Re: [AMBER] RMS Fluctuation limit and difference in Temperature maximum Density (TMD)

From: David A Case via AMBER <amber.ambermd.org>
Date: Wed, 19 Jul 2023 15:37:37 -0400

On Wed, Jul 19, 2023, Zafar,Muhammad Saqlain wrote:


Please send amber-related questions to the mail reflector, amber.ambermd.org,
and not to me personally. That way, many people can see your question and try
to help, and the answers can help others with similar questions. See
http://lists.ambermd.org/mailman/listinfo/amber for information on how to
subscribe.

>I am taking densityy after equilibration. The whole NPT run for 10ns and i
>took from range of 2ns-10ns.
>
>I get density from output file that generated from NPT of each time frame
>of 0.00005.

Look at (plot) the time dependence of the density: is it changing with time?
Is there any pattern to the fluctuations? It is very odd to see the density
fluctuations you reported in a previous email, and (as mentioned) the
average density is way off.

I would also recommend visualizing the trajectory (after using autoimage in
cpptraj). I'm still concerned that you say that your unit cell had was 30
Ang on each side, which is very far from what it should be.

We would probably need to get access to files that would enable the problem
to be replicated.

....dac


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 19 2023 - 13:00:02 PDT
Custom Search