From: Yinglong Miao (
Date: Thu Apr 08 2010 - 10:10:17 CDT

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!

Yinglong Miao