From: Axel Kohlmeyer (
Date: Fri Sep 25 2009 - 12:16:30 CDT

On Fri, 2009-09-25 at 18:55 +0200, Luca Gelisio wrote:


> So, please, could you give me new version of *psfgen*, if possible?
> I'm planning of increase more box size in order to try to do better
> x-ray
> diffraction studies (best box size is not known at the moment)... It's
> really interesting that peaks calculates from "your water" seems to
> fit
> really good real water peaks, apart obviously for illuminated sample
> size
> (and here is my interest in increasing box size)...

please keep in mind that if you do not run an equilibration MD on
the generated structure (and it would take a _long_ time to _properly_
equilibrate a sample this large directly), all you are seeing is a
"crystal" of the replicated small reference box with some water
molecules cut off at three of the sides, so they won't overlap
with the molecules where they will be placed next to, due to PBC.

it would probably be more efficient, to double the initial water
box in x-, y-, and z-direction, re-equilibrate this until the "memory"
of the small system is lost and then double up from there again
and re-equilibrate and so on. when running MD on non-commensurate box
sizes, you have to expect a shockwave running through your system
in all directions to close the gap that was introduced. thanks to
PBC, this is something that will wear off very slowly (using langevin
dynamics with a large friction, or fixing some atom positions
strategically can help to reduce this) and will become an increasing
problem with larger system size, as the wavelengths of this can
can longer and longer.

in summary: to get meaningful information, it always
takes more effort as one would assume initially.


> Cheers,
> luca

Dr. Axel Kohlmeyer 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.