NAME

obminimize — optimize the geometry, minimize the energy for a molecule

SYNOPSIS

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 numer 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:

Minimize the energy for the molecule(s) in file test.mol2:

Minimize the energy for the molecule(s) in file test.mol2 using the Ghemical forcefield:

Minimize the energy for the molecule(s) in file test.mol2 by taking at most 300 geometry optimization steps

Minimize the energy for the molecule(s) in file test.mol2 using the steepest descent algorithm and convergence criteria 1e-5:

SEE ALSO

obabel(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 current 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.