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
============================================
----------------------------------------------------------------------------
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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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Received on Sun Aug 06 2006 - 06:07:07 PDT
