OpenSMOG

OpenSMOG constructs structure-based (Gō-like) models and OpenMM-compatible force fields to simulate biomolecular dynamics for analysis of polymer-ligand interactions and large-scale molecular rearrangements.

Key Features:

• Structure-Based Modeling: Implements structure-based (Gō-like) models that explicitly define intra- and inter-molecular interactions to stabilize experimentally-determined structures and probe dynamics.
• Customization and Distribution: Supports customization and distribution of structure-based models tailored to specific polymer-ligand systems.
• Integration with OpenMM: With SMOG 2 version 2.4, generates force fields specifically designed for use with OpenMM to enable efficient large-scale molecular dynamics simulations.
• User-Defined Force Field Customization: Provides tools to incorporate user-defined modifications to force fields for customized simulation energetics.
• Hybrid Model Support: Allows incorporation of non-structure-based energetics, including AMBER-based terms, to create hybrid classes of models.

Scientific Applications:

• SARS-CoV-2 Spike Protein: Simulation of large-scale rearrangements of the Spike protein to analyze structural dynamics relevant to viral entry.
• HIV-1 Capsid Dynamics: Simulation of HIV-1 capsid behavior in the presence of explicit ions to investigate ionic contributions to capsid stability and function.
• Ribosomes and Protein Crystals: Modeling of crystallographic lattices of ribosomes and proteins to study structural organization and assembly in lattice environments.

Methodology:

Uses structure-based (Gō-like) models that define intra- and inter-molecular interactions to stabilize experimentally-determined structures; generates OpenMM-compatible force fields via the OpenSMOG module (SMOG 2 v2.4); and supports incorporation of AMBER-based energetics for hybrid models.