Crescat Scientia

This website hosts the software suites COPSS (Continuum--Particle Simulation Suite) and SSAGES (Software Suite for Advanced Generalized Ensemble Simulations), which augment standard molecuar dynamics and Monte-Carlo codes, permitting particle--field coupling (COPSS), and calculation of of reaction coordinates, reactive pathways and free energies (SSAGES). Each presents not only a set of methods, but also aims to provide a unified, extensible framework adaptable to generic molecular simulations.

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IME-CODES

Open Source Project

IME codes SSAGES and COPSS are open-source, distributed under the BSD 3-clause license.

Seamless Integration

SSAGES and COPSS are designed from the ground up to connect to arbitrary molecular simulation codes through minimal programming effort. Initial releases target specific interoperability with the open-source code LAMMPS, and will grow to incorporate other open-source, proprietary, and bespoke codes.

Under the Hood

SSAGES implements several methods for reactive pathway identification and free energy measurement, including Forward Flux Sampling, Metadynamics, and Nudged Elastic Band methods.

COPSS

The continuum--particle coupling provided by COPSS enables the spanning of multiple timescales in simulation. The initial suite of routines is built around the General-geometry Ewald-like Method (GgEM) which enables simulations such as that shown below, where a discrete polymer chain, modeling DNA, is embedded in a background solvent, and confined to a nanoscopic channel; without coupling algorithms such as GgEM, such simulations are impossible.