Re: [AMBER] minimizing a pyridine in water

From: Debarati DasGupta <>
Date: Mon, 27 Apr 2020 18:53:48 +0000

Hello Prof Case,
I see segfault when running from the main console!


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From: David A Case<>
Sent: 27 April 2020 14:28
To: Debarati DasGupta<>
Subject: Re: [AMBER] minimizing a pyridine in water

On Sun, Apr 26, 2020, Debarati DasGupta wrote:
>Ans: Page 329 of AMBER18 manual says “Since SHAKE is an algorithm based
>on dynamics, the minimizer is not aware of what SHAKE is doing; for this
>reason, minimizations generally should be carried out without SHAKE”. I
>thought we did not use SHAKE in minimization steps...

It's still worth seeing if SHAKE makes a difference. Having your job
seemingly stop, but not exit from slurm, may reflect something about the
queue manager. Running 1000 steps on a small system should take a
minimal amount of time: could you run this outside the queueing system,
just to eliminate that as a possible source of confusion?


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Received on Mon Apr 27 2020 - 12:00:03 PDT
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