Nope, (unless some one develop PME-like method for GB).
Otherwise, you should use a small GPU clusters.
Hai
On Tue, Jan 24, 2017 at 2:15 PM, Thakur, Abhishek <axt651.miami.edu> wrote:
> Thank you Hai,
>
> Is it that you I should use other GB model for such simulation?
>
> ______________
__________________
> From: Hai Nguyen <nhai.qn.gmail.com>
> Sent: Tuesday, January 24, 2017 8:01:44 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] REMD_just_1.10ns/day
>
> yes, implicit solvent in this case is Generalized Born model. It does not
> scale very well with the number of atoms.
> So getting that slow speed is expected. The strength of GB model is to make
> conformation searching much more
> efficient than explicit water simulation.
>
> btw, your system is very big and very challenging for REMD (you can do
> literature search).
>
> For your input: You should exclude "rgbmax=15.0" and let AMBER to use the
> default value.
>
> Hai
>
> On Tue, Jan 24, 2017 at 1:53 PM, Thakur, Abhishek <axt651.miami.edu>
> wrote:
>
> > Hi every one,
> >
> > I am running REMD on 128 processors with 10706 atoms implicitly and just
> > getting 1.1ns/day.
> >
> > Is it normal that such calculation run so slow?
> >
> > Or can there be a possibility of some fault in my script?
> >
> > Here is what I am using
> >
> >
> > &cntrl
> > irest=1, ntx=5,
> > nstlim=100, dt=0.004,
> > ntt=3, gamma_ln=50.0,
> > temp0=XXXXX, ig=RANDOM_NUMBER,
> > ntc=2, ntf=2, nscm=1000,
> > ntb=0, igb=5,
> > cut=999.0, rgbmax=15.0,
> > ntpr=100, ntwx=1000, ntwr=100000,
> > nmropt=1,
> > numexchg=100000,
> > saltcon=0.2,
> > /
> > &wt TYPE='END'
> > /
> > DISANG=WT_chir.dat
> >
> >
> > Thanking you,
> >
> > -AT
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Received on Tue Jan 24 2017 - 12:00:02 PST
