From: Narasimhan LOGANATHAN (Narasimhan.Loganathan_at_etu.univ-provence.fr)
Date: Wed Feb 20 2013 - 11:55:31 CST
I did simple distance collective variable(CV) simulations between two atom groups using the CV module in NAMD.
I have the histogram and the colvars trajectory file. I tried to use WHAM code by Dr. Alan Grossfield for obtaining PMF.
However, i get only a straight line with a negative slope (highly strange). I tried to look at the histograms
and i see sufficient overlap of the windows. I double checked the value and units of force constant.
In namd i am using relatively high k value (250kcal/mol/Ang^2 and scaled k-2.5 kcal/mol for width of 0.1Ang).
I used 250kcal/mol/Ang^2 in WHAM analysis. I understand that this is little to do with the NAMD.
But, i want to understand why i have a strange results by discussion.
Also, Could you please kindly let me know how i can resolve it.
Thanks in advance,
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