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

From: Norman Geist (
Date: Thu Jun 06 2013 - 02:12:01 CDT



I guess he meant the long range electrostatics (PME) which is anyway
incompatible with non-periodic simulations. So to turn it off, just remove
the PME related flags or explicitly tell "PME off". In that case, you will
still have the cutoff electrostatics left.


Norman Geist.


Von: [] Im Auftrag
von Aron Broom
Gesendet: Mittwoch, 5. Juni 2013 17:48
An: Jose Borreguero
Cc: NAMD-l
Betreff: Re: namd-l: how to do a vacuum minimization without electrostatics
and periodic boundary conditions?


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 <>

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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