From: Chris Chipot (Christophe.Chipot_at_edam.uhp-nancy.fr)
Date: Fri Dec 23 2005 - 01:22:32 CST
Manori,
could you, please, provide me with additional detail about the system
you are running?
In the meantime, I can comment on the values that you used in the ABF
section of your input file:
abf dxi 0.04
abf forceConst 0.1
abf applyBias yes
abf fullsamples 20
The choice of dxi depends on how fast the free energy varies. 0.04 Å
is what I would use for a very fast changing free energy profile.
The forceconst variable controls the walls at the border of the path
you are sampling. 0.1 kcal/mol/Ų constitutes an excessively weak
restraint unlikely to prevent sampling to go beyond the bounds defined
by ximin and ximax.
More worrisome, too small a value of fullsamples is prone to drive
your system out of equilibrium. Keep in mind that the samples are
accrued in dxi-wide bins prior to application of -?F??? ??. In other
words, fullsamples controls the convergence of ?F???. It is inherently
system-dependent and varies as a function of how fast the different
degrees of freedom relax. Too small a value of fullsamples is
equivalent to applying an erroneous average force that will often
overshoot the barriers of the free energy landscape.
Chris Chipot
_______________________________________________________________________
Chris Chipot, Ph.D.
Equipe de dynamique des assemblages membranaires
Unité mixte de recherche CNRS/UHP No 7565
Université Henri Poincaré - Nancy 1 Phone: (33) 3-83-68-40-97
B.P. 239 Fax: (33) 3-83-68-43-87
54506 Vandoeuvre-lès-Nancy Cedex
E-mail: Christophe.Chipot_at_edam.uhp-nancy.fr
http://www.edam.uhp-nancy.fr
To sin by silence when we should protest makes cowards out of men
Ella Wheeler Wilcox
_______________________________________________________________________
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