obminimize (1) - Linux Manuals

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

NAME

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

SYNOPSIS

[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"

AUTHORS

The minimize program was contributed by An Tim Vandermeersch.

An -nosplit Open Babel is developed by a cast of many, including currrent maintainers An Geoff Hutchison , An Chris Morley , An 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.