From: Bhargava (
Date: Thu Apr 08 2010 - 11:10:51 CDT

Have a look at the pbctools manual


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:
> Does anyone know how VMD set the center of unit cell? Are there functions
> we 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!
> Best,
> Yinglong Miao