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
Regards,
JP Mahalik
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