Efficient implementation of Monte Carlo algorithms on graphical processing units for simulation of adsorption in porous materials

Z Li, K Shi, D Dubbeldam, M Dewing… - Journal of Chemical …, 2024 - ACS Publications
We present enhancements in Monte Carlo simulation speed and functionality within an open-
source code, gRASPA, which uses graphical processing units (GPUs) to achieve significant …

New features of the open source Monte Carlo software Brick-CFCMC: Thermodynamic integration and hybrid trial moves

HM Polat, HS Salehi, R Hens, DO Wasik… - Journal of Chemical …, 2021 - ACS Publications
We present several new major features added to the Monte Carlo (MC) simulation code
Brick-CFCMC for phase-and reaction equilibria calculations (https://gitlab …

Py-MCMD: python software for performing hybrid Monte Carlo/molecular dynamics simulations with GOMC and NAMD

MS Barhaghi, B Crawford, G Schwing… - Journal of chemical …, 2022 - ACS Publications
py-MCMD, an open-source Python software, provides a robust workflow layer that manages
communication of relevant system information between the simulation engines NAMD and …

MoSDeF-GOMC: Python software for the creation of scientific workflows for the Monte Carlo simulation engine GOMC

B Crawford, U Timalsina, CD Quach… - Journal of Chemical …, 2023 - ACS Publications
MoSDeF-GOMC is a python interface for the Monte Carlo software GOMC to the Molecular
Simulation Design Framework (MoSDeF) ecosystem. MoSDeF-GOMC automates the …

[PDF][PDF] alchemlyb: the simple alchemistry library

Z Wu, D Dotson, I Alibay, B Allen… - Journal of Open Source …, 2024 - hal.science
Summary alchemlyb is an open-source Python software package for the analysis of
alchemical free energy calculations, an important method in computational chemistry and …

Coarse-Grained Molecular Dynamics Simulation of Cobalt Nanoparticle in the n-Octacosane–Water Mixture: The Effect of Water Concentration and Nanoparticle Size

KD Papavasileiou, LD Peristeras… - The Journal of …, 2022 - ACS Publications
The Fischer–Tropsch synthesis (FTS) is central in the Gas-to-Liquids (GTL) process, which is
commercially used in the production of environmentally benign transportation fuels from …

Avoiding pitfalls in molecular simulation of vapor sorption: Example of propane and isobutane in metal–organic frameworks for adsorption cooling applications

F Formalik, H Chen, RQ Snurr - The Journal of Chemical Physics, 2024 - pubs.aip.org
This study introduces recommendations for conducting molecular simulations of vapor
adsorption, with an emphasis on enhancing the accuracy, reproducibility, and comparability …

[PDF][PDF] MoSDeF-dihedral-fit: A lightweight software for fitting dihedrals within MoSDeF

B Crawford, CD Quach, NC Craven… - The Journal of …, 2024 - researchportal.hw.ac.uk
Molecular Mechanics (MM) simulations (eg, molecular dynamics and Monte Carlo) provide a
third method of scientific discovery, adding to the traditional theoretical and experimental …

Force Field for Calculation of the Vapor-Liquid Phase Equilibrium of trans-Decalin

IP Anashkin, AV Klinov - ChemEngineering, 2023 - mdpi.com
Based on the TraPPE force field, previously unknown values of the parameters of the
intermolecular interaction potential of trans-decalin were determined. Parametrization was …

Thermal Fluctuations and Framework Flexibility of IRMOF-1 upon CH4 and CO2 Adsorption

S Parashar, NJ Corrente, AV Neimark - 2024 - chemrxiv.org
Flexibility of metal-organic frameworks (MOFs) plays an important role in their applications
for adsorption separations, energy and gas storage, and drug delivery. Here, we …