We present an open-source, performant, pure-python molecular dynamics (MD) suite for non-ideal plasmas. The code, Sarkas, aims to accelerate the research process by providing an MD code but also pre- and post-p
Python openmm/openmm Star1.6k Code Issues Pull requests Discussions OpenMM is a toolkit for molecular simulation using high performance GPU code. simulationmolecular-dynamics UpdatedFeb 27, 2025 C++ MDAnalysis is a Python library to analyze molecular dynamics simulations. ...
Recurrent neural networks have led to breakthroughs in natural language processing and speech recognition. Here we show that recurrent networks, specifically long short-term memory networks can also capture the temporal evolution of chemical/biophysical
machine-learning structural-biology molecular-dynamics-simulation antimicrobial-peptides antibiotics Updated Aug 6, 2014 Shell shubhamkrpandey19 / gmx_automated_MDsimulation Star 0 Code Issues Pull requests This bash script requires gromacs and python installed on your system. production molecular-dyn...
DeePMD-kit is a package written in Python/C++, designed to minimize the effort required to build deep learning-based model of interatomic potential energy and force field and to perform molecular dynamics (MD). This brings new hopes to addressing the accuracy-versus-efficiency dilemma in molecular...
Metadynamics is a powerful method to accelerate molecular dynamics simulations, but its efficiency critically depends on the identification of collective variables that capture the slow modes of the process. Unfortunately, collective variables are usuall
We present OpenMM-Python-Force, a plugin designed to extend OpenMM's functionality by enabling integration of energy and force calculations from external Python programs via a callback mechanism. During molecular dynamics simulations, data exchange can be implemented through this http URL or this http...
Code Ocean capsule: https://codeocean.com/capsule/5271472 Licensing provisions: BSD 3-clause Programming language: Python, C++ Nature of problem: Atomic environment analysis and generation of the initial structure are important in molecular dynamics simulations. Many analysis methods relying on particle...
niquetoacceleratesamplingratesofmoleculardynamicssimulationsby performinganumberofparallelreplicasimulationsatdifferenttempera tures(seeFigure1).Periodically,thetemperaturesbetweenpairsofreplica simulationsareswitchedwithaprobability � (E 1 i −E
Molecular simulation communities have faced the accuracy-versus-efficiency dilemma in modeling the potential energy surface and interatomic forces for decades. Deep Potential, the artificial neural network force field, solves this problem by combining the speed of classical molecular dynamics (MD) simulatio...