[gmx-users] Removing periodic boundary conditions using trjconv

Bob Johnson robertjo at physics.upenn.edu
Thu Aug 18 18:40:23 CEST 2005

Hello everyone,
I'm simulating the interactions between single stranded DNA and an infinite
carbon nanotube. I finally got the simulations to work (thank you David and
everyone else for your input). The DNA adsorbs to the nanotube pretty quickly
but wanders around  along the surface of the tube. It's seems that it maintains
a fixed radial distance from the tube center but moves along the z (tube axis)
and the phi (tube circumference) directions. Sometimes the DNA slides into the
next periodic box in the z direction.

When I view the trajectory in VMD, a portion of the DNA moves to the right and
goes into the next box. Of course, because of periodic boundary conditions, an
exact replica of this portion is then shifted back into the box. However, VMD
tries to draw bonds between the DNA and the portion that has been shifted.
Thus, long bonds are drawn across the nanotube's length. I was playing around
with trjconv to see if I could suppress the periodic boundary conditions for
the purpose of visualization. I've used all the different -pbc options already
and none of them helped. Any suggestions on how to go about doing this? In the
end, it may be a problem with how VMD represents a trajectory.
Bob Johnson

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