[gmx-users] Problem - can't set dodecahedrons box
Mark.Abraham at anu.edu.au
Tue Feb 9 02:20:53 CET 2010
On 09/02/10 12:12, Maurício Menegatti Rigo wrote:
> I'm facing a problem with GROMACS that appears pretty simple, actually.
> I'm trying to set a dodecahedron box but all I can get is a triclinic
> box. For that, I'm using the following line:
> editconf -f pMHC -bt dodecahedron -o -d 1 /
Since all box types are special cases of a triclinic box, they are all
described in the same way as the latter. I expect the values are
suitable for dodecahedron, but resemble triclinic.
> Am I doing something wrong?? Another problem, different from this one,
> is that my protein, during the simulation, is escaping/comming
> off/"running away" (sorry I'm butchering the english) from the water
> box. I tried to use periodic boundaries conditions, but didn't work (I
> added a line in my .mdp file - pbc = xyz). Someone could help me with
> that, please?
The .mdp file controls the algorithms of the simulation. What you do
afterwards to visualise the results of a simulation is the business of
your visualisation software, and/or your usage of trjconv to keep
yourself happy with what you can see.
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