From: Ashar Malik (
Date: Sat Feb 25 2017 - 14:43:39 CST

Load the trajectory into vmd

Run the following

package require pbctools
pbc unwrap

The last command by default unwraps everything but if you want to unwrap a
selection follow it by

-sel *your selection*

This should unwrap the trajectory.

You should then be able to run the analysis on that (I think). Or you could
save the unwrapped trajectory using "animate"

Hope this works. Other wise write back.


On Feb 26, 2017 09:01, "zoran matovic" <> wrote:

Dear VMD users,

I ran 60 ns NAMD trajectory of protein dimmer. RMSD calculated by VMD is
attached. RMSD spikes are obviously due to the periodic box and the system
appeared to be equilibrated. I turned on “wrapAll” option in config file.
Protein monomers stacked together but due to PB transition I have rmsd
spikes. May be some of u people know how to eliminate these spikes?