On Tue, May 27, 2014 at 9:04 AM, Massimiliano Porrini <
m.porrini.iecb.u-bordeaux.fr> wrote:
> On 26 May 2014 21:21, Jason Swails <jason.swails.gmail.com> wrote:
>
> > One other comment I'll make is that you can actually have ParmEd run
> OpenMM
> > simulations for you directly. There is an "OpenMM" command that behaves
> > exactly like sander -- it reads sander/pmemd input files, runs a
> > calculation with OpenMM, and writes sander-formatted trajectories and
> > restart files. You would use this command exactly the same way as you
> > would run sander or pmemd on the command-line.
> >
> > $ parmed.py -p my.prmtop
> > loadRestrt my.inpcrd
> > OpenMM -O -i mdin -o mdout -x mdcrd -i mdinfo ...etc
> >
> > This may make it a bit easier to use OpenMM coming from an Amber
> > background.
> >
>
> I assume this is only available in Amber14, like you had already mentioned
> it in a previous
> email of yours. And in my group unfortunately we do not have Amber14...
>
This is actually in AmberTools 14 -- freely available under an open source
license. It should (hopefully) be easy enough to install. (And again, you
can download and install ParmEd separately if you wish to keep up-to-date
with the OpenMM-related developments).
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue May 27 2014 - 06:30:02 PDT
