Re: Protein moving out of PBC water box

From: Jérôme Hénin (
Date: Tue Feb 08 2005 - 17:08:05 CST


If you use the default thermostat and PME electrostatics, there is not much
you can do to prevent your protein from diffusing (partly) out of the unit
cell over long simulation times. The physics happening in your simulation is
of course unaffected. Well, actually, you *could* add position restraints,
but you had better not.

WrapNearest is only relevant if your periodic cell has non-right angles. In a
"rectangular" cell, the periodic image closest to the origin is always
located in the unit cell, so wrapNearest has no effect.


Le mardi 08 Février 2005 22:23, Leyla Celik a écrit :
> Hi,
> I am running a NPT simulation with PBC and my protein moves out of the box.
> I am using "wrapWater" and "wrapAll" options but the "wrapNearest" confuses
> me a bit...
> Could anyone help me?

Jérôme Hénin
Equipe de Dynamique des Assemblages Membranaires
Université Henri Poincaré / CNRS
Tel : (33) 3 83 68 43 95        Fax : (33) 3 83 68 43 71

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