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

From: Ye MEI <>
Date: Tue, 15 Mar 2011 21:41:53 +0800

Dear Daniel,

thank you very much for your quick reply.
The idea in this paper is very illuminating.
It seems that the difficulty lies on how to build a series of hamiltonians with scaled biasing potential in REMD simulation. Is it possible to run such a simulation without any change to the amber code?



From: Daniel Sindhikara
Date: 2011-03-15 14:04:52
To: AMBER Mailing List
Subject: Re: [AMBER] how to choose the biasing potential based on the coarsefree energy curve
This is possible, but no formalism has been published on it (yet). There has
other adaptations to ABMD that may be helpful to you though. Please see, for
J. Chem. Phys. *132*, 104108 (2010); doi:10.1063/1.3355621 (*10 pages*)
 Conformational free energies of methyl-**-L-iduronic and
acids in water
 Volodymyr Babin and Celeste Sagui
On Tue, Mar 15, 2011 at 1:21 PM, Ye MEI <> 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
> _______________________________________________
> AMBER mailing list
Dr. Daniel J. Sindhikara
Institute for Molecular Science
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Received on Tue Mar 15 2011 - 07:00:05 PDT
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