This website hosts the software suites SSAGES (Software
Suite for Advanced General Ensemble Simulations) and
COPSS (Continuum--Particle Simulation Software)
which augment standard molecular dynamics and Monte-Carlo codes,
permitting particle--field coupling (COPSS), calculation of
reaction coordinates and 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.
This site also hosts the GPU-accelerated molecular dynamics engine DASH.
The engine is controllable through a powerful Python interface. DASH is specifically designed to couple with SSAGES for fast, state of the art advanced sampling calculations .
MICCoM codes SSAGES, COPSS, and DASH are open-source
and distributed under the GNU General Public License (v3.0). These codes were developed at Argonne National Laboratory
in conjunction with the University of Chicago and the University of Notre Dame.
MICCoM also supports the development of WEST and Qbox.
The Materials Science Division at Argonne National Laboratory (Building 241)
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 open-source codes GROMACS and LAMMPS, and
will grow to incorporate other open-source,
proprietary, and bespoke codes.
SSAGES
SSAGES implements several methods for reactive pathway
identification and free energy measurement, including
Forward Flux Sampling, Metadynamics, and Nudged Elastic
Band methods. A video showing the isomerization of alanine dipeptide is shown here,
with all calculations having been performed in SSAGES.
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, representing DNA, is embedded in a background solvent, and
confined to a nanoscopic channel; without coupling
algorithms such as GgEM, such simulations are
impossible.
The continuum--particle coupling of COPSS permits efficient
simulation of many-body systems such as the DNA nanoslit (see video) on the timescales of
polymer diffusion. In the first video, 84 kilobase DNA is simulated under confinement in a nanochannel with full
hydrodynamic coupling to itself and the system boundaries.
COPSS also permits the simulation of electrostatic interactions with polarization effects in heterogeneous
dielectric media in an accurate, highly efficient manner. In the second video, 10 polarizable micron-sized particles are
simulated in an vacuum environment where only long-range electrostatic interaction and short-range excluded
volume interaction affect their motion. The electrostatic forces are calculated by COPSS at each time step,
and the particles' positions are evolved by coupling COPSS with LAMMPS.
DASH
DASH is a GPU-accelerated molecular dynamics software package designed for both atomistic and coarse grained simulations.
DASH is controlled via a powerful Python interface, which gives the user full control to set up, modify, and analyze
simulations all within one script. Using efficient parallel algorithms, DASH also provides the facility to compute arbitrarily
complex user-defined types of data while maintaining high performance.
DASH is specifically optimized for running with the the advanced sampling package SSAGES,
allowing up to double the performance of leading competitors. With plain molecular dynamics, performance in DASH is comparable
to the fastest codes available.
DASH supports several water models including TIP3P, TIP4P (and variants), as well as the E3B model, a fast and robust 3-body
water model parameterized to capture much of the water phase diagram (Kumar, JPC, 2008).
In addition to these features, DASH provides all the standard functionality users have come to expect from a batteries-included
molecules dynamics package, including a variety of thermostats, barostats, elegant methods for dealing with molecules, long range
charge computation, multiple force fields, and much more.
