From: Axel Kohlmeyer (
Date: Tue Mar 18 2014 - 01:10:34 CDT

On Mon, Mar 17, 2014 at 7:08 PM, Kipp Johnson <> wrote:
> 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:
> After:
> Can anyone offer suggestions on how to correctly unwrap this?

you did the unwrapping correctly, but now you have to wrap it again,
but with -compound fragment to keep molecules intact and centered on
the protein.


> Thank you,
> Kipp Johnson

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.