1) Adding replicas to any kind of REMD run disrupts the detailed balance
between states and thus a separate simulation is required. The old data is
still valid in the sense that it was drawn from the different states with
appropriate weight, but those weights with respect to the new data will not
be correct without some kind of re-weighting scheme.
2) -ng and -groupfile are only valid arguments for MPI executables. You
want pmemd.cuda.MPI. I don't know if you can run multiple simulations on a
single GPU, but even if you can it is probably not recommended.
Regards,
Brian
On Wed, Aug 6, 2014 at 1:43 PM, M Olivia Kim <olivijuly.gmail.com> wrote:
> Hi,
>
> I have been using the pH-REMD by Jason Swails, implemented in the Amber 14
> release and have a couple questions:
>
> 1) I ran the pH-REMD for the pH range between 2 to 7.5, and want to add
> new replicas at pH 1, 1.5, 8, and 8.5. In that case, should I rerun the
> entire production run involving the new, extended pH ladder (pH 1-8.5)? Or
> can I restart the production run by adding the new replicas to the restart
> files from the old pH-REMD of pH 2-7.5?
>
> 2) Jason Swails mentioned in his wiki that he implemented the pH-REMD on
> GPU. However, when I try to run the pH-REMD on GPU like:
>
> pmemd.cuda -ng 12 -groupfile groupfile ……
>
> it crashes with an error message saying that -ng is not a valid option for
> pmemd.cuda. It basically requires the usual command like -O -i …… Does
> anyone have idea how to make it run on GPU?
>
> Thank you in advance!
>
> Thanks,
> Olivia
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>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for
Integrative Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
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Received on Wed Aug 06 2014 - 12:00:05 PDT
