Philip Shushkov wrote:
Dear Mark,
I have checked this possibility and it turned out that the positional
restraints and constraints did not lead to MD instabilities when run in
serial mode. Unfortunately, the system is pretty large (it consists of
27255 atoms) so it runs quite slowly in serial mode. That is why, I do
want to run mdrun in parallel mode and make an advantage of our cluster.
Thus, I would like to ask you for some advice how to get around the problem.
OK, well to do this you need to identify the actual source of problems.
Try simplifying your chemical system somehow, and/or changing which
parts of it have constraints and/or restraints. You should also be
describing to us what your system contains, and where the LINCS errors
were occuring, else we're guessing in the dark.
Mark
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