openmm
lammps
openmm | lammps | |
---|---|---|
2 | 7 | |
1,385 | 2,052 | |
2.5% | 1.8% | |
8.6 | 10.0 | |
2 days ago | 1 day ago | |
C++ | C++ | |
- | GNU General Public License v3.0 only |
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openmm
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Developers of Software used in Modelling
Gromacs: https://gitlab.com/gromacs/gromacs OpenMM: https://github.com/openmm/openmm Dalton: https://gitlab.com/dalton/dalton/tree/release/2020
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Strange display with disconnected lines, does anyone know what this means?
Thanks for reporting. I haven't used CHARMMGUI myself, but I do see a similar issue that was resolved here: https://github.com/openmm/openmm/issues/3250 By chance is this relevant and/or address your problem?
lammps
- Lammps – A flexible simulation tool for particle-based materials modeling
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Efficiently spreading 1K + agents
Look into verlet lists or cell lists for your task, which are typically used with a discrete element method such as LAMMPS for what you seem to be describing.
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Where to find a dynamic charge density animation/simulation?
Your choices are an n-body simulation (e.g., LAMMPS) with Coulomb interactions or, if your electrons are sufficiently sparse, a particle-in-cell (e.g., Starfish). Your best bets for visualization are going to be matplotlib or something more user-friendly like Visit or Paraview. Without a neutralizing background, however, your electrons are just going to repel each other, hit the walls, and disappear - there's not going to be much interesting to visualize. What are you actually trying to simulate? With more information maybe you could receive some more targeted advice.
- Lammps Molecular Dynamics Simulator
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👀 Chem.py has started development 🎉 A python library for doing chemistry simulations!! It's open-source too!!!!
Is this just a personal /learning project? I see "chemical simulations" and think quantum-espresso, LAMMPS, NWChem, etc. If this is a personal project, I apologize for my bluntness above.
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If we invert the velocity of all molecules in a closed system, can we reverse its entropy?
Actually, the LAMMPS website has a similar example: Just hover over the "LAMMPS" logo in yellow and blue.
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Active Matter Simulation using LAMMPS
Modify the file to add what you need. In your case, modify the post_force functions in the files, since those will allow you to define the integration steps for the Vicsek model and its variations.
What are some alternatives?
gromacs
espresso - The ESPResSo package
senpai - Molecular dynamics simulation software [Moved to: https://github.com/Chelsea486MHz/senpai]
EventMolecularDynamics - A program implementing event driven molecular dynamics for hard smooth spheres, using OpenGL for displaying
Blender-FLIP-Fluids - The FLIP Fluids addon is a tool that helps you set up, run, and render high quality liquid fluid effects all within Blender, the free and open source 3D creation suite.
plumed2 - Development version of plumed 2
The-Powder-Toy - Written in C++ and using SDL, The Powder Toy is a desktop version of the classic 'falling sand' physics sandbox, it simulates air pressure and velocity as well as heat.
SolarSystem - A solar system simulator with Verlet, using OpenGL for displaying.
chemispy - A library for using chemistry in your applications
awesome-python-chemistry - A curated list of Python packages related to chemistry
miniMD - MiniMD Molecular Dynamics Mini-App