[gmx-users] Gromacs 4.0.7 failing in parallel mode

Jyoti Mahalik jmahalik at polysci.umass.edu
Tue Sep 28 00:17:36 CEST 2010

  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  
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

JP Mahalik

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