https://gitlab.com/simnavi/shapespyer

The project provides Python tool-chain and shell scripts for molecular simulation workflows: preparation, running and analysing molecular dynamics (MD) simulations of bio- and organic soft condensed matter.

3D Atomistic simulations Biochemistry Colloidal Self-Assembly Data Structures Mesoscale Modelling and Simulations SAXS Sample atomisitc automation bash biomolecular biomolecular simulation coarse-grain coarse-grained condensed matter equilibration framework free software full atom full-atom git gitlab library molecular aggregates molecular arrangement molecular dynamics molecular modeling molecular structures multiscale multiscale modeling numerical simulation organic molecule physical-chemistry post-processing post-simulation analyses post-simulation analysis python python3 sans sas script self-aggregation self-assembly shape shapes shapespyer simulation simulation-framework smiles notation smiles strings soft matter software development template workflow workflow automation

Last synced: 15 Feb 2026