On Tue, Jun 18, 2013, Bailey, Steven wrote:
>
> I have just changed my executable from pmemd.MPI to sander.MPI.
> This resulted in a fairly obvious error: Must have more residues than
> processors. As I have only 3 molecules in this test case then in
> retrospect I would have expected this. Nevertheless this error did not
> show up on the pmemd.MPI run.
This is expected: pmemd handles parallelization in a different way than
sander, and has different restrictions.
>
> I then ran the job in serial mode sander and low and behold have
> 'jiggling' molecules.
We would need more information: be sure you are using ntt=3 if you just have
three molecules in your system. Did you rms fit your trajectory before
visualizing it? If so, try it without doing that. But without knowing how
you really ran the two simulations, it is hard to provide any real answers:
generally speaking, pmemd and sander should give equivalent results.
...dac
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Received on Tue Jun 18 2013 - 08:30:12 PDT
