OpenMM System Preparation

This protocol prepares a OpenMM MD System prior to its simulation from a AtomStruct object.

This protein must have all the atoms including hydrogens, we recommend you to prepare it first with any of our integrated protocols for receptor preparation.

Input

Note

All parameters include a help button that gives further information for each of them.

OpenMM System Preparation form

The result of this protocol is a OpenMMSystem, containing the prepared system including receptor and solvent. It can be visualized using Analyze Results.

OpenMM System Preparation output

Test

This protocol has an integrated test that can be run using the following command:

scipion3 tests openmm.tests.test_openmm.TestOpenMMPrepareSystem