Hi, I am doing some research on molecular crystal nanoparticles. My simulation needs to construct a nanoparticle for the molecular crystal material. However, the tools I found online (e.g. Atomsk, LAMMPS, ASE) can only build the particle out of some simple metallic material, such as Aluminum, Copper and NaCl.
I was wondering if there is a software (or packages can be used in Python development environment) that I can use to build a nanoparticle ?
I think the following Python Packages can help:
1- https://wiki.fysik.dtu.dk/ase/index.html https://wiki.fysik.dtu.dk/ase/ase/cluster/cluster.html The Atomic Simulation Environment (ASE) is a set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations. The code is freely available under the GNU LGPL license. There are modules for creating nanoparticles (clusters) with a given crystal structure by specifying either the number of layers in different directions, or by making a Wulff construction.
2- https://www.mdanalysis.org/ MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. It can write most of these formats, too, together with atom selections suitable for visualization or native analysis tools. Conference Paper MDAnalysis: a Python package for the rapid analysis of molec...
3-https://github.com/datreant/MDSynthesis
4-https://pysimm.org/
5-https://simtk.org/projects/pyopenmm
6-http://dirac.cnrs-orleans.fr/MMTK/
7-https://github.com/SCM-NV/PLAMS
8-http://nznano.blogspot.com/2017/11/molecular-dynamics-in-python.html
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