[gmx-users] Lennard Jones spheres

Chiara Parravicini parravicini.chiara at gmail.com
Tue Feb 19 16:44:08 CET 2008

Dear Mark,
thanks for your reply!

I'll try to better focus my issue: my intent is to perform simulations
similar to which described in some recently published papers in which
cavities are expanded by means of  LJ spheres, using methods called
"pressure guided MD" or "active-site pressurization" (Kimura et al.,
Proteins 2008 Jan 3; Mazanetz et al., Biochemical Society Transactions
2008). I'm working with a receptor model but experimental informations about
the ligand binding mode are not available to date. I don't want to introduce
bias in my MD simulations using a structure with the ligand already inserted
so, inspired by that papers, I was thinking about LJ spheres.
How can I apply this approach with gromacs?


On Feb 19, 2008 2:06 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:

> Chiara Parravicini wrote:
> > Hi Mark,
> >
> > I just want make use of the volumes of the spheres to enlarge the pocket
> > without the use of any ligands.
> How about using a ligand with charges set to zero? Or that and
> tinkered-LJ parameters?
> Mark
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