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