Hi Dr.Simmerling,
I have ran with same mdind file MD with some what less processor but ot gave me around 7-8ns/day.
than is why I am more shocked that REMD is giving so slow.
With aMD I have got 6ns/day.
________________________________
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Tuesday, January 24, 2017 9:50:28 AM
To: AMBER Mailing List
Subject: Re: [AMBER] REMD_just_1.10ns/day
I would suggest doing the benchmarking without REMD. Do your MD speeds
match published benchmarks for similar size systems? REMD should not add
much overhead but can add complications if your computer system is not
configured well. It's best to try to isolate the factors and test MD alone.
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 - 13:00:03 PST
