From: Robert Elder (rmelder_at_gmail.com)
Date: Tue Jul 12 2011 - 16:48:48 CDT
I'm a little unclear about the units of the force constant (K) for the
new 'tilt' collective variable. The units of the output for this
colvar appear to be cos(angle in radians), such that I can extract the
angle in degrees using acos(colvars output) * (180/pi).
I have been using the raw output from the colvars module (i.e.
cos(radians)) and the force constant in my colvars configuration file
(no clue what the units are) for WHAM. However, it appears to me that
using this force constant may be incorrect, based on a) the expected
results of the simulations and b) some testing with lower force
constants, which show behavior more closely resembling what I expect.
So this made me wonder if I need to convert the K from colvars.conf to
some other set of units where the value of K would be lower. Of
course, I don't want to choose random numbers until I get desirable
So, my questions (maybe Jerome or Giacomo can comment):
1. Do I need to convert the tilt force constant to some other set of
units for WHAM? Or should I just continue to use the value as it is in
my colvars.conf file?
2. Is the factor of 1/2 included in the colvars calculations? That is,
is the potential K/2*(x-x0)^2 or simply K*(x-x0)^2? The manual
suggests the 1/2 is included, but I'm still unclear.
I can provide more details if necessary.
University of Colorado at Boulder
Chemical and Biological Engineering
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