Giovanni M. Pavan Research Group

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Swarm-CG

A software designed for automatically optimizing the bonded terms of a coarse-grained (CG) model of a molecule, in explicit or implicit solvent, with respect to a reference (e.g. all-atom (AA)) trajectory and starting from a preliminary CG model (topology and non-bonded parameters). The package is designed for usage with Gromacs and contains 3 modules for:

  1. Evaluating the bonded parametrization of a CG model
  2. Optimizing bonded terms of a CG model
  3. Monitoring an optimization procedure

GitHub
https://github.com/GMPavanLab/Swarm-CG

Publication
C. Empereur-Mot, L. Pesce, G. Doni, D. Bochicchio, R. Capelli, C. Perego and G. M. Pavan*
“Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-Based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization”
ACS Omega 2020, 5, 32823–32843