I checked the file.mdoutand watch the trajectory using VMD everything looks
good, until now.
On Fri, Jul 27, 2018 at 7:07 PM, Supriyo Bhattacharya <sup27606.yahoo.com>
wrote:
> 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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> >
> >
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>
>
>
> --
> Parviz Seifpanahi
> Ph.D. Candidate
> Department of Physics
> Virginia Tech, Blacksburg, Va 24061
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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 - 16:30:04 PDT
