Aswathy wrote:
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.
Isn't SMD usually referred to pulling at some finite pulling speed? That
would not be umbrella sampling.
Anyway, you'll have to provide a lot more data to enable us to help you.
Jochen
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
--
---------------------------------------------------
Dr. Jochen Hub
Molecular Biophysics group
Dept. of Cell & Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4714451 Fax: +46-18-511755
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