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