a problem about pbc in a namd trajectory

From: (jinxj10_at_lzu.edu.cn)
Date: Mon Aug 26 2013 - 02:44:23 CDT

Dear professor,
 
   We simulated a pentamer protein with NAMD. I am confused about that some part of the pemtamer fluctuated in and out of the box. I dealed with pbctools in vmd and failed. The command used are at below.

  package require pbctools
  pbc readxst xstfile
  pbc box_draw
  pbc wrap -all

  The unrecognizable code was displayed when I opened the processed trajectory using VMD.
  Would you tell me the reason and the solution?
  

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