From: mjyang (mjyang_at_hku.hk)
Date: Mon Nov 01 2010 - 09:49:17 CDT

Thanks for the detailed explanation of Jerome and Giacomo. It is helpful to my understanding of this method.

After reading the papers about ABF, I still have some confusions about the sampling along the defined order parameter. In ABF theory, the acceleration of the order parameter is elminated by the biased force. Then, the order parameter will progress according to its initial velocity during MD simulation. Do I have a correct understanding of this process? If so, which parameters will impact the efficiency of the sampling? If a dihedral is used as the reaction coordinate from 0 to 180 degree, how long a MD simulation is required to sample the whole range? In my protein system, I defined the dihedral between the center of mass of a larger immoble domain and a smaller flexible domain.

Many thanks.

Mingjun

________________________________
From: giacomo.fiorin_at_gmail.com [giacomo.fiorin_at_gmail.com] On Behalf Of Giacomo Fiorin [giacomo.fiorin_at_temple.edu]
Sent: Friday, October 29, 2010 4:33 AM
To: mjyang
Cc: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: questions about ABF simulations

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

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Dr. Giacomo Fiorin
ICMS - Institute for Computational Molecular Science - Temple University
1900 N 12 th Street, Philadelphia, PA 19122
giacomo.fiorin_at_temple.edu<mailto:giacomo.fiorin_at_temple.edu>
---- ----

On Thu, Oct 28, 2010 at 2:26 PM, mjyang <mjyang_at_hku.hk<mailto: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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