[gmx-users] Truncated Octahedron Box
spoel at xray.bmc.uu.se
Mon May 31 22:05:41 CEST 2004
On Mon, 2004-05-31 at 19:06, Seonah Kim wrote:
> Hello All,
> I asked Villin Benchmark for octahedron box and Dr. Spoel replied to me that if
> I use trjconv command, I can see the octahedron box.
> I still have one more question about trjconv.
> I used trjconv option like,
> >trjconv -f full.trr -s full.tpr -o full.pdb
add -pbc compact (or something like that)
> Now, I got the full.pdb file and upload this pdb file using VMD but it still
> looks like cubic box instead of octahedron box. Did I miss something to see
> octahedron box? If someone knows this solution, I'll greatly happy for this. :)
> Thank you for your help in advance...
> Seonah Kim
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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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