[gmx-users] Visualizing non-rectangular boxes

[chris.neale at utoronto.ca]

> It is a dodecahedron, as far as I can see. The last line says:
>
>   3.44971   3.44971   2.43931   0.00000   0.00000   0.00000    
> 0.00000   1.72486   1.72486

Here's a test. Copy this into a file and chmod +x it and then run it  
and vmd c.gro. Is it dodecahedron? It should be.

#!/bin/bash
echo "title">a.gro
echo "0">>a.gro
echo "  3.44971   3.44971   2.43931   0.00000   0.00000   0.00000    
0.00000   1.72486   1.72486" >> a.gro

genbox -cp a.gro -cs spc216.gro -o b.gro
pdb2gmx -f b.gro -p b.top -ff oplsaa
touch empty.mdp
grompp -f empty.mdp -p b.top -c b.gro -o b.tpr

echo 0 | trjconv -f b.gro -s b.tpr -ur compact -o c.gro

### End of script


Other Suggestions:
1) Look at your output from trjconv carefully. Did you do exactly what  
you posted? (trjconv -ur compact -s topol.tpr -f config.gro -o  
filenew.pdb) Note that some options don't work together e.g. -ur  
compact and -pbc whole
2) Try the trjconv -ur compact and output a .gro (although a .pdb  
works fine for me)
3) Try upgrading your VMD to the most recent version
4) Go back to a simple system and try again.