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 - 11:30:02 PST
