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.
- -c criteria
-
Set convergence criteria (default=1e-6)
- -cg
-
Use conjugate gradients algorithm (default)
- -sd
-
Use steepest descent algorithm
- -newton
-
Use Newton2Num linesearch (default=Simple)
- -ff forcefield
-
Select the forcefield
- -o format
-
Select the output file format
- -h
-
Add hydrogen atoms
- -n steps
-
Specify the maximum number of steps (default=2500)
- -cut
-
Use cut-off (default=don't use cut-off)
- -rvdw rvdw
-
Specify the VDW cut-off distance (default=6.0)
- -rele rele
-
Specify the Electrostatic cut-off distance (default=10.0)
- -pf freq
-
Specify the frequency to update the non-bonded pairs (default=10)
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
obabel(1), obenergy(1), obrotamer(1).
The web pages for Open Babel can be found at: <https://openbabel.org/>
The web pages for Open Babel Molecular Mechanics can be found at: <https://openbabel.org/docs/Forcefields/Overview.html>
AUTHORS
The minimize program was contributed by Tim Vandermeersch.
Open Babel is developed by a cast of many, including current maintainers Geoff Hutchison, Chris Morley, Michael Banck, and innumerable others who have contributed fixes and additions. For more contributors to Open Babel, see <https://openbabel.org/docs/Introduction/thanks.html>
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.