[gmx-users] PMF of ligand transport

Jochen Hub jochen at xray.bmc.uu.se
Thu May 6 09:26:07 CEST 2010

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.


> 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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