[gmx-users] triclinic box

[Anton Feenstra]

"T. Zaraiskaya" wrote:
> 
> 1)i am using editconf to generate .gro from .pdb for crystal simulation;
> the crystal is triclinic.

it is by definition... ;-)

> doing:
> % editconf -f <in.pdb> -o <out.gro> -bf tric -box a b c -angles bc ac ab
> 
> the last line of out.gro looks like:
>    1.12020 0.92620 6.259008 0.00000 0.00000 0.00000 0.00000 -0.99134 0.00000
> 
> what are these 9 values in this case? (angles, unit cell vectors..) why nine?

They are the XX YY ZZ XY XZ YX YZ ZX ZY components of the three
box vectors. The ordering is a bit counterintuitive, but that is
because it keeps the XX YY ZZ 'cubic' part of the box vectors in
the beginning, so it corresponds to the case where only the three
box-edge lengths are defined for a cubic box.

> 2)can genbox generate a triclinic box of solvent?

Yes and no. You don't need a triclinic shaped box of solvent to fill
a triclinic system. So genbox generates a 'brick' shaped box of solvent,
but since both a brick and a triclinic box will 'fill' a three
dimensional
space, it doesn't matter. Check your local mathematician for more info
on space filling 'tilings' of different box shapes... trjconv has an
option '-ur' which will reorient your system into different possible
box shape representations.


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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