[gmx-users] Jarzynski equality in pulling simulation
psamrat10 at yahoo.com
Tue Jul 27 23:59:01 CEST 2010
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.
Thanks in advance,
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