On Fri, Aug 15, 2014 at 12:46 PM, DEBOSTUTI GHOSHDASTIDAR <
debostutighosh.gmail.com> wrote:
> Hi Daniel
>
> I have 8000 water in the system run in NPT at 298K and 1atm pressure.
>
You can't compute temporal properties in this ensemble. If you want
time-dependent properties (diffusion, relaxation times, etc.) you need to
run NVE with good energy conservation.
For example, set a very tight constraint tolerance (a couple orders of
magnitude smaller than the default). And use a 1 fs time step with SHAKE.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Aug 15 2014 - 12:30:02 PDT
