fullSamples in ABF: applied at restart?

From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Sun Nov 20 2011 - 22:19:00 CST

> 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).


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

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