From: Joshua D. Moore (jdmoore_at_unity.ncsu.edu)
Date: Fri Jul 08 2005 - 15:46:41 CDT
I would like to use the SPC/E water model and use "rigidBonds Water".
1) How are the values of Kb and Ktheta determined for the TIP3P water
model to use here? Are they arbitrary?
2) Is the angle information required for the "rigidBonds water" call?
It is my understanding that when using rigidBonds Water, only the bond
information is required in the parameter file, namely K, the coefficient
in front of the bond term in the potential energy function and Do, the
equilibrium distance. I don't find much of a description in the NAMD 2.5
Manual, but the NAMD 1.5 Manual describes the use of both Shake and Rattle
and seems to imply the need of only the distance between the hydrogens and
the distance between the hydrogen and oxygen?
For example, in the Charm22 All-Hydrogen Parameter File for Proteins and
Lipids, for TIP3P water it appears there is information given for both
bonds and angles:
HT HT 0.000 1.5139
OT HT 450.000 0.9572
HT OT HT 55.000 104.5200
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