Related papers: Software package for simulations using the coarse-…
A modular, maintainable and extensible particle beam simulation architecture is presented. Design considerations for single particle, multi particle, and rms envelope simulations (in two and three dimensions) are outlined. Envelope…
QMCPACK is an open source quantum Monte Carlo package for ab-initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum…
The purpose of this paper is to introduce Condensed-Matter-Laboratory (CML) application for simulating solids and nanostructures and calculating different properties of them by density functional theory and using Green's function theory in…
During the last decade coarse-grained nucleotide models have emerged that allow us to DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a coarse-grained, sequence-specific model that captures the hybridisation…
Soft matter materials and polymers are widely used in the controlled delivery of drugs. Simulation and modeling provide insight at the atomic scale enabling a level of control unavailable to experiments. We present a workflow protocol for…
The simulation of quantum circuits on classical computers is an important problem in quantum computing. Such simulation requires representations of distributions over very large sets of basis vectors, and recent work has used symbolic…
This chapter discusses how the PLUMED plugin for molecular dynamics can be used to analyze and bias molecular dynamics trajectories. The chapter begins by introducing the notion of a collective variable and by then explaining how the free…
Transitions between different conformational states are ubiquitous in proteins, being involved in signaling, catalysis and other fundamental activities in cells. However, modeling those processes is extremely difficult, due to the need of…
DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials (MLP) known as Deep Potential (DP) models. This package, which was released in 2017, has been widely…
Scalable and efficient numerical simulations continue to gain importance, as computation is firmly established as the third pillar of discovery, alongside theory and experiment. Meanwhile, the performance of computing hardware grows through…
An approach for incorporating embedded simulation and analysis capabilities in complex simulation codes through template-based generic programming is presented. This approach relies on templating and operator overloading within the C++…
Motivation: Computational models in biology can increase our understanding of biological systems, be used to answer research questions, and make predictions. Accessibility and reusability of computational models is limited and often…
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…
Computer simulations have become a very powerful tool for scientific research. In order to facilitate research in computational biology, the BioDynaMo project aims at a general platform for biological computer simulations, which should be…
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…
Classical molecular dynamics (MD) simulations are important tools in life and material sciences since they allow studying chemical and biological processes in detail. However, the inherent scalability problem of particle-particle…
Systems composed of soft matter (e.g., liquids, polymers, foams, gels, colloids, and most biological materials) are ubiquitous in science and engineering, but molecular simulations of such systems pose particular computational challenges,…
Here we present a program aimed at free-energy calculations in molecular systems. It consists of a series of routines that can be interfaced with the most popular classical molecular dynamics (MD) codes through a simple patching procedure.…
Biomolecular condensates are formed via liquid-liquid phase separation of proteins, often together with nucleic acids, typically driven by interactions between low-affinity binding sites. The computational study of such condensates that…
Coarse-grained (CG) molecular dynamics simulations enable efficient exploration of protein conformational ensembles. However, reconstructing atomic details from CG structures (backmapping) remains a challenging problem. Current approaches…