Dear All,
I am simulating a protein in water to check the ligand movement over a
time span. I have minimized the system in STEEP and CG and after that
heated from 0K - 300K within a time span of 300 ps. Then, I performed the
NPT production runs. In two clusters I have got different results, like in
one I see the ligand came out of the protein and in other it stayed inside
the protein cavity, after a same (comparable) time duration. Now, while
running the same job (same .mdp file) in different numbers of cores (in the
same machine) I'm getting different behaviors, e.g., in protein ligand
distance plots etc. I don't know the reason behind this. I'm running all my
jobs in gromacs-4.5.5 version.
Recently I have visited this post [
http://redmine.gromacs.org/issues/1012 ], but could not able to conclude
properly. Anyone's help would be greatly appreciated.
Thanks and regards
Tarak
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