[gmx-users] Re: Jarzynski equality in pulling simulation

Samrat Pal psamrat10 at yahoo.com
Wed Jul 28 20:18:48 CEST 2010

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.
Samrat Pal  

From: Samrat Pal <psamrat10 at yahoo.com>
To: Discussion list for GROMACS users <gmx-users at 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 

(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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