Re: [AMBER] Very high values of Diffusion coefficient of water

From: Jason Swails <>
Date: Fri, 15 Aug 2014 15:27:41 -0400

On Fri, Aug 15, 2014 at 12:46 PM, DEBOSTUTI GHOSHDASTIDAR <> 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.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Aug 15 2014 - 12:30:02 PDT
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