I change the maximum charge group size defined in the include/types/nblist.h header from 32 to 267. Then grompp worked fine but the mdrun did not start. The following error came out
Program mdrun_jptlc, VERSION 4.5.3 Source code file: ns.c, line: 2417 Fatal error: Max #atoms in a charge group: 267 > 64 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors In ns.c the relevant section (in bold) is the following: void init_ns(FILE *fplog,const t_commrec *cr, gmx_ns_t *ns,t_forcerec *fr, const gmx_mtop_t *mtop, matrix box) { int mt,icg,nr_in_cg,maxcg,i,j,jcg,ngid,ncg; t_block *cgs; char *ptr; /* Compute largest charge groups size (# atoms) */ nr_in_cg=1; for(mt=0; mt<mtop->nmoltype; mt++) { cgs = &mtop->moltype[mt].cgs; for (icg=0; (icg < cgs->nr); icg++) { nr_in_cg=max(nr_in_cg,(int)(cgs->index[icg+1]-cgs->index[icg])); } } * /* Verify whether largest charge group is <= max cg.* * * This is determined by the type of the local exclusion type * * * Exclusions are stored in bits. (If the type is not large* * * enough, enlarge it, unsigned char -> unsigned short -> unsigned long)* * */* * maxcg = sizeof(t_excl)*8;* * if (nr_in_cg > maxcg)* * {* * gmx_fatal(FARGS,"Max #atoms in a charge group: %d > %d\n",* * nr_in_cg,maxcg);* * }* ngid = mtop->groups.grps[egcENER].nr; snew(ns->bExcludeAlleg,ngid); for(i=0; i<ngid; i++) { ns->bExcludeAlleg[i] = TRUE; for(j=0; j<ngid; j++) { if (!(fr->egp_flags[i*ngid+j] & EGP_EXCL)) { ns->bExcludeAlleg[i] = FALSE; } } } if (fr->bGrid) { /* Grid search */ ns->grid = init_grid(fplog,fr); init_nsgrid_lists(fr,ngid,ns); } else { /* Simple search */ snew(ns->ns_buf,ngid); for(i=0; (i<ngid); i++) { snew(ns->ns_buf[i],SHIFTS); } ncg = ncg_mtop(mtop); snew(ns->simple_aaj,2*ncg); for(jcg=0; (jcg<ncg); jcg++) { ns->simple_aaj[jcg] = jcg; ns->simple_aaj[jcg+ncg] = jcg; } } /* Create array that determines whether or not atoms have VdW */ snew(ns->bHaveVdW,fr->ntype); for(i=0; (i<fr->ntype); i++) { for(j=0; (j<fr->ntype); j++) { ns->bHaveVdW[i] = (ns->bHaveVdW[i] || (fr->bBHAM ? ((BHAMA(fr->nbfp,fr->ntype,i,j) != 0) || (BHAMB(fr->nbfp,fr->ntype,i,j) != 0) || (BHAMC(fr->nbfp,fr->ntype,i,j) != 0)) : ((C6(fr->nbfp,fr->ntype,i,j) != 0) || (C12(fr->nbfp,fr->ntype,i,j) != 0)))); } } if (debug) pr_bvec(debug,0,"bHaveVdW",ns->bHaveVdW,fr->ntype,TRUE); ns->nra_alloc = 0; ns->bexcl = NULL; if (!DOMAINDECOMP(cr)) { /* This could be reduced with particle decomposition */ ns_realloc_natoms(ns,mtop->natoms); } ns->nblist_initialized=FALSE; /* nbr list debug dump */ { char *ptr=getenv("GMX_DUMP_NL"); if (ptr) { ns->dump_nl=strtol(ptr,NULL,10); if (fplog) { fprintf(fplog, "GMX_DUMP_NL = %d", ns->dump_nl); } } else { ns->dump_nl=0; } } } Any ideas ?
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