Freeze groups do something along these lines. See manual.
Mark
----- Original Message -----
From: TJ Mustard <musta...@onid.orst.edu>
Date: Tuesday, September 28, 2010 10:46
Subject: [gmx-users] Psuedo ONIOM gromacs MD run
To: "gmx-users@gromacs.org" <gmx-users@gromacs.org>
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>
Hello all,
Is it possible to do a pseudo ONIOM MD run where you hold all atoms rigid
except for a small sphere of some radius. I was wondering if I could do this
with posres.itp files or a define argument. It would be beneficial if the atoms
held rigid had no energies, trajectories, vectors, etc calculated for them as
to speed up calculations. I was thinking of first minimizing the energy of the
system before restricting the system.
I came upon this idea first as a "box" inside your solvent md box that
held all atoms and bonds that the box's planes intersected with and held those
rigid allowing the atoms on the outside of the box to be rigid or removed and
the atoms on the inside to be dynamic.
Is this possible? I was hoping to test this as a possible promoter of
FEP. Of course this could increase or implement artifacts.
Thank you,
TJ Mustard
> Email: musta...@onid.orst.edu
|
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