From: Giacomo Fiorin (giacomo.fiorin_at_temple.edu)
Date: Thu Oct 28 2010 - 15:33:19 CDT
Hi Mingjun:
1) lowerWallConstant and upperWallConstant shouldn't play a role, unless you
set either boundary on or near the barrier. But the barrier should ideally
be at the center of your interval, to be sampled correctly.
2) No, the ABF method samples forces on the variables that you use, and does
not compute the free energies from the histogram of the variables' values
(such as e.g. umbrella sampling with WHAM, metadynamics etc would do).
3) Yes, this seems a very sensible starting point.
Giacomo
---- ----
Dr. Giacomo Fiorin
ICMS - Institute for Computational Molecular Science - Temple University
1900 N 12 th Street, Philadelphia, PA 19122
giacomo.fiorin_at_temple.edu
---- ----
On Thu, Oct 28, 2010 at 2:26 PM, mjyang <mjyang_at_hku.hk> wrote:
> Dear NAMD users,
>
> It is the first time I use the adaptive biased force simulation (ABF) to
> study the relative free energy change between two distinct conformations of
> a protein. After reading the corresponding mannual and tutorial, I still
> have some confusions required your kind help:
>
> 1. If the barrier is not known along an order parameter, how large should I
> set the value for the force constant for efficient sampling, e.g.
> lowerWallConstant and upperWallConstant?
> 2. Is WHAM used to calculate the free energy based on the simulation
> samplings?
> 3. How large should I set the "width" keyword? I performed 1000,000 MD
> steps and printed the standard deviation by turning on the "analysis". Is it
> ok to set the value of "width" to 2 times of the largest deviation?
>
> Many thanks.
>
> Mingjun
>
>
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