From: Nicolas Martin (
Date: Fri Feb 19 2016 - 08:30:12 CST

Dear users,

I recently run a simulation in NAMD of a pentameric membrane protein
using the wrapping option. Even tough the water and membrane are
correctly wrapped, the protein diffuse in the simulation box and end ups
crossing the periodic boundaries. Doing so, the protein is not kept
full, but 2 chains over 5 jump on the other side of the box. The
wrapping in namd is made so there is no long bonds and only full chains
move to the other side of the box.

I need all the chains to be put back together at the center of the box
for further analysis.

I tried to follow the documentation for doing so and the best I could
end up with is a protein more or less (the com seems to be moving
significantly) well centered in the box and several frames over a long
trajectory with stretched bonds. Here is the routine I used over all
trajectory frames:

pbc unwrap -sel protein -now
pbc wrap -compound res -center com -centersel "protein" -now

I also used bigdcd (that's why the option -now and not -all was used
above) for reading trajectories and wrote wrapped dcds every 1000 frames
to avoid memory problems (otherwise it's a ~30GB trajectory).

I also tried using the Join keyword on the first frame which had no
significant effect.

What procedure would you advice me to use in order to get a perfectly
re-centered and wrapped trajectory in the case of my multi-chains system?

Thanks you in advance for your help,