Re: expected speed up after fixing atoms?

From: Aron Broom (
Date: Wed Sep 24 2014 - 13:10:45 CDT

I don't think you'd expect any speed up actually. Fixing the atoms just
means they don't move, but they are still involved in all the pair-wise
force calculations for the system which is the vast bulk of the
computational work.

On Wed, Sep 24, 2014 at 1:44 PM, Jose Borreguero <>

> Dear NAMD users,
> I have a system where I can fix the positions of more than half the atoms
> without affecting much the dynamics I'm interested in. I was wondering what
> is (approximately) the expected speed up in the simulation after I do this.
> Even more important: What will happen if I run a parallel job with this
> system? Will some of the CPU end up doing no calculations if the fixed
> atoms are assigned to those CPU's?
> Best regards,
> Jose Borreguero

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:52 CST