On Sun, Jun 24, 2012, Adam Jion wrote:
>
> I have a system in which a large number of molecules need to be
> position-restraint under NPT.
The barostat in Amber is not designed to handle situations like you describe.
Depending on the geometry of the fixed molecules, it is possible that bad
results (like bubbles) might occur. There haven't been any changes in Amber12
in this regard, and I don't know even in principle how the issue could be
"resolved". Use short time steps and slow volume equilibration, if you are
not doing that already.
....dac
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Received on Mon Jun 25 2012 - 05:00:02 PDT
