VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Mar 18 2014 - 01:10:34 CDT

On Mon, Mar 17, 2014 at 7:08 PM, Kipp Johnson <kippjohnson_at_uchicago.edu> 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: 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?

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.

axel.

>
> Thank you,
> Kipp Johnson
>
>
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.