Re: ABF Method

From: Eric H. Lee (
Date: Wed Jul 02 2008 - 10:45:15 CDT

I suggest you try picking a narrower sampling window for distance-
com. For example, lets say you want to sample over a total range of
20A extension. You can try two 10A sampling windows instead (i.e. run
two separate simulations). If you continue one run from the other, it
should read your old hist and dat files and then you can splice the
PMF data from both runs together afterwards.

Another suggestion would be to do a few quick SMD runs to evaluate
potential reaction coordinates. This may help you consider new
pathways to sample with ABF.


On Jul 2, 2008, at 9:19 AM, Bonnie A Merchant wrote:

> I am currently studying the transport mechanism of leucine through
> the leucine transporter. I have been using the ABF method and
> distance-com. Once the leucine moves half-way through from the
> extracellualar side to the binding pocket, it appears to stop and
> will not move any further. Even when using stronger forces, it will
> not proceed through the rest of the trasnporter.
> Does anyone have any suggestions? Should be be using Zcoord?
> Bonnie Merchant

Eric H. Lee
Medical Scholars Program
Theoretical and Computational Biophysics Group, UIUC

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