Re: [AMBER] multinode NPT runs on GPU

From: Sourav Purohit <sour000.gmail.com>
Date: Fri, 9 May 2014 19:49:06 +0530

Even After 50 ns long NPT simulation I saw that the pressure values are all
negative and fluctuating about -500. The system consists of a large number
of DNA fragments initially arranged in a crystal with a water buffer of 30
Ang.. I wanted to see the type of LC phase the system attains.
The density also attained a large value.
I had heard from my colleagues about similar problems with multinode
multigpu NPT simulations. I just wanted to make sure that all the results
that I get are right. Do you feel that the observations of a high density
and negative pressure even after a long run are okay for the system I am
simulating?? Kindly help.

Thanks.


On Fri, May 9, 2014 at 7:30 PM, Jason Swails <jason.swails.gmail.com> wrote:

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> On Fri, 2014-05-09 at 19:13 +0530, Sourav Purohit wrote:
> > The pressure values are all negative. Thats why I had a doubt.
>
> This is to be expected when the box size starts to shrink. tleap
> creates solvent boxes that are too large, so while the box shrinks the
> pressure should be negative. Once the density 'equilibrates', you
> should see large pressure fluctuations around 0 to 1 bar (high positive
> to high negative).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Fri May 09 2014 - 07:30:04 PDT