Obminimize
Name
obminimize -- optimize the geometry, minimize the energy for a molecule
Synopsis
obminimize [OPTIONS] filename
Description
The obminimize tool can be used to minimize the energy for molecules inside (multi-)molecule files (e.g., MOL2, etc.)
Options
If no filename is given, obminimize will give all options including the available forcefields.
- -n steps
- Specify the maximum number of steps (default=2500)
- -cg
- Use conjugate gradients algorithm (default)
- -sd
- Use steepest descent algorithm
- -c criteria
- Set convergence criteria (default=1e-6)
- -ff forcefield
- Select the forcefield
Examples
View the possible options, including available forcefields:
obminimize
Minimize the energy for the molecule(s) in file test.mol2:
obminimize test.mol2
Minimize the energy for the molecule(s) in file test.mol2 using the Ghemical forcefield:
obminimize -ff Ghemical test.mol2
Minimize the energy for the molecule(s) in file test.mol2 by taking at most 300 geometry optimization steps
obminimize -n 300 test.mol2
Minimize the energy for the molecule(s) in file test.mol2 using the steepest descent algorithm and convergence criteria 1e-5:
obminimize -sd -c 1e-5 test.mol2
See Also
The web pages for Open Babel Molecular Mechanics can be found at: <http://openbabel.sourceforge.net/wiki/Molecular_mechanics>
Authors
The obminimize program was contributed by Tim Vandermeersch.
Open Babel is developed by a cast of many, including currrent maintainers Geoff Hutchison, Chris Morley, Michael Banck, and innumerable others who have contributed fixes and additions. For more contributors to Open Babel, see the Contributor list
Copyright
Copyright (C) 2007 Tim andermeersch.
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License, version 2, as published by the Free Software Foundation.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.