Re: [AMBER] Restarting a heating simulation

From: David A Case <>
Date: Thu, 11 Feb 2016 21:50:39 +0900

On Thu, Feb 11, 2016, Elisa Pieri wrote:
> *Implicit solvent constant pH initial heating mdin &cntrl imin=0,
> irest=0, ntx=1, ntpr=500, ntwx=500, nstlim=1000000, dt=0.002, ntt=3,
> tempi=10, temp0=300, tautp=2.0, ig=-1, ntp=0, ntc=2, ntf=2,
> cut=30, ntb=0, igb=2, tol=0.000001, nrespa=1, saltcon=0.1,
> icnstph=1, ntcnstph=100000000, gamma_ln=5.0, ntwr=500, ioutfm=1,
> nmropt=1, / &wt TYPE='TEMP0', ISTEP1=1, ISTEP2=500000, VALUE1=10.0,
> VALUE2=300.0, / &wt TYPE='END' /*
> First of system has 3744 atoms and I'm running pmemd on 36 cores
> (Intel X5675 3.06 GHz). It has an average of 10.5 minutes per picosecond,
> so it will take more than two weeks to finish. Is it normal? Isn't it VERY
> slow?

Try reducing the cutoff (to say, 20 Ang.). Also see if lowering the number of
cores makes the program go faster (depends a *lot* on the details of your
machine, so it is hard to make generalizations.) Also check whether the
presence of a non-zero value for icnstph is having an effect on timings.

If you do the run in pieces, set ntx=5 and irest=1 when you restart, using
the restart file from the first run as the input to the second run.


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Received on Thu Feb 11 2016 - 05:00:08 PST
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