Re: [AMBER] pmemd.cuda incomplete output file

From: Andreas Tosstorff <>
Date: Sun, 18 Dec 2016 14:27:12 +0100

Dear David and Niel,

Thank you very much for your suggestions!

The error is not fully reproducible, meaning that the equilibration stops at
different times. Sometimes after 90 ps sometimes after 200 ps.
I set ntpr=100 and printed out stderr with "pmemd.cuda .... > out 2>error"
but no error messages were printed neither in the error file nor the output.

-----Original Message-----
From: David A Case []
Sent: Friday, December 16, 2016 3:02 PM
To: AMBER Mailing List <>
Subject: Re: [AMBER] pmemd.cuda incomplete output file

On Thu, Dec 15, 2016, Andreas Tosstorff wrote:
> I have been running some MD simulations and I just realized that the
> equilibration runs are not being completed. Instead they appear to b
> just canceled without any warning or error.

In addition to makeing sure you are not missing some errors (e.g. by
redirecting stderr to a file), you can debug by setting ntpr to a small
value, so that you can more information about what is happening at the time
the program stops.

I'm gathering from you emails, although I'm not sure that you have
explicitly said this, that this behavior is fully reproducible: the
pmemd.cuda run stops in exactly the same place every time.


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