In that case, are you sure the simulation is stable. In my experience, implicit solvent simulations can slow down a lot if the system becomes unstable and atoms start flying out.
On Friday, July 27, 2018, 4:02:05 PM PDT, Parviz Seifpanahi Shabane <sparviz.vt.edu> wrote:
No system software upgrades and there is not any other job running on this
GPU!!!
On Fri, Jul 27, 2018 at 5:10 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> And per David, do you e.g.
>
> $ watch -n 0.5 nvidia-smi
>
>
> On 7/27/18 2:05 PM, Supriyo Bhattacharya wrote:
> > Also, do a nvidia-smi and check what other processes might be running
> on the gpu to slow down the MD.
> > On Friday, July 27, 2018, 1:35:06 PM PDT, Bill Ross <
> ross.cgl.ucsf.edu> wrote:
> >
> > How long ago did you last get the better results? What software has
> > changed, particularly drivers? What OS?
> >
> > Bill
> >
> >
> > On 7/27/18 1:15 PM, Parviz Seifpanahi Shabane wrote:
> >> Dear AMBER user,
> >>
> >> I am running a simulation on 1 GPU (GTX980), with almost 4000 atmos with
> >> using implicit water (igb=8) and no cutoff (cut=999). everything works
> but
> >> the problem is it is very slow (72 ns/day !!!) I used to get 500 ns/day
> >> for the almost same system on the same GPU. Any idea?
> >> Best
> >
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--
Parviz Seifpanahi
Ph.D. Candidate
Department of Physics
Virginia Tech, Blacksburg, Va 24061
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Received on Fri Jul 27 2018 - 16:30:03 PDT
