Half of the structure goes out of the simulation box!

From: faride badalkhani (farideh.khamseh_at_gmail.com)
Date: Fri Sep 30 2016 - 05:18:51 CDT

Dear NAMD experts,

I have performed a simulation on a nanostructure in a water box and I did
not get any errors. However, when I load the dcd file in VMD I see that
almost half of the structure remains in the water box and the remain part
of the molecule is out of the box. Could you tell me what is wrong with the
simulation, please?


This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:22:30 CST