Re: Rigid bonds and non-bonded energy

From: Brian Radak (
Date: Fri Oct 16 2015 - 17:42:34 CDT

Is your structure generated in accord with those constraints? Since you
are running dynamics, I believe RATTLE will have a go at coordinate
resetting. In that case the energy you get will not be the energy of
the input structure if the constraints are not satisfied.

On 10/16/2015 04:39 PM, Grzegorz Nawrocki wrote:
> Dear NAMD users,
> I run simulation with number of steps equal to zero, since I want to
> calculate energy of a single structure. Log file says that kinetic
> energy is zero, that is fine, but non-bonded energies, both VDW and
> electrostatic, significantly depend on rigid bonds are turned on or
> off. How it is possible?
> Best regards,
> --
> Grzegorz Nawrocki

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

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