VMD-L Mailing List

From: Prof. Eddie (eackad_at_siue.edu)
Date: Tue Jun 12 2012 - 12:03:39 CDT

Hello all,

I completed a run with namd using both wrapWater on and wrapAll on for a
solvated protein with period boundary condition. I did so because my
protein kept escaping the water box (when I only used wrapWater). I'd like
to check that this worked so I visualized it in vmd expecting that when a
piece of my protein crossed the boundary I'd see it appear on the other
side of the box. Instead I see part of the protein leave the water box. The
water "reflects" well.

In the initial output of the code I saw:
Info: WRAPPING WATERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.

Is there something wrong with my expectation of seeing the protein "break
up" and reform as it hits the boundary? should it simply look like a
protein sticking out of a box because of some intelligent thing vmd is
doing? Is there any other way to ensure the wrapAll worked besides
visualization?
Thanks,
Eddie 

-- 
_________________________________________________________
Edward Ackad, Ph.D <http://www.siue.edu/%7Eeackad>
Assistant Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390
-- 
_________________________________________________________
Edward Ackad, Ph.D <http://www.siue.edu/%7Eeackad>
Assistant Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390
-- 
_________________________________________________________
Edward Ackad, Ph.D <http://www.siue.edu/%7Eeackad>
Assistant Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390