have you performed normal MD before doing REMD? Did you compare the timings?
On Tue, Aug 23, 2011 at 8:51 PM, Catein Catherine <askamber23.hotmail.com>wrote:
>
> 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
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 23 2011 - 18:00:03 PDT
