[gmx-users] PMF of ligand transport
ammasachu at gmail.com
Thu May 6 08:20:28 CEST 2010
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.
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