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 - 11:00:02 PDT
