VMD-L Mailing List

From: Marc Q. Ma (qma_at_oak.njit.edu)
Date: Wed Feb 23 2005 - 11:45:36 CST

Hi Margaret,

My understanding on PBC is as follows, which partially answers your
question -- which I do not understand fully -- and please clarify your
questions:

 From computation point of view, PBC is just a means to allow fast
electrostatics calculation in MD simulations, such as PME or P3ME or
MultiGrid summation. For the biomolecular systems such as solvated
proteins, the replicated identical images are not phyiscal. For
crystals it might be a different story. Also, for systems that charges
are not balanced, or with charged particles going out of one side of
unitcell and enter from the other side, PBC may have some problems,
too.

Best,

Marc
On Feb 23, 2005, at 10:42 AM, Margaret Shun Cheung wrote:

>
>
>
> Hey VMD wizards,
>
> I wonder how the rules of PBC (periodic boundary condition) were
> implemented if the box includes several identical biomolecules. How
> the referenced coordinates that define edges of the box were
> justified?
> Thank you.
>
> Margaret S. Cheung,
> Ph. D. Postdoctoral Fellow,
>
> ------------------------------------------------------------
> Room 2117 Tel: (301) 405-4892
> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
> University of Maryland http://glue.umd.edu/~mscheung
> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
> ------------------------------------------------------------
>