Thank you so much
________________________________
From: Hai Nguyen <nhai.qn.gmail.com>
Sent: Tuesday, November 15, 2016 4:13:20 AM
To: AMBER Mailing List
Subject: Re: [AMBER] simulating with "gbsa=1" on gpu give only 0.18ns per/day
On Tue, Nov 15, 2016 at 10:01 AM, Thakur, Abhishek <axt651.miami.edu> wrote:
> Hi everyone,
>
>
> I am trying to do (GB/SA) calculation with intrinsic water model. In my
> simulation I also want to include surface area so I was planning to use
> "gbsa=1" .
As I am running on GPU I am getting only 0.18ns per day only, bust as soon
> I am removing "gbsa=1" I am getting decent speed of 10ns per day.
>
>
> So simulating while use "gbsa=1" seems to be impossible.
>
> Can anyone suggest me what should I do?
>
>
>
> This is my script
>
> imin=0,irest=1,ntx=5,
> nstlim=10000000,dt=0.001,
> ntf=2,ntc=2,ntb=0,
> igb=8,gbsa=1,cut=9999.0,rgbmax=15.0,
> ntpr=500, ntwx=500, ntwr=10000,
> saltcon=0.2,
> temp0=300.0,
> ntt=1,tautp=1.0,
> nscm=0,
>
>
Addition to what Adrian said, I have few comments about your input
- use dt=0.004 with hydrogen mass repartitioning. Please check manual for
this. You should get 40 ns /day.
- just use the default rgbmax ( = 30 if I remember correctly).
Hai
>
>
>
> Thanking you,
>
> Abhishek
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Received on Tue Nov 15 2016 - 09:30:02 PST
