questions about ABF simulations

From: mjyang (mjyang_at_hku.hk)
Date: Thu Oct 28 2010 - 13:26:59 CDT

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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