[gmx-users] Lennard Jones spheres

Chiara Parravicini parravicini.chiara at gmail.com
Tue Feb 19 09:26:16 CET 2008

Hi Mark,

I just want make use of the volumes of the spheres to enlarge the pocket
without the use of any ligands.
Thanks in advance!


On Feb 19, 2008 1:12 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:

> Chiara Parravicini wrote:
> > Hi gromacs users,
> >
> > I would like to add LJ spheres into the protein cavitities, but I don't
> > know how to define input parameters and files to set the run. Should I
> > define spheres as "dummy atoms"? Any suggestion will be greatly
> appreciated!
> How do you want these spheres to interact with the system?
> Mark
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