VMD-L Mailing List

From: Zhimin Xiong (zhimin.xiong_at_gmail.com)
Date: Tue Jul 03 2007 - 23:58:00 CDT

Hi, all, I am asking for your help when viewing molecular dynamics
trajectory. For example, I want to display the polymer chain configuration
from MD trajectory file, however, given the psf file that contains the
connectivity of the monomer along the chain, some of the bonds cross over
the box boundary, so the bonds displayed is not true. One way I thought to
solve it is to view a specific frame of the trajectory file and give the
connectivity psf file for this frame that don't connect the crossing bonds,
but it is not convenient to view a lot of frames sequentially. Any
suggestion is appreciated! 

-- 
Zhimin Xiong
State Key Lab. of Polymer Physics & Chemistry
Institute of Chemistry
Chinese Academy of Sciences