Quick question - when you say serial pmemd works fine, do you mean it
completes all 850000 steps? Is it able to complete more steps than the
parallel run? Usually when you receive a message like this:
On Wed, Aug 17, 2011 at 10:13 PM, Danny Xu <quantum_mania.yahoo.com> wrote:
> Coordinate resetting cannot be accomplished,
> deviation is too large
and see behavior like this:
> If I disable SHAKE (ntc=1, ntf=1), pmemd.MPI job will run, but energies blow up in a short period of time.
it means your starting coordinates are not well-minimized.
-Dan
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Received on Wed Aug 17 2011 - 21:30:03 PDT
