[gmx-users] Umbrella sampling force autocorrelation
gozdeeergin at gmail.com
Thu Nov 26 17:02:12 CET 2015
Dear Gromacs user,
I did umbrella sampling by pulling a water molecule from gas phase to
organic coated bulk water.
By clicking the link below you can see my PMF profile.
In order to estimate the transmission coefficient, I put the pulled
molecule on the top of the PMF barrier and did simulation for 600 ps.
I extracted the instantaneous force of z direction on this molecule by
using the command of :
*g_traj -f traj.trr -s md.tpr -of force.xvg -n index.ndx -nox -noy*
And to estimate the auto-correlation for instantaneous force:
*g_analyze -f force.xvg -ac auto_corr.xvg -temp 300 -nonormalize*
However I wonder why the fluctuation on auto-correlation is big and never
converges to the zero.
Please find the profile.xvg, force.xvg and auto_corr.xvg on
I would greatly appreciate of any respond.
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