obminimize1

Usage

Overview

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 the forcefield

-o format

Select the output file format

-h

Add hydrogen atoms

-n steps

Specify the maximum number 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