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
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
