From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Thu Oct 28 2010 - 14:37:29 CDT
On 28 October 2010 20:26, 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?
Those do not affect the sampling efficiency, they are just for
confining the variable within some interval. For distance-like
variables, use something on the order of 10 or 20 kcal/mol/A^2.
> 2. Is WHAM used to calculate the free energy based on the simulation samplings?
No, in ABF the free energy is calculated based on thermodynamic
integration (TI). I recommend reading some of the ABF articles before
using it. Your question is equivalent to someone saying "okay, now I'm
going to drive this truck. What's the big wheel for?"
> 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?
This is not very helpful for ABF. It depends a lot on the kind of
coordinate you are using. Think about it that way: in the end you are
going to obtain a discretized free energy profile. How big should the
steps to be for the actual profile to be well-described by the
discretized one? For distances, typical choices are 0.1 or 0.2
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