From: sruthi c k (cksruthikvr_at_gmail.com)
Date: Thu Jan 07 2016 - 06:49:51 CST
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
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
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
This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:20:06 CST