From: Mo Chen (mochen.mmm_at_gmail.com)
Date: Mon Jul 21 2014 - 15:03:30 CDT
Dear NAMD developers,
Regarding the "forceConstant" (the scaled force constant) in harmonic
restraints, as demonstrated in NAMD user guide. I have two questions:
1) Does this mean that if setting a 2D umbrella sampling, there is no way
to individually define the force constants (with the unit of kcal/mol A^2
or kcal/mol degree^2) for distance and angle? If there is a way to
individually define them, how should that be done?
2) May I confirm with you about my understanding of the "forceConstanct"?
According to the biased potential in case that the reaction coordinate is
the distance, W = K/2*( r - r_ref)^2, here it basically says W is defined
by "Forceconstants" and that K is dependent on W and r_ref?
Thank you very much!
forceConstant < (harmonic) Scaled force constant (kcal/mol) >
Acceptable Values: positive decimal
Default Value: 1.0
Description: This defines a scaled force constant for the harmonic
potential. To ensure
consistency for multidimensional restraints, it is divided internally by
the square of the specific
width for each colvar involved (which is 1 by default), so that all colvars
dimensionless and of commensurate size. For instance, setting a scaled
force constant of
10 kcal/mol acting on two colvars, an angle with a width of 5 degrees and a
distance with a
width of 0.5 °A, will apply actual force constants of 0.4 kcal/mol×degree−2
for the angle and
40 kcal/mol/°A2 for the distance.
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