[gmx-users] PMF of ligand transport

Aswathy 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.
Thank you.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100506/e605b8b6/attachment.html>

More information about the gromacs.org_gmx-users mailing list