[gmx-users] unexpected trajectory

Vivek Raut vraut at CLEMSON.EDU
Tue Jun 10 16:08:00 CEST 2003

i loaded the .trr file in VMD. My system has middle layer of molecules 
fixed, & molecules in upper/ lower layer are free to move. All the 
molecules are in cubical box.

the trajectory shows that lower half molecules maintained the box shape & 
were shown moving within the shape, but the molecules in upper half wander 
off & disperse in all directions, not following the periodic boundary 

what maybe the reason ?

Vivek Raut
Graduate Research Assistant
Department of Bioengineering
Clemson University
Clemson, SC- 29631. USA
Email: vraut at clemson.edu
Phone: 864-650-1431

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