I'm a little late to the party here, but if you needed the added
performance of GPUs for the 12-6-4 model, OpenMM supports it (using native
Amber prmtop and inpcrd files).
And parmed has an "OpenMM" command that will read basic sander/pmemd input
files and generate NetCDF trajectories (with a sander-like set of
command-line options) for the small subset of functionality that is
supported by that interface (for the most part, just basic MD with
optionally some simple restraints).
HTH,
Jason
On Tue, Jan 31, 2017 at 4:40 AM, Andreas Tosstorff <
andreas.tosstorff.cup.uni-muenchen.de> wrote:
> Hi all,
>
> I want to run some REMD simulations with a peptide/Zinc system.
>
> I wanted to use th 12-6-4 LJ-Type Nonbonded model.
>
> I generated the parm7 and crd files according to the manual and ran my
> first simulation using pmemd.cuda.
>
> lj1264 is set to 1 and the simulation ran without any errors, however it
> did not produce the expected outcome, meaning that Zn2+ would bind to a
> HIE residue in its proximity.
>
> I read in the manual that lj1264 is not supported by pmemd.cuda.
>
> Is this information outdated or is pmemd.cuda just ignoring lj1264=1?
>
> Should I rather use 12-6 LJ-Type with pmemd.cuda?
>
>
> Kind regards,
>
>
> Andreas
>
>
> --
> M.Sc. Andreas Tosstorff
> Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
> Department Pharmazie
> LMU München
> Butenandtstr. 5-13 ( Haus B)
> 81377 München
> Germany
> Tel.: +49 89 2180 77059
>
>
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>
--
Jason M. Swails
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Received on Thu Feb 02 2017 - 18:30:02 PST
