Hi Andreas,
No, unfortunately GPU code was never written for the 12-6-4 LJ model so it is CPU only I am afraid. However, it's strange that the GPU code would just run with it. At the time 12-6-4 was added to PMEMD a check should have been added to the GPU startup code to quit if 12-6-4 was detected. The authors of the 12-6-4 model should check this.
All the best
Ross
> On Jan 31, 2017, at 04:40, 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 Is this information outdated or is pmemd.cuda just ignoring lj1264=1?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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Received on Tue Jan 31 2017 - 04:30:03 PST
