From: Joshua D. Moore (jdmoore_at_unity.ncsu.edu)
Date: Sun Jun 05 2005 - 21:39:09 CDT
I am using a user defined parameter file to use the OPLS-AA force field, so
my naming of things differs from normal CHARMM parameter files. However, my
parameter file is in CHARMM format, and I specify this with "paraTypeCharmm
on". I was wondering how NAMD uses the rigidBonds water command.
Specifically, how does NAMD determine what is water? I think that "oxygen"
just has to have an atom name in the .psf file of OT and "hydrogen" HT?
These then call the parameter file and use OT and HT to match with my .psf
file. Is this correct?
Also, is NAMD setup to use TIP4P and TIP5P water models? Would it be
difficult to use "rigidBonds water" with these models?
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