I am looking for a paid/open-source software which can generate 3D model structures of self-assemblies (like vesicles, nanotubes, fibrils and other 3D structures) on command. I have attached an example of the kind of 3D structures I am looking to model. The attached 3D model has been manually drawn using Blender, which is time consuming.
So, I need a software in which if I feed the structure of the monomer to the software and command it to model a multi-lamellar vesicle structure formed by self-assembly of the monomers, the software should be able to produce a 3D model.
Few examples:
1. LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator): LAMMPS is a widely used molecular dynamics simulation software that can simulate various self-assembled structures. With the appropriate force fields and input commands, LAMMPS can generate and simulate self-assembled systems in 3D.
2. GROMACS: GROMACS is another popular molecular dynamics simulation package that can generate self-assembled structures. It offers various tools and modules for constructing and simulating self-assemblies, including lipid bilayers, micelles, and protein complexes.
3. VMD (Visual Molecular Dynamics): VMD is a molecular visualization and analysis software that can also be used to generate self-assembled structures. It provides a user-friendly interface for constructing and visualizing complex molecular assemblies.
4. Materials Studio: Materials Studio is a comprehensive software suite for materials modeling and simulation. It includes tools for building and simulating self-assembled structures, such as surfactant micelles, nanoparticles, and polymers.
5. CHARMM (Chemistry at HARvard Macromolecular Mechanics): CHARMM is a molecular modeling software package that can be used to generate and simulate self-assembled structures. It offers a range of force fields and simulation modules to model various self-assembling systems.
Hope it helps
Yes, there are various scientific software that can be useful for creating 3D models of self-assemblies.
1. Materials Studio
2. CHARMM (Chemistry at Harvard Molecular Mechanics):
3. LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator): GROMACS
4. VMD (Visual Molecular Dynamics)
The flowing program is the 2D Python, open-source, celluoar automaton program that can be used to understand the very principles of self-organization and emergence.
Game of life generalization, Python, educative program GoL-N24:
https://www.researchgate.net/publication/365477118_Exploring_Emergence_Python_Program_GoL-N24_Simulating_the_'Game_of_Life'_Using_8_Neighbors_from_24_Possible
Video-database and its future updates:
https://www.researchgate.net/publication/373806519_Exploring_Emergence_Video-Database_of_Emergents_Found_in_Advanced_Cellular_Automaton_'Game_of_Life'_Using_GoL-N24_Software
The review covering the relevant research and its relationship to many scientific disciplines:
https://www.researchgate.net/publication/373044641_EMERGENT_INFORMATION_PROCESSING_OBSERVATIONS_EXPERIMENTS_AND_FUTURE_DIRECTIONS
(follow for the final version)
- Badges
- Science topic
- Similar topics
- Mathematics