[gmx-users] box vectores
feenstra at chem.vu.nl
Tue Oct 21 09:05:02 CEST 2003
Nuno R. L. Ferreira wrote:
> My problem, is that I don't know how to draw those lines for this polyhedra
> based again on 3 vectores only.
> Can anyone point me a book, or some other kind of information on how to do this?
> P.S. ngmx draws the box only on cubes, triclinic and octahedrons. It doesn't
> draw the box around the rhombic dodecahedron. At least, I was not successful.
Right - all box types are unified in Gromacs as triclinic boxes.
Octahedrons, dodecahedrons etc. can be represented as well as triclinic,
with certain ratio of vector lenghts and certain angles.
I've seen one of the Gromacs tools (trjconv or editconf, IIRC) with an
option to draw atoms at the corners and 'conect' statements in the .pdb
file to represent the vertices. But I don't remember if that version
made it into the distribution (it may have become a hidden option, check
with 'trjconv -h -hidden' or 'editconf -h -hidden'), otherwise I'm sure
Berk Hess could answer that...
Another option is something like '-ur compact', which is an option to
trjconv (which can also work on single .pdb or .gro files!), that will
'pack' your water molecules into the 'compact' representation of your
box, corresponding to the intuitive rhombic box-shape you would want to see...
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| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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