Re: peridic boundary condition

From: Edward Patrick Obrien (edobrien_at_Glue.umd.edu)
Date: Fri Mar 11 2005 - 13:09:43 CST

>> (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

There is a physical justification for using PBC, PBC conserve the momentum of
the system. It is my understanding that without PBC conservation of momentum is
violated.

Ed

On Fri, 11 Mar 2005, Marc Q. Ma wrote:

> 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.
>
> Best,
>
> Marc
>
>> Thanks.
>> Debashis
>>
>>
>>
>> -----------------------------------------------------------------------
>> DEBASHIS SIKDAR
>> Ph.D. Student
>> Department of Civil Engineering
>> North Dakota State University
>> Fargo, North Dakota-58105.
>> U.S.A.
>> Phone(Office):701-231-6491.
>> Phone(Residence):701-231-4069.
>> E-mail: Debashis.Sikdar_at_ndsu.edu
>> Sikdardebashis_at_rediffmail.com
>> -----------------------------------------------------------------------
>>
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:18:39 CST