Re: how to do a vacuum minimization without electrostatics and periodic boundary conditions?

From: Aron Broom (
Date: Wed Jun 05 2013 - 10:47:48 CDT

you certainly shouldn't have periodic conditions if doing a vacuum
simulation anyway, at any point. Getting rid of that is easy, just don't
write any periodic flags to your config file, e.i. PBC, cellBasisVector and
so forth. Maybe double check the manual to ensure PBC on isn't the
default, in which case you'd just have to explicitly turn it off.

I don't know how to turn off the electrostatics. Are you confident that's
a good assumption? How massive is this chain that it would add so much to
the computational time? If you leave a cutoff (which is questionable for
vacuum) then in the extended form there will be few pairs, so you won't
start doing a lot of long range calculations until the chain collapses


On Wed, Jun 5, 2013 at 11:20 AM, Jose Borreguero <>wrote:

> Dear NAMD users,
> I have a long linear chain. I want to remove steric clashes and simulate
> for a while in order for the chain to shrink in length. For this purpose, I
> can do away without electrostatics and periodic boundary conditions. This
> should speed up the initial relaxation.
> Could anyone please help me with the input configuration file settings to
> accomplish this?
> Best regards,
> Jose Borreguero

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

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