This is the Molecular Dynamics software ESPResSo ("Extensible Simulation Package for the Research on Soft Matter Systems").
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 as for example polymers, liquid crystals, colloids, ferrofluids and biological systems such as 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, MMMxD). Rigid bodies can be modelled by virtual site interactions, and it can integrate rotationally non-invariant particles.
ESPResSo is free, open-source software (GPL). It is parallelized and can be employed on desktop machines, convenience clusters as well as on supercomputers with hundreds of CPUs. The parallel code is controlled via the scripting language Python, which gives the software its great flexibility and allows for many unconventional simulation protocols, as are often required when studying coarse-grained models.
ESPResSo is used in scientific working groups all over the world both as a production platform as well as a research platform for developing new algorithms and methods and designing new models for coarse-grained simulations. It is mainly developed at the Institute for Computational Physics of the University of Stuttgart, but has contributors from all over the world.
You can find documentation on how to compile, use and develop ESPResSo on the homepage at http://espressomd.org/html/doc/index.html.
ESPResSo is intended to be used by people that have proper knowledge of simulation techniques and know how to use them. We do not take responsibility if you use ESPResSo to create and publish bogus results. You have been warned!
PLEASE CITE US!
If you use ESPResSo and obtain scientific results that you publish, we would ask you to acknowledge the usage of ESPResSo by referencing
Hans-Jörg Limbach, Axel Arnold, Bernward A. Mann and Christian Holm. "ESPResSo - An Extensible Simulation Package for Research on Soft Matter Systems". Comput. Phys. Commun. 174(9) (704-727), 2006.
For a BibTeX record, please refer to the key "espresso" in doc/ug/citations.bib.
A number of algorithms in ESPResSo are fairly advanced and unique to ESPResSo. The authors of these contributions kindly ask you to cite the relevant publications, as indicated in the ESPResSo User's Guide (see http://espressomd.org or doc/ug/ug.pdf). For your convenience, the BibTeX records are compiled in doc/ug/citations.bib.
The following files are licensed and copyrighted as indicated below:
doc/dg/figs/bond_angle.fig doc/dg/figs/datastorage.gif doc/dg/figs/dihedral_angle.fig doc/dg/figs/directions.fig doc/dg/figs/elc_errordist.gif doc/dg/figs/ghost_cells.fig doc/dg/figs/ghost_communication.fig doc/dg/figs/linked_cells.fig doc/dg/figs/logo.png doc/dg/figs/move_to_p_buf.fig doc/dg/figs/particles.fig doc/ug/figures/diamond.png doc/ug/figures/dihedral-angle.fig doc/ug/figures/dihedral-angle.pdf doc/ug/figures/fullerene.png doc/ug/figures/hbond.fig doc/ug/figures/hbond.pdf doc/ug/figures/logo.png doc/ug/figures/maggs-charge-assignment.pdf doc/ug/figures/maggs-initial-scheme.pdf doc/ug/figures/maggs-rotation.pdf doc/ug/figures/nacl-rdf.pdf doc/ug/figures/salt.png doc/tutorials/tut2/figures/data/neutral-rho.data doc/tutorials/tut2/figures/data/nonneutral-rho.data doc/tutorials/tut2/figures/data/rdf_from_melt_00.data doc/tutorials/tut2/figures/data/rdf_from_melt_10.data doc/tutorials/tut2/figures/data/rdf_from_melt_11.data doc/tutorials/tut2/figures/data/rdf_lj_00.data doc/tutorials/tut2/figures/nacl-rdf.pdf doc/tutorials/tut2/figures/nacl.plot doc/tutorials/tut2/figures/neutral-rho.pdf doc/tutorials/tut2/figures/nonneutral-rho.pdf doc/tutorials/tut2/figures/salt.png packages/mbtools/doc/colloid_model.jpg packages/mbtools/doc/cylinder_membrane.jpg packages/mbtools/doc/flat_membrane.jpg packages/mbtools/doc/protein_model.jpg packages/mbtools/doc/sphere_membrane.jpg packages/mbtools/doc/torus_membrane.jpg packages/mbtools/doc/wrapped_colloid_densitymap.jpg packages/mbtools/examples/forcetables/9_095_11.tab packages/mbtools/examples/forcetables/n9_c140_22.tab packages/mbtools/examples/forcetables/n9_c160_22.tab packages/mbtools/examples/forcetables/sr_e10_c25.tab samples/adress/bond_tetra.tab samples/adress/cg_ic_tetra.tab samples/adress/cg_tetra.tab samples/adress/thermo_force.tab samples/maggs_correct_rdf.dat samples/object-in-fluid/object-in-fluidUG/figures/arealocal.eps samples/object-in-fluid/object-in-fluidUG/figures/bending.eps samples/object-in-fluid/object-in-fluidUG/figures/bloodCell.eps samples/object-in-fluid/object-in-fluidUG/figures/stretching.eps samples/object-in-fluid/object-in-fluidUG/figures/volume.eps testsuite/analysis_system.data.00.gz testsuite/analysis_system.data.01.gz testsuite/analysis_system.data.02.gz testsuite/analysis_system.data.03.gz testsuite/analysis_system.data.04.gz testsuite/analysis_system.data.05.gz testsuite/analysis_system.data.06.gz testsuite/analysis_system.data.07.gz testsuite/analysis_system.data.08.gz testsuite/analysis_system.data.09.gz testsuite/analysis_system.data.10.gz testsuite/analysis_system.data.chk testsuite/angle_cosine.data testsuite/angle_cossquare.data testsuite/angle_harmonic.data testsuite/comfixed_system.data testsuite/comforce_system.data testsuite/constraints_system.data testsuite/dh_system.data testsuite/el2d_system.data testsuite/el2d_system_die.data testsuite/gb_system.data testsuite/lb_system.data testsuite/lj-cos_system.data testsuite/lj_system.data testsuite/maggs_correct_rdf.data testsuite/mass_system.data testsuite/mdlc_expected_energy.data testsuite/mdlc_expected_force_torque.data testsuite/mdlc_system.data testsuite/mmm1d_system.data testsuite/npt_lj_system.data testsuite/object_in_fluid_system-final.data testsuite/object_in_fluid_system-init.data testsuite/object_in_fluid_system-nodes.data testsuite/object_in_fluid_system-triangles.data testsuite/p3m_magnetostatics2_expected.data testsuite/p3m_magnetostatics2_system.data testsuite/p3m_magnetostatics.data testsuite/p3m_system.data testsuite/p3m_wall_system.data testsuite/pe_micelle.data testsuite/tabulated_system.data testsuite/thermostat.data testsuite/thermostat_rot.data
"Copyright (C) 2010,2011,2012,2013,2014,2015,2016 The ESPResSo project Copyright (C) 2002,2003,2004,2005,2006,2007,2008,2009,2010 Max-Planck-Institute for Polymer Research, Theory Group
This file is part of ESPResSo.
ESPResSo is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
ESPResSo is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/."
This file is licensed as follows:
Copyright (C) 2010,2011,2012,2013,2014 The ESPResSo project
Copying and distribution of this file, with or without modification, are permitted in any medium without royalty provided the copyright notice and this notice are preserved. This file is offered as-is, without any warranty.