Dear Prof. Simmerling,
Thank you very much for your instruction. I think the reasons why my jobs runs so slowly is because I have to use do 8 replicas in a 8 nodes. An the memory demand for this calculation is very large. Are there any way to solve this problem?
Best regards,
Annie
> From: carlos.simmerling.gmail.com
> Date: Tue, 23 Aug 2011 13:44:47 -0400
> To: amber.ambermd.org
> Subject: Re: [AMBER] Is it possible to do REMD for a 12000 atom molecule?
>
> 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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Received on Tue Aug 23 2011 - 18:00:03 PDT
