Re: expected speed up after fixing atoms?

From: Aron Broom (
Date: Wed Sep 24 2014 - 14:07:32 CDT

Yes, that's true that there isn't a point in calculating the forces between
two atoms that are both fixed. It may be that NAMD will bypass that, but I
think that it may currently not be coded that way. The reason being, that
in general, a situation where it would actually be beneficial would almost
never arise in a reasonable simulation.

For instance, say you have 10,000 atoms, and you want to fix 1000 of them.
The total number of atom-atom interactions (assuming no cutoff) is
10,000^2, and the total number you could potentially save if the
fixed-fixed ones were ignored is 1000^2. In that case, you are only saving
on 1% of the calculations. So, implementing a check for the atoms being
fixed, which itself will take some compute time, isn't really worthwhile
until you have quite a substantial amount of the system fixed, at which
point, you are quite likely simulating something so unphysical that the
results may not be meaningful anyway.

On Wed, Sep 24, 2014 at 2:41 PM, Jose Borreguero <>

> 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

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

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