From: zeynab hoseyni (
Date: Sat Apr 23 2016 - 09:32:06 CDT

Dear all,

I ran NVT simulation of a nano-tubes in addition to a dimer solvated in
water. In the namd conf file
I turned on the wrapAll and wrapWater options. I saw that the nano-tube and
dimer were so
much moving around and going out of the simulation box frequently during
the simulation. Since I already turned
on the wrap options then sometimes either nano-tube or dimer jump from one
side to the other side
of simulation box, depending on which one catching the side wall, not
suitable for doing some
calculations. I then decided to unwrap the nano-tube (resname CNT) and
dimer (resname ARG)
by following command in vmd:

pbc unwrap -sel "resname CNT or resname ARG" -all

Doing so I calculated the total energy of the wrapped and unwrapped
trajectories using namd energy
plugin. I expected they show the same plot of total energy versus time, but
they show slightly different plots.

Can anyone help on this? In addition to this I don't have a
clear understanding of what wrapping option
does in namd or vmd as I see sometimes nano-tube or dimer traverses the
cell side (one part pass the side
and one part still in the box) but it isn't wrapped and sometimes it is in
the similar situations and it would be wrapped..
Don't know exactly what it does.. Can anyone introduce me some reference or
tutorial to understand more?