[gmx-users] Jarzynski equality in pulling simulation

Samrat Pal psamrat10 at yahoo.com
Tue Jul 27 23:59:01 CEST 2010

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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