[gmx-users] Question about WHAM
sup27606 at yahoo.com
Tue Feb 23 23:01:05 CET 2016
Hello,This question is more about the WHAM technique in general, but I take the liberty to ask it in this forum, hoping somebody can point me in the right direction.
I am calculating the free energy difference between two wells separated by an energy barrier using an umbrella potential restraining an inter-residue distance.
After running the umbrella sampling, I find that some of the histograms have shifted to some extent from their intended positions, with the peak shifted from the restraining distance value. This happens close to the barrier region. So, I have sampled the barrier region separately with a stronger umbrella potential to prevent the 'slippage'.
Now my questions are:1. Can I mix two different umbrella potentials for two different regions (well and barrier) in gmx wham?
2. Would it be wrong to include those simulations where the histograms shifted from the restraining distance in the WHAM calculations?
Many thanks in advance,Supriyo
p.s. If something is unclear in my posting, please let me know and I will try to clarify as much as possible.
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