[gmx-users] Villin Benchmarks

David van der Spoel spoel at xray.bmc.uu.se
Fri May 28 09:31:42 CEST 2004

On Thu, 2004-05-27 at 21:46, Seonah Kim wrote:
> Hello All,
> I was tryied to use Villin Benchmark for studying Gromacs.
> I have some question about it.
> When I check my molecule after mdrun using VMD, they have cubic box instead of 
> octahedron box. I used .gro file and .trr file for the input of VMD. Do you know 
> why I have cubic box instead of octahedron box? 
you don't, but VMD doesn't display the box. In addition gromacs uses a
triclinic box rather than a truncated octahedron (which is identical
mathematically). You can use trjconv to make a a trajectory in trunc.
oct. shape.
> Thank you for you 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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