Re: [AMBER] MC barostat cause the system to stuck indefinitely

From: David A Case <>
Date: Mon, 13 May 2019 08:44:29 -0400

On Sat, May 11, 2019, Zhiyi Wu wrote:

>I was trying to run an explicit solvent cpHMD simulation on a membrane
>protein system with amber18. After equilibrating the system in NVT
>ensemble for 200ps, I tried to move the system to NPT ensemble with
>MC barostat. However, MC barostat will cause the system to stuck
>indefinitely (~12 hours) in the first step but Berendsen will keep the
>system going normally.

Do the tests in AMBERHOME/test/tip4p/Run.tip4p_mcbar work OK for you, in
both serial and parallel? Are you using sander or pmemd?

Could you try a short calculation turning of constant pH? That might
help indicate whether the problem might be with the combination of
barostat=2 with constant pH.


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Received on Mon May 13 2019 - 06:00:05 PDT
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