Re: [AMBER] Any help on the error

From: David Case <>
Date: Tue, 7 Jan 2020 13:59:45 +0000

On Mon, Jan 06, 2020, Debarati DasGupta wrote:
> [cid:image001.png.01D5C4A4.520900A0]
> Please find my input files.
> This error pops up right after the minimization step. ( I am using
> pmemd.cuda)

I don't know which step is the one that follows minimization. But what
happens if you run a 10-step simulation with ntpr=1? Does the energy at
the first step of MD match that at the last step of minimization? Do
you get the same values if you run the 10-step simulation on the CPU?
(Do the energies at the end of minimization look OK? Have you
visualized the structure to make sure something bad didn't happen during

It looks like something is happening when you go from minimization to
MD. You need to try to figure out what has changed. Just seeing the
input files is not going to allow others to help you very much. You
will need to debug this yourself, and running *short* simulations is
usually a necessary first step.


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Received on Tue Jan 07 2020 - 06:30:02 PST
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