VMD-L Mailing List

From: Kipp Johnson (kippjohnson_at_uchicago.edu)
Date: Mon Mar 17 2014 - 18:08:45 CDT

Dear VMD List,

I am interested in analyzing the water around a protein in a NAMD
simulation where the protein has multiple chains and some of the chains
move out of the box during the simulation.

I unwrapped the system with the command "pbc unwrap -first 0". This works
well for the protein, which is correctly unwrapped. However, the waters do
not behave as expected. At the first frame, they all remain inside of the
water box and periodic boundary limits. However, as the trajectory
continues, they spread outside of the water box and form a low-density
sphere around the protein.

Here are pictures describing what I am observing after I unwrap the
trajectory:

Before: http://home.uchicago.edu/~/kippjohnson/protein_frame1.png
After: http://home.uchicago.edu/~/kippjohnson/protein_frame2.png

Can anyone offer suggestions on how to correctly unwrap this?

Thank you,
Kipp Johnson