<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div>Dear All,<br> 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 -<br><br>(1) running multiple trajectories and apply Jarzynski equality to get free energy <br> OR <br>(2) running a single trajectory and taking configurations at different distances and then apply umbrella sampling to compute PMF.<br><br>Please
advise. <br>Thanks in advance,<br>Samrat Pal<br></div>
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