Rigid bonds for United Atom Methylene Chloride CH2Cl2

From: Joshua D. Moore (jdmoore_at_unity.ncsu.edu)
Date: Wed May 17 2006 - 15:22:41 CDT


I am using a rigid CH2Cl2 united atom model, (CH2 as a united atom bonded
to two Cl atoms). I want to restrain the bond length between the CH2 and
the Cl atoms and also the Cl-CH2-Cl angle. Since this is essentially a 3
atom (or beaded) molecule like water, is it possible to use Settle in NAMD
to apply these restraints?

I think I could trick NAMD, by calling the Cl atoms hydrogens (HT) and the
CH2 united atom (OT) and apply Settle with "rigid water". However, is
there any easier way to apply these restraints?

Does anyone know the details about how NAMD knows that water is water? Is
it the OT and HT atom types in the .psf file?



Joshua D. Moore
Graduate Student
North Carolina State University
Department of Chemical and Biomolecular Engineering
Box 7905 Centennial Campus
Engineering Building I
911 Partners Way
Raleigh, NC 27695-7905
Phone: (919) 513-2051
Fax: (919) 513-2470
Email: jdmoore_at_unity.ncsu.edu

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