I think you are not setting the number of exchanges you want.
So unless there is a default (I doubt it), it will go to nstlim and then
I am not sure what will happen.
In any case, as Carlos said, each remd replica should take basically the
same time if it part of a remd run or not.
Check that first
Adrian
On 8/23/11 1:44 PM, Carlos Simmerling wrote:
> your question isn't clear. REMD should not be much slower than
> standard MD for the same system in sander. Did you compare these?
>
>
> On Tue, Aug 23, 2011 at 1:18 PM, Catein Catherine
> <askamber23.hotmail.com> wrote:
>>
>> Dear Sir/Madam,
>> I am trying to do an REMD equilibrium as tutorial A7.
>> I found the work done very very slow for my system with 12000 atoms. Is it too large that I should not be able to do REMD with such a large protein? I found the job hang at the first beginning and then die when I call up job by "mpirun -np 8 $AMBERHOME/exe/sander.MPI -ng 8 -groupfile equilibrate.groupfile"
>> Is there any other way to speed up the process by changing these parameters below:
>> Equilibration&cntrl irest=0, ntx=1, nstlim=100000, dt=0.002, irest=0, ntt=3, gamma_ln=1.0, temp0=512.9, ig=15184, ntc=2, ntf=2, nscm=1000, ntb=0, igb=5, cut=12.0, ntpr=500, ntwx=500, ntwr=100000, nmropt=1, /&wt TYPE='END' /DISANG=my_chir.dat
>>
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--
Dr. Adrian E. Roitberg
Professor
Quantum Theory Project, Department of Chemistry
University of Florida
roitberg.ufl.edu
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Received on Tue Aug 23 2011 - 11:00:03 PDT
