VMD-L Mailing List

From: yzliu (nk.liuyz_at_gmail.com)
Date: Thu Jul 16 2009 - 02:06:34 CDT

Dear all,

  I have simulated a membrane system with NAMD.
  And I want to calculate the sasa of each lipid with
  the command "measure" in VMD.

  But first of all, the PBC must be used to reduce edge
  effect. My idea is replicating the cell 3 * 3 times in
  the xy plane to a big box. Only the central image of
  the replicated system is used for analysis.

  My problem is how to replicate the cell in my trajectories.

  Thanks in advanced.

   Regards,

   Yingzhe 

-- 
==============================
Yingzhe Liu
PHD Student of Analytical Chemistry
Chemistry Department
Nankai University
Tianjin, P.R.China,30071
Email: nk.liuyz_at_gmail.com
==============================