Not the same system, the number of atoms was 1354 (I checked now), but
still, does not make sense to get 72 ns/day for 400 atoms!!!
On Fri, Jul 27, 2018 at 7:13 PM, Parviz Seifpanahi Shabane <sparviz.vt.edu>
wrote:
> 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
>
--
Parviz Seifpanahi
Ph.D. Candidate
Department of Physics
Virginia Tech, Blacksburg, Va 24061
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Received on Fri Jul 27 2018 - 16:30:05 PDT
