PolymerMD is a software that performs Langevin dynamics of proteins, represented by means of a minimalistic coarse-grained model: the Elastic Folder Model.
Such a model, presented by S. Najafi and R. Potestio in this article, describes the protein as a simple chain of beads, each representing an amino-acid. The beads interact via a set of potentials encoding the known native state, following the common phylosophy of Go-models. The model adopted by PolymerMD is peculiar as the structure information is implemented only via angular potentials, without native contact interactions.
Moreover, the potential is optimized to reach the folded state with high efficiency and reproducibility. In order to achieve this, the parameters of the angular potential are tuned through a stochastic procedure. In this work I have proposed an evolutionary-based improvement of the original strategy proposed by Najafi and Potestio.
PolymerMD has been implemented by R. Potestio and me. The Langevin dynamics, and of the original stochastic optimization, is the work of R. Potestio, while I have taken care of the parallelization, and of the evolutionary optimization part.
If you are interested in the code you can download it here.
For any question about installation and usage don’t hesitate to contact me!