCOUL14][0] +
> 0.5*(grps->estat.ee[egCOUL14][1] + grps->estat.ee[egCOUL14][2]);  
>   epot[F_COUL_LR]  = grps->estat.ee[egCOULLR][0] +
> 0.5*(grps->estat.ee[egCOULLR][1] + grps->estat.ee[egCOULLR][2]);
>   epot[F_LJ_LR]    = grps->estat.ee[egLJLR][0] + 0.5*(grps->estat.ee[egLJLR][1]
> + grps->estat.ee[egLJLR][2]);
> /* lattice part of LR doesnt belong to any group
>  * and has been added earlier
>  */
>   epot[F_BHAM]     = grps->estat.ee[egBHAMSR][0] +
> 0.5*(grps->estat.ee[egBHAMSR][1] + grps->estat.ee[egBHAMSR][2]);
>   epot[F_BHAM_LR]     = grps->estat.ee[egBHAMLR][0] +
> 0.5*(grps->estat.ee[egBHAMLR][1] + 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];
> }
>
> I thank you very much for your help!!
>
> 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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>   

-- 
/Regards,/
Yang Ye
/Computational Biology Lab
School of Biological Sciences
Nanyang Technological University
Singapore
Tel: 6316-2884
/