Re: [AMBER] how to choose the biasing potential based on the coarse free energy curve

From: Daniel Sindhikara <sindhikara.gmail.com>
Date: Tue, 15 Mar 2011 15:03:15 +0900

This is possible, but no formalism has been published on it (yet). There has
been
other adaptations to ABMD that may be helpful to you though. Please see, for
example,

J. Chem. Phys. *132*, 104108 (2010); doi:10.1063/1.3355621 (*10 pages*)
 Conformational free energies of methyl-**-L-iduronic and
methyl-**-D-glucuronic
acids in water
 Volodymyr Babin and Celeste Sagui


On Tue, Mar 15, 2011 at 1:21 PM, Ye MEI <ymei.itcs.ecnu.edu.cn> wrote:

> Dear Amber users,
>
> I am studying the loop dynamics of a large protein. I defined a 1D
> reaction coordinate and already obtained a nearly converged free energy
> curve using ABMD. But this free energy curve is not that smooth, further
> refinement is required. However, due to its large size, computational
> expense will be very demanding. So, I am thinking that maybe I can use
> umbrella sampling to further refine this curve. My question is that whether
> these is any rule to choose the biasing potential at any reaction
> coordinates based on the coarse free energy curve.
> Please feel free to correct me if my idea is not correct. Any comments or
> suggestions are appreciated.
>
> best wishes,
>
> Ye
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>



-- 
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sindhikara.gmail.com
Website: http://sites.google.com/site/dansindhikara/
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Received on Mon Mar 14 2011 - 23:30:02 PDT
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