[gmx-users] umbrella sampling-Bimodal Histograms

chris.neale at utoronto.ca chris.neale at utoronto.ca
Mon Jun 21 16:44:38 CEST 2010

Please clarify:

Are doing SMD or are you doing US? If you're doing SMD then you should  
not be using WHAM and you should not really be able to generate any  
sampling histograms.

Are the histograms that you are referring to population densities of  
the sampling along your reaction coordinate?

My guess -- if you're doing US -- is that you have some incorrect pull  
group settings. Bimodal distributions are indeed possible, but should  
require very long sampling times to achieve, and I doubt that you are  
at those times yet. Your Fc is fine. Post your pull settings.


-- original message --

When i did the Umbrella sampling of frames from an SMD (of ligand
transport), I am getting bimodal histograms in some cases.

Do you think this is because , the force constant that i used is very low (i
used pull_k1=1000).? Are these bimodal peaks may cause any deviation in my
PMF result? Do I need to repeat the sampling again with another pull_k1
value(higher value)?

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