Related papers: OpenMM-Python-Force: Deploying Accelerated Python …
Tensor product state (TPS) based methods are powerful tools to efficiently simulate quantum many-body systems in and out of equilibrium. In particular, the one-dimensional matrix-product (MPS) formalism is by now an established tool in…
(Abridged) We have developed a numerical software library for collisionless N-body simulations named "Phantom-GRAPE" which highly accelerates force calculations among particles by use of a new SIMD instruction set extension to the x86…
In this work, we present a general purpose deep neural network package for representing energies, forces, dipole moments, and polarizabilities of atomistic systems. This so-called recursively embedded atom neural network model takes both…
We provide an introduction to molecular dynamics simulations in the context of the Kob-Andersen model of a glass. We introduce a complete set of tools for doing and analyzing the results of simulations at fixed NVE and NVT. The modular…
Compound AI applications, which compose calls to ML models using a general-purpose programming language like Python, are widely used for a variety of user-facing tasks, from software engineering to enterprise automation, making their…
Ongoing advances in force field and computer hardware development enable the use of molecular dynamics (MD) to simulate increasingly complex systems with the ultimate goal of reaching cellular complexity. At the same time, rational design…
The MeMC is an open-source software package for monte-carlo simulation of elastic shells. It is designed as a tool to interpret the force-distance data generated by indentation of biological nano-vesicles by atomic force microscopes. The…
We propose an enhanced approach to the extrapolation of mean potential forces acting on atoms of solute macromolecules due to their interactions with solvent atoms in complex biochemical liquids. It improves and extends previous…
Molecular mechanics (MM) potentials have long been a workhorse of computational chemistry. Leveraging accuracy and speed, these functional forms find use in a wide variety of applications in biomolecular modeling and drug discovery, from…
We present a polarizable embedding quantum mechanics/molecular mechanics (QM/MM) framework for ground- and excited-state Complete Active Space Self-Consistent Field (CASSCF) calculations on molecules within complex environments, such as…
Python has become the de-facto language for training deep neural networks, coupling a large suite of scientific computing libraries with efficient libraries for tensor computation such as PyTorch or TensorFlow. However, when models are used…
DL_MONTE is an open source, general-purpose software package for performing Monte Carlo simulations. It includes a wide variety of force fields and MC techniques, and thus is applicable to a broad range of problems in molecular simulation.…
We introduce GMTHRASHpy, a Python-based application to do forward convolution fits of crossed molecular beams experiments. The code is designed to be easy-to-use and widely-available, so as to be of value to anyone wanting to reproduce data…
The development of reliable and extensible molecular mechanics (MM) force fields -- fast, empirical models characterizing the potential energy surface of molecular systems -- is indispensable for biomolecular simulation and computer-aided…
-Molecular simulations allow the study of properties and interactions of molecular systems. This article presents an improved version of the Adaptive Resolution Scheme that links two systems having atomistic (also called fine-grained) and…
The scale of large pre-trained models (PTMs) poses significant challenges in adapting to downstream tasks due to the high optimization overhead and storage costs associated with full-parameter fine-tuning. To address this, many studies…
Large-scale pre-training has brought unimodal fields such as computer vision and natural language processing to a new era. Following this trend, the size of multi-modal learning models constantly increases, leading to an urgent need to…
The Tree-Particle-Mesh (TPM) N-body algorithm couples the tree algorithm for directly computing forces on particles in an hierarchical grouping scheme with the extremely efficient mesh based PM structured approach. The combined TPM…
We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small computer cluster reactions as complex as protein folding,…
This article presents an innovative open-source software named ModelFLOWs-app, written in Python, which has been created and tested to generate precise and robust hybrid reduced order models (ROMs) fully data-driven. By integrating modal…