[gmx-users] Using umbrella sampling at constant force

[Justin Lemkul]

On 10/17/12 11:01 AM, Sanku M wrote:
> Hi,
>    I am trying to compute free energy of a polymer in presence of a constant force.
> If I understand correctly, I need to use two pull-option here in gromacs: one for performing umbrella sampling and other for applying  constant force. But, as far as I know I can not specify two pull option in single mdp file of gromacs.
> So, I was wondering whether there is any way out in gromacs regarding this issue.

I think some clarification is necessary here.  To what are you applying a force? 
  The ends of the polymer?  What is the desired reaction coordinate for the 
umbrella sampling?  If it is the end-to-end distance, you can't do this because 
you have a constant force and thus nothing varies.  If it's some other distance, 
you might find ways around the problem.

A harmonic potential (umbrella potential) by definition results in a variable 
force depending upon the extension of the spring.  A constant force restraint is 
a very different idea.  Gromacs calculates the PMF from the umbrella potential, 
but if you have a constant force, then you already know the energies (PMF = 
potential of mean force).

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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