obminimize

Table of Contents

## 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 a 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:

    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: <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.

Table of Contents

- Name
- Synopsis
- Description
- Options
- Examples
- See Also
- Authors
- Copyright