[gmx-users] PMF of ligand transport

[Aswathy]

Hi gromacs users,

I am using Gromacs 4.0.4 package. I am doing SMD of a ligand transport
through a channel.

I performed SMD and did umbrella sampling (Thanks to Justin for his
tutorial). Extracted frames with a window spacing interval  of ~0.12nm. and
did 1ns sampling. Histograms are with reasonabvle overlap. Then I used
g_wham for plotting PMF considering first 300ps as equilibration.

I am getting a plot , but potential is increasing constantly. ie, PMF is not
converged as mentioned the tutorial? Do I need to extend the sampling ? or
any other reason?

Please help me.
Thank you.

-Aswathy
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