DragonFly On-Line Manual Pages

obminimize(1)       DragonFly General Commands Manual (urm)      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.

Open Babel 2.2                   July 4, 2008                   Open Babel 2.2