Molecular enhanced sampling with autoencoders: On‐the‐fly collective variable discovery and accelerated free energy landscape exploration
Sign Up to like & getrecommendations! Published in 2018 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.25520
Abstract: Macromolecular and biomolecular folding landscapes typically contain high free energy barriers that impede efficient sampling of configurational space by standard molecular dynamics simulation. Biased sampling can artificially drive the simulation along prespecified collective variables (CVs),… read more here.
Keywords: enhanced sampling; molecular enhanced; energy; exploration ... See more keywords
CHARMM‐GUI Enhanced Sampler for various collective variables and enhanced sampling methods
Sign Up to like & getrecommendations! Published in 2022 at "Protein Science"
DOI: 10.1002/pro.4446
Abstract: Enhanced sampling methodologies modifying underlying Hamiltonians can be used for the systems with a rugged potential energy surface that makes it hard to observe convergence using conventional unbiased molecular dynamics (MD) simulations. We present CHARMM‐GUI… read more here.
Keywords: gui enhanced; enhanced sampling; enhanced sampler; charmm gui ... See more keywords
Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21: A Machine-Learning-Aided Enhanced Sampling Study
Sign Up to like & getrecommendations! Published in 2024 at "Journal of Chemical Information and Modeling"
DOI: 10.1021/acs.jcim.4c01166
Abstract: MicroRNAs (miRNAs) are short, non-coding RNA strands that regulate the activity of messenger RNAs (mRNAs) by affecting the repression of protein translation, and their dysregulation has been implicated in several pathologies. miR21 in particular has… read more here.
Keywords: dynamics pre; pre mir21; drug; conformational dynamics ... See more keywords
Moltiverse: Molecular Conformer Generation Using Enhanced Sampling Methods
Sign Up to like & getrecommendations! Published in 2025 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.5c00871
Abstract: Accurately predicting the diverse bound-state conformations of small molecules is crucial for successful drug discovery and design, particularly when detailed protein-ligand interactions are unknown. Established tools exist, but efficiently exploring the vast conformational space remains… read more here.
Keywords: generation; enhanced sampling; conformer generation; using enhanced ... See more keywords
An Efficient Gaussian-Accelerated Molecular Dynamics (GaMD) Multilevel Enhanced Sampling Strategy: Application to Polarizable Force Fields Simulations of Large Biological Systems.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.1c01024
Abstract: We introduce a novel multilevel enhanced sampling strategy grounded on Gaussian-accelerated Molecular Dynamics (GaMD). First, we propose a GaMD multi-GPUs-accelerated implementation within the Tinker-HP molecular dynamics package. We introduce the new "dual-water" mode and its… read more here.
Keywords: enhanced sampling; multilevel enhanced; polarizable force; force ... See more keywords
Toward Convergence in Folding Simulations of RNA Tetraloops: Comparison of Enhanced Sampling Techniques and Effects of Force Field Modifications.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.1c01222
Abstract: Atomistic molecular dynamics simulations represent an established technique for investigation of RNA structural dynamics. Despite continuous development, contemporary RNA simulations still suffer from suboptimal accuracy of empirical potentials (force fields, ffs) and sampling limitations. Development… read more here.
Keywords: enhanced sampling; rna tetraloops; toward convergence; convergence ... See more keywords
LINES: Log-Probability Estimation via Invertible Neural Networks for Enhanced Sampling.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.2c00254
Abstract: It is very challenging to sample a molecular process with large activation energies using molecular dynamics simulations. Current enhanced sampling methodologies, such as umbrella sampling and metadynamics, rely on the identification of appropriate reaction coordinates… read more here.
Keywords: enhanced sampling; probability estimation; reaction; log probability ... See more keywords
MDexciteR: Enhanced Sampling Molecular Dynamics by Excited Normal Modes or Principal Components Obtained from Experiments.
Sign Up to like & getrecommendations! Published in 2023 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.2c00599
Abstract: Molecular dynamics with excited normal modes (MDeNM) is an enhanced sampling method for exploring conformational changes in proteins with minimal biases. The excitation corresponds to injecting kinetic energy along normal modes describing intrinsic collective motions.… read more here.
Keywords: enhanced sampling; molecular dynamics; normal modes; excited normal ... See more keywords
Rare Event Kinetics from Adaptive Bias Enhanced Sampling.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.2c00806
Abstract: We introduce a novel enhanced sampling approach named on-the-fly probability enhanced sampling (OPES) flooding for calculating the kinetics of rare events from atomistic molecular dynamics simulation. This method is derived from the OPES approach [Invernizzi… read more here.
Keywords: enhanced sampling; adaptive bias; rare event; kinetics adaptive ... See more keywords
Reweighted Manifold Learning of Collective Variables from Enhanced Sampling Simulations
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Chemical Theory and Computation"
DOI: 10.1021/acs.jctc.2c00873
Abstract: Enhanced sampling methods are indispensable in computational chemistry and physics, where atomistic simulations cannot exhaustively sample the high-dimensional configuration space of dynamical systems due to the sampling problem. A class of such enhanced sampling methods… read more here.
Keywords: learning collective; enhanced sampling; reweighted manifold; manifold learning ... See more keywords
High-performance QM/MM Enhanced Sampling Molecular Dynamics Simulations with GENESIS SPDYN and QSimulate-QM
Sign Up to like & getrecommendations! Published in 2025 at "Journal of Chemical Theory and Computation"
DOI: 10.1021/acs.jctc.5c00163
Abstract: A new module for quantum mechanical/molecular mechanical (QM/MM) calculations is implemented in a molecular dynamics (MD) program, SPDYN in GENESIS, interfaced with an electronic structure program, QSimulate-QM. The periodic boundary condition (PBC) in QM/MM simulation… read more here.
Keywords: sampling molecular; high performance; molecular dynamics; performance enhanced ... See more keywords