[gmx-users] Umbrella sampling question

chris.neale at utoronto.ca chris.neale at utoronto.ca
Mon Sep 20 14:52:49 CEST 2010


We can't tell if you did US correctly unless you post what you have  
done. You must give more info and you must copy and paste the actual  
input / .mdp parameters that you used.

As for if your PMF is correct, then we can never tell you that. You  
can, however, ensure that your sampling distributions are compatible  
with the PMF that you get out of WHAM by looking at the probability  
histograms and ensuring that they tend away from the center of  
restraint and toward local minima on your PMF.

There are hundreds of reasons why your PMF might be wrong (note that  
it also might be correct!) but that is impossible for us to tell with  
the information that you have provided. At the very least, one would  
need to see the PMF and all of the info I mentioned above. Also, you  
should check (and show us!) convergence. If you PMF is still drifting  
with increasing sampling (or increased initial time discarded as  
equilibration) then you are simply not converged for sure.


-- original message --

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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