Re: peridic boundary condition

From: Marc Q. Ma (
Date: Fri Mar 11 2005 - 10:38:15 CST

Hi, Debashis,

You must be new in this list. There are already tons of info regarding
your questions. Here are some quick answers:

> (1) the meaning of periodic boundary condition?

The system of interest is infinitely replicated in x, y, and z
directions -- for simple box shaped cell. for other complicated cell
shapes, the replication is more complex.

> (2)How NAMD utilize the periodic boundary condition in it's simulation?

For biomolecules, PBC is not physical. Maybe PBC makes more sense for
crystals. NAMD, or any other MD software, uses PBC as an artificial way
to speed up numerical evaluation of electrostatic forces. Fast
electrostatics algorithms include MultiPole, MultiGrid, and PME. NAMD
implements PME and Multipole.

> (3)How the value of periodic boundary condition or cell basis vector
> influence the simulation result.

If you solvate your molecule with a box of water, you better make cell
basis vectors such that they are just a little bit (half angstroms or 1
AA) bigger than the water box. If you make cell basis vectors too big,
you introduce artificial vacuum in your system. Your waters will fill
in the bigger box and the density will become smaller. Or small bubbles
will form along some directions, usually close to the boundaries.

Besides PBC, NAMD also supports cylindrical, spherical and vacuum
boundary conditions. Setting up BCs is dependent on your needs and the
particular systems you work with.



> Thanks.
> Debashis
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> Department of Civil Engineering
> North Dakota State University
> Fargo, North Dakota-58105.
> U.S.A.
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