[gmx-users] Varying results due to parallel processing (1 node versus 2 nodes)

Sanket Ghawali sanket.ghawali at gmail.com
Mon Sep 19 11:11:09 CEST 2016

Dear Gromacs users

I am trying to simulate peptide in 30% TFE/water complex. Using parallel
processing, I ran this system for 100ns using 2 nodes. The peptide is known
to obtain helical conformation in this system. After 100ns, the peptide was
found to be 37% helical. I ran the same system again on 1 node instead of
2, with no changes in the parameter or the input files. After 100ns of the
simulation, the peptide was found to be 44% helical. Why is there so much
change in the results? Which of the two should be considered?

The following commands were used:

Simulation run on 1 node:

mpirun –np 12 –hostfile host /share/apps/gromacs/bin/mdrun_mpi –v –deffnm

Simulation run on 2 nodes:

mpirun –np 24 –hostfile host /share/apps/gromacs/bin/mdrun_mpi –v –deffnm

Kindly help.

Sanket B Ghawali
Junior Research Fellow
ICMR-Biomedical Informatics Centre
National Institute for Research in Reproductive Health
Parel, Mumbai.

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