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

Yinghong xieyh at hkusua.hku.hk
Fri Mar 10 00:43:06 CET 2006

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.

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.

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.


Xie Yinghong
Hong Kong University
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