From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Mon Nov 21 2011 - 02:51:55 CST
Dear Jerome,
Thanks. That was very informative.
However, if we specify a different fullSamples value in a colvar config
file, will it override the value specified initially (ie. one found in the
restart files)?
-Neela
On Mon, Nov 21, 2011 at 1:40 PM, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>wrote:
> Dear Neela,
>
> fullSamples applies to the number of samples in each bin. That number
> is saved and read from restart files, so when restarting from a
> simulation with sufficient sampling, the bias is applied immediately.
>
> Your second question is about choosing the value of fullSamples. The
> bad news is that it is difficult to make an informed choice; the good
> news is that the outcome is not very sensitive to this parameter, so
> there is a range of safe values. The role of fullSamples is wait until
> some of the noise in the measured force is averaged out before
> applying the bias. In many cases, the system force contains a large
> amplitude, high-frequency noise due to bond vibrations. Because of the
> high frequency, this noise component is much reduced with values of
> fullSample of 100 or 200 steps, i.e. a few periods of typical bond
> vibrations.
>
> The only reason I see to use larger values is to protect a "fragile"
> system from distortion due to non-equilibrium forces. By fragile, I
> mean a system that is likely to be pushed out of the most relevant
> configurations by moderate non-equilibrium forces applied in the
> initial regime of ABF. In such a case, larger values of fullSamples
> can be used to deliberately slow down the process and keep the initial
> regime even closer to equilibrium. The cost of this, of course, is
> less effective exploration of configuration space.
>
> Best,
> Jerome
>
> On 21 November 2011 05:19, Neelanjana Sengupta <senguptan_at_gmail.com>
> wrote:
> >>
> > In addition, I would like to know people's experience regarding accuracy
> of
> > PMF profiles (if any) by increasing/decreasing the fullSamples steps.
> What
> > if one uses a default of 100? (I understand it is situation dependent,
> but
> > would still like to pose this question).
> >
> > Thanks,
> > Neela
> >
> > On Mon, Nov 21, 2011 at 9:44 AM, Neelanjana Sengupta <
> senguptan_at_gmail.com>
> > wrote:
> >>
> >> Dear NAMD experts,
> >>
> >> I need a clarification about an Adaptive Biasing Force (ABF) parameter
> in
> >> colvars.
> >>
> >> Due to large fluctuations of the biasing force, the fullSamples option
> >> (default 200 steps) is used to obtain accurate estimate of the reaction
> >> coordinate before applying the bias.
> >> However, is this applied only the very first time, or at each restart
> >> step? (ie. if someone uses the .restart.colvar files, etc to continue
> >> another calculation, will fullSamples be applied again)?
> >>
> >> Thanks and regards,
> >> Neela
> >
> >
> >
> > --
> > ~~~~~~~~~~~~~~~~~~~~
> > Neelanjana Sengupta, PhD
> > Physical Chemistry Division
> > National Chemical Laboratory
> > Dr. Homi Bhaba Road
> > Pune 411008, India
> > Phone: +91-20-2590 2087
> > Fax: +91-20-2590 2636
> > ~~~~~~~~~~~~~~~~~~~~
> >
>
-- ~~~~~~~~~~~~~~~~~~~~ Neelanjana Sengupta, PhD Physical Chemistry Division National Chemical Laboratory Dr. Homi Bhaba Road Pune 411008, India Phone: +91-20-2590 2087 Fax: +91-20-2590 2636 ~~~~~~~~~~~~~~~~~~~~
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