[gmx-users] Umbrella sampling question

Aswathy ammasachu at gmail.com
Fri Sep 17 12:50:53 CEST 2010

Hi Gromacs users,
Let me give an idea about what i am doing.
I was doing a Steered Molecular dynamics of ligand transport through
the transporter channel. I want to do the PMF calculation using
Umbrella sampling. I followed the steps provided in the (Justin's)
tutorial. I have generated all configurations, then used the perl
script to find out the distance. I made  one index group for 3 back
bone atoms at the center of the channel and another for the ligand.
(Therefore I will get the distance between the center of the channel
and ligand).
Then I sampled each frame with a window spacing of 0.1nm. The frame
close to the center of the channel is taken at the 0 th
coordinate(pull_init=0 0 0). above this point is +Z coordinate and
below this point is -Z coordinate. I had  good overlapped histograms
and went ahead with plotting PMF.

Am I doing the correct procedure for Umbrella sampling?
Why I doubt because,
 I run g_wham and I had a PMF plot in which at the starting of the
transport (from extracellular), I have free energy value of
-35kcal/mol. Then as it moves along the pathway it increases and
finally it reaches a positive value, +5kcal (when at intracellular).

I know its hard give explanation to my observation, but I am confused
due to several reasons.
1.The energy increases is not much explainable with interactions of
ligand and transporter.
2.If I take the free energy barrier value it is great value than I
expected. Nearly 170KJ/mol
3.In similar kind of ligand transport Smds the PMF was continuous
maxima and minima.

Can any one tell whether my US procedures were right or not?



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