From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed Feb 13 2019 - 12:24:51 CST
Are you sure the energy is what you think it is? If I compare the documentation for the respective modules (http://www.ks.uiuc.edu/Research/namd/2.13/ug/node57.html#SECTION000126400000000000000 for colvars, section 8.1.2 for Grossfield's implementation of WHAM), they both have the factor of 1/2. Looking back at my own analysis, the value I put down for the force constant (assuming the width of the colvar is 1), is the same value you feed to WHAM. When you say the width shows it is missing a factor of 1/2, how did you test this?
On 2019-02-13 11:13:03-07:00 owner-namd-l_at_ks.uiuc.edu wrote:
I am using colvar module for running umbrella sampling (1D) with window width of 1A and a force constant (1 kCal/mol). Since, NAMD defines energy as (k x^2) to rescale the force constant (as can be seen in log file by modifying the width of the window) but in case of WHAM ( by Grossfield) , the energy is defined as 1/2 k x^2. I am wondering if I need to use different force-constant to match the exact value used in simulation -- in my case 2kCal/mol/A^2 while doing the free energy calculation.
I would like to point out that I am getting exactly double the value of the free energy when I doubled the force constant.
I appreciate your help.
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