[gmx-users] unexpected trajectory

[Vivek Raut]

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 
conditions.

what maybe the reason ?

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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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