From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Mon Dec 08 2014 - 06:48:19 CST
I am currently doing Umbrella Sampling using colvars in NAMD. I am
moving a protein towards a membrane and sampling a vertical distance
of 30A in 21 windows and with width of 0.25 in colvars. The result
histogram shows very "concentrated" distribution at distances
representing the centers of each window. This actually makes sense as
the system should be confined to be near the center defined in colvars
by some harmonic restraints.
My question is
1. Is such histogram agrees with the principle of Umbrella Sampling in
which a "overlapping" histogram is required? As in fact the
distribution does not even "touch" any of the adjacent windows.
2. Can anyone explain more about the width option in colvars? The
manual sometimes confuses me: it says that width helps to rescale the
"value" for harmonic restraints. So what should I do if I would like
to broaden the distribution of histogram? Increase the width or
decrease the force constant, or they are actually the same thing?
Thanks in advance, I will greatly appreciate it if anyone could share
City University of Hong Kong
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:23:06 CST