[gmx-users] Small V.S. Large simulation box.

Mark Abraham Mark.Abraham at anu.edu.au
Thu Mar 9 09:11:18 CET 2006

Yinghong wrote:
> Dear Gmxers:
> For some particular reasons, I need to adopt a very small simulation 
> box, in which box boundary is only ~0.2nm to the surfuce of solute, and 
> PME is used as coulombtype.

Unless you are attempting to simulate a crystal, the odds are are
excellent that your simulation, which significant pertubative effects
from the periodicity and the high effective solute concentration, will
bear no resemblance to a physical one. Even if it does appear to
resemble one, nobody well-informed is likely to believe that it does.

> Roughly speaking, I want to observe the displacement of some atoms, 
> which is however 30% lower than expected. If I enlarge the box, 
> everything goes smoothly. Has anybody ever used such a small box? Any 
> suggestion will be greatly appreciately.

Don't use it :-)

> As I think, Maybe, the problem is from periodic boundary condition and 
> long-range interactions treatment? But I can not find the relevant 
> information both in manual and in mailinglist.

We can't tell from what you've told us. Moreover, I doubt anybody has
relevant experience of doing such simulations.


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