ESPResSO

ESPResSo is a highly versatile software package for performing and analyzing scientific Molecular Dynamics many-particle simulations of coarse-grained atomistic or bead-spring models as they are used in soft matter research in physics, chemistry and molecular biology.

Policy

ESPResSO is freely available to users at HPC2N, published under the GNU General Public License (GPL3).

Citations

If you use ESPResSO in your research, please cite them in your scientific papers. How to cite ESPResSO is described here.

Overview

ESPResSo is a highly versatile software package for performing and analyzing scientific Molecular Dynamics many-particle simulations of “coarse-grained” bead-spring models as they are used in soft matter research in physics, chemistry and molecular biology. It can be used to simulate systems such as polymers, liquid crystals, colloids, ferrofluids and biological systems, for example DNA and lipid membranes.

In “coarse-grained” models, a whole group of atoms or molecules are treated as a single bead. Although many details are coarse-grained away in these models, they can often predict qualitative properties, such as for example the scaling behavior of a system, and can give insight into theoretical models. Due to the drastic reduction of degrees of freedom, coarse-graining allows to investigate systems which would be out of reach of the commonly used atom-based simulations, due to the large time- and length scales of the studied processes.

ESPResSo is capable of doing classical Molecular dynamics simulations of many types of systems in different statistical ensembles (NVE, NVT, NpT) and non-equilibrium situations, using standard potentials such as the Lennard-Jones or Morse potential. It contains many advanced simulation algorithms, which take into account hydrodynamic (lattice-Boltzmann) and electrostatic interactions (P3M, ELC, MMM1D). Rigid bodies can be modelled by virtual site interactions, and it can integrate rotationally non-invariant particles.

Usage at HPC2N

On HPC2N we have ESPResSO available as a module.

Loading

To use the ESPResSO module, add it to your environment. You can find versions with 

module spider ESPResSO

and you can then find how to load a specific version (including prerequisites), with 

module spider ESPResSO/<VERSION>

Note

There is both CPU-only and GPU-enabled versions available. Load the prerequisites containing CUDA in order to get the GPU-enabled version.

EXAMPLE:

Loading ESPResSo/4.1.4-Python-3.7.4 for CPUs: 

ml GCC/8.3.0 OpenMPI/3.1.4 ESPResSo/4.1.4-Python-3.7.4

Loading ESPResSo/4.1.4-Python-3.7.4 for GPUs: 

GCC/8.3.0 CUDA/10.1.243 OpenMPI/3.1.4 ESPResSo/4.1.4-Python-3.7.4

Running

The executable is named 

pypresso

Additional info