Osprey-DPD / osprey-dpd

Open Source Polymer Research Engine codebase

Welcome to the official distribution of the Osprey simulation engine.

Osprey-DPD - Open Source Polymer Research Engine-Dissipative Particle Dynamics - is free software distributed under the BSD 3-clause license. It was developed by the author at the Max Planck Institute of Colloids and Interfaces, Germany, 1999-2007. You may use the code in any way you wish, modify and redistribute it or embed it in other software, subject to the conditions of the license. See the license file for details. For further information, please contact the author: jsnano "at" me "." com

The code is written in standard C++03 and uses the STL. It has run successfully on Linux, Mac OS X and Windows 10 platforms.

The User Guide describes how to compile and run the code, and explains many of the code features.

On Linux platforms, the code is compiled and linked using the GNU C++ compiler with the following two commands executed in the source code directory:

$ g++ -c -O3 -std=c++11 *.cpp
$ g++ -o dpd *.o -pthread

One can also build it using cmake:

$ mkdir build
$ cd build

# for Release
$ cmake ..
$ make

# for Debug
$ cmake .. -DCMAKE_BUILD_TYPE=Debug
$ make

# or using Ninja
$ cmake .. -GNinja
$ ninja

The main() routine is in the file "dmpc.cpp".

The code is executed by entering its name at the command line and providing a single argument that is the extension of the required text input file that must be named "dmpci.nnn" where "nnn" is a user-defined alphanumeric string. This command

$ ./dpd  001

will invoke the code and cause it to read its input from the file "dmpci.001" that must be located in the current directory. If the specified file is not found, the code creates a default input file that can then be modified as desired. Some simple input files for various cases can be found in the /examples directory.

Publications using Osprey-DPD

Macromolecular crowding is surprisingly unable to deform the structure of a model biomolecular condensate, J. C. Shillcock, D. B. Thomas, J. H. Ipsen, A. D. Brown, Biology, 2023, 12, 181.

Model biomolecular condensates have heterogeneous structure quantitatively dependent on the interaction profile of their constituent macromolecules, J. C. Shillcock, C. Lagisquet, J. Alexandre, L. Vuillon, J. H. Ipsen, Soft Matter, 2022, 18, 6674-6693.

Investigating the morphological transitions in an associative surfactant ternary system, H. Honaryar, J. A. LaNasa, R. J. Hickey, J. C. Shillcock, Z. Niroobakhsh, Soft Matter, 2022, 18:2611-2633.

Non-monotonic fibril surface occlusion by GFP tags from coase-grained molecular simulations, J. C. Shillcock, J. Hastings, N. Riguet, H. A. Lashuel, Computational and Structural Biotechnology Journal, 2022, 20, 309-321.

Coupling bulk phase separataion of disordered proteins to membrane domain formation in molecular simulations on a bespoke compute fabric, J. C. Shillcock, D. B. Thomas, J. R. Beaumont, G. M. Bragg, M. L. Vousden, A. D. Brown, Membranes, 2022, 12, 17

Phase behaviour and structure of a model biomolecular condensate, J. C. Shillcock, M. Brochut, E. Chenais, J. H. Ipsen, Soft Matter, 2020, 16, 6413.