Hi all,
Just one thing to add. Generally for PMF calculation the pulling is done in
one direction (N N Y in mdp file for pulling in z direction). But, as I will be
pulling a protein, I think, it will be Y Y Y i.e. in all directions. Is that
OK?
If that so, would I be able to calculate PMF in the conventional way?
Please suggest.
Thanks
Samrat Pal
________________________________
From: Samrat Pal <psamra...@yahoo.com>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Sent: Tue, July 27, 2010 2:59:01 PM
Subject: Jarzynski equality in pulling simulation
Dear All,
I am trying to do unfolding simulation of a protein by applying
pulling code in GROMACS. Now, as the pulling speed is much more faster than the
optical trap experiment or the AFM experiment, what would be more logical to
get
the PMF/free energy of the simulation -
(1) running multiple trajectories and apply Jarzynski equality to get free
energy
OR
(2) running a single trajectory and taking configurations at different
distances
and then apply umbrella sampling to compute PMF.
Please advise.
Thanks in advance,
Samrat Pal
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