RMPCDMD: Simulations of Colloids with Coarse-grained Hydrodynamics, Chemical Reactions and External Fields
The RMPCDMD software package performs hybrid Molecular Dynamics simulations, coupling Multiparticle Collision Dynamics to model the solvent and Molecular Dynamics to model suspended colloids, including hydrodynamics, thermal fluctuations, and chemically active solvent particles and catalytic colloid...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Ubiquity Press
2017-01-01
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| Series: | Journal of Open Research Software |
| Subjects: | |
| Online Access: | http://openresearchsoftware.metajnl.com/articles/142 |
| _version_ | 1811201186844377088 |
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| author | Pierre de Buyl Mu-Jie Huang Laurens Deprez |
| author_facet | Pierre de Buyl Mu-Jie Huang Laurens Deprez |
| author_sort | Pierre de Buyl |
| collection | DOAJ |
| description | The RMPCDMD software package performs hybrid Molecular Dynamics simulations, coupling Multiparticle Collision Dynamics to model the solvent and Molecular Dynamics to model suspended colloids, including hydrodynamics, thermal fluctuations, and chemically active solvent particles and catalytic colloids. The main usage of RMPCDMD is the simulation of chemically powered nanomotors, but other setups are considered: colloids in the presence of a thermal gradients or forced flows. RMPCDMD is developed in Fortran 2008 with OpenMP for multithreaded operation and uses the HDF5-based H5MD file format for storing data. RMPCDMD comes with documentation and a tutorial for the simulation of chemically powered nanomotors. |
| first_indexed | 2024-04-12T02:17:49Z |
| format | Article |
| id | doaj.art-4c54992ec42e4486bd05083655b33a32 |
| institution | Directory Open Access Journal |
| issn | 2049-9647 |
| language | English |
| last_indexed | 2024-04-12T02:17:49Z |
| publishDate | 2017-01-01 |
| publisher | Ubiquity Press |
| record_format | Article |
| series | Journal of Open Research Software |
| spelling | doaj.art-4c54992ec42e4486bd05083655b33a322022-12-22T03:52:13ZengUbiquity PressJournal of Open Research Software2049-96472017-01-015110.5334/jors.142110RMPCDMD: Simulations of Colloids with Coarse-grained Hydrodynamics, Chemical Reactions and External FieldsPierre de Buyl0Mu-Jie Huang1Laurens Deprez2KU LeuvenUniversity of TorontoKU LeuvenThe RMPCDMD software package performs hybrid Molecular Dynamics simulations, coupling Multiparticle Collision Dynamics to model the solvent and Molecular Dynamics to model suspended colloids, including hydrodynamics, thermal fluctuations, and chemically active solvent particles and catalytic colloids. The main usage of RMPCDMD is the simulation of chemically powered nanomotors, but other setups are considered: colloids in the presence of a thermal gradients or forced flows. RMPCDMD is developed in Fortran 2008 with OpenMP for multithreaded operation and uses the HDF5-based H5MD file format for storing data. RMPCDMD comes with documentation and a tutorial for the simulation of chemically powered nanomotors.http://openresearchsoftware.metajnl.com/articles/142Molecular DynamicsColloidsHydrodynamicsNanomotorsFortranPython |
| spellingShingle | Pierre de Buyl Mu-Jie Huang Laurens Deprez RMPCDMD: Simulations of Colloids with Coarse-grained Hydrodynamics, Chemical Reactions and External Fields Journal of Open Research Software Molecular Dynamics Colloids Hydrodynamics Nanomotors Fortran Python |
| title | RMPCDMD: Simulations of Colloids with Coarse-grained Hydrodynamics, Chemical Reactions and External Fields |
| title_full | RMPCDMD: Simulations of Colloids with Coarse-grained Hydrodynamics, Chemical Reactions and External Fields |
| title_fullStr | RMPCDMD: Simulations of Colloids with Coarse-grained Hydrodynamics, Chemical Reactions and External Fields |
| title_full_unstemmed | RMPCDMD: Simulations of Colloids with Coarse-grained Hydrodynamics, Chemical Reactions and External Fields |
| title_short | RMPCDMD: Simulations of Colloids with Coarse-grained Hydrodynamics, Chemical Reactions and External Fields |
| title_sort | rmpcdmd simulations of colloids with coarse grained hydrodynamics chemical reactions and external fields |
| topic | Molecular Dynamics Colloids Hydrodynamics Nanomotors Fortran Python |
| url | http://openresearchsoftware.metajnl.com/articles/142 |
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