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obminimize - Online in the Cloud

Run obminimize in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command obminimize that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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

Use obminimize online using onworks.net services


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