VMD-L Mailing List

From: OPC3_at_pitt.edu
Date: Thu Oct 28 2010 - 12:12:51 CDT

Hello everyone,

To start with, I am new to PBCtools.

During my MD simulations using Charmm, the protein-membrane system moves
down and the ATP in my system crosses lower hexagonal Periodic boundary
and appear on the upper side of the cell. To correct this, I translated
protein membrane system to the center of the box using PBCtools. now I
would like to rewrap ATP from upper boundary to lower bulk.

PBCtools manual doesn't provide any wrapping information for hexagonal
periodic cells. I wonder if there is a way I could do this?

thanks for your time
Owen