[gmx-users] unexpected trajectory

[David van der Spoel]

On Mon, 2003-06-09 at 16:08, Vivek Raut wrote:
> 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.
are you sure you have pbc=xyz in your mdp file?
> 
> 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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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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