[gmx-users] PMF with nanotube

Vijayaraj vijayaraj81 at gmail.com
Thu Nov 17 17:36:44 CET 2011


I am trying to find the PMF for the diffusion of small molecule through a
nanotube. I have generated the umbrella sampling windows from
pull_geometry=direction simulation and umbrella sampling with
pull_geometry=position. I guess the PMF for this system can be obtained by
combining the g_wham output of above and below of reference nanotube. I got
negative PMF curve for the above reference part and positive curve for the
below reference part. I should get a complete PMF curve when I combine the
above and below part. I dont understand why these two parts have different

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