From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Thu Nov 12 2009 - 01:23:16 CST
As I read from the ug ( http://www.ks.uiuc.edu/Research/namd/2.7b1/ug/node23.html#SECTION00081100000000000000
), the bonded energy function is defined as : U = k * (r_i - r_0)^2.
My question is: is the k used in calculating the energy the same as
the one read from the charmm formated parameter file?
P P 1.493 4.7
Does k = 1.493 or k = 1/2 * 1.493?
Does the same rule apply to the restraining constant defined in the
extrabond file :
# bond atom1 atom2 k ref
Thanks for your help!
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