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How to work with WHAM for PMF calculations ?
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+ Computational biophysics
+ Protein analysis
Posted by
Kathryn Barker
How to work with WHAM for PMF calculations ?
I am trying to calculate the PMF of NaCl dissociation by doing Umbrella Sampling and further for removing bias using WHAM, Umbrella Integration (This is just for testing the codes). I checked the overlaps of umbrellas at various positions and they are in good overlap. When i tried to use WHAM, i found that the PMF generated is not in correspondence with the reported literature. Although i am getting the CIP, SSIP positions perfect but the plot shows ions like to stay in SSIP region rather than CIP which is in-correct. Further when i tried to use umbrella integration then it worked. Now, i am confused why WHAM is not working properly.
