diff --git a/patches/gromacs-4.5.7.diff b/patches/gromacs-4.5.7.diff index 8eeb506acd56ffc698dfa40261063c5f8b68de42..5fd6d46659aec5e7ac397d041e0975ad02d1ea27 100644 --- a/patches/gromacs-4.5.7.diff +++ b/patches/gromacs-4.5.7.diff @@ -51,7 +51,7 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/kernel/md.c" << \EOF_EOF { if (mdatoms->cFREEZE && (state->flags & (1<<estV))) { -@@ -588,10 +601,57 @@ +@@ -588,10 +601,60 @@ } } fprintf(fplog,"\n"); @@ -65,7 +65,10 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/kernel/md.c" << \EOF_EOF + /* setting kbT is only implemented with api>1) */ + real kbT=ir->opts.ref_t[0]*BOLTZ; + if(pversion>1) plumed_cmd(plumedmain,"setKbT",&kbT); -+ ++ if(pversion>2){ ++ int res=1; ++ if( (Flags & MD_STARTFROMCPT) ) plumed_cmd(plumedmain,"setRestart",&res); ++ } + if(cr->ms && cr->ms->nsim>1) { + if(MASTER(cr)) plumed_cmd(plumedmain,"GREX setMPIIntercomm",&cr->ms->mpi_comm_masters); + if(PAR(cr)){ @@ -109,7 +112,7 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/kernel/md.c" << \EOF_EOF print_date_and_time(fplog,cr->nodeid,"Started mdrun",runtime); wallcycle_start(wcycle,ewcRUN); if (fplog) -@@ -898,10 +958,17 @@ +@@ -898,10 +961,17 @@ state,&f,mdatoms,top,fr, vsite,shellfc,constr, nrnb,wcycle,do_verbose); @@ -127,7 +130,7 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/kernel/md.c" << \EOF_EOF if (MASTER(cr) && do_log && !bFFscan) { -@@ -1038,16 +1105,50 @@ +@@ -1038,16 +1108,50 @@ * in do_force. * This is parallellized as well, and does communication too. * Check comments in sim_util.c