Re: expected speed up after fixing atoms?

From: Jose Borreguero (
Date: Wed Sep 24 2014 - 13:41:02 CDT

Isn't it the case that calculations involving interactions between fixed
atoms are bypassed? What's the point of calculating forces between atoms
that won't move?

On Wed, Sep 24, 2014 at 2:10 PM, Aron Broom <> wrote:

> 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 <>
> wrote:
>> 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

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