On 4/30/2011 9:06 AM, Juliette N. wrote:
Dear experts,
I just tried the command mpirun -np 4 mdrun on 4.5.4 but after a few
steps I get LINCS error:
step 400, will finish Sat Apr 30 05:20:45 2011
Step 750, time 1.5 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 10.116560, max 72.359520 (between atoms 314 and 315)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
301 302 61.0 0.1090 0.1841 0.1090
I tried to run using the same input files on 4.0.7 and simulation
worked fine. I mean the LINCS is not because of flawed topology or
instability issue. I am wondering this is happening because of MPI or
installation ..Please help!
Normally, a successful MPI installation would have produced an mdrun_mpi
executable, not mdrun. 15 minutes before this email you didn't manage to
configure successfully with --enable-mpi. So probably you are not
running in parallel. Look at the number of .log files produced, and
their first line.
Regarding the LINCS error, your simulation was probably marginally
stable, and got lucky with the integration in 4.0.7 and unlucky in 4.5.
That's life - you should consider the management strategies here
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
Mark
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