[gmx-users] Psuedo ONIOM gromacs MD run

Mark Abraham mark.abraham at anu.edu.au
Tue Sep 28 02:52:55 CEST 2010

Freeze groups do something along these lines. See manual.


----- Original Message -----
From: TJ Mustard <mustardt at onid.orst.edu>
Date: Tuesday, September 28, 2010 10:46
Subject: [gmx-users] Psuedo ONIOM gromacs MD run
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>


      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: mustardt at onid.orst.edu
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