Thakur, you need togive us much better data if we are to help youy.
What does "somewhat less processor" means?
You said you used 128 cores for REMD. How many replicas ?
How many cores did you use to run without REMD?
adrian
On 1/24/17 3:58 PM, Thakur, Abhishek wrote:
> 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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--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Tue Jan 24 2017 - 13:30:02 PST
