From: Aryan Vahedi-Faridi (
Date: Thu Jul 30 2015 - 15:04:12 CDT


I am having an issue with unwrapping molecules from a simulation I
conducted. First off, the simulation involves the interaction of a protein
with SWCNT. In one case I had 1GFL and the SWCNT, and in the other I had
1CEL with SWCNT. To my knowledge, both were simulations were run with
similar configuration. After getting my trajectories, I wanted to solve
contact area between them in each case so I used the script featured below.
Now what is unusual is the resulting charts (please see Google Drive link
below to view charts). When the 1GFL calculation was done, the unwrapped
result was fine and comparable to the wrapped result (without the huge
gaps). But when I did the same with 1CEL, the resulting charts are
completely different (unwrapped vs. wrapped). I was expecting the gaps to
be filled but instead I have a completely different result. Indeed, the
trajectory is much different after unwrapping. After unwrap, the SWCNT no
longer appears to be adsorbing onto CEL like when it was wrapped.

Can anyone help me understand why my contact area chart is looking so
different? I know that I used a minimize command in some of the simulation
runs for 1CEL. I am not sure if that has anything to do with this issue.
That is the only difference I was aware of in terms of the runs. I am not
sure what else could be the issue. I have tried unwrapping the Protein and
CNT separately. The issue seems to occur when I unwrap the CNT in
particular. I did not provide the graphs for this but basically the chart
and trajectory look very different right after I unwrap the CNT. If I
unwrap the protein only and look at the resulting chart it is exactly the
same as if I had not unwrapped anything at all. Thanks everyone for the
help. Items to refer to are below. Please let me know if there is anything
else you need to know or see.

Morgan State University

Unwrap Commands Used
>pbc unwrap -sel "protein"
>pbc unwrap -sel "resname CNT"

Contact Area Script

Contact Area Charts

CEL NAMD Run Conf File

GFP NAMD Run Conf File