From: Udaya Dahal (dahal.udaya_at_gmail.com)
Date: Wed Feb 13 2019 - 13:08:44 CST
Thank you Giacomo. That was exactly what I was looking and got confused and
thanks for the clarification that colvars uses 1/2 kx^2.
Vermass, I also got confused what is right value to use after looking at
those two documents you mentioned and the NAMD output. Now, it seems
obvious from Giacomo's comment that we need to use the same force constant
as in colvar module ( when the width is 1A ). For the test of force
constant, what I did was I just changed the width of the window(should be
other than 1 to get this output in log file) and checked the line "rescaled
force constant " in the output. That will show us the rescaled value of
force constant and you can easily see it is using kx^2 to rescale the value.
On Wed, Feb 13, 2019 at 1:24 PM Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
> Hi Udaya,
> Are you sure the energy is what you think it is? If I compare the
> documentation for the respective modules (
> 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.
> Best Regards,
> Udaya Dahal
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