Jason,
too bad about hybrid remd on cuda.
I'm doing small polysaccharides, the T generator is for proteins and couldn't get good results. I just found out that I may be having issues with the starting structures for some Ts. I think I'll be able to work it out.
Thanks,
Hugo
On Wednesday, September 3, 2014 4:30 PM, Jason Swails <jason.swails.gmail.com> wrote:
On Wed, Sep 3, 2014 at 3:53 PM, Hugo Azurmendi <hazur_99.yahoo.com> wrote:
> I'm trying to run a hybrid T-replica exchange on Amber 14 using
> pmemd.cuda.MPI in a GPU, but the parameters numwatkeep and hybridgb
> apparently are not recognized.
Hybrid REMD is supported only in sander. It will require a lot of work to
get it working on GPUs.
>
> I didn't find information on this on the manual nor a cuda test in
> $AMBERHOME. My system is relatively small and the T_remd runs OK
(ignoring
> the
>
> mentioned parameters) , but I'm having problems to set temp0 to have
> relatively uniform exchanges through the replicas (trying with 10 now) and
>
>
> I believe using a hybrid EP strategy might help to improve exchange rates.
>
Have you used the T-REMD temperature generator (there is a link on the
tutorial page). In my experience, that gets really close to the desired
exchange rates (like, within 2-5%).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Sep 03 2014 - 14:30:02 PDT
