Re: [AMBER] Incomplete trajectory due to calculation halted error

From: David A Case <>
Date: Wed, 9 Jun 2021 08:48:59 -0400

On Tue, Jun 08, 2021, Razil Tahir wrote:

>My question is why the subsequent steps continue and the outputs from
>unfinished steps can be used as the input file for the next step even
>though it is incomplete?

Presumably, the subsequent steps are looking for a certain file name that
contains coordinates. pmemd will save intermediate restart files, even
before the calculation is completed. So these (incomplete) results are
probably being picked up for the next stage of the calculation.

Check your densities: if they are very far from the final value (using
near 1.0 gm/cc), you might want to specify the closeness parameter in your
solvateBox or solvateOct commands (if you are using those). A value of 0.8
generally works well for me. Or, you may just need to use the CPU version
to do a short initial relaxation to something close to a density of 1.0.


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Received on Wed Jun 09 2021 - 06:00:04 PDT
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