AMBER Archive (2006)

Subject: Re: AMBER: Maximum system size in simulated annealing

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Thu Aug 03 2006 - 05:26:58 CDT

you don't give much information, but you might
try normal constant temperature MD before you try annealing.
Also you probably need to run constant P for a while to
equilibrate the box size- perhaps you have bad contacts at the box edge.
you also may need to do careful equilibration- you haven't said
how that was done.

I don't think that the system size should be a problem.

Juraj Kotulic Bunta wrote:

> Dear Amber people,
>
> I would like to ask a question concerning simulated annealing
> procedure. I performed several simulations using Amber 7 on PC cluster
> with Red Hat Linux 9, based on input file from the manual, however,
> slightly modified and with several additional parameters based on
> observing the behavior of the system.
>
> I had a trouble to tune the input up so that the simulation would not
> terminate with error.
>
> I succeeded, however, the problem is that I cannot avoid rather high
> velocities (vlimit) being often of the order of tens (sometimes
> hundreds). I think it is caused by the large size of the overall
> system which I simulate – it consists of almost 180 thousands atoms
> (10 thousands of heavy, 8 thousand of hydrogens within the crystal and
> the rest is water solvent). Is it reasonable to use Amber annealing
> for such a big system? Is the numerical procedure consistent with so
> many atoms?
>
> I suspect that it is not, because the result is quite strange – it
> seems like several parts of the system are “frozen”, despite I did not
> use any special constrains, and there are only something like “waves”
> or “pressure shocks” moving through the system. The temperature was
> 1200 K, could it be caused by the fact that I used constant volume
> choice (and thus the pressure could cause the “frozing”?). I am afraid
> that in the case of constant pressure the system will blow up.
>
> Therefore, I used also smaller system – without water (igb=1), the
> result was much less “frozen” and seemed more realistic, however, I am
> not convinced that the system is “small” enough.
>
> Do you have some experience or recommendation for simulated annealing
> for large systems? What’s is an expected limit for the size of the system?
>
> The system was, of course, very carefully minimized (belly and
> nonbelly, around 60 thousands steps) before annealing simulation.
>
> Many thanks for your answer.
>
> Juraj Kotulic Bunta, Ph.D
>
> Japan Atomic Energy Agency
>
> Please find following my two input files (the case with and without
> explicit water solvent – due to the length of calculation I used many
> restart files, these are only the first initial ones at the beginning
> of the heating):
>
> ============================================
>
> &cntrl
>
> nstlim=2500, ntt=1,
>
> scee=1.2,
>
> ntpr=50,
>
> vlimit=50,
>
> nmropt=1,
>
> ntb=1,
>
> ntf=3, ntc=3,
>
> DT=0.0001,
>
> TOL=0.00005,
>
> &end
>
> &ewald
>
> eedmeth=5,
>
> &end
>
> #
>
> #
>
> &wt type='TEMP0', istep1=0,istep2=2500,value1=0.0,
>
> value2=20.0, &end
>
> #
>
> #
>
> &wt type='TAUTP', istep1=0,istep2=2500,value1=0.0005,
>
> value2=0.0005, &end
>
> #
>
> #
>
> &wt type='REST', istep1=0,istep2=2500,value1=1.0,
>
> value2=1.0, &end
>
> #
>
> &wt type='END' &end
>
> LISTOUT=POUT
>
> ============================================
>
> ============================================
>
> &cntrl
>
> nstlim=250, ntt=1,
>
> scee=1.2,
>
> ntpr=50,
>
> vlimit=50,
>
> nmropt=1,
>
> ntb=1, ntx=5, irest=1,
>
> ntf=3, ntc=3,
>
> ntb=0, igb=1,
>
> &end
>
> &ewald
>
> eedmeth=5,
>
> &end
>
> #
>
> #
>
> &wt type='TEMP0', istep1=0,istep2=250,value1=0.0,
>
> value2=20.0, &end
>
> #
>
> #
>
> &wt type='TAUTP', istep1=0,istep2=250,value1=0.01,
>
> value2=0.01, &end
>
> #
>
> #
>
> &wt type='REST', istep1=0,istep2=250,value1=1.0,
>
> value2=1.0, &end
>
> #
>
> &wt type='END' &end
>
> LISTOUT=POUT
>
> ============================================
>
> ---------------------------------------------------------------------------------
>
> KOTULIC BUNTA, Juraj, Ph.D
>
> Japan Atomic Energy Agency
>
> Nuclear Energy Basic Engineering Research Sector
>
> Environment and Radiation Engineering Unit
>
> Research Group for Radiation Effect Analysis
>
> Tokai-mura, Naka-gun, Ibaraki-ken, 319-1195
>
> JAPAN
>
> Tel. +81-29-282-5583 Fax. +81-29-282-6768
>
> ---------------------------------------------------------------------------------
>
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