obminimize(1)
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
babel(1), obenergy(1), obrotamer(1).
The web pages for Open Babel can be found at: <http://openbabel.org/>
The web pages for Open Babel Molecular Mechanics can be found at:
<http://openbabel.org/wiki/Molecular_mechanics>
AUTHORS
The minimize 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 <http://openbabel.org/wiki/THANKS>
COPYRIGHT
- Copyright (C) 2007 by Tim Vandermeersch.
- This program is free software; you can redistribute it and/or modify it
- under the terms of the GNU General Public License as published by the
Free Software Foundation version 2 of the License.
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.