Try using barostat=2, this is a monte carlo barostat optimized for GPU
use. You can find more info in the amber16 manual.
Best,
Andy
On 04/05/2017 04:27 PM, Sofia Vasilakaki wrote:
> Hi to all,
>
> I am running an MD simulation of a protein attached to a lipid membrane in
> water. The system is 262628 atoms and the input file is:
>
> imin=0, ntx=5, irest=1,
> ntc=2, ntf=2,
> nstlim=3500000, ntt=3,gamma_ln=1.0,
> temp0=310.0,
> ntpr=20000, ntwr=500000,ntwx=20000,
> dt=0.002,ig=-1,
> ntb=2, ntp=2, cut=10.0, barostat=1, ioutfm=1, ntxo=2
>
>
> On a Tesla K40m is 7.50ns/day, on GTX980 P2P is 10.35ns/day and on GTX1080
> is 12.57ns/day. Is there any way I could improve performance?
>
> Thank you in advance.
>
> Kind Regards,
> Sofia V.
>
>
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--
M.Sc. Andreas Tosstorff
Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
Department Pharmazie
LMU München
Butenandtstr. 5-13 ( Haus B)
81377 München
Germany
Tel.: +49 89 2180 77059
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Received on Wed Apr 05 2017 - 08:00:02 PDT
