From: Parisa Akhski (Parisa.Akhshi_at_chem.queensu.ca)
Date: Thu Dec 15 2011 - 09:24:36 CST
Dear NAMD experts,
I am using NAMD to run Umbrella Sampling on an ion channel. I am using a "harmonic force constant" to keep the ion in the center of bin in each window and I know that this value is scaled by the square of the specific width as mentioned in the manual. So, if I define "forceConstant=1" and use width=0.1, NAMD actually applied K=100 in the calculations.
Then, I am processing the trajectory files by using WHAM to produce PMF. I know that WHAM assumes that the biasing potential is V=1/2K(X-X0)^2 whereas CHARMM just defines it as V=K(X-X0)^2. This means if I am using K=100 in NAMD, I should define K=200 in WHAM.
Since I already have the PMF profile from ABF calculations for the same system, I know how the profile should look like and what are the energy barriers in my system. Comparing theses results with the ones from Umbrella Sampling and WHAM, the shape of the profile makes sense but not the amount of the barriers. However, if I change the K value from 200 in WHAM to 50, everything makes sense. I double checked this with WHAM experts to make sure I am using the correct K (200) in WHAM.
Could you please let me know whether you have any suggestions,... to solve this issue?
Many thanks for your time,
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