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PLUMED-NEST provides all the data needed to reproduce the results of a PLUMED-enhanced molecular dynamics simulation or analysis contained in a published paper. Furthermore, PLUMED-NEST monitors the compatibility of the provided PLUMED input files with the current and development versions of the code and integrates links from these files to the PLUMED manual.

Here is the list of projects already deposited in PLUMED-NEST, while a complete bibliography can be found here.

plumID Name Category Keywords Contributor Actions
24.013 Estimating Free Energy Surfaces and their Convergence from multiple, independent static and history-dependent biased molecular-dynamics simulations with Mean Force Integration methods Mean Force Integration, Convergence, FES, Umbrella Sampling Salvalaglio M. BIASVALUE MOLINFO MATHEVAL COMMITTOR PRINT RESTART COORDINATIONNUMBER METAD RESTRAINT DISTANCE FLUSH TORSION ENERGY
24.003 Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations chemistry steered molecular dynamics, foldamers, peptoids, bio-inspired Torkelson K. GYRATION MOVINGRESTRAINT COORDINATION COM INCLUDE PRINT DISTANCE TORSION ALPHABETA WHOLEMOLECULES
23.039 Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation chemistry metadynamics, ligand dissociation Beyerle E. MOLINFO PRINT CENTER FIXEDATOM COMBINE DUMPMASSCHARGE RESTRAINT METAD DISTANCE UPPER_WALLS
23.029 An accurate and efficient SAXS/SANS implementation including solvation layer effects suitable for restrained Molecular Dynamics simulations bio SAXS, SANS, SAS, metainference, proteins, nucleic-acid Ballabio F. ENSEMBLE BIASVALUE MOLINFO WRAPAROUND PRINT CENTER GROUP DISTANCE SAXS RMSD UPPER_WALLS STATS
23.019 Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors bio binding pathway, binding energy, sketch-map, drug development Bobrovs R. TRANSPOSE DISSIMILARITIES COLLECT_FRAMES VORONOI PRINT COM SKETCHMAP_PROJECTION LANDMARK_SELECT_FPS CUSTOM VSTACK SKETCHMAP METAD PATHMSD DISTANCE UPPER_WALLS WHOLEMOLECULES
23.009 Deep Learning Collective Variables from Transition Path Ensemble methods TPI-Deep-TDA, Deep-TDA, Transition Path, OPES, OPES Flooding, Machine Learning, Protein folding, Ligand binding Ray D. MATHEVAL CENTER GROUP DISTANCE FIT_TO_TEMPLATE PYTORCH_MODEL CUSTOM ANGLE RMSD WHOLEMOLECULES COMMITTOR INCLUDE FIXEDATOM COMBINE OPES_METAD LOWER_WALLS CONTACTMAP UPPER_WALLS MOLINFO PRINT COORDINATION ENDPLUMED ENERGY
22.045 Binding mode and mechanism of enzymatic polyethylene terephthalate degradation bio metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation Colizzi F. PRINT MOVINGRESTRAINT COM METAD LOWER_WALLS DISTANCE ANGLE UPPER_WALLS WHOLEMOLECULES
22.035 Deciphering the alphabet of disorder — Glu and Asp act differently on local but not global properties bio intrinsically disordered proteins, parallel bias metadynamics, protein Lindorff-Larsen K. GYRATION MOLINFO PBMETAD TORSION WHOLEMOLECULES
22.025 Bubble nucleation rate predictions in a Lennard-Jones fluid materials free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation Bal K. ANN BIASVALUE COMMITTOR PRINT MOVINGRESTRAINT UNITS LOAD CUSTOM DUMPGRID COORDINATIONNUMBER RESTRAINT VOLUME FLUSH REWEIGHT_BIAS CONVERT_TO_FES UPPER_WALLS HISTOGRAM
22.015 Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome bio photodynamics, bacteriophytochrome, variationally enhanced sampling Rydzewski J. OPT_AVERAGED_SGD TD_UNIFORM PRINT TORSION VES_LINEAR_EXPANSION BF_FOURIER
22.004 Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques chemistry reaction discovery, OPES, collective variables Raucci U. MATHEVAL PRINT COORDINATION UNITS COM OPES_METAD_EXPLORE LOAD CUSTOM PYTORCH_MODEL GROUP OPES_METAD LOWER_WALLS DISTANCE UPPER_WALLS
21.047 Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations materials pair entropy, metadynamics, ves, solids, crystallization Piaggi P. OPT_AVERAGED_SGD PRINT RESTART LOAD COMBINE BF_LEGENDRE METAD VOLUME PAIRENTROPY TD_WELLTEMPERED VES_LINEAR_EXPANSION ENERGY
21.037 Molecular Dynamics simulations of RBD/hACE2 complexes bio SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain Bonomi M. RMSD DISTANCE PRINT
21.027 EGFR activating mutations mechanism bio metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA Gervasio F. MOLINFO MATHEVAL PRINT INCLUDE ALPHARMSD METAD LOWER_WALLS DISTANCE CONTACTMAP UPPER_WALLS WHOLEMOLECULES ENERGY
21.017 All-atom simulations of the Vav1 AD construct bio metadynamics, parallel-bias, well-tempered Orioli S. MOLINFO PBMETAD PRINT ALPHARMSD RESTART GROUP METAD CONTACTMAP REWEIGHT_BIAS ALPHABETA WHOLEMOLECULES
21.007 Sampling enhancement by metadynamics driven by machine learning and de novo protein modelling bio metadynamics, machine learning, protein folding Spiwok V. MOLINFO MATHEVAL FIT_TO_TEMPLATE ALPHARMSD COMBINE WHOLEMOLECULES POSITION
20.032 Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil materials clustering, conformational isomers Salvalaglio M. TORSION ENDPLUMED PRINT
20.022 Unified Approach to Enhanced Sampling methods OPES, expanded ensembles, importance sampling Invernizzi M. MATHEVAL ECV_UMBRELLAS_LINE Q6 ECV_LINEAR VOLUME TORSION OPES_EXPANDED ECV_MULTITHERMAL ECV_MULTITHERMAL_MULTIBARIC UNITS CUSTOM RMSD WHOLEMOLECULES UPPER_WALLS POSITION MOLINFO PRINT LOAD ENDPLUMED ENVIRONMENTSIMILARITY ENERGY
20.012 Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies bio metadynamics, well-tempered ensemble, ligand binding, binding affinity calculations, novel COLVAR, funnel restraints, Hamiltonian replica-exchange, PathCV, COMetPath, SWISH Gervasio F. BIASVALUE MOLINFO MATHEVAL PRINT INCLUDE COM FUNCPATHGENERAL LOAD CONSTANT GROUP METAD LOWER_WALLS PROJECTION_ON_AXIS DISTANCE CONTACTMAP UPPER_WALLS WHOLEMOLECULES
20.002 Exploring conformational dynamics of the extracellular Venus flytrap domain of the GABAB receptor, a path-metadynamics study bio Metadynamics, path CVs Ocello R. MOLINFO PRINT RESTART GROUP METAD PATHMSD UPPER_WALLS WHOLEMOLECULES
19.076 Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones bio molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics Assenza S. GYRATION PRINT MOVINGRESTRAINT UNITS ENDPLUMED
19.066 Finding ligand unbinding reaction pathways methods maze, ligand unbinding Rydzewski J. MAZE_SIMULATED_ANNEALING PRINT UNITS MAZE_OPTIMIZER_BIAS MAZE_LOSS POSITION
19.056 maze methods maze, ligand unbinding Rydzewski J. MAZE_SIMULATED_ANNEALING PRINT UNITS MAZE_OPTIMIZER_BIAS MAZE_LOSS POSITION
19.036 Thermodynamics and kinetics of G protein-coupled receptor activation bio metadynamics, allostery, receptor conformation, GPCR, pharmacology Provasi D. FUNCPATHMSD PRINT COM METAD ENDPLUMED CONTACTMAP DISTANCE RMSD WHOLEMOLECULES
19.026 Ice Nucleation on Cholesterol Crystals materials forward flux sampling, crystal nucleation, water, ice, organic crystals Sosso G. OUTPUT_CLUSTER COMMITTOR Q6 CLUSTER_NATOMS ENDPLUMED MFILTER_MORE LOCAL_Q6 FLUSH CLUSTER_WITHSURFACE DFSCLUSTERING CONTACT_MATRIX
19.016 Succinnic acid gamma polymorph materials Succinnic acid, conformers, polymorphs, metadynamics Salvalaglio M. MATHEVAL PRINT COMBINE METAD ENDPLUMED VOLUME CELL LOWER_WALLS TORSION UPPER_WALLS ENERGY
19.006 Flying Gaussian proof methods flying Gaussians, alanine dipeptide Spiwok V. TORSION METAD PRINT
24.012 Molecular simulations to investigate the impact of N6-methylation in RNA recognition bio metadynamics, alchemistry, RNA modification, RNA:protein interactions Bussi G. PRINT COORDINATION GROUP BIASVALUE DISTANCE LOWER_WALLS MOLINFO DEBUG UPPER_WALLS METAD CENTER GHBFIX COMBINE COM
24.002 Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes chemistry metadynamics, ligand design, solvent extraction Wang X. PRINT RESTART UNITS METAD TORSION
23.038 Determinants of Neutral Antagonism and Inverse Agonism in the β2-adrenergic receptor bio protein coupled receptor, beta-adrenergic, receptor activation, antagonism, inverse agonism, metadynamics Clark T. PRINT WHOLEMOLECULES DISTANCE MOLINFO METAD MATHEVAL RMSD
23.028 Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process chemistry Ammonia decomposition; Dynamics;OPES; Neural Network potential Yang M. ZDISTANCES COORDINATIONNUMBER PRINT GROUP OPES_METAD DISTANCE LOWER_WALLS CUSTOM COMMITTOR UPPER_WALLS UNITS DISTANCES MATHEVAL FLUSH FIXEDATOM ENERGY COM
23.018 Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention materials metadynamics, surface binding, peptide adsorption Torkelson K. PRINT DISTANCE UPPER_WALLS GYRATION PBMETAD COM
23.008 PBMetaD simulations of Histatin5 bio metadynamics, IDP, Rg, PPII Pesce F. PRINT GROUP WHOLEMOLECULES MOLINFO TORSION GYRATION PBMETAD
22.044 Colloid Crystallisation Analyses materials Q4, Q6, Pair Entropy, DFS Finney A. COORDINATIONNUMBER Q4 MFILTER_LESS CLUSTER_NATOMS GROUP PRINT Q6 LOCAL_Q6 MFILTER_MORE LOCAL_Q4 CONTACT_MATRIX DFSCLUSTERING COMBINE LOCAL_AVERAGE
22.034 Rationalising the difference in crystallisability of two Sulflowers using efficient in silico methods materials metadynamics, crystallizability, crystal structure prediction, sulflower, persulforated coronene Salvalaglio M. PRINT LOWER_WALLS COMMITTOR CUSTOM UPPER_WALLS METAD MATHEVAL CELL DRMSD
22.024 Conformational Entropy as a Potential Liability of Computationally Designed Antibodies bio metadynamics, conformational entropy, antibody, nanobody Löhr T. PRINT ALPHARMSD WHOLEMOLECULES ANTIBETARMSD RESTART MOLINFO ALPHABETA TORSION PBMETAD COM
22.014 Quasi Liquid Layer Order Parameters materials Quasi-Liquid Layer, Steinhardt Order Parameter, Entropy Fingerprint Shi J. Q4 ENDPLUMED HISTOGRAM Q6 LOCAL_Q6 UNITS DUMPMULTICOLVAR LOCAL_Q4 PAIRENTROPIES LOAD LOCAL_Q3 DUMPGRID LOCAL_AVERAGE Q3
22.003 Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling methods opes, metadynamics, reweighting, alanine, muller Invernizzi M. PBMETAD PRINT ENDPLUMED OPES_METAD BIASVALUE ECV_MULTITHERMAL LOWER_WALLS ECV_UMBRELLAS_FILE OPES_EXPANDED CUSTOM UPPER_WALLS UNITS METAD TORSION POSITION OPES_METAD_EXPLORE ENERGY
21.046 Ubiquitin Interacting Motifs, Duality Between Structured and Disordered Motifs bio wt metadynamics, ubiquitin, ataxin-3, short linear motifs, ubiquitin binding motif, moonlight functions, intrinsic disorder Papaleo E. PRINT GROUP WHOLEMOLECULES ENDPLUMED LOWER_WALLS ALPHABETA UPPER_WALLS METAD GYRATION
21.036 Modelling the structure and interactions of intrinsically disordered peptides with multiple-replica, metadynamics-based sampling methods and force-field combinations bio Bias Exchange Metadynamics, PTWTE-metaD Salvalaglio M. PARABETARMSD PRINT COORDINATION ALPHARMSD GROUP WHOLEMOLECULES ANTIBETARMSD RANDOM_EXCHANGES LOWER_WALLS MOLINFO UPPER_WALLS METAD GYRATION ENERGY DIHCOR
21.026 Probing allosteric regulations with coevolution-driven molecular simulations bio metadynamics, coevolution, allostery, adenylate cyclase Colizzi F. PRINT WHOLEMOLECULES DISTANCE UPPER_WALLS UNITS METAD PATHMSD COM
21.016 MD SAXS GTPase associated center bio metadynamics, RNA, folding, SAXS Bussi G. PRINT GROUP WHOLEMOLECULES ERMSD LOWER_WALLS MOLINFO CUSTOM UPPER_WALLS METAD CENTER SAXS GYRATION INCLUDE
21.006 OPES, On-the-fly Probability Enhanced Sampling Method methods opes, alanine dipeptide, well-tempered, multithermal, multiumbrella Invernizzi M. PRINT ENDPLUMED OPES_METAD ECV_MULTITHERMAL OPES_EXPANDED TORSION ECV_UMBRELLAS_LINE ENERGY
20.031 Soft fluorescent nanoshuttles targeting receptors chemistry polymers, receptors, nanoparticles, fluorescent probes Pietropaolo A. PRINT COORDINATION WHOLEMOLECULES CENTER PBMETAD
20.021 Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins. bio phi-values, restrained MD, transition-state, protein folding, disordered proteins, protein evolution Paissoni C. PRINT COORDINATION WHOLEMOLECULES STATS MOLINFO RESTRAINT
20.011 Uremic toxin analysis bio metadynamics, uremic toxin, serum albumin Pfaendtner J. PRINT COORDINATION GROUP WHOLEMOLECULES RESTART DISTANCE DISTANCES CENTER
20.001 Conformational stability and dynamics in solution and in crystals report similarly on unfolding and aggregation propensity of amyloidogenic proteins bio metainference, metadynamics, NMR, protein dynamics, b2m, protein crystals Camilloni C. PRINT GROUP WHOLEMOLECULES ENDPLUMED ANTIBETARMSD BIASVALUE LOWER_WALLS MOLINFO ALPHABETA UPPER_WALLS CS2BACKBONE FLUSH PBMETAD
19.075 PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python other Python, automatic differentiation Giorgino T. PRINT COMBINE GROUP ENDPLUMED DISTANCE DUMPDERIVATIVES CUSTOM ANGLE CENTER TORSION RESTRAINT
19.065 Molecular Enhanced Sampling with Autoencoders methods enhanced sampling, collective variables, deep learning Chen W. COMBINE POSITION ANN RESTRAINT COM
19.055 Flying Gaussian method methods flying Gaussians, alanine dipeptide, peptide bond, Met-enkephalin Spiwok V. PRINT DISTANCE METAD MATHEVAL TORSION COMBINE
19.045 Adsorption free energy of Ca/CO3 ions on calcite steps in contact with water materials metadynamics, well-tempered, multiple walkers, LAMMPS Pierre M. PRINT COORDINATION GROUP RESTART LOWER_WALLS UPPER_WALLS UNITS METAD POSITION FLUSH
19.035 Dimerization of GPCRs from coarse-grained umbrella sampling bio Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization Provasi D. PRINT GROUP DISTANCE TORSION RESTRAINT COM
19.025 Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide bio metainference, NMR, protein dynamics, force-fields Camilloni C. PRINT RDC ENDPLUMED WHOLEMOLECULES ENSEMBLE BIASVALUE MOLINFO STATS METAINFERENCE CS2BACKBONE TORSION FLUSH GYRATION PBMETAD JCOUPLING
19.015 Ibuprofen conformational dynamics and thermodynamics surface materials Ibuprofen, crystal, surface, solvents, conformers, metadynamics Salvalaglio M. PRINT DISTANCE LOWER_WALLS COMMITTOR UPPER_WALLS METAD CENTER TORSION
19.005 Cmyc small molecule interaction bio metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP Heller G. PRINT COORDINATION GROUP WHOLEMOLECULES DISTANCE MOLINFO ALPHABETA METAINFERENCE CS2BACKBONE CENTER GYRATION PBMETAD INCLUDE
24.011 Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble methods committor, machine learning Kang P. TORSION PRINT RMSD MATHEVAL WHOLEMOLECULES POSITION ENDPLUMED MOLINFO INCLUDE ENERGY UPPER_WALLS DISTANCE LOWER_WALLS BIASVALUE CELL GROUP CUSTOM UNITS COORDINATION LOAD
24.001 A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations bio OPES, OPES-Flooding, QM/MM, Kinetics, Enzyme Catalysis Ray D. TORSION PRINT UNITS UPPER_WALLS FLUSH COMMITTOR DISTANCE COMBINE CUSTOM LOWER_WALLS OPES_METAD
23.037 Estimating binding free energy of solid binding peptides without extensive sampling bio metadynamics, solid binding peptides Qi X. PRINT UPPER_WALLS GYRATION DISTANCE LOWER_WALLS COM MOLINFO PBMETAD
23.027 CmuMD simulations of NaCl(aq) at NaCl chemistry CmuMD, DFS, Q3, Pair Entropy Finney A. LOCAL_AVERAGE HISTOGRAM PRINT UNITS Q3 FIXEDATOM COORDINATIONNUMBER AROUND CLUSTER_DISTRIBUTION DFSCLUSTERING GROUP CONTACT_MATRIX RESTRAINT LOAD DENSITY CLUSTER_NATOMS LOCAL_Q3 DUMPGRID
23.017 How and When Does an Enzyme React? Unraveling α-Amylase Catalytic Activity with Enhanced Sampling Techniques bio enzymatic reaction discovery, reaction mechanism, catalysis, ligand-binding modes, water, alpha-amylase, sugar, QM/MM MD, OPES, OPES explore, graph CV, machine learning, Deep TDA CV, path CV Das S. TORSION PRINT UNITS UPPER_WALLS CENTER DISTANCE COORDINATION CUSTOM GROUP WHOLEMOLECULES PATH FIT_TO_TEMPLATE LOWER_WALLS OPES_METAD OPES_METAD_EXPLORE PYTORCH_MODEL FIXEDATOM
23.007 Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains bio metadynamics, peptoids, parallel-bias metadynamics Pfaendtner J. TORSION PRINT GYRATION RESTRAINT COORDINATION WHOLEMOLECULES COM INCLUDE PBMETAD
22.043 Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES bio OPES, RNA, Tetraloop, Folding Zerze G. PRINT OPES_EXPANDED WHOLEMOLECULES ECV_MULTITHERMAL ECV_UMBRELLAS_LINE ENERGY CONTACTMAP
22.033 Reciprocal barrier restraint. Application to PROTAC passive permeability prediction methods PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR Kolossvary I. BIASVALUE PRINT UNITS FLUSH DISTANCE CUSTOM COM DRR METAD
22.023 Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy bio CryoEM, MEMMI,EMMI, Metadynamics, Metainference, IAPP, structural ensemble Brotzakis F. BIASVALUE TORSION PRINT UPPER_WALLS COORDINATION RMSD GROUP RESTART WHOLEMOLECULES COM MOLINFO EMMI PBMETAD
22.013 Ligand dissociation from PreQ1 riboswitch bio ligand, RNA, metadynamics, pRAVE Wang Y. PRINT COORDINATIONNUMBER COMBINE DISTANCE COMMITTOR RMSD WHOLEMOLECULES COM MOLINFO METAD
22.002 GAMBES_SAMPL5_RATES other GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding Debnath J. PRINT UPPER_WALLS CENTER FLUSH COMMITTOR DISTANCE COORDINATION GROUP WHOLEMOLECULES MATHEVAL LOAD FIT_TO_TEMPLATE ENDPLUMED PYTORCH_MODEL ANGLE ENERGY FIXEDATOM
21.045 QM/MM metadynamics of thiol-disulfide exchange between methylthiolate and dimethyldisulfide in water with an imposed external electrostatic potential (ESP) chemistry metadynamics, QM/MM, electrostatic potential, thiol-disulfide exchange Maag D. PRINT UPPER_WALLS COORDINATIONNUMBER COMBINE DISTANCE COORDINATION LOWER_WALLS METAD
21.035 CmuMD simulations of NaCl(aq) at NaCl chemistry CmuMD, interface Finney A. PRINT DISTANCE RESTRAINT GROUP LOAD FIXEDATOM
21.025 Computational and biochemical analysis of type IV pilus dynamics and stability bio molecular dynamics, calcium binding, Type IV pilus Karami Y. DISTANCE LOWER_WALLS PRINT UPPER_WALLS
21.015 Coarse-grained metadynamics and umbrella sampling simulations to investigate interactions of carbohydrate-binding modules with chitin bio metadynamics, umbrella sampling, coarse-grained, MARTINI, chitin, carbohydrate-binding module Courtade G. PRINT CENTER REWEIGHT_BIAS RESTRAINT COORDINATION RESTART WHOLEMOLECULES MATHEVAL POSITION METAD
21.005 Crystallization Collective Variable methods Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA Karmakar T. PRINT UPPER_WALLS FLUSH GROUP MATHEVAL LOAD LOWER_WALLS OPES_METAD PYTORCH_MODEL
20.030 Converging experimental and computational views of the knotting mechanism of the smallest knotted protein bio phi-values, transition state, knotted proteins Paissoni C. PRINT COMBINE RESTRAINT COORDINATION WHOLEMOLECULES MOLINFO STATS
20.020 Parallel Bias Metadynamics methods pbmetad, trp-cage, folding Bonomi M. ALPHABETA PRINT DIHCOR GYRATION COORDINATION WHOLEMOLECULES MOLINFO INCLUDE PBMETAD
20.010 Phase equilibrium of liquid water and hexagonal ice from enhanced sampling molecular dynamics simulations materials water, ice, TIP4P, crystallization, EnvironmentSimilarity, RefCV, kernel, VES, variationally enhanced sampling Piaggi P. PRINT UPPER_WALLS VOLUME TD_WELLTEMPERED Q6 RESTART VES_LINEAR_EXPANSION MATHEVAL BF_LEGENDRE OPT_AVERAGED_SGD OPT_DUMMY ENVIRONMENTSIMILARITY
20.000 Muscarinic M2 receptor-ligand funnel metadynamics bio multiple walker metadynamics, well-tempered metadynamics, funnel metadynamics, MC-HLDA, GPCR, receptor, Adiabatic Bias MD Capelli R. HISTOGRAM PRINT UPPER_WALLS COMBINE DISTANCE MATHEVAL ENDPLUMED LOWER_WALLS COM ABMD REWEIGHT_METAD CONVERT_TO_FES METAD READ DUMPGRID
19.074 Asymmetric base pair opening in nucleic acids bio double helix, DNA, RNA, unwindability Bussi G. DISTANCE RESTRAINT COORDINATION WHOLEMOLECULES ENDPLUMED LOWER_WALLS
19.064 Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations materials metadynamics, peptide-surface binding Pfaendtner J. PRINT UPPER_WALLS GYRATION DISTANCE COM MOLINFO METAD ENERGY
19.054 MetaFEP methods metadynamics, chemistry, free energy perturbation Piccini G. PRINT UNITS UPPER_WALLS FLUSH COMBINE DISTANCE LOWER_WALLS METAD ENERGY
19.044 Multithermal-multibaric simulations using VES methods ves, Wang Landau, multicanonical, water, density anomaly Piaggi P. HISTOGRAM AVERAGE PRINT REWEIGHT_BIAS REWEIGHT_TEMP_PRESS COMBINE VOLUME RESTART VES_LINEAR_EXPANSION BF_LEGENDRE TD_MULTITHERMAL_MULTIBARIC CONVERT_TO_FES OPT_AVERAGED_SGD OPT_DUMMY ENERGY READ DUMPGRID
19.024 PT-MetaD-WTE methods metadynamics, WTE, trp cage, PT Pfaendtner J. COORDINATION EXTERNAL GROUP METAD ENERGY
19.014 MIL101(Cr) SBUs assembly materials MOFs, nucleation, self-assembly, metadynamics Salvalaglio M. PRINT COORDINATIONNUMBER GYRATION RESTART DISTANCES ENDPLUMED METAD
19.004 MI Ubiquitin bio metainference, NMR Bonomi M. CS2BACKBONE PRINT GROUP WHOLEMOLECULES MOLINFO RDC METAINFERENCE
24.010 Oxytocin metadynamics simulation bio metadynamics, oxytocin, peptide Beránek J. METAD FLUSH TORSION RESTART WHOLEMOLECULES PRINT
24.000 Ammonia Decomposition on Non-stoichiometric Lithium Imide chemistry ammonia decomposition, non-stoichiometric lithium imide, machine learning interatomic potentials, enhanced sampling, heterogeneous catalysis Mambretti F. UPPER_WALLS FIXEDATOM FLUSH GROUP OPES_METAD UNITS PRINT ZDISTANCES COORDINATIONNUMBER DISTANCE
23.036 Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? bio NaCl, nucleation, metadynamics Wang R. METAD VOLUME COMBINE MATHEVAL Q6 ENERGY Q4 PRINT COORDINATIONNUMBER
23.026 Machine Learning Nucleation Collective Variables with Graph Neural Networks chemistry Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks Dietrich F. PRINT METAD COMBINE MFILTER_MORE MOVINGRESTRAINT GROUP Q6 LOWER_WALLS LOCAL_Q6 COORDINATIONNUMBER
23.016 Activation/deactivation free-energy profiles for the β2-adrenergic receptor: Ligand modes of action bio G protein coupled receptor, beta-adrenergic, receptor activation, partial agonism, metadynamics Clark T. METAD READ CONVERT_TO_FES DUMPGRID MATHEVAL REWEIGHT_METAD MOLINFO RMSD HISTOGRAM WHOLEMOLECULES PRINT DISTANCE
23.006 Transcription factor unbinding bio metadynamics, DNA, conformational changes Lüking M. METAD CONTACTMAP ANGLE MOLINFO DUMPFORCES COM PRINT ALPHARMSD DISTANCE
22.042 Metadynamics of NSP10 and variants bio metadynamics, NSP10, crystal structure, variants Haider S. METAD TORSION PRINT
22.032 Reciprocal barrier restraint. Application to path-meta-eABF methods restraint, upper wall, lower wall, path colvar, meta-eABF, metadynamics, DRR, protein conformational transition, PROTAC Kolossvary I. METAD BIASVALUE PATHMSD FLUSH DRR CUSTOM PRINT
22.022 Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir bio RMSD, protein-ligand interactions Grothaus I. PRINT RMSD
22.012 Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT bio contact maps, protein-protein interactions Grothaus I. DISTANCE PRINT CENTER CONTACTMAP
22.001 Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials methods enhanced sampling, variationally enhanced sampling, ves, metadynamics, bias representation, wavelets, adam Pampel B. OPT_AVERAGED_SGD UNITS METAD UPPER_WALLS OPT_ADAM VES_OUTPUT_BASISFUNCTIONS DISTANCE BF_GAUSSIANS TD_UNIFORM FLUSH ENERGY VES_LINEAR_EXPANSION BF_CHEBYSHEV COORDINATION PRINT TD_WELLTEMPERED BF_WAVELETS INCLUDE BF_CUBIC_B_SPLINES POSITION BF_LEGENDRE
21.044 NaCl nucleation chemistry metadynamics, DFS clustering Finney A. METAD FIXEDATOM DUMPGRID COMBINE MFILTER_MORE CONTACT_MATRIX CLUSTER_NATOMS GROUP INSPHERE Q6 LOCAL_Q6 HISTOGRAM CLUSTER_DISTRIBUTION DFSCLUSTERING PRINT COORDINATIONNUMBER
21.034 Efficient sampling of high-dimensional free energy landscapes using adaptive reinforced dynamics bio reinforced dynamics, bias-exchange metadynamics, parallel-bias metadynamics Wang D. METAD ENDPLUMED RANDOM_EXCHANGES TORSION PBMETAD PRINT INCLUDE
21.024 Property map collective variable as a useful tool for force field correction chemistry molecular mechanics Spiwok V. METAD BIASVALUE TORSION PROPERTYMAP WHOLEMOLECULES PRINT
21.014 how to determine statistically accurate conformational ensembles bio metadynamics, metainference, errors, cv, SAXS, ensemble determination Paissoni C. METAD BIASVALUE CONTACTMAP GYRATION TORSION ALPHABETA STATS MOLINFO ANTIBETARMSD PBMETAD CENTER ENSEMBLE WHOLEMOLECULES PRINT SAXS
21.004 Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy bio machine learning, well-tempered metadynamics, path collective variable, potential of mean force, standard binding free energy calculations, host-guest, protein-ligand unbinding Gobbo D. METAD UPPER_WALLS PATHMSD LOWER_WALLS RESTART WHOLEMOLECULES PRINT
20.029 High Conformational Flexibility of the E2F1/DP1/DNA complex bio SAXS, protein-DNA complex, hySAXS, ensemble determination Paissoni C. BIASVALUE RESTRAINT STATS GROUP MOLINFO CENTER ENSEMBLE WHOLEMOLECULES PRINT SAXS DISTANCE INCLUDE
20.019 Systematic finite-temperature reduction of crystal energy landscapes materials crystals, organics, structure prediction Salvalaglio M. METAD UPPER_WALLS VOLUME MATHEVAL ENERGY LOWER_WALLS PRINT CELL
20.009 The dynamics of linear polyubiquitin bio saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics Camilloni C. GYRATION TORSION ALPHABETA STATS FLUSH MOLINFO METAINFERENCE PBMETAD CENTER ENSEMBLE WHOLEMOLECULES PRINT SAXS DISTANCE
19.083 Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis chemistry metadynamics, chemical reactions, reaction discovery Rizzi V. METAD UPPER_WALLS ENDPLUMED COMBINE FLUSH GROUP DISTANCES RESTART UNITS PRINT COORDINATIONNUMBER
19.073 On the role of enthalpic and entropic contributions on the conformational free energy landscape of MIL-101(Cr) building units materials metadynamics, MOF, MIL101Cr, conformational Salvalaglio M. METAD UPPER_WALLS ENDPLUMED GYRATION DISTANCES ENERGY LOWER_WALLS PRINT COORDINATIONNUMBER
19.063 Protein-ligand binding through metadynamics with path CVs bio metadynamics, path CVs, ligand binding Bernetti M. METAD UPPER_WALLS PATHMSD LOWER_WALLS WHOLEMOLECULES PRINT
19.053 Capillary fluctuations with PLUMED methods nucleation, surface tension, capillary fluctuations Tribello G. FCCUBIC MULTICOLVARDENS DUMPGRID FIND_CONTOUR_SURFACE GROUP CENTER MORE_THAN UNITS FOURIER_TRANSFORM
19.043 Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) methods metadynamics, chemistry, HLDA Piccini G. METAD UPPER_WALLS COMBINE FLUSH DISTANCES RESTART UNITS PRINT DISTANCE
19.023 RECT methods metadynamics, replica exchange Bussi G. METAD GYRATION TORSION WHOLEMOLECULES PRINT
19.013 RNA FF FITTING methods force field, RNA Bussi G. BIASVALUE TORSION MATHEVAL CONSTANT MOLINFO PUCKERING INCLUDE
19.003 EMMI ClpP bio metainference, cryo-EM Bonomi M. BIASVALUE EMMI GROUP MOLINFO PRINT
24.009 Weighted Shape Gaussian Mixture Models bio metadynamics, clustering Hocky G. GROUP TORSION PRINT METAD UNITS
23.046 Lasso Peptides - HLDA CV bio metadynamics, protein folding, HLDA, harmonic Hora G. DISTANCE WHOLEMOLECULES COMBINE PRINT METAD UNITS
23.035 An Extended Metadynamics Protocol for Binding/Unbinding of Peptide Ligands to Class A G-Protein Coupled Receptors bio G protein coupled receptor, peptide ligands, metadynamics, multiple-walker Clark T. CONSTANT DISTANCE CENTER WHOLEMOLECULES MATHEVAL LOWER_WALLS UPPER_WALLS BIASVALUE PRINT METAD
23.025 Probing ion binding to G-quadruplexes and related events chemistry metadynamics, repulsive potential, nucleic acids, G-quadruplexes Poleto M. COM GROUP WRAPAROUND POSITION DISTANCE WHOLEMOLECULES DUMPATOMS FIT_TO_TEMPLATE FLUSH MATHEVAL LOWER_WALLS DISTANCES UPPER_WALLS PRINT RESTART METAD UNITS
23.015 MPCs aggregation bio opes_explore, dimerization, MPCs, self-assembly Tiwari V. COM GROUP COORDINATION DISTANCE CENTER WHOLEMOLECULES CUSTOM OPES_METAD_EXPLORE LOWER_WALLS UPPER_WALLS PRINT METAD
23.005 A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs bio metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A Clark T. MOLINFO READ HISTOGRAM RMSD DISTANCE DUMPGRID WHOLEMOLECULES CONVERT_TO_FES MATHEVAL REWEIGHT_METAD PRINT METAD
22.041 Skipping the Replica Exchange Ladder with Normalizing Flows methods OPES, alanine, normalizing flows, replica exchange Invernizzi M. OPES_EXPANDED ECV_MULTITHERMAL POSITION ENERGY ENDPLUMED TORSION PRINT OPES_METAD UNITS
22.031 Rare Event Kinetics from Adaptive Bias Enhanced Sampling methods OPES Flooding, Kinetics, Rate, OPES, Machine Learning Ray D. CONSTANT DISTANCE CUSTOM COMBINE BIASVALUE MOLINFO GROUP RMSD WHOLEMOLECULES CONTACTMAP COMMITTOR ENDPLUMED ENERGY TORSION INCLUDE UNITS PYTORCH_MODEL POSITION PRINT OPES_METAD
22.021 Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations chemistry Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella Bore S. OPES_EXPANDED INCLUDE LOWER_WALLS ECV_UMBRELLAS_LINE PRINT ENVIRONMENTSIMILARITY UPPER_WALLS
22.011 Accelerating all-atom simulations and gaining mechanistic understanding of biophysical systems through State Predictive Information Bottleneck methods metadynamics, membrane permeation, protein folding Mehdi S. MOLINFO COM YANGLES DISTANCE WHOLEMOLECULES ZANGLES CUSTOM COMBINE XANGLES MATHEVAL LOWER_WALLS UPPER_WALLS TORSION ALPHABETA PRINT METAD
22.000 Amyloid precursor protein processing by human γ-secretase bio Bias Exchange Metadynamics, Helix unfolding, coupled binding Lu X. MOLINFO ANTIBETARMSD COORDINATION UNITS ALPHARMSD CENTER DISTANCE PRINT INCLUDE RANDOM_EXCHANGES METAD CONTACTMAP
21.043 Predicting the Conformational Variability of Oncogenic GTP-bound G12D Mutated KRas-4B Proteins at Cell Membranes chemistry well-tempered metadynamics, KRas-4B, anionic membrane, conformational variability Lu H. FIT_TO_TEMPLATE FIXEDATOM TORSION PRINT METAD
21.033 Multiple-path-metadynamics applied to DNA base-pairing transitions bio path-CV, metadynamics, multiple-walker, dna Pérez-de-Alba-Ortíz A. CONSTANT DISTANCE CENTER WHOLEMOLECULES MOVINGRESTRAINT CUSTOM COMBINE LOAD UPPER_WALLS TORSION RESTRAINT PRINT INCLUDE METAD UNITS
21.023 Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling methods enhanced sampling, collective variables, machine learning Rydzewski J. CONSTANT DISTANCE CUSTOM ENERGY BIASVALUE REWEIGHT_METAD TORSION PRINT INCLUDE METAD UNITS
21.013 Role of vibrational excitation in heterogeneous catalysis chemistry catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption Bal K. COORDINATIONNUMBER REWEIGHT_BIAS DISTANCE DUMPGRID COMBINE FLUSH LOAD LOWER_WALLS DISTANCES VES_LINEAR_EXPANSION REWEIGHT_METAD UWALLS EXTERNAL METAD CONVERT_TO_FES OPT_AVERAGED_SGD UPPER_WALLS RESTRAINT UNITS BF_CHEBYSHEV HISTOGRAM COORDINATION TD_GRID ANGLES PRINT
21.003 aSYN SAXS metainference bio metainference, SAXS Lindorff-Larsen K. MOLINFO GROUP GYRATION CENTER ALPHARMSD WHOLEMOLECULES PBMETAD FLUSH METAINFERENCE BIASVALUE EEFSOLV PRINT SAXS
20.028 Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane bio metadynamics, KRas-4B, anionic membrane Lu H. DISTANCE CENTER FIT_TO_TEMPLATE PRINT RESTART METAD
20.018 Free energy barriers from biased molecular dynamics simulations methods kinetics, free energy barriers, chemical reactions, nucleation, metadynamics Bal K. COORDINATIONNUMBER CONTACT_MATRIX REWEIGHT_BIAS DISTANCE DUMPGRID COMBINE DENSITY FLUSH LOAD LOWER_WALLS VOLUME REWEIGHT_METAD PAIRENTROPY METAD Q6 LOCAL_AVERAGE SPRINT CONVERT_TO_FES ENERGY UPPER_WALLS UNITS HISTOGRAM COORDINATION CENTER PRINT
20.008 Simulating solvation and acidity in complex mixtures with first-principles accuracy. The case of CH3SO3H and H2O2 in phenol chemistry proton trasfer, metadynamics Rossi K. COORDINATION CUSTOM DISTANCES PRINT METAD UNITS
19.082 Ammonia Borane Dehydrogenation chemistry metadynamics, reaction discovery, hydrogen production, chemistry Rizzi V. COORDINATIONNUMBER GROUP COMBINE FLUSH EXTERNAL ENDPLUMED PRINT RESTART METAD UNITS
19.072 SINE hairpin MD+NMR bio metadynamics, RNA, NMR Bussi G. MOLINFO COM MAXENT COORDINATION DISTANCE WHOLEMOLECULES SORT FLUSH MATHEVAL TORSION PRINT INCLUDE METAD
19.062 Elucidating molecular design principles for charge-alternating peptides bio peptide folding, metadynamics, well-tempered ensemble, parallel tempering Pfaendtner J. GYRATION WHOLEMOLECULES ENERGY PRINT METAD
19.052 Gibbs free energy of homogeneous nucleation materials nucleation, surface excess free energy Tribello G. CELL FCCUBIC ENDPLUMED UPPER_WALLS PRINT METAD UNITS
19.042 Harmonic Linear Discriminant Analysis (HLDA) methods metadynamics, chemistry, HLDA Piccini G. DISTANCE COMBINE FLUSH ENERGY UPPER_WALLS PRINT METAD UNITS
19.032 Chemical reaction in solution using path collective variables based on coordination patterns chemistry chemical reactions, solutions, metadynamics, coordination patterns Pietrucci F. FLUSH DISTANCES UPPER_WALLS PATH PRINT RESTART METAD
19.022 eABF simulation of NANMA (alanine dipeptide) methods eABF, DRR, alanine dipeptide Chen H. TORSION PRINT DRR
19.012 Martini-Beads multi-scale SAXS methods metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex Camilloni C. MOLINFO GROUP STATS RMSD DISTANCE CENTER WHOLEMOLECULES ENDPLUMED BIASVALUE UPPER_WALLS RESTRAINT PRINT INCLUDE SAXS
19.002 EMMI STRA6 bio metainference, cryo-EM Bonomi M. MOLINFO GROUP EMMI BIASVALUE PRINT
24.008 yCD Metadynamics bio volume-based MetaD, path CVs, infrequent MetaD, product release McCarty J. WRAPAROUND FIXEDATOM COORDINATION RMSD READ MATHEVAL COMMITTOR DISTANCE COM ENDPLUMED CONTACTMAP REWEIGHT_METAD GROUP FIT_TO_TEMPLATE HISTOGRAM METAD PATH CONVERT_TO_FES MOLINFO DUMPGRID PRINT INCLUDE FLUSH WHOLEMOLECULES UPPER_WALLS
23.045 Minute-timescale simulations of G Protein Coupled Receptor A2A activation mechanism reveal a receptor pseudo-active state bio Path CVs Metadynamics, GPCRs activation transition Limongelli V. FUNCPATHMSD PATHMSD MOLINFO CONTACTMAP INCLUDE ALPHARMSD PRINT METAD LOWER_WALLS UPPER_WALLS DISTANCE
23.034 Urea nucleation in water: do long-range forces matter? materials LMF theory, Metadynamics, Nucleation Zou Z. LOAD COORDINATIONNUMBER GROUP INCLUDE PRINT METAD CENTER
23.024 Permutationally Invariant Networks for Enhanced Sampling (PINES) methods collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent Herringer N. PRINT PBMETAD LOAD
23.014 Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 bio metadynamics, oligomerization, chemokine receptors, GPCR, membrane Limongelli V. COM FLUSH WHOLEMOLECULES COMBINE PRINT TORSION METAD UPPER_WALLS DISTANCE
23.004 Melting curves of ice polymorphs in the vicinity of the liquid-liquid critical point chemistry water, liquid-liquid transition, second critical point, ice, polymorphs, melting curves, environment similarity, opes, density-functional theory, scan, machine learning potential Piaggi P. OPES_EXPANDED DUMPGRID PRINT LOWER_WALLS HISTOGRAM RESTART ENVIRONMENTSIMILARITY UPPER_WALLS ECV_UMBRELLAS_LINE
22.040 From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure bio SARS-CoV-2, Spike, Omicron Wieczór M. WHOLEMOLECULES PRINT METAD PCAVARS LOWER_WALLS UPPER_WALLS
22.030 Mixing physics across temperatures with generative artificial intelligence methods REMD, Generative AI, DDPM Wang Y. PRINT TORSION WHOLEMOLECULES
22.020 Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix–Junction–Helix RNA bio RNA force field, Helix-Junction-Helix RNA, SAXS, Well tempered metadynamics He W. COM WHOLEMOLECULES GROUP PRINT TORSION METAD DISTANCE
22.009 Glycosylation in calixarenes capsule chemistry Metadynamics, glycosylation, supramolecular catalysis Piccini G. FLUSH UNITS COORDINATION WHOLEMOLECULES GROUP COMBINE PRINT FIT_TO_TEMPLATE BRIDGE DISTANCES RMSD ANGLE METAD MATHEVAL LOWER_WALLS UPPER_WALLS DISTANCE
21.052 On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets materials Ibuprofen, unbinding, WTmetaD Salvalaglio M. ENDPLUMED COORDINATIONNUMBER PRINT TORSION METAD CENTER COMMITTOR DISTANCE
21.042 Peptoid-mediated Au nanocrystal growth materials parallel-bias metadynamics, peptoid, Au Qi X. COM MOLINFO GYRATION PRINT PBMETAD UPPER_WALLS DISTANCE
21.032 Metal-coupled folding mechanism to metallothionein bio parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination Diaz M. DRMSD UNITS COORDINATION REWEIGHT_METAD WHOLEMOLECULES GROUP COORDINATIONNUMBER MFILTER_MORE COMBINE HISTOGRAM CONVERT_TO_FES DUMPGRID PRINT READ REWEIGHT_BIAS PBMETAD
21.022 Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly materials parallel bias metadynamics, adsorption, peptide Qi X. COM ENERGY MOLINFO GYRATION PRINT PBMETAD LOWER_WALLS UPPER_WALLS DISTANCE
21.012 NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition bio funnel metadynamics Pfaendtner J. COM PRINT FUNNEL_PS FUNNEL METAD LOWER_WALLS UPPER_WALLS DISTANCE
21.002 Phase equilibrium of water with hexagonal and cubic ice using the SCAN functional materials ice, water, SCAN, OPES, VES, multithermal, crystallization, environment similarity, refcv, reweighting Piaggi P. OPES_EXPANDED ENERGY BF_LEGENDRE VOLUME PRINT Q6 MATHEVAL ECV_MULTITHERMAL_MULTIBARIC RESTART OPT_AVERAGED_SGD TD_UNIFORM VES_LINEAR_EXPANSION ENVIRONMENTSIMILARITY UPPER_WALLS ECV_UMBRELLAS_LINE
20.027 Allosteric Regulation of SARS-CoV-2 Protease. Towards Informed Structure-Based Drug Discovery bio SARS-CoV2, MPro, Covid-19, Molecular Dynamics, Metadynamics, Computer-Aided Drug Discovery Abdel-Maksoud K. PRINT METAD TORSION DISTANCE
20.017 FISST methods FISST, force, peptide, sampling, tempering Hocky G. ENERGY RESTRAINT UNITS BIASVALUE GYRATION GROUP PRINT FISST MATHEVAL DISTANCE
20.007 Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics bio metadynamics, loop movement, artificial intelligence Tiwary P. MOLINFO WHOLEMOLECULES COMBINE PRINT RMSD TORSION RESTART METAD UPPER_WALLS DISTANCE
19.081 Calculation of phase diagrams in the multithermal-multibaric ensemble methods VES, variationally enhanced sampling, multithermal-multibaric, energy, Wang Landau, RefCV, kernel, bcc, fcc, sodium, aluminum Piaggi P. OPT_DUMMY ENERGY BF_LEGENDRE COMBINE REWEIGHT_TEMP_PRESS CELL READ VES_LINEAR_EXPANSION MATHEVAL VOLUME HISTOGRAM RESTART LOWER_WALLS TD_WELLTEMPERED CONVERT_TO_FES DUMPGRID PRINT REWEIGHT_BIAS OPT_AVERAGED_SGD TD_MULTITHERMAL_MULTIBARIC LOAD Q6 UPPER_WALLS
19.071 Time-independent free energies from metadynamics via Mean Force Integration methods metadynamics, mean force integration, MFI, thermodynamic integration Salvalaglio M. BIASVALUE CONVERT_TO_FES EXTERNAL DUMPGRID REWEIGHT_METAD PRINT HISTOGRAM REWEIGHT_BIAS TORSION READ METAD MATHEVAL COMMITTOR DISTANCE
19.061 Diffusion in porous materials materials metadynamics, porous materials, diffusion Jelfs K. COM GROUP PRINT UPPER_WALLS RESTART METAD LOWER_WALLS CENTER DISTANCE
19.051 Solid liquid interfacial free energy out of equilibrium materials metadynamics, nucleation, surface excess free energy Tribello G. ENDPLUMED UNITS PRINT FCCUBIC CELL METAD AROUND LOWER_WALLS UPPER_WALLS
19.041 Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces bio metadynamics, collective variables, conformational changes, multiple walkers, Well-Tempered MetaD, peptide, binding, phosphorylation, post-transitional motif, sio2, adsorption Pfaendtner J. COM ENERGY PRINT METAD UPPER_WALLS DISTANCE
19.031 Ice nucleation using PIV-based path coordinates materials phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics Pipolo S. FUNCPATHMSD PRINT CELL METAD PIV LOWER_WALLS UPPER_WALLS
19.021 Coarse-Grained Directed Simulation methods experiment directed simulation, coarse-grain, bias Hocky G. RESTRAINT COMBINE PRINT TORSION EDS DISTANCE
19.011 Automatic Gradient Computation for Collective Variables other gradient, differentiation, curvature Giorgino T. ENDPLUMED
19.001 RNA SHAPE bio metadynamics, RNA, ligand binding Bussi G. FLUSH MOLINFO ERMSD INCLUDE COMBINE DISTANCES PRINT RANDOM_EXCHANGES ANGLE METAD LOWER_WALLS UPPER_WALLS DISTANCE
24.007 SWISH-X bio swish-x, SWISH-X, swish, expanded SWISH Borsatto A. MOLINFO ECV_MULTITHERMAL ENERGY WHOLEMOLECULES CONTACTMAP UPPER_WALLS PRINT OPES_EXPANDED INCLUDE
23.044 Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition materials metadynamics, interlocked molecules Leanza L. DUMPGRID ENDPLUMED HISTOGRAM COMMITTOR PRINT METAD GROUP CONVERT_TO_FES READ COORDINATION
23.033 DNA G-quadruplex and G-hairpin folding with ST-metaD protocol bio DNA, G4, GQ, quadruplex, hairpin, folding, metadynamics, REST2, ST-metaD Pokorná P. BIASVALUE MOLINFO WHOLEMOLECULES COORDINATION METAD GHBFIX ERMSD PRINT COMBINE
23.023 Rational design of novel biomimetic sequence-defined polymers for mineralization applications methods metadynamics, surface binding, biomimetic mineralization Torkelson K. COM PBMETAD DISTANCE GYRATION PRINT UPPER_WALLS COORDINATION
23.013 Path meta-eABF simulation of large scale conformational change in STING protein methods meta-eABF, path CV, large scale conformational change, STING protein, reciprocal barrier restraint Kolossvary I. UNITS BIASVALUE DRR CUSTOM LOWER_WALLS METAD FLUSH UPPER_WALLS TIME PATHMSD PRINT
23.003 Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations methods metadynamics, alchemical variable, alchemical free energy calculations Hsu W. METAD EXTRACV READ PRINT TORSION
22.039 Driving and characterizing nucleation of urea and glycine polymorphs in water bio metadynamics, nucleation, amino acids, polymorphism Beyerle E. Q6 COORDINATIONNUMBER Q4 LOAD METAD MATHEVAL GROUP PAIRENTROPY CENTER PRINT COMBINE INCLUDE
22.029 Angiotensin-1-7_Metadynamics bio Metadynamics, Angiotensin-(1-7), peptide Chi L. WHOLEMOLECULES GYRATION METAD PRINT FLUSH GROUP UPPER_WALLS LOWER_WALLS COORDINATION
22.019 Exploring aspartic protease inhibitor binding to design selective antimalarials bio ligand binding, loop opening, path CV, funnel metadynamics, drug development Bobrovs R. COM FUNNEL LOWER_WALLS WHOLEMOLECULES DISTANCE METAD UPPER_WALLS PATHMSD PRINT FUNNEL_PS
22.008 Ab initio metadynamics determination of temperature-dependent free-energy landscape in ultrasmall silver clusters materials Well tempered metadynamics, ab-initio, ase Sucerquia D. UNITS COORDINATIONNUMBER COM DISTANCE GYRATION METAD FLUSH UPPER_WALLS LOWER_WALLS COORDINATION COMBINE
21.051 Automatic learning of hydrogen-bond fixes in an AMBER RNA force field methods force field, RNA Bussi G. BIASVALUE MOLINFO WHOLEMOLECULES PRINT METAD ERMSD COORDINATION COMBINE
21.041 Nucleating a Different Coordination in a Crystal under Pressure. A Study of the B1−B2 Transition in NaCl by Metadynamics methods metadynamics, structural phase transitions, pressure-induced phase transition, martensitic transitions Badin M. CUSTOM ENDPLUMED PRINT METAD VOLUME COORDINATION COMBINE
21.031 Photo-switchable sulfonulureas in KATP channel bio metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels Walczewska-Szewc K. UNITS COM WHOLEMOLECULES DISTANCE METAD UPPER_WALLS LOWER_WALLS PRINT
21.021 ATLAS methods Machine Learning, Metadynamics Giberti F. UNITS BIASVALUE COORDINATIONNUMBER DUMPATOMS DISTANCE WHOLEMOLECULES METAD GYRATION COORDINATION MATHEVAL GROUP PRINT TORSION
21.011 CmuMD simulations of NaCl(aq) at graphite chemistry CmuMD, DFS clustering Finney A. FIXEDATOM CONTACT_MATRIX DFSCLUSTERING DENSITY COORDINATIONNUMBER MULTICOLVARDENS MFILTER_MORE DUMPGRID CLUSTER_NATOMS LOAD AROUND GROUP RESTRAINT CLUSTER_DISTRIBUTION PRINT
21.001 Substrate recognition and catalysis by glycosaminoglycan sulfotransferases bio metadynamics, well-tempered metadynamics, puckering, coordination Ferreira T. DUMPGRID MOLINFO HISTOGRAM ENERGY DISTANCE WHOLEMOLECULES METAD PUCKERING COORDINATION RANDOM_EXCHANGES GROUP UPPER_WALLS LOWER_WALLS REWEIGHT_METAD PRINT INCLUDE
20.026 Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor bio Metadynamics, Umbrella sampling Peters B. DUMPGRID HISTOGRAM METAD MULTI_RMSD RESTRAINT CONVERT_TO_FES REWEIGHT_METAD PRINT
20.016 Predicting polymorphism in molecular crystals using orientational entropy materials metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy Piaggi P. LOAD METAD GROUP UPPER_WALLS CENTER VOLUME PRINT INCLUDE
20.006 Class B GPCR activation mechanism bio metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding Gervasio F. RMSD MOLINFO ENERGY WHOLEMOLECULES DISTANCE METAD MATHEVAL UPPER_WALLS LOWER_WALLS CENTER PRINT COMBINE
19.080 Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium methods ves, variationally enhanced sampling, vibrational excitation, chemical reactions Bal K. UNITS ANGLE TD_WELLTEMPERED EXTERNAL BF_CHEBYSHEV DUMPGRID VES_LINEAR_EXPANSION LOWER_WALLS HISTOGRAM DISTANCE PRINT FLUSH CONVERT_TO_FES UPPER_WALLS OPT_AVERAGED_SGD TD_GRID COORDINATION COMBINE
19.070 Unexpected Dynamics in the UUCG RNA Tetraloop bio well-tempered metadynamics, RNA, UUCG, maximum entropy Bottaro S. RMSD MOLINFO WHOLEMOLECULES DISTANCE METAD ERMSD PRINT TORSION
19.060 Neural networks-based variationally enhanced sampling methods ves, neural networks Bonati L. UNITS POSITION Q6 ENDPLUMED ENERGY LOAD PRINT ENVIRONMENTSIMILARITY TORSION
19.050 Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes chemistry metadynamics, membranes, Willard Chandler surface Tribello G. RESTART DUMPGRID REWEIGHT_BIAS HISTOGRAM METAD DISTANCE_FROM_CONTOUR CONVERT_TO_FES UPPER_WALLS READ PRINT COMBINE
19.040 Optimal Metric for Path Collective Variables bio metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path Gervasio F. ENDPLUMED METAD MATHEVAL PRINT TORSION
19.030 Coarse-Grained MetaDynamics (CG-MetaD) bio Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy Limongelli V. COM WHOLEMOLECULES DISTANCE METAD UPPER_WALLS LOWER_WALLS PRINT
19.020 PTMetaD-WTE simulation of the Ntail IDP bio metadynamics, IDPs, protein folding Bernetti M. ALPHARMSD MOLINFO ENDPLUMED ENERGY WHOLEMOLECULES GYRATION METAD PRINT
19.010 Multi-domain protein dynamics bio metainference, NMR, protein dynamics Camilloni C. DHENERGY DIHCOR ALPHABETA MOLINFO ENDPLUMED PBMETAD STATS METAINFERENCE WHOLEMOLECULES DISTANCE RDC PRINT GROUP RESTRAINT UPPER_WALLS CENTER ENSEMBLE TORSION
19.000 VesDeltaF methods VES, convergence, suboptimal CVs Invernizzi M. UNITS RESTART POSITION ENDPLUMED ENERGY LOAD METAD VES_DELTA_F PRINT TORSION
24.006 Water vapor condensation chemistry metadynamics, homogeneous condensation, chemical potential Zhong S. UNITS CONTACT_MATRIX METAD DFSCLUSTERING UPPER_WALLS CLUSTER_PROPERTIES PRINT COORDINATIONNUMBER CLUSTER_NATOMS
23.043 Modeling the ferroelectric phase transition in barium titanate with DFT accuracy and converged sampling materials Barium Titanate, ferroelectric phase transition, Machine Learning, polarization order parameters Gigli L. FLUSH MATHEVAL METAD TRANSPOSE INCLUDE SUM PRINT SELECT_COMPONENTS
23.032 Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics bio metadynamics, tSNE, neural network, machine learning, trp-cage, folding Spiwok V. ANN COMBINE POSITION METAD MOLINFO ALPHARMSD PRINT WHOLEMOLECULES FIT_TO_TEMPLATE
23.022 A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar methods collective variables, machine learning, toy model Trizio E. UNITS ENDPLUMED BIASVALUE CUSTOM UPPER_WALLS LOWER_WALLS OPES_METAD PRINT POSITION PYTORCH_MODEL
23.012 JAK2 2D meta-eABF PMF with statistical analysis bio 2D meta-eABF, path CV, PMF Kolossvary I. PRINT FLUSH METAD BIASVALUE PATHMSD CUSTOM UPPER_WALLS LOWER_WALLS DRR
23.002 Critical comparison of general-purpose collective variables for crystal nucleation methods metadynamics, umbrella sampling, commitor, entropy, PIV Lam J. PIV UNITS VOLUME Q6 METAD PAIRENTROPY Q4 LOCAL_AVERAGE CUSTOM UPPER_WALLS FUNCPATHMSD PRINT ENERGY RESTRAINT
22.038 Enhanced Sampling Aided Design of Molecular Photoswitches chemistry reaction discovery, OPES explore, graph CV Raucci U. UNITS PRINT OPES_METAD_EXPLORE CUSTOM PYTORCH_MODEL COORDINATION
22.028 N-glycan conformer distributions in atomistic simulation bio REST2, RECT, N-glycan, pucker Grothaus I. METAD MOLINFO PUCKERING READ CONVERT_TO_FES DUMPGRID TORSION PRINT HISTOGRAM
22.018 Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations bio ligand binding, docking, EMMI, LAT1 Bonomi M. GROUP MOLINFO EMMIVOX BIASVALUE PRINT WHOLEMOLECULES LOAD
22.007 Characterization of a natural variant of human NDP52 and its functional consequences on mitophagy bio metadynamics, well-tempered, protein-protein interactions, disordered proteins, mutations autophagy Papaleo E. COORDINATION DISTANCE PRINT FLUSH METAD MOLINFO ALPHARMSD ALPHABETA TORSION UPPER_WALLS ANGLE WHOLEMOLECULES
21.050 N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity methods bio Grothaus I. PRINT DISTANCE CENTER
21.040 A structural ensemble of a tau-microtubule complex reveals regulatory tau phosphorylation and acetylation mechanisms bio EMMI, CryoEM, tau-microtubules, post-translational modifications, chemical mutagenesis, structural ensemble, Metainference Brotzakis F. GROUP DISTANCE COM MOLINFO EMMI BIASVALUE UPPER_WALLS PRINT WHOLEMOLECULES RESTART
21.030 Thermodynamic Basis for Stabilization of Helical Peptoids by Chiral Sidechains bio parallel bias parallel tempered metadynamics in WTE, synthetic foldamers, self-assembly, peptoid secondary structure Pfaendtner J. DISTANCE COM METAD INCLUDE GYRATION ALPHABETA TORSION PBMETAD PRINT COORDINATION ENERGY
21.020 Reweighted Jarzynski sampling methods free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions Bal K. UPPER_WALLS MOVINGRESTRAINT RESTRAINT ANN FLUSH CONVERT_TO_FES REWEIGHT_METAD DUMPGRID COORDINATIONNUMBER TD_WELLTEMPERED UNITS CONSTANT CUSTOM BF_CHEBYSHEV PRINT OPT_AVERAGED_SGD COMBINE DISTANCE REWEIGHT_BIAS METAD BIASVALUE VES_LINEAR_EXPANSION OPES_METAD HISTOGRAM LOAD
21.010 Step by Step Strecker Amino Acid Synthesis from Ab Initio Prebiotic Chemistry chemistry Strecker reaction, free energy landscape, ab initio molecular dynamics, glycine, prebiotic synthesis Magrino T. PRINT
21.000 Uremic toxin time scale dynamics bio uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs) Pfaendtner J. GROUP DISTANCE COM PRINT WHOLEMOLECULES
20.025 The role of water in host-guest interaction bio ligand binding, water, opes, SAMPL5 Rizzi V. GROUP COORDINATION ANGLE DISTANCE ENDPLUMED CENTER PRINT MATHEVAL FIXEDATOM UPPER_WALLS OPES_METAD PYTORCH_MODEL WHOLEMOLECULES ENERGY FIT_TO_TEMPLATE
20.015 Rational design of ASCT2 inhibitors using an integrated experimental-computational approach bio ASCT2 transporter, small-molecules, cryo-EM, metainference Bonomi M. GROUP DUMPATOMS MOLINFO EMMIVOX BIASVALUE PRINT WHOLEMOLECULES LOAD
20.005 Muscarinic M2 receptor/ligand Frequency-Adaptive Metadynamics and QM/MM calculations bio Frequency-adaptive metadynamics, multiple-walkers metadynamics, well-tempered metadynamics, GPCR, receptor, Adiabatic Bias MD Capelli R. CONTACTMAP UPPER_WALLS FLUSH MOLINFO CONVERT_TO_FES REWEIGHT_METAD DUMPGRID ENDPLUMED COM FUNCPATHMSD PRINT COMBINE DISTANCE ABMD METAD READ LOWER_WALLS HISTOGRAM WHOLEMOLECULES
19.079 Impact of Glutamate Carboxylation in the Adsorption of the alpha-1 Domain of Osteocalcin to Hydroxyapatite and Titania bio metadynamics, peptide adsorption, parallel tempering, well-tempered ensemble Alamdari S. GROUP DISTANCE COM METAD MOLINFO GYRATION UPPER_WALLS PRINT ENERGY
19.069 Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen materials ibuprofen, crystal, solvent, surface Salvalaglio M. GROUP DISTANCE ENDPLUMED DISTANCES CENTER DUMPMULTICOLVAR INCLUDE GYRATION PRINT
19.059 cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide bio bias-exchange metadynamics, cis-trans isomerization Marinelli F. METAD INCLUDE RANDOM_EXCHANGES TORSION PRINT
19.049 Determining the sizes of solid/liquid clusters in MD trajectories of nucleation methods nucleation, metadynamics, clustering, Steinhardt order parameters Tribello G. Q6 CONTACT_MATRIX LOCAL_Q6 DISTANCES MATRIX_VECTOR_PRODUCT CLUSTER_NATOMS METAD SMAC CUSTOM DFSCLUSTERING CLUSTER_PROPERTIES OUTPUT_CLUSTER OUTER_PRODUCT PRINT ONES CLUSTER_DISTRIBUTION COORDINATIONNUMBER MORE_THAN
19.039 Funnel Metadynamics bio funnel-metadynamics, absolute binding free energy, ligand-receptor complexes Limongelli V. DISTANCE FUNNEL_PS COM METAD FUNNEL UPPER_WALLS LOWER_WALLS PRINT WHOLEMOLECULES RMSD
19.029 WTE-metaD of FF domain of URNF1 C57D variant bio metadynamics, mutations, post-translational modification, ff domain Papaleo E. GROUP METAD MOLINFO ALPHABETA GYRATION UPPER_WALLS LOWER_WALLS PRINT WHOLEMOLECULES
19.019 FA-MetaD-JCP-Wang-et-al bio Frequency adaptive metadynamics; peptide Lindorff-Larsen K. COMBINE FLUSH METAD MOLINFO ALPHABETA PRINT COMMITTOR
19.009 RNA tetraloops folding bio metadynamics, RNA, folding Bussi G. ENDPLUMED METAD MOLINFO PRINT WHOLEMOLECULES RMSD ERMSD
24.005 Learning Markovian Dynamics with Spectral Maps methods spectral map, collective variables, machine learning Rydzewski J. UNITS DISTANCE BIASVALUE PRINT CUSTOM
23.041 Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference methods EMMIVox, cryo-EM, single-structure refinement, ensemble refinement, Bayesian inference, B-factors, structural ensembles Hoff S. UPPER_WALLS EMMIVOX GROUP WRAPAROUND INCLUDE MOLINFO DISTANCE BIASVALUE PRINT WHOLEMOLECULES
23.031 Identifying small molecules binding sites in RNA conformational ensembles with SHAMAN bio RNA, metadynamics, probes, mixed-solvent MD, small molecules, binding sites Bonomi M. UPPER_WALLS SHADOW GROUP WRAPAROUND POSITION FIT_TO_TEMPLATE MOLINFO DISTANCES PRINT METAD CENTER WHOLEMOLECULES
23.021 Into the Dynamics of Rotaxanes at Atomistic Resolution materials metadynamics, rotaxanes, molecular shuttles, molecular machines Leanza L. UPPER_WALLS FIXEDATOM MATHEVAL DISTANCE TORSION PRINT METAD CUSTOM CENTER
23.011 OneOPES, a combined enhanced sampling method to rule them all bio OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding Rizzi V. OPES_EXPANDED ENERGY MOLINFO DISTANCE TORSION PRINT ECV_MULTITHERMAL METAD OPES_METAD_EXPLORE ENDPLUMED
23.001 Quantum phase diagram of water chemistry Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella Bore S. UPPER_WALLS OPES_EXPANDED RESTART INCLUDE LOWER_WALLS PRINT ENVIRONMENTSIMILARITY ECV_UMBRELLAS_LINE
22.037 Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site chemistry metadynamics, DNA, abasic Jones M. DISTANCE DISTANCES PRINT METAD
22.027 Molecular Dynamics simulations of BANAL-236 RBD-hACE2 complexes bio SARS-CoV-2, COVID-19, MD, human-ACE2, spike, BANAL-236, receptor-binding domain Bonomi M. PRINT RMSD
22.017 Water regulates the residence time of Benzamidine in Trypsin bio ligand binding, water, opes, benzamidine trypsin, unbinding rates, machine learning, Deep-LDA, Deep-TICA Ansari N. UPPER_WALLS OPES_METAD FIXEDATOM GROUP MATHEVAL LOWER_WALLS FIT_TO_TEMPLATE WHOLEMOLECULES DISTANCE PRINT PYTORCH_MODEL COMMITTOR COORDINATION RMSD CUSTOM CENTER
22.006 Peptide framework for screening the effects of amino acids on assembly bio metadynamics, peptides White A. DUMPGRID CONVERT_TO_FES GYRATION GROUP COMBINE INCLUDE PRINT HISTOGRAM METAD REWEIGHT_BIAS COM DISTANCES
21.049 Multiple-path-metadynamics and PathMaps methods path-CV, metadynamics, multiple-walker, multiple paths, pathmap Pérez-de-Alba-Ortíz A. UPPER_WALLS UNITS MOVINGRESTRAINT ENSEMBLE COMBINE LOWER_WALLS LOAD CONSTANT TORSION RESTRAINT PRINT METAD CUSTOM
21.039 Deep learning the slow modes for rare events sampling methods collective variables, machine learning, slow modes, deep-tica, opes Bonati L. COMBINE INCLUDE DISTANCE PYTORCH_MODEL WHOLEMOLECULES ENDPLUMED UNITS LOAD TORSION MOLINFO ECV_MULTITHERMAL ENVIRONMENTSIMILARITY Q6 OPES_METAD GROUP CONTACTMAP FLUSH RMSD OPES_EXPANDED ENERGY VOLUME PRINT
21.029 Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs bio metadynamics, small peptide, machine learning Tiwary P. ENERGY EXTERNAL RESTART TORSION MOLINFO PRINT FLUSH
21.019 Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations materials Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen Salvalaglio M. TORSIONS MATHEVAL DISTANCE PRINT KDE COM
21.009 Nucleation rates from small scale atomistic simulations and transition state theory materials kinetics, free energy barriers, nucleation, droplets, metadynamics Bal K. UPPER_WALLS CONVERT_TO_FES DUMPGRID REWEIGHT_METAD UNITS MOVINGRESTRAINT LOAD COMMITTOR PRINT FLUSH HISTOGRAM METAD COORDINATIONNUMBER
20.034 Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations bio RNA, SARS-CoV-2, partial tempering Bottaro S. ERMSD RESTART MOLINFO DISTANCE PRINT TORSION ABMD CENTER
20.024 Gaussian Mixture Based Enhanced Sampling (GAMBES) methods enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias Debnath J. UPPER_WALLS UNITS ENERGY GROUP COMBINE LOWER_WALLS LOAD TORSION DISTANCE PRINT DISTANCES
20.014 amyloid beta small molecule interaction bio intrinsically disordered proteins, disordered proteins, IDPs, fuzzy binding, small molecule, drugs, entropy, binding, Alzheimer’s disease, amyloid beta Heller G. PARABETARMSD DIHCOR COMBINE INCLUDE ENDPLUMED WHOLEMOLECULES GYRATION METAINFERENCE CS2BACKBONE ANTIBETARMSD MOLINFO TORSION GROUP FLUSH COORDINATION STATS PBMETAD ALPHARMSD ENSEMBLE PRINT
20.004 Data-driven collective variables for enhanced sampling methods collective variables, machine learning, deep-lda Bonati L. UPPER_WALLS OPES_METAD UNITS GROUP MATHEVAL LOWER_WALLS LOAD DISTANCE TORSION PRINT PYTORCH_MODEL FLUSH COM ENDPLUMED
19.078 Iterative unbiasing of quasi-equilibrium sampling methods metadynamics, reweighting Giberti F. COLLECT_FRAMES UNITS MATHEVAL DUMPATOMS DISTANCE BIASVALUE PRINT COORDINATIONNUMBER METAD REWEIGHT_BIAS
19.068 Rethinking Metadynamics methods metadynamics, opes, convergence Invernizzi M. OPES_METAD UNITS EXTERNAL POSITION TORSION PRINT METAD ENDPLUMED
19.058 Constrained MD for maintaining a cavity in a calculation chemistry constrained MD, porous molecules, porosity, cavity Jelfs K. MOVINGRESTRAINT RESTART INPLANEDISTANCES PRINT FLUSH COM DISTANCES
19.048 Understanding Ligand Binding Selectivity in a Prototypical GPCR Family bio metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding Gervasio F. UPPER_WALLS MATHEVAL LOWER_WALLS CONSTANT DISTANCE BIASVALUE PRINT METAD COM WHOLEMOLECULES
19.038 native state dynamics of human and mouse b2m bio metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation Camilloni C. UPPER_WALLS CS2BACKBONE GROUP RESTART LOWER_WALLS ANTIBETARMSD ENDPLUMED MOLINFO BIASVALUE PRINT FLUSH PBMETAD ALPHABETA WHOLEMOLECULES
19.028 pRAVE methods RAVE, reaction coordinate, deep learning, metadynamics, kinetics Tiwary P. EXTERNAL COMBINE RESTART DISTANCE TORSION PRINT COMMITTOR COM ALPHABETA WHOLEMOLECULES
19.018 Excited state FEP/Metadynamics simulations chemistry metadynamics, FEP, excited states, conjugated polymers, torsional potential Pietropaolo A. MATHEVAL CONSTANT TORSION BIASVALUE PRINT METAD WHOLEMOLECULES
19.008 anncolvar methods neural network, dimensionality reduction Spiwok V. ALPHARMSD MATHEVAL COMBINE POSITION FIT_TO_TEMPLATE MOLINFO PRINT METAD WHOLEMOLECULES
24.004 Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables materials metadynamics, nucleation, machine learning Zou Z. GROUP CENTER RESTART COM PRINT INCLUDE LOAD METAD
23.040 Supramolecular capsules assembly dynamics chemistry Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics Capelli R. WHOLEMOLECULES GROUP CENTER DISTANCES DISTANCE COM PRINT POSITION CUSTOM UNITS METAD FLUSH
23.030 Data Driven Classification of Ligand Unbinding Pathways bio OPES Explore, OPES Flooding, Benzene T4 Lysozyme, Ligand unbinding, Pathway classification, Kinetics, Residence time Ray D. WHOLEMOLECULES UPPER_WALLS ENDPLUMED GROUP OPES_METAD COM DISTANCE MOLINFO MATHEVAL TORSION FIT_TO_TEMPLATE PRINT OPES_METAD_EXPLORE UNITS COORDINATION CENTER BIASVALUE CUSTOM FLUSH WRAPAROUND LOWER_WALLS ENERGY POSITION COMMITTOR
23.020 FEP simulations of ATOX1 homodimer chemistry parallel bias metadynamics, FEP, free-energy of metal ion dissociation Pietropaolo A. WHOLEMOLECULES ANGLE DISTANCE PRINT BIASVALUE MATHEVAL PBMETAD CONSTANT
23.010 An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G‑Protein-Coupled Receptor Ligands bio GPCR, binding free energy, free energy surface Clark T. WHOLEMOLECULES UPPER_WALLS LOWER_WALLS DISTANCE PRINT BIASVALUE MATHEVAL CONSTANT METAD
23.000 Atomistic simulations of RNA tetraloop folding via PTWTE-WTM bio parallel tempering, well-tempered metadynamics, well-tempered ensemble, RNA, Tetraloop, Folding Zerze G. WHOLEMOLECULES UPPER_WALLS LOWER_WALLS ENERGY CONTACTMAP PRINT METAD
22.036 Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction bio Well-tempered MetaDynamics with Hamiltonian Replica Exchange Krepl M. UPPER_WALLS GROUP GHBFIX MOLINFO PRINT BIASVALUE METAD CUSTOM LOAD COMBINE FLUSH COORDINATION
22.026 Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification materials Peptoid, silica Pfaendtner J. UPPER_WALLS GYRATION COM DISTANCE MOLINFO PRINT PBMETAD
22.016 Homogeneous ice nucleation in an ab initio machine learning model of water chemistry ice, water, nucleation, seeding, environment similarity, interfacial free energy, interfaces Piaggi P. AROUND UPPER_WALLS VOLUME OPES_METAD ENERGY HISTOGRAM CUSTOM PRINT DUMPGRID ENVIRONMENTSIMILARITY RESTART
22.005 Collective Variable for Metadynamics Derived from AlphaFold Output bio AlphaFold, protein folding, protein structure prediction, metadynamics, deep learning, free energy simulation, collective variable Spiwok V. WHOLEMOLECULES LOAD PRINT METAD
21.048 Enhancing ligand exploration within a channel pore and fenestrations using metadynamics bio well-tempered metadynamics, protein-ligand enhanced sampling, sodium channel, Nav, small molecule drug Tao E. UPPER_WALLS LOWER_WALLS COM DISTANCE PRINT CUSTOM UNITS METAD TORSION
21.038 Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics materials metadynamics, SGOOP, nucleation, urea Zou Z. GROUP CENTER VOLUME ENERGY PRINT COORDINATIONNUMBER METAD INCLUDE LOAD COMBINE
21.028 From Enhanced Sampling to Reaction Profiles methods collective variables, multi-state, machine learning, Deep-TDA Trizio E. WHOLEMOLECULES UPPER_WALLS ENDPLUMED GROUP OPES_METAD DISTANCE MATHEVAL TORSION ANGLE FIT_TO_TEMPLATE PRINT UNITS COORDINATION CENTER PYTORCH_MODEL DISTANCES LOWER_WALLS FIXEDATOM LOAD
21.018 Localized Volume-based Metadynamics bio LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification Capelli R. WHOLEMOLECULES UPPER_WALLS ENDPLUMED GROUP COM DISTANCE READ DUMPGRID MATHEVAL RMSD PRINT COORDINATION CONVERT_TO_FES REWEIGHT_METAD HISTOGRAM FLUSH FIXEDATOM POSITION METAD
21.008 Multi-replica biased sampling for photoisomerization processes in conjugated polymers methods metadynamics, FEP, replica-exchange Pietropaolo A. WHOLEMOLECULES PRINT BIASVALUE PBMETAD MATHEVAL TORSION RESTART CONSTANT
20.033 COVID-19 Spike protein opening transition mechanism bio EMMI, CryoEM, COVID-19, Spike, Metainference Brotzakis F. WHOLEMOLECULES RMSD CONVERT_TO_FES GROUP EMMI HISTOGRAM DISTANCES MOLINFO READ PRINT DUMPGRID BIASVALUE
20.023 metadynminer and metadynminer3d methods metadynamics, visualization, R Spiwok V. TORSION PRINT METAD
20.013 Improving accuracy of biased Alchemistic simulations methods flying Gaussian method, Alchemistic simulations, thermodynamic integration, reweighting Spiwok V. TORSION PRINT METAD
20.003 Enhanced sampling of transition states methods Variationally Enhanced Sampling, Target distribution, Transition state, Enhanced Sampling, Nucleation, chemical reaction Debnath J. BF_LEGENDRE OPT_AVERAGED_SGD ENERGY UNITS VES_LINEAR_EXPANSION PRINT POSITION LOAD
19.077 Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations materials metadynamics, peptide-surface binding Pfaendtner J. UPPER_WALLS GYRATION ENERGY COM DISTANCE MOLINFO PRINT METAD
19.067 Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways bio metadynamics, ligand unbinding Rydzewski J. UPPER_WALLS LOWER_WALLS PATHMSD RESTART PRINT UNITS METAD
19.057 SAXS ensembles using Martini-Beads multi-scale SAXS methods metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics Paissoni C. WHOLEMOLECULES STATS ENDPLUMED GROUP CENTER ANGLE SAXS ENSEMBLE MOLINFO PRINT BIASVALUE PBMETAD MATHEVAL INCLUDE ALPHABETA COMBINE COORDINATION
19.047 Close Structure methods metadynamics, RMSD, path collective variables, property map Spiwok V. WHOLEMOLECULES PROPERTYMAP PRINT METAD
19.037 Scission free energy of organic dyes chemistry metadynamics, multiple walkers, matheval/lepton Raiteri P. UPPER_WALLS DISTANCE PRINT MATHEVAL UNITS RESTART FLUSH METAD
19.027 Multithermal-multibaric simulations using VES methods ves, Wang Landau, multicanonical, liquid sodium, density anomaly Piaggi P. AVERAGE BF_LEGENDRE CONVERT_TO_FES OPT_DUMMY OPT_AVERAGED_SGD REWEIGHT_TEMP_PRESS RESTART ENERGY HISTOGRAM READ PRINT DUMPGRID REWEIGHT_BIAS TD_MULTICANONICAL VES_LINEAR_EXPANSION UNITS COMBINE
19.017 Ligand binding pathways exploration bio metadynamics, ligand binding Capelli R. WHOLEMOLECULES WRAPAROUND UPPER_WALLS ENDPLUMED CONVERT_TO_FES GROUP REWEIGHT_METAD HISTOGRAM COM FIT_TO_TEMPLATE PRINT READ DUMPGRID POSITION MATHEVAL METAD FLUSH COORDINATION
19.007 EMMI Microtubules bio metainference, cryo-EM Bonomi M. WHOLEMOLECULES GROUP EMMI MOLINFO PRINT BIASVALUE