Module: Molecule Optimizer ()

Description:

This module optimizes the coordinates of a molecule by minimizing its MMFF94 force field energy.

To be able to start the minimization the MMFF parameterization needs to be available as attributes of the molecule. MMFF94 parameters can be computed with the MoleculeEditor or with the molecule tcl command addMMFFParameterization.

The computation will create a Molecule Trajectory containing each minimization timestep. The trajectory will also contain a float observable with the name 'energy' which contains the total MMFF94 energy value (in kJ/mol) for each step.

Connections:

Data [required]
The molecule that is optimized.

Ports:

Method

Method defines the minimization method used. SD (steepest descent) is a first order gradient method following the negative gradient at each step. BFGS (Broyden-Fletcher-Goldfarb-Shanno) is a second order gradient method which works well for small molecules but will fail for large ones because of its storage requirements. CG (conjugate gradient) is a second order gradient method which has less storage demand than BFGS and is therefor better suited for larger molecules with the tradeoff of slower convergence. All three methods are local minimizers, i.e., they will find the closest local minimum.

Fixed

With the fixed port the user can set the current selection of atoms as fixed during the minimization. Fixed atoms will not move but still influence the atoms surrounding them.

Max Steps

The maximum number of steps during the minimization. The minimization will be terminated after this step except if another termination criteria is reached.

Cutoff

Cutoff is the nonbonded cutoff distance in Angstrom.

Min Diff

The minimum difference of energies (in kJ/mol) between two consecutive steps. When the difference becomes smaller the minimization will be terminated.