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

From: Nicolas Cheron <>
Date: Tue, 13 Nov 2018 11:03:57 +0100

Dear David,

Thank you for your answer. Setting ntpr to 1 doesn't change anything: a
Prod.out file is written but is empty, and the .e and .o file are similar
to those already posted.

I can share the files (the system is DHFR in water). Should I send them
directly to the list, or post them somewhere online?

Thank you


Le lun. 12 nov. 2018 à 23:20, David Case <> a écrit :

> 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
> >
> >#
> >&cntrl
> >imin=0, irest=1, ntx=5,
> >ntpr=500, ntwr=500,
> >ntwx=500, ntwe=500, ntwv=500,
> >nstlim=50000, dt=.001,
> >ntt=0,
> >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.
> ....dac
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Received on Tue Nov 13 2018 - 02:30:02 PST
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