does fixedAtoms modify velocities?

From: Brian Radak (
Date: Tue Jul 07 2015 - 12:25:32 CDT

I'm having a hard time fully figuring out what happens when fixedAtoms is
turned on. If velocities are read in with binVelocities, are these zeroed
out for atoms that are frozen or are just the forces?

What I'd like to have happen is that I read in coordinates and velocities
and then run dynamics on just a portion of the system with everything else
held as is (that is, both the coordinates and thevelocities). Based on a
drop in the kinetic energy before and after turning on fixedAtoms, it looks
like the velocities are all discarded. Can anyone verify this?


Brian Radak
Postdoctoral Scholar
University of Chicago
Department of Biochemistry & Molecular Biology
Gordon Center for Integrative Science, W323A
929 E. 57th St.
Chicago, IL 60637-1454
Tel: 773/834-2812

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