OBMINIMIZE(1)

💅 obminimize — like, the geometry optimizer of your dreams

okay so bestie, welcome to obminimize, from the Open Babel User's Reference Manual ✨ this is the little icon that takes your molecule and goes "no babe, that bond angle is not it" and gently smooshes it into a lower-energy shape. we stan a glow-up.

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✨ SYNOPSIS ✨

obminimize [OPTIONS] filename

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🦋 DESCRIPTION 🦋

so the obminimize tool can be used to minimize the energy for molecules inside (multi-)molecule files (like, MOL2, etc.) — yes, multi-molecule files, she's not scared of a crowd 💅

it literally just takes your structure and finds the chillest, lowest-energy version of it. main character energy for your atoms, fr fr.

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🎀 OPTIONS 🎀

okay so here's the tea. if no filename is given, obminimize will give you all the options including the available forcefields — so obminimize with no args is basically her saying "here's my whole personality, pick something" 🫶

• -c criteria — set the convergence criteria (default is 1e-6). like how picky she is about "close enough" ✨
• -cg — use the conjugate gradients algorithm (this is the default, she's already on that grind)
• -sd — use the steepest descent algorithm
• -newton — use the Newton2Num linesearch (default is Simple)
• -ff forcefield — select the forcefield. yes you get to choose her whole vibe
• -o format — select the output file format
• -h — add hydrogen atoms 💖 (the little guys deserve to be there)
• -n steps — specify the maximum number of steps (default is 2500). a hard limit, bestie, she will stop
• -cut — use cut-off (default is don't use cut-off)
• -rvdw rvdw — specify the VDW cut-off distance (default is 6.0)
• -rele rele — specify the electrostatic cut-off distance (default is 10.0)
• -pf freq — specify the frequency to update the non-bonded pairs (default is 10)

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🌸 EXAMPLES 🌸

view the possible options, including available forcefields — literally just her showing off:

obminimize

minimize the energy for the molecule(s) in file test.mol2 — the classic, no notes:

obminimize test.mol2

minimize the energy for the molecule(s) in file test.mol2 using the Ghemical forcefield — a whole different flavor:

obminimize -ff Ghemical test.mol2

minimize the energy for the molecule(s) in file test.mol2 by taking at most 300 geometry optimization steps — when you're in a hurry:

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 — -sd girlies rise:

obminimize -sd -c 1e-5 test.mol2

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🧚 SEE ALSO 🧚

go give her friends some love too: 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>

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👑 AUTHORS 👑

the minimize program was contributed by Tim Vandermeersch — ty king 💜

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> — it's giving community, it's giving collaborative slay 🌈

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💀 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. (no cap, that part's important — no promises, bestie 😭)

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ok real talk: that's the whole page. every flag, every default, every number — nothing skipped, nothing invented. she's thorough 💅

and that's the wrap, bestie — Open Babel 3.2, dated May 26, 2026, signing off 🎀✨💖