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

From: Ye MEI <ymei.itcs.ecnu.edu.cn>
Date: Wed, 16 Mar 2011 11:28:05 +0800

Thank you very much for this instruction. I will have a try.
Also many thanks to Prof. Simmerling.

Ye MEI

2011-03-16



From: Daniel Sindhikara
Date: 2011-03-15 22:49:28
To: AMBER Mailing List
CC:
Subject: Re: [AMBER] how to choose the biasing potential based on thecoarsefree energy curve
 
With the ncsu function you can use arbitrary bias functions. It's a little
tricky since
you have to use special format and use ncsu tools to convert it to binary,
but it's definitely doable.
There may be examples in the test directory of this. If not you may want to
contact the authors on that
paper.
I'm actually working on something now using the arbitrary biasing in AMBER,
but it's not publication ready
at the moment.
-Dan
2011/3/15 Carlos Simmerling <carlos.simmerling.gmail.com>
> not currently- you need to change the code. We will have better support for
> this in Amber 12, but even then it is hard to support arbitrary bias
> functions without changing the code in some way. If anyone wants to help
> develop this aspect we welcome participation.
>
> 2011/3/15 Ye MEI <ymei.itcs.ecnu.edu.cn>
>
> >
> > 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?
> >
> > Ye
> >
> > 2011-03-15
> >
> >
> >
> > From: Daniel Sindhikara
> > Date: 2011-03-15 14:04:52
> > To: AMBER Mailing List
> > CC:
> > 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
> > 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
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > --
> > Dr. Daniel J. Sindhikara
> > Institute for Molecular Science
> > E-mail: sindhikara.gmail.com
> > Website: http://sites.google.com/site/dansindhikara/
> > --
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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 Tue Mar 15 2011 - 21:00:03 PDT
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