Re: [AMBER] Files work with sander and not pmemd

From: David Case <>
Date: Mon, 12 Nov 2018 22:20:22 +0000

On Wed, Nov 07, 2018, Nicolas Cheron wrote:
>I have files that were used previously to perform EVB simulations with
>sander (prmtop and rst). I now want to perform simulation on a pure VB
>state (no more EVB) and was thinking of using pmemd, however I can't. For
>example, with this file
>imin=0, irest=1, ntx=5,
>ntpr=500, ntwr=500,
>ntwx=500, ntwe=500, ntwv=500,
>nstlim=50000, dt=.001,
>ntb=1, ntp=0,
>ntc=2, ntf=2,

Usual debugging idea: try a short run with pmemd, but set ntpr=1.
Examine the output: does the crash happen before the first step, or some
time later?

However, you may have found some code problem as well. If the pmemd run
suggested above doesn't seem to provide any help, you will probably have
to post the relevant files (if that is possible) so that we can try to
reproduce the problem.


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Received on Mon Nov 12 2018 - 14:30:04 PST
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