----- Original Message ----- From: Jyoti Mahalik <[email protected]> Date: Tuesday, September 28, 2010 9:19 Subject: [gmx-users] Gromacs 4.0.7 failing in parallel mode To: [email protected]
> Hi, > I am simulating two protein units in water and it works > fine in the single processor but when I use the parallel version > of the GROMACS, it fails. > > My script: > grompp_mpi_d -f md.mdp -c hba_b4md.gro -r hba_b4md.gro -p > hba.top -o hba_md.tpr > mpirun -np $NPROCS mdrun_mpi_d -np $NPROCS -ddorder pp_pme -s > hba_md.tpr -o hba_md.trr -c hba_pmd.gro -g md.log -e md. edr > > Error Messages: > Step 0, time 0 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms nan, max inf (between atoms 1 and 2) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, > constraint length > 1 > 2 90.0 > 0.1000 inf 0.1000 > 712 714 > 90.0 0.1250 > inf 0.1250 > 712 713 > 90.0 0.1250 > inf 0.1250 > 710 711 > 90.0 0.1000 > inf 0.1000 > 709 710 > 90.0 0.1430 > inf 0.1430 > > > Program mdrun_mpi_d, VERSION 4.0.7 > Source code file: constr.c, line: 136 > > Fatal error: > Too many LINCS warnings (1286) > If you know what you are doing you can adjust the lincs warning > threshold in your mdp file > or set the environment variable GMX_MAXCONSTRWARN to -1, > but normally it is better to fix the problem See http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings Probably your single processor version was also fairly unhappy, but was lucky enough to succeed. Reconsider your system preparation workflow in the light of the "blowing up" page on the above link. Mark
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
