From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu Jan 07 2016 - 08:37:07 CST
Hi Sruthi,
If you are looking at a radius of gyration, keep in mind that that
coordinate experiences a strong Jacobian force especially at small values.
Essentially, entropy tends to pull the particles apart, while cohesive
forces from the force field keep it together - those would be almost always
negative. Did you activate the hideJacobian option?
Jerome
On 7 January 2016 at 13:49, sruthi c k <cksruthikvr_at_gmail.com> wrote:
> Dear NAMD developers,
>
> I have some queries about the system forces that are calculated in the
> COLVAR module implemented in NAMD.
>
> I was trying to generate the free-energy surface by integrating the
> <F_system> on the colvar obtained from an unconstrained and unbiased MD
> simulation.
>
> I did 200 ns equilibrium molecular dynamics (NPT) simulation (NO BIAS
> APPLIED) and collected the system force acting on the colvar. The
> <F_system> for a given bin of the colvar was then calculated by taking the
> average of the system forces corresponding to the rg values falling in that
> bin.
>
> What I observe is that <F_system> is a straight-line but it is all
> negative numbers. I was expecting that <F_system> will be equal to zero
> where the histogram of colvar has a peak and +ve and -ve on either side of
> it.
>
> Could you please help me in understanding this?
> Thanks in advance
>
> Regards
> Sruthi
>
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