Re: [AMBER] Minimization of a small molecule in gas phase

From: David A Case <>
Date: Thu, 21 Jul 2016 21:22:45 -0400

On Thu, Jul 21, 2016, Tiffani Rovira wrote:
> I would like to know if pmemd.cuda allows to perform a minimization of a
> small molecule in gas phase. Also I need help with the keywords that I have
> to use in the input file.
> I already have the topology and rst file of the molecule but without box
> parameters.

pmemd.cuda is way overkill; you can just use pmemd or sander for this
process. The calculation should take at most a few seconds.

A sample minimization input file is the first one in section 18.3 of
the Amber Manual (you can leave out the restraint lines).


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Received on Thu Jul 21 2016 - 18:30:02 PDT
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