From: Axel Kohlmeyer (
Date: Thu Apr 08 2010 - 11:13:45 CDT

On Thu, Apr 8, 2010 at 11:10 AM, Yinglong Miao <> wrote:
> Dear VMDers,
> From what I found in posts of NAMD and VMD mailing lists, only the x, y, z
> length of the simulation box and three angles are stored as unit cell
> information in NAMD dcd files, but not the center of the unit cell (origin
> in xst files). As a consequence, VMD pbctools 2.5 don't have the center of
> unit cell set correctly. Even when reading xst files for pbcset, the origin
> information is lost when calling pbc_namd2vmd. A PBC box won't be displayed
> properly by calling "pbc box" as shown in post:

you have to tell pbc box the location of your origin. there is a flag
for you. check the online documentation.

> Does anyone know how VMD set the center of unit cell? Are there functions we

vmd does nothing at all. it just takes coordinates.

> can call to get/set its values? And also how does it affect "pbwithin" as
> implemented in vmd1.8.7? Thanks in advance for your help!

it should not affect pbwithin at all. to compute periodic neighbors
you only need the cell lengths and angles provided the cell is
oriented properly, which is a given in namd.


> Best,
> Yinglong Miao

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.