[gmx-users] Using umbrella sampling at constant force
jalemkul at vt.edu
Wed Oct 17 19:41:38 CEST 2012
On 10/17/12 11:01 AM, Sanku M wrote:
> 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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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