Browse the eggs in PLUMED-NEST
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 | Modules |
|---|---|---|---|---|---|---|
| 24.018 | A new route to the prebiotic synthesis of glycine via ab initio-based machine learning calculations | chemistry | prebiotic chemistry, glycine, Strecker synthesis, ab initio calculations, machine learning | Léon HUET | DISTANCE PRINT | generic colvar |
| 24.017 | Absolute Binding Free Energies with OneOPES | methods | protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy | Francesco Gervasio | MOLINFO COORDINATION CONSTANT GROUP ECV_MULTITHERMAL INCLUDE OPES_EXPANDED COM BIASVALUE PRINT WHOLEMOLECULES RMSD WRAPAROUND MATHEVAL CUSTOM TORSION ENERGY OPES_METAD_EXPLORE UPPER_WALLS METAD RESTART LOWER_WALLS PROJECTION_ON_AXIS CONTACTMAP | core setup colvar opes bias function vatom generic |
| 24.008 | yCD Metadynamics | bio | volume-based MetaD, path CVs, infrequent MetaD, product release | James McCarty | CONVERT_TO_FES COMBINE FLUSH DUMPGRID READ PATH MOLINFO COORDINATION GROUP DISTANCE INCLUDE COM PRINT WHOLEMOLECULES RMSD FIXEDATOM WRAPAROUND MATHEVAL ENDPLUMED HISTOGRAM COMMITTOR UPPER_WALLS METAD GPATH REWEIGHT_METAD FIT_TO_TEMPLATE CONTACTMAP | mapping core gridtools colvar bias function vatom generic |
| 23.039 | Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation | chemistry | metadynamics, ligand dissociation | Eric Beyerle | COMBINE PRINT UPPER_WALLS METAD CENTER DISTANCE FIXEDATOM DUMPMASSCHARGE MOLINFO RESTRAINT | colvar bias function vatom generic |
| 23.027 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, DFS, Q3, Pair Entropy | Aaron Finney | DUMPGRID COMBINE OUTER_PRODUCT MORE_THAN SUM DFSCLUSTERING Q3 LOCAL_Q3 SPHERICAL_HARMONIC DENSITY ONES GROUP CLUSTER_DISTRIBUTION LOCAL_AVERAGE MATRIX_PRODUCT MEAN PRINT UNITS AROUND FIXEDATOM CLUSTER_NATOMS HIGHEST VSTACK TRANSPOSE RESTRAINT ACCUMULATE COORDINATIONNUMBER KDE CUSTOM LOAD HISTOGRAM MATRIX_VECTOR_PRODUCT CLUSTER_WEIGHTS CONTACT_MATRIX | adjmat volumes core setup gridtools symfunc clusters matrixtools bias function vatom valtools generic |
| 23.014 | Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 | bio | metadynamics, oligomerization, chemokine receptors, GPCR, membrane | Vittorio Limongelli | COMBINE FLUSH PRINT TORSION WHOLEMOLECULES UPPER_WALLS METAD DISTANCE COM | colvar bias function vatom generic |
| 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 | Pablo Piaggi | DUMPGRID MORE_THAN ENVIRONMENTSIMILARITY SUM DISTANCE_MATRIX ONES GROUP OPES_EXPANDED MEAN PRINT ACCUMULATE KDE CUSTOM HISTOGRAM UPPER_WALLS RESTART MATRIX_VECTOR_PRODUCT LOWER_WALLS ECV_UMBRELLAS_LINE | adjmat core setup gridtools opes matrixtools bias function generic envsim |
| 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 | Kresten Lindorff-Larsen | TORSION WHOLEMOLECULES MOLINFO PBMETAD GYRATION | generic colvar bias |
| 22.029 | Angiotensin-1-7_Metadynamics | bio | Metadynamics, Angiotensin-(1-7), peptide | L.-América Chi | FLUSH PRINT WHOLEMOLECULES UPPER_WALLS GROUP METAD LOWER_WALLS COORDINATION GYRATION | generic colvar bias core |
| 22.025 | Bubble nucleation rate predictions in a Lennard-Jones fluid | materials | free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation | Kristof Bal | CONVERT_TO_FES DUMPGRID FLUSH MOVINGRESTRAINT SUM ONES LESS_THAN GROUP BIASVALUE MEAN PRINT UNITS REWEIGHT_BIAS ANN RESTRAINT COORDINATIONNUMBER VOLUME CUSTOM LOAD HISTOGRAM COMMITTOR UPPER_WALLS MATRIX_VECTOR_PRODUCT CONTACT_MATRIX | adjmat annfunc core setup gridtools colvar symfunc matrixtools bias function generic |
| 22.002 | GAMBES_SAMPL5_RATES | other | GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding | Jayashrita Debnath | LOAD PRINT FLUSH PYTORCH_MODEL ENERGY GROUP WHOLEMOLECULES UPPER_WALLS CENTER FIXEDATOM DISTANCE COMMITTOR ANGLE COORDINATION MATHEVAL ENDPLUMED FIT_TO_TEMPLATE | core setup colvar bias function vatom generic pytorch |
| 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 | Elena Papaleo | COMBINE PRINT TORSION ALPHABETA CONSTANT WHOLEMOLECULES UPPER_WALLS GROUP METAD LOWER_WALLS SUM ENDPLUMED GYRATION CUSTOM | multicolvar core colvar bias function generic |
| 21.044 | NaCl nucleation | chemistry | metadynamics, DFS clustering | Aaron Finney | DUMPGRID COMBINE OUTER_PRODUCT MORE_THAN BETWEEN SUM LOCAL_Q6 DFSCLUSTERING SPHERICAL_HARMONIC Q6 ONES LESS_THAN GROUP CLUSTER_DISTRIBUTION MFILTER_MORE MEAN MATRIX_PRODUCT PRINT INSPHERE FIXEDATOM CLUSTER_NATOMS HIGHEST VSTACK TRANSPOSE ACCUMULATE COORDINATIONNUMBER CUSTOM KDE HISTOGRAM METAD MATRIX_VECTOR_PRODUCT CLUSTER_WEIGHTS CONTACT_MATRIX | adjmat volumes core multicolvar gridtools symfunc clusters matrixtools bias function vatom valtools generic |
| 21.039 | Deep learning the slow modes for rare events sampling | methods | collective variables, machine learning, slow modes, deep-tica, opes | Luigi Bonati | COMBINE FLUSH MORE_THAN ENVIRONMENTSIMILARITY SUM MOLINFO SPHERICAL_HARMONIC Q6 DISTANCE_MATRIX ONES ECV_MULTITHERMAL GROUP DISTANCE INCLUDE OPES_METAD OPES_EXPANDED MEAN PRINT UNITS WHOLEMOLECULES RMSD ENDPLUMED VOLUME CUSTOM LOAD TORSION ENERGY MATRIX_VECTOR_PRODUCT PYTORCH_MODEL CONTACT_MATRIX CONTACTMAP | adjmat core setup colvar symfunc opes matrixtools function generic pytorch envsim |
| 20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Adriana Pietropaolo | PRINT WHOLEMOLECULES CENTER COORDINATION PBMETAD | generic colvar vatom bias |
| 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 | Kevin Rossi | DISTANCES PRINT UNITS GROUP METAD CENTER DISTANCE SUM COORDINATION CUSTOM | core setup multicolvar colvar bias function vatom generic |
| 19.080 | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | methods | ves, variationally enhanced sampling, vibrational excitation, chemical reactions | Kristof Bal | CONVERT_TO_FES COMBINE VES_LINEAR_EXPANSION BF_CHEBYSHEV FLUSH DUMPGRID COORDINATION ONES DISTANCE TD_GRID OPT_AVERAGED_SGD TD_WELLTEMPERED EXTERNAL PRINT UNITS ACCUMULATE CUSTOM KDE HISTOGRAM UPPER_WALLS LOWER_WALLS ANGLE | setup gridtools colvar ves bias function generic |
| 19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Riccardo Capelli | CONVERT_TO_FES DUMPGRID FLUSH READ COORDINATION ONES GROUP COM PRINT WHOLEMOLECULES WRAPAROUND MATHEVAL ACCUMULATE ENDPLUMED CUSTOM KDE HISTOGRAM POSITION UPPER_WALLS METAD REWEIGHT_METAD FIT_TO_TEMPLATE | core gridtools colvar bias function vatom generic |
| 19.011 | Automatic Gradient Computation for Collective Variables | other | gradient, differentiation, curvature | Toni Giorgino | ENDPLUMED | generic |
| 19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Michele Invernizzi | LOAD PRINT TORSION UNITS ENERGY POSITION METAD RESTART ENDPLUMED VES_DELTA_F | setup colvar ves bias generic |
| 24.009 | Weighted Shape Gaussian Mixture Models | bio | metadynamics, clustering | Glen Hocky | METAD GROUP PRINT UNITS TORSION | generic bias colvar setup core |
| 24.004 | Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables | materials | metadynamics, nucleation, machine learning | Ziyue Zou | METAD GROUP PRINT CENTER LOAD INCLUDE RESTART COM | generic vatom bias setup core |
| 24.002 | Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes | chemistry | metadynamics, ligand design, solvent extraction | Xiaoyu Wang | METAD PRINT RESTART UNITS TORSION | bias generic colvar setup |
| 23.030 | Data Driven Classification of Ligand Unbinding Pathways | bio | OPES Explore, OPES Flooding, Benzene T4 Lysozyme, Ligand unbinding, Pathway classification, Kinetics, Residence time | Dhiman Ray | PRINT FLUSH TORSION COMMITTOR GROUP MOLINFO LOWER_WALLS CUSTOM WHOLEMOLECULES COORDINATION BIASVALUE CENTER WRAPAROUND UNITS OPES_METAD FIT_TO_TEMPLATE POSITION ENDPLUMED COM ENERGY UPPER_WALLS MATHEVAL OPES_METAD_EXPLORE DISTANCE | generic function vatom bias colvar opes setup core |
| 23.024 | Permutationally Invariant Networks for Enhanced Sampling (PINES) | methods | collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent | Nicholas Herringer | LOAD PBMETAD PRINT | setup bias generic |
| 23.021 | Into the Dynamics of Rotaxanes at Atomistic Resolution | materials | metadynamics, rotaxanes, molecular shuttles, molecular machines | Luigi Leanza | METAD MATHEVAL PRINT CENTER CUSTOM UPPER_WALLS DISTANCE TORSION FIXEDATOM | generic function vatom bias colvar |
| 23.008 | PBMetaD simulations of Histatin5 | bio | metadynamics, IDP, Rg, PPII | Francesco Pesce | GROUP MOLINFO PRINT PBMETAD TORSION WHOLEMOLECULES GYRATION | generic core bias colvar |
| 22.044 | Colloid Crystallisation Analyses | materials | Q4, Q6, Pair Entropy, DFS | Aaron Finney | CONTACT_MATRIX GROUP LOCAL_Q6 LOCAL_AVERAGE MFILTER_LESS PRINT COMBINE Q4 CLUSTER_NATOMS MFILTER_MORE DFSCLUSTERING LOCAL_Q4 COORDINATIONNUMBER Q6 | generic multicolvar symfunc clusters function core adjmat |
| 22.021 | Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn Løland Bore | OPES_EXPANDED MORE_THAN MATRIX_VECTOR_PRODUCT ENVIRONMENTSIMILARITY PRINT GROUP INCLUDE DISTANCE_MATRIX LOWER_WALLS ONES CUSTOM MEAN UPPER_WALLS SUM ECV_UMBRELLAS_LINE | generic envsim function bias opes matrixtools core adjmat |
| 22.013 | Ligand dissociation from PreQ1 riboswitch | bio | ligand, RNA, metadynamics, pRAVE | Yihang Wang | METAD CONTACT_MATRIX MATRIX_VECTOR_PRODUCT GROUP PRINT MOLINFO COMBINE RMSD ONES MEAN CUSTOM COM DISTANCE SUM COORDINATIONNUMBER COMMITTOR WHOLEMOLECULES | generic symfunc function vatom bias colvar matrixtools core adjmat |
| 22.011 | Accelerating all-atom simulations and gaining mechanistic understanding of biophysical systems through State Predictive Information Bottleneck | methods | metadynamics, membrane permeation, protein folding | Shams Mehdi | ZANGLES PRINT COMBINE TORSION METAD MOLINFO YANGLES LOWER_WALLS CUSTOM MEAN ALPHABETA SUM WHOLEMOLECULES COM UPPER_WALLS XANGLES MATHEVAL DISTANCE CONSTANT | generic multicolvar function vatom bias colvar |
| 22.000 | Amyloid precursor protein processing by human γ-secretase | bio | Bias Exchange Metadynamics, Helix unfolding, coupled binding | Xiaoli Lu | METAD COORDINATION CONTACTMAP MOLINFO ANTIBETARMSD CENTER PRINT INCLUDE SECONDARY_STRUCTURE_RMSD UNITS LESS_THAN RANDOM_EXCHANGES DISTANCE ALPHARMSD SUM | generic function vatom bias secondarystructure colvar setup |
| 21.049 | Multiple-path-metadynamics and PathMaps | methods | path-CV, metadynamics, multiple-walker, multiple paths, pathmap | Alberto Pérez-de-Alba-Ortíz | METAD PRINT LOAD COMBINE LOWER_WALLS UNITS CUSTOM RESTRAINT UPPER_WALLS TORSION CONSTANT MOVINGRESTRAINT ENSEMBLE | generic function bias colvar setup |
| 21.038 | Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics | materials | metadynamics, SGOOP, nucleation, urea | Ziyue Zou | METAD CONTACT_MATRIX MATRIX_VECTOR_PRODUCT GROUP PRINT CENTER COMBINE LOAD INCLUDE VOLUME ONES MEAN ENERGY COORDINATIONNUMBER | generic symfunc function vatom bias colvar matrixtools setup core adjmat |
| 21.031 | Photo-switchable sulfonulureas in KATP channel | bio | metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels | Katarzyna Walczewska-Szewc | METAD PRINT UNITS LOWER_WALLS UPPER_WALLS DISTANCE COM WHOLEMOLECULES | generic vatom bias colvar setup |
| 20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Faidon Brotzakis | KDE GROUP PRINT READ MOLINFO BIASVALUE EMMI HISTOGRAM RMSD ONES CUSTOM DUMPGRID CONVERT_TO_FES DISTANCES ACCUMULATE WHOLEMOLECULES | generic multicolvar function bias gridtools colvar isdb core |
| 20.032 | Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil | materials | clustering, conformational isomers | Matteo Salvalaglio | ENDPLUMED PRINT TORSION | generic colvar |
| 20.024 | Gaussian Mixture Based Enhanced Sampling (GAMBES) | methods | enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias | Jayashrita Debnath | GROUP PRINT CENTER LOAD COMBINE UNITS LOWER_WALLS HIGHEST CUSTOM DISTANCES UPPER_WALLS DISTANCE TORSION ENERGY SUM | generic multicolvar function vatom bias colvar setup core |
| 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 | Cristina Paissoni | COORDINATION MOLINFO PRINT RESTRAINT STATS WHOLEMOLECULES | bias generic function colvar |
| 20.015 | Rational design of ASCT2 inhibitors using an integrated experimental-computational approach | bio | ASCT2 transporter, small-molecules, cryo-EM, metainference | Max Bonomi | EMMIVOX GROUP MOLINFO BIASVALUE PRINT LOAD DUMPATOMS WHOLEMOLECULES | generic bias isdb setup core |
| 19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_LOSS MAZE_OPTIMIZER_BIAS MAZE_SIMULATED_ANNEALING PRINT UNITS POSITION | maze generic colvar setup |
| 19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | GiovanniMaria Piccini | METAD PRINT COMBINE UNITS LOWER_WALLS FLUSH UPPER_WALLS DISTANCE ENERGY | generic function bias colvar setup |
| 19.047 | Close Structure | methods | metadynamics, RMSD, path collective variables, property map | Vojtech Spiwok | METAD PROPERTYMAP WHOLEMOLECULES PRINT | bias colvar generic |
| 19.040 | Optimal Metric for Path Collective Variables | bio | metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path | Francesco Luigi Gervasio | METAD MATHEVAL PRINT ENDPLUMED TORSION | bias function generic colvar |
| 19.025 | Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide | bio | metainference, NMR, protein dynamics, force-fields | Carlo Camilloni | CS2BACKBONE METAINFERENCE MOLINFO PRINT BIASVALUE PBMETAD JCOUPLING ENDPLUMED FLUSH TORSION STATS ENSEMBLE WHOLEMOLECULES RDC GYRATION | generic function bias colvar isdb |
| 19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Jim Pfaendtner | METAD COORDINATION GROUP ENERGY EXTERNAL | bias core colvar |
| 19.023 | RECT | methods | metadynamics, replica exchange | Giovanni Bussi | METAD PRINT TORSION WHOLEMOLECULES GYRATION | bias generic colvar |
| 19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Haochuan Chen | DRR PRINT TORSION | generic colvar drr |
| 19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Glen Hocky | PRINT COMBINE EDS RESTRAINT DISTANCE TORSION | generic function bias colvar eds |
| 24.011 | Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble | methods | committor, machine learning | Peilin Kang | WHOLEMOLECULES UNITS DISTANCE CUSTOM ENERGY TORSION MOLINFO UPPER_WALLS CELL COORDINATION MATHEVAL LOWER_WALLS INCLUDE PRINT BIASVALUE RMSD LOAD GROUP ENDPLUMED POSITION | bias generic colvar core function setup |
| 23.046 | Lasso Peptides - HLDA CV | bio | metadynamics, protein folding, HLDA, harmonic | Gabriel da Hora | PRINT WHOLEMOLECULES UNITS DISTANCE METAD COMBINE | bias generic colvar function setup |
| 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 | Lorenzo Gigli | MATHEVAL SELECT_COMPONENTS PRINT FLUSH INCLUDE TRANSPOSE SUM METAD | valtools bias generic function matrixtools |
| 23.037 | Estimating binding free energy of solid binding peptides without extensive sampling | bio | metadynamics, solid binding peptides | Xin Qi | PRINT COM LOWER_WALLS MOLINFO GYRATION UPPER_WALLS PBMETAD DISTANCE | colvar vatom generic bias |
| 23.032 | Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics | bio | metadynamics, tSNE, neural network, machine learning, trp-cage, folding | Vojtech Spiwok | PRINT LESS_THAN WHOLEMOLECULES MOLINFO ALPHARMSD SECONDARY_STRUCTURE_RMSD SUM ANN POSITION FIT_TO_TEMPLATE METAD COMBINE | colvar generic bias function annfunc secondarystructure |
| 23.028 | Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process | chemistry | Ammonia decomposition; Dynamics;OPES; Neural Network potential | Manyi Yang | ZDISTANCES COM OPES_METAD UNITS DISTANCE CUSTOM ENERGY CONTACT_MATRIX DISTANCES FLUSH FIXEDATOM UPPER_WALLS MATHEVAL ONES LOWER_WALLS CENTER MATRIX_VECTOR_PRODUCT MEAN COORDINATIONNUMBER COMMITTOR PRINT GROUP SUM LESS_THAN | opes vatom colvar generic bias core function symfunc setup multicolvar adjmat matrixtools |
| 23.025 | Probing ion binding to G-quadruplexes and related events | chemistry | metadynamics, repulsive potential, nucleic acids, G-quadruplexes | Marcelo Poleto | COM WHOLEMOLECULES UNITS DISTANCE FIT_TO_TEMPLATE LOWEST DISTANCES FLUSH UPPER_WALLS RESTART METAD MATHEVAL WRAPAROUND LOWER_WALLS CENTER DUMPATOMS PRINT GROUP POSITION | vatom generic colvar bias core function setup multicolvar |
| 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 | Sudip Das | WHOLEMOLECULES OPES_METAD UNITS DISTANCE FIT_TO_TEMPLATE CUSTOM PDB2CONSTANT LOWEST TORSION CONSTANT FIXEDATOM UPPER_WALLS PYTORCH_MODEL EUCLIDEAN_DISTANCE COORDINATION LOWER_WALLS CENTER OPES_METAD_EXPLORE COMBINE PRINT GROUP SUM PATH | opes vatom generic colvar bias pytorch refdist core function mapping setup |
| 23.002 | Critical comparison of general-purpose collective variables for crystal nucleation | methods | metadynamics, umbrella sampling, commitor, entropy, PIV | Julien Lam | Q4 PIV PRINT PAIRENTROPY RESTRAINT FUNCPATHMSD UNITS Q6 UPPER_WALLS ENERGY METAD VOLUME CUSTOM LOCAL_AVERAGE | bias generic piv colvar function gridtools symfunc setup |
| 22.041 | Skipping the Replica Exchange Ladder with Normalizing Flows | methods | OPES, alanine, normalizing flows, replica exchange | Michele Invernizzi | PRINT ECV_MULTITHERMAL OPES_METAD POSITION UNITS ENDPLUMED OPES_EXPANDED ENERGY TORSION | colvar opes generic setup |
| 22.031 | Rare Event Kinetics from Adaptive Bias Enhanced Sampling | methods | OPES Flooding, Kinetics, Rate, OPES, Machine Learning | Dhiman Ray | WHOLEMOLECULES OPES_METAD UNITS DISTANCE ENERGY CUSTOM TORSION CONSTANT MOLINFO PYTORCH_MODEL INCLUDE COMBINE COMMITTOR PRINT CONTACTMAP BIASVALUE RMSD ENDPLUMED GROUP POSITION | opes pytorch generic colvar bias core function setup |
| 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 | Faidon Brotzakis | EMMI PRINT COM MOLINFO WHOLEMOLECULES BIASVALUE GROUP DISTANCE RESTART UPPER_WALLS | vatom core generic bias colvar isdb setup |
| 21.035 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, interface | Aaron Finney | PRINT LOAD FIXEDATOM GROUP DISTANCE RESTRAINT | vatom core generic colvar bias setup |
| 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 | Jim Pfaendtner | COORDINATION PRINT ALPHABETA COM TORSION INCLUDE GYRATION SUM DISTANCE PBMETAD ENERGY METAD CUSTOM COMBINE CONSTANT | vatom colvar generic bias function multicolvar |
| 21.027 | EGFR activating mutations mechanism | bio | metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA | Francesco Gervasio | MATHEVAL PRINT CONTACTMAP LESS_THAN LOWER_WALLS MOLINFO WHOLEMOLECULES INCLUDE ALPHARMSD UPPER_WALLS DISTANCE SUM METAD ENERGY SECONDARY_STRUCTURE_RMSD | colvar generic bias function secondarystructure |
| 21.026 | Probing allosteric regulations with coevolution-driven molecular simulations | bio | metadynamics, coevolution, allostery, adenylate cyclase | Francesco Colizzi | PRINT COM WHOLEMOLECULES UNITS PATHMSD UPPER_WALLS DISTANCE METAD | vatom bias generic colvar setup |
| 21.020 | Reweighted Jarzynski sampling | methods | free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions | Kristof Bal | HISTOGRAM OPES_METAD UNITS DISTANCE OPT_AVERAGED_SGD CUSTOM CONTACT_MATRIX CONSTANT FLUSH MORE_THAN TD_WELLTEMPERED UPPER_WALLS METAD VES_LINEAR_EXPANSION ONES KDE REWEIGHT_METAD BF_CHEBYSHEV MATRIX_VECTOR_PRODUCT DUMPGRID MEAN ANN COORDINATIONNUMBER ACCUMULATE COMBINE PRINT REWEIGHT_BIAS BIASVALUE LOAD MOVINGRESTRAINT GROUP SUM RESTRAINT CONVERT_TO_FES | opes colvar ves generic bias core function gridtools symfunc annfunc setup adjmat matrixtools |
| 21.013 | Role of vibrational excitation in heterogeneous catalysis | chemistry | catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption | Kristof Bal | HISTOGRAM ANGLES UNITS DISTANCE OPT_AVERAGED_SGD CUSTOM CONTACT_MATRIX DISTANCES FLUSH UPPER_WALLS METAD VES_LINEAR_EXPANSION COORDINATION ONES EXTERNAL KDE REWEIGHT_METAD UWALLS BF_CHEBYSHEV LOWER_WALLS MATRIX_VECTOR_PRODUCT DUMPGRID MEAN COORDINATIONNUMBER ACCUMULATE COMBINE TD_GRID COORD_ANGLES REWEIGHT_BIAS PRINT LOAD GROUP RESTRAINT CONVERT_TO_FES | colvar ves generic bias core function gridtools symfunc setup multicolvar adjmat matrixtools |
| 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 | Théo Magrino | generic | |
| 20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Carlo Camilloni | CONSTANT ENSEMBLE METAINFERENCE SAXS FLUSH ALPHABETA PRINT MOLINFO WHOLEMOLECULES CENTER STATS GYRATION DISTANCE SUM PBMETAD CUSTOM COMBINE TORSION | vatom generic colvar bias function isdb multicolvar |
| 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 | Riccardo Capelli | HISTOGRAM COM WHOLEMOLECULES DISTANCE CUSTOM ABMD FLUSH MOLINFO UPPER_WALLS METAD ONES KDE LOWER_WALLS REWEIGHT_METAD FUNCPATHMSD DUMPGRID ACCUMULATE COMBINE READ PRINT CONTACTMAP ENDPLUMED CONVERT_TO_FES | vatom colvar generic bias function gridtools |
| 19.076 | Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones | bio | molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics | Salvatore Assenza | PRINT MOVINGRESTRAINT UNITS GYRATION ENDPLUMED | setup generic bias colvar |
| 19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Giovanni Bussi | COORDINATION LOWER_WALLS WHOLEMOLECULES ENDPLUMED DISTANCE RESTRAINT | colvar generic bias |
| 19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Gareth Tribello | AROUND FCCUBIC UNITS CUSTOM CONTACT_MATRIX MORE_THAN UPPER_WALLS METAD CELL ONES LOWER_WALLS MATRIX_VECTOR_PRODUCT MEAN FCCUBIC_FUNC PRINT GROUP SUM ENDPLUMED LESS_THAN | volumes bias colvar generic core function symfunc setup adjmat matrixtools |
| 19.046 | Optimal Collective from short simulations for Benzamidine-Trypsin ligand binding | bio | VAC-MetaD, optimised collective variables, binding free energy, unbinding rates, benzamidine trypsin, Structure Activity Relation | Faidon Brotzakis | DISTANCES PRINT ALPHABETA COM FUNNEL MOLINFO WHOLEMOLECULES LOWER_WALLS RMSD REWEIGHT_METAD BRIDGE UPPER_WALLS GROUP DISTANCE METAD COMBINE TORSION | vatom generic bias colvar core function funnel multicolvar adjmat |
| 19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | DISTANCES PRINT FLUSH UNITS UPPER_WALLS DISTANCE RESTART METAD COMBINE | generic bias colvar function setup multicolvar |
| 19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Paolo Raiteri | MATHEVAL PRINT FLUSH UNITS UPPER_WALLS DISTANCE RESTART METAD | generic bias colvar function setup |
| 19.030 | Coarse-Grained MetaDynamics (CG-MetaD) | bio | Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy | Vittorio Limongelli | PRINT COM LOWER_WALLS WHOLEMOLECULES UPPER_WALLS DISTANCE METAD | colvar vatom generic bias |
| 19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Gabriele Cesare Sosso | COMMITTOR DFSCLUSTERING FLUSH CLUSTER_NATOMS OUTPUT_CLUSTER CLUSTER_WITHSURFACE Q6 ENDPLUMED LOCAL_Q6 MFILTER_MORE CONTACT_MATRIX | generic clusters symfunc multicolvar adjmat |
| 19.013 | RNA FF FITTING | methods | force field, RNA | Giovanni Bussi | CONSTANT MATHEVAL INCLUDE MOLINFO BIASVALUE PUCKERING TORSION | colvar function generic bias |
| 19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Max Bonomi | EMMI PRINT MOLINFO WHOLEMOLECULES BIASVALUE GROUP | core generic bias isdb |
| 19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Max Bonomi | EMMI PRINT MOLINFO BIASVALUE GROUP | core generic bias isdb |
| 24.000 | Ammonia Decomposition on Non-stoichiometric Lithium Imide | chemistry | ammonia decomposition, non-stoichiometric lithium imide, machine learning interatomic potentials, enhanced sampling, heterogeneous catalysis | Francesco Mambretti | UNITS CONTACT_MATRIX GROUP SUM COORDINATIONNUMBER MEAN UPPER_WALLS CUSTOM OPES_METAD ZDISTANCES FLUSH MATRIX_VECTOR_PRODUCT CENTER DISTANCE ONES PRINT FIXEDATOM | matrixtools multicolvar opes bias colvar generic function setup symfunc core adjmat vatom |
| 23.033 | DNA G-quadruplex and G-hairpin folding with ST-metaD protocol | bio | DNA, G4, GQ, quadruplex, hairpin, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | WHOLEMOLECULES COMBINE PRINT BIASVALUE METAD COORDINATION GHBFIX ERMSD MOLINFO | generic bias colvar function |
| 23.031 | Identifying small molecules binding sites in RNA conformational ensembles with SHAMAN | bio | RNA, metadynamics, probes, mixed-solvent MD, small molecules, binding sites | Max Bonomi | DISTANCES WHOLEMOLECULES FIT_TO_TEMPLATE SUM GROUP POSITION SHADOW UPPER_WALLS METAD WRAPAROUND CENTER DISTANCE CUSTOM PRINT MOLINFO | multicolvar bias colvar function isdb core generic vatom |
| 23.023 | Rational design of novel biomimetic sequence-defined polymers for mineralization applications | methods | metadynamics, surface binding, biomimetic mineralization | Kaylyn Torkelson | COM UPPER_WALLS PBMETAD GYRATION DISTANCE COORDINATION PRINT | generic bias colvar vatom |
| 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 | Timothy Clark | READ WHOLEMOLECULES ACCUMULATE MATHEVAL MOLINFO KDE DUMPGRID CUSTOM REWEIGHT_METAD METAD HISTOGRAM CONVERT_TO_FES DISTANCE ONES PRINT RMSD | bias colvar function gridtools generic |
| 23.015 | MPCs aggregation | bio | opes_explore, dimerization, MPCs, self-assembly | Vikas Tiwari | WHOLEMOLECULES OPES_METAD_EXPLORE GROUP COM UPPER_WALLS METAD LOWER_WALLS CENTER DISTANCE COORDINATION CUSTOM PRINT | opes bias colvar function core generic vatom |
| 22.033 | Reciprocal barrier restraint. Application to PROTAC passive permeability prediction | methods | PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR | Istvan Kolossvary | UNITS COM BIASVALUE DRR METAD FLUSH DISTANCE CUSTOM PRINT | bias colvar drr setup function generic vatom |
| 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 | Narjes Ansari | WHOLEMOLECULES FIT_TO_TEMPLATE COMMITTOR GROUP MATHEVAL PYTORCH_MODEL UPPER_WALLS OPES_METAD LOWER_WALLS CENTER DISTANCE COORDINATION CUSTOM PRINT RMSD FIXEDATOM | opes bias colvar function pytorch core generic vatom |
| 22.009 | Glycosylation in calixarenes capsule | chemistry | Metadynamics, glycosylation, supramolecular catalysis | GiovanniMaria Piccini | SUM BRIDGE_MATRIX MEAN UPPER_WALLS FLUSH PRINT DISTANCES DISTANCE RMSD UNITS COMBINE GROUP MATHEVAL LOWER_WALLS CENTER WHOLEMOLECULES FIT_TO_TEMPLATE BRIDGE METAD ANGLE COORDINATION | multicolvar bias colvar generic function setup core adjmat vatom |
| 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 | Matteo Salvalaglio | RANDOM_EXCHANGES SUM UPPER_WALLS PRINT LOWEST GYRATION GROUP LESS_THAN PARABETARMSD LOWER_WALLS SECONDARY_STRUCTURE_RMSD ENERGY ALPHARMSD DIHCOR WHOLEMOLECULES ANTIBETARMSD METAD DIHEDRAL_CORRELATION COORDINATION MOLINFO | multicolvar bias colvar secondarystructure function core generic |
| 21.021 | ATLAS | methods | Machine Learning, Metadynamics | Federico Giberti | UNITS WHOLEMOLECULES CONTACT_MATRIX GROUP MATHEVAL TORSION COORDINATIONNUMBER BIASVALUE DUMPATOMS MEAN METAD MATRIX_VECTOR_PRODUCT GYRATION DISTANCE COORDINATION ONES PRINT | matrixtools bias colvar function setup symfunc core generic adjmat |
| 21.017 | All-atom simulations of the Vav1 AD construct | bio | metadynamics, parallel-bias, well-tempered | Simone Orioli | ALPHABETA WHOLEMOLECULES COMBINE SUM GROUP REWEIGHT_BIAS CONTACTMAP TORSION LESS_THAN CONSTANT PBMETAD RESTART SECONDARY_STRUCTURE_RMSD METAD CUSTOM PRINT ALPHARMSD MOLINFO | multicolvar bias colvar secondarystructure function setup core generic |
| 21.006 | OPES, On-the-fly Probability Enhanced Sampling Method | methods | opes, alanine dipeptide, well-tempered, multithermal, multiumbrella | Michele Invernizzi | TORSION ENDPLUMED OPES_METAD ECV_MULTITHERMAL OPES_EXPANDED ENERGY PRINT ECV_UMBRELLAS_LINE | generic opes colvar |
| 21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Tarak Karmakar | GROUP LOAD MATHEVAL PYTORCH_MODEL UPPER_WALLS OPES_METAD LOWER_WALLS FLUSH PRINT | bias generic function setup pytorch core opes |
| 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 | Sandro Bottaro | TORSION RESTART CENTER DISTANCE ABMD PRINT ERMSD MOLINFO | bias colvar setup generic vatom |
| 20.030 | Converging experimental and computational views of the knotting mechanism of the smallest knotted protein | bio | phi-values, transition state, knotted proteins | Cristina Paissoni | WHOLEMOLECULES COMBINE RESTRAINT STATS COORDINATION PRINT MOLINFO | generic bias colvar function |
| 20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Max Bonomi | ALPHABETA WHOLEMOLECULES DIHCOR COMBINE SUM INCLUDE TORSION PBMETAD CONSTANT GYRATION DIHEDRAL_CORRELATION COORDINATION CUSTOM PRINT MOLINFO | multicolvar bias colvar function generic |
| 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 | Pablo Piaggi | SUM MEAN UPPER_WALLS TD_WELLTEMPERED DISTANCE_MATRIX OPT_DUMMY PRINT VOLUME ENVIRONMENTSIMILARITY BF_LEGENDRE VES_LINEAR_EXPANSION MATRIX_VECTOR_PRODUCT CUSTOM ONES COMBINE CONTACT_MATRIX GROUP MORE_THAN MATHEVAL RESTART Q6 SPHERICAL_HARMONIC OPT_AVERAGED_SGD | matrixtools bias colvar generic function setup symfunc core ves adjmat envsim |
| 20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Pratyush Tiwary | WHOLEMOLECULES COMBINE MOLINFO TORSION UPPER_WALLS RESTART METAD DISTANCE PRINT RMSD | bias colvar setup function generic |
| 20.002 | Exploring conformational dynamics of the extracellular Venus flytrap domain of the GABAB receptor, a path-metadynamics study | bio | Metadynamics, path CVs | Riccardo Ocello | WHOLEMOLECULES PRINT GROUP UPPER_WALLS RESTART METAD PATHMSD MOLINFO | bias colvar setup core generic |
| 19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Luigi Bonati | UNITS LOAD POSITION TORSION ENDPLUMED ENVIRONMENTSIMILARITY Q6 ENERGY PRINT | colvar setup symfunc generic envsim |
| 19.059 | cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide | bio | bias-exchange metadynamics, cis-trans isomerization | Fabrizio Marinelli | RANDOM_EXCHANGES INCLUDE TORSION METAD PRINT | generic bias colvar |
| 19.056 | maze | methods | maze, ligand unbinding | Jakub Rydzewski | UNITS MAZE_SIMULATED_ANNEALING MAZE_LOSS POSITION MAZE_OPTIMIZER_BIAS PRINT | maze generic colvar setup |
| 19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Davide Provasi | WHOLEMOLECULES FUNCPATHMSD CONTACTMAP ENDPLUMED COM METAD DISTANCE PRINT RMSD | bias colvar function generic vatom |
| 19.027 | Multithermal-multibaric simulations using VES | methods | ves, Wang Landau, multicanonical, liquid sodium, density anomaly | Pablo Piaggi | ACCUMULATE OPT_DUMMY PRINT REWEIGHT_TEMP_PRESS KDE DUMPGRID BF_LEGENDRE VES_LINEAR_EXPANSION AVERAGE ONES CUSTOM UNITS COMBINE TD_MULTICANONICAL RESTART CONVERT_TO_FES ENERGY HISTOGRAM OPT_AVERAGED_SGD READ REWEIGHT_BIAS | bias colvar function setup gridtools ves generic |
| 19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Mattia Bernetti | WHOLEMOLECULES SUM ENDPLUMED LESS_THAN SECONDARY_STRUCTURE_RMSD METAD GYRATION ENERGY PRINT ALPHARMSD MOLINFO | bias colvar secondarystructure function generic |
| 19.008 | anncolvar | methods | neural network, dimensionality reduction | Vojtech Spiwok | WHOLEMOLECULES FIT_TO_TEMPLATE COMBINE SUM POSITION MATHEVAL LESS_THAN METAD SECONDARY_STRUCTURE_RMSD PRINT ALPHARMSD MOLINFO | bias colvar generic function secondarystructure |
| 19.003 | EMMI ClpP | bio | metainference, cryo-EM | Max Bonomi | GROUP BIASVALUE EMMI PRINT MOLINFO | isdb generic bias core |
| 24.019 | Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning | bio | Metadynamics, Adaptive Sampling, Machine Learning | Yong Wang | GYRATION LESS_THAN DISTANCE COMBINE CUSTOM SECONDARY_STRUCTURE_RMSD SUM TORSION OPES_METAD PRINT ALPHARMSD WHOLEMOLECULES COORDINATION MOLINFO | secondarystructure function colvar generic opes |
| 24.010 | Oxytocin metadynamics simulation | bio | metadynamics, oxytocin, peptide | Jan Beránek | RESTART PRINT TORSION WHOLEMOLECULES FLUSH METAD | setup generic colvar bias |
| 24.005 | Learning Markovian Dynamics with Spectral Maps | methods | spectral map, collective variables, machine learning | Jakub Rydzewski | DISTANCE CUSTOM PRINT UNITS BIASVALUE | bias function colvar generic setup |
| 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 | Vittorio Limongelli | PATHMSD LESS_THAN DISTANCE SECONDARY_STRUCTURE_RMSD INCLUDE SUM PRINT ALPHARMSD FUNCPATHMSD LOWER_WALLS CONTACTMAP UPPER_WALLS MOLINFO METAD | secondarystructure bias function colvar generic |
| 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 | Timothy Clark | DISTANCE MATHEVAL PRINT CONSTANT WHOLEMOLECULES LOWER_WALLS BIASVALUE UPPER_WALLS CENTER METAD | vatom bias function colvar generic |
| 23.034 | Urea nucleation in water: do long-range forces matter? | materials | LMF theory, Metadynamics, Nucleation | Ziyue Zou | GROUP MORE_THAN CUSTOM INCLUDE SUM PRINT METAD ONES CONTACT_MATRIX MATRIX_VECTOR_PRODUCT MEAN COORDINATIONNUMBER CENTER LOAD | vatom adjmat bias function setup generic symfunc core matrixtools |
| 23.020 | FEP simulations of ATOX1 homodimer | chemistry | parallel bias metadynamics, FEP, free-energy of metal ion dissociation | Adriana Pietropaolo | PBMETAD DISTANCE MATHEVAL PRINT CONSTANT WHOLEMOLECULES BIASVALUE ANGLE | bias generic function colvar |
| 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 | Timothy Clark | DISTANCE MATHEVAL PRINT CONSTANT WHOLEMOLECULES LOWER_WALLS BIASVALUE UPPER_WALLS METAD | bias generic function colvar |
| 23.006 | Transcription factor unbinding | bio | metadynamics, DNA, conformational changes | Malin Lüking | LESS_THAN DISTANCE SECONDARY_STRUCTURE_RMSD SUM PRINT ALPHARMSD COM METAD CONTACTMAP DUMPFORCES MOLINFO ANGLE | secondarystructure vatom bias function colvar generic |
| 22.045 | Binding mode and mechanism of enzymatic polyethylene terephthalate degradation | bio | metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation | Francesco Colizzi | DISTANCE PRINT COM WHOLEMOLECULES LOWER_WALLS MOVINGRESTRAINT ANGLE UPPER_WALLS METAD | bias generic colvar vatom |
| 22.040 | From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure | bio | SARS-CoV-2, Spike, Omicron | Miłosz Wieczór | RMSD COMBINE PCAVARS CUSTOM SUM PRINT SELECT_COMPONENTS CONSTANT WHOLEMOLECULES MATRIX_VECTOR_PRODUCT LOWER_WALLS BIASVALUE UPPER_WALLS METAD | bias function colvar generic mapping valtools matrixtools |
| 22.039 | Driving and characterizing nucleation of urea and glycine polymorphs in water | bio | metadynamics, nucleation, amino acids, polymorphism | Eric Beyerle | Q4 CUSTOM SUM MATRIX_VECTOR_PRODUCT COORDINATIONNUMBER LOAD GROUP MATHEVAL INCLUDE PRINT Q6 PAIRENTROPY ONES MORE_THAN COMBINE CONTACT_MATRIX MEAN SPHERICAL_HARMONIC CENTER METAD | vatom adjmat bias function core generic gridtools symfunc setup matrixtools |
| 22.026 | Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification | materials | Peptoid, silica | Jim Pfaendtner | GYRATION PBMETAD DISTANCE PRINT COM UPPER_WALLS MOLINFO | bias generic colvar vatom |
| 22.022 | Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir | bio | RMSD, protein-ligand interactions | Isabell Grothaus | RMSD PRINT | generic colvar |
| 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 | Elena Papaleo | LESS_THAN DISTANCE COMBINE CUSTOM ALPHABETA SECONDARY_STRUCTURE_RMSD SUM TORSION PRINT ALPHARMSD CONSTANT WHOLEMOLECULES METAD COORDINATION FLUSH UPPER_WALLS MOLINFO ANGLE | secondarystructure bias function multicolvar colvar generic |
| 22.004 | Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques | chemistry | reaction discovery, OPES, collective variables | Umberto Raucci | DISTANCE PYTORCH_MODEL GROUP MATHEVAL CUSTOM OPES_METAD_EXPLORE UNITS PRINT OPES_METAD COM LOWER_WALLS COORDINATION UPPER_WALLS LOAD | pytorch vatom bias function colvar setup generic core opes |
| 21.051 | Automatic learning of hydrogen-bond fixes in an AMBER RNA force field | methods | force field, RNA | Giovanni Bussi | COMBINE PRINT ERMSD WHOLEMOLECULES COORDINATION BIASVALUE MOLINFO METAD | bias generic function colvar |
| 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 | Elaine Tao | DISTANCE CUSTOM UNITS TORSION PRINT COM LOWER_WALLS UPPER_WALLS METAD | vatom bias function colvar generic setup |
| 21.018 | Localized Volume-based Metadynamics | bio | LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification | Riccardo Capelli | KDE CUSTOM COORDINATION UPPER_WALLS REWEIGHT_METAD GROUP MATHEVAL PRINT ACCUMULATE POSITION COM WHOLEMOLECULES ONES RMSD DISTANCE READ HISTOGRAM ENDPLUMED CONVERT_TO_FES FLUSH METAD FIXEDATOM DUMPGRID | vatom bias function colvar generic gridtools core |
| 21.012 | NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition | bio | funnel metadynamics | Jim Pfaendtner | DISTANCE PRINT UPPER_WALLS COM FUNNEL_PS LOWER_WALLS FUNNEL METAD | vatom bias colvar generic funnel |
| 21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Tarsis Ferreira | KDE CUSTOM ENERGY COORDINATION UPPER_WALLS REWEIGHT_METAD GROUP INCLUDE PRINT ACCUMULATE WHOLEMOLECULES ONES DISTANCE HISTOGRAM RANDOM_EXCHANGES PUCKERING MOLINFO METAD LOWER_WALLS DUMPGRID | bias function colvar generic gridtools core |
| 20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Vojtech Spiwok | PRINT TORSION METAD | bias generic colvar |
| 20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Michele Invernizzi | ECV_MULTITHERMAL CUSTOM ECV_LINEAR SUM ENERGY MATRIX_VECTOR_PRODUCT UPPER_WALLS LOAD GROUP ECV_UMBRELLAS_LINE MATHEVAL PRINT UNITS Q6 POSITION WHOLEMOLECULES OPES_EXPANDED ONES RMSD MORE_THAN ENDPLUMED COMBINE TORSION DISTANCE_MATRIX MEAN CONTACT_MATRIX VOLUME SPHERICAL_HARMONIC MOLINFO ENVIRONMENTSIMILARITY ECV_MULTITHERMAL_MULTIBARIC | adjmat bias function colvar core generic envsim opes symfunc setup matrixtools |
| 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 | Matteo Salvalaglio | LOWEST SUM ENERGY MATRIX_VECTOR_PRODUCT COORDINATIONNUMBER UPPER_WALLS GROUP DISTANCES PRINT ONES DISTANCE MORE_THAN ENDPLUMED CONTACT_MATRIX MEAN CENTER METAD GYRATION LOWER_WALLS | vatom adjmat bias function multicolvar colvar generic symfunc core matrixtools |
| 19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Matteo Salvalaglio | DISTANCE READ HISTOGRAM REWEIGHT_METAD MATHEVAL CONVERT_TO_FES PRINT TORSION EXTERNAL COMMITTOR DUMPGRID BIASVALUE REWEIGHT_BIAS METAD | bias function colvar generic gridtools |
| 19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Matteo Salvalaglio | DISTANCE GROUP ENDPLUMED INCLUDE PRINT CENTER | core generic colvar vatom |
| 19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Gareth Tribello | GROUP CELL MORE_THAN ENDPLUMED CUSTOM UNITS SUM PRINT FCCUBIC_FUNC MATRIX_VECTOR_PRODUCT CONTACT_MATRIX MEAN FCCUBIC UPPER_WALLS ONES METAD | adjmat bias function colvar setup generic symfunc core matrixtools |
| 19.048 | Understanding Ligand Binding Selectivity in a Prototypical GPCR Family | bio | metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | DISTANCE MATHEVAL PRINT COM WHOLEMOLECULES CONSTANT LOWER_WALLS BIASVALUE UPPER_WALLS METAD | vatom bias function colvar generic |
| 19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | DISTANCE COMBINE UNITS PRINT ENERGY FLUSH UPPER_WALLS METAD | bias function colvar generic setup |
| 19.032 | Chemical reaction in solution using path collective variables based on coordination patterns | chemistry | chemical reactions, solutions, metadynamics, coordination patterns | Fabio Pietrucci | RESTART DISTANCES PRINT FLUSH UPPER_WALLS PATH METAD | bias multicolvar generic mapping setup |
| 19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Matteo Salvalaglio | GYRATION RESTART GROUP MORE_THAN ENDPLUMED DISTANCES CENTER DISTANCE SUM PRINT LOWEST MATRIX_VECTOR_PRODUCT CONTACT_MATRIX MEAN COORDINATIONNUMBER ONES METAD | vatom adjmat bias function multicolvar colvar core generic symfunc setup matrixtools |
| 19.006 | Flying Gaussian proof | methods | flying Gaussians, alanine dipeptide | Vojtech Spiwok | PRINT TORSION METAD | bias generic colvar |
| 24.014 | Learning Collective Variables with Synthetic Data Augmentation through Physics-inspired Geodesic Interpolation | methods | data augmentation, geodesic interpolation, collective variables, protein folding | Juno Nam | COORDINATION UPPER_WALLS LOWER_WALLS MOLINFO PYTORCH_MODEL DRR PRINT METAD RMSD WHOLEMOLECULES FLUSH | colvar bias generic drr pytorch |
| 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 | Matteo Salvalaglio | BIASVALUE COMMITTOR RESTRAINT MOLINFO COORDINATIONNUMBER TORSION RESTART PRINT METAD DISTANCE MATHEVAL FLUSH ENERGY | setup colvar bias symfunc generic function |
| 24.006 | Water vapor condensation | chemistry | metadynamics, homogeneous condensation, chemical potential | Shenghui Zhong | ONES CLUSTER_PROPERTIES UPPER_WALLS MEAN SUM CONTACT_MATRIX GROUP DFSCLUSTERING PRINT LESS_THAN METAD MATRIX_VECTOR_PRODUCT COORDINATIONNUMBER UNITS CLUSTER_NATOMS | setup clusters bias symfunc generic matrixtools function core adjmat |
| 24.003 | Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations | chemistry | steered molecular dynamics, foldamers, peptoids, bio-inspired | Kaylyn Torkelson | COORDINATION ALPHABETA GYRATION TORSION INCLUDE PRINT DISTANCE MOVINGRESTRAINT WHOLEMOLECULES COM | vatom multicolvar colvar bias generic |
| 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 | Samuel Hoff | UPPER_WALLS BIASVALUE MOLINFO EMMIVOX GROUP INCLUDE PRINT WRAPAROUND DISTANCE WHOLEMOLECULES | isdb colvar bias generic core |
| 23.005 | A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs | bio | metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A | Timothy Clark | ONES KDE CUSTOM HISTOGRAM MOLINFO READ CONVERT_TO_FES PRINT ACCUMULATE METAD DUMPGRID REWEIGHT_METAD DISTANCE MATHEVAL RMSD WHOLEMOLECULES | colvar bias generic function gridtools |
| 23.003 | Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations | methods | metadynamics, alchemical variable, alchemical free energy calculations | Wei-Tse Hsu | EXTRACV TORSION READ PRINT METAD PUT | core bias generic colvar |
| 22.038 | Enhanced Sampling Aided Design of Molecular Photoswitches | chemistry | reaction discovery, OPES explore, graph CV | Umberto Raucci | COORDINATION CUSTOM PYTORCH_MODEL PRINT UNITS OPES_METAD_EXPLORE | setup opes colvar generic function pytorch |
| 22.036 | Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction | bio | Well-tempered MetaDynamics with Hamiltonian Replica Exchange | Miroslav Krepl | COORDINATION UPPER_WALLS CUSTOM BIASVALUE GHBFIX MOLINFO COMBINE GROUP PRINT METAD LOAD FLUSH | setup colvar bias generic function core |
| 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 | Istvan Kolossvary | PATHMSD CUSTOM BIASVALUE DRR PRINT METAD FLUSH | colvar bias generic function drr |
| 22.030 | Mixing physics across temperatures with generative artificial intelligence | methods | REMD, Generative AI, DDPM | Yihang Wang | TORSION PRINT WHOLEMOLECULES | generic colvar |
| 22.006 | Peptide framework for screening the effects of amino acids on assembly | bio | metadynamics, peptides | Andrew White | ONES GYRATION CONVERT_TO_FES KDE METAD DISTANCE MEAN SUM DISTANCES COMBINE INCLUDE PRINT ACCUMULATE DUMPGRID COM CUSTOM HISTOGRAM REWEIGHT_BIAS GROUP CENTER | vatom multicolvar colvar bias generic function core gridtools |
| 21.052 | On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets | materials | Ibuprofen, unbinding, WTmetaD | Matteo Salvalaglio | ONES MEAN COMMITTOR CONTACT_MATRIX TORSION ENDPLUMED GROUP CENTER PRINT METAD DISTANCE COORDINATIONNUMBER MATRIX_VECTOR_PRODUCT | vatom colvar bias symfunc generic matrixtools function core adjmat |
| 21.050 | N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity | methods | bio | Isabell Louise Grothaus | CENTER PRINT DISTANCE | vatom generic colvar |
| 21.024 | Property map collective variable as a useful tool for force field correction | chemistry | molecular mechanics | Vojtech Spiwok | PROPERTYMAP BIASVALUE TORSION PRINT METAD WHOLEMOLECULES | bias generic colvar |
| 21.019 | Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations | materials | Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen | Matteo Salvalaglio | KDE PRINT TORSIONS DISTANCE MATHEVAL COM | vatom multicolvar colvar generic function gridtools |
| 21.016 | MD SAXS GTPase associated center | bio | metadynamics, RNA, folding, SAXS | Giovanni Bussi | UPPER_WALLS CUSTOM LOWER_WALLS ERMSD GYRATION MOLINFO GROUP INCLUDE SAXS CENTER PRINT METAD WHOLEMOLECULES | vatom isdb colvar bias generic function core |
| 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 | Khaled Abdel-Maksoud | TORSION METAD PRINT DISTANCE | bias generic colvar |
| 20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Matteo Salvalaglio | UPPER_WALLS LOWER_WALLS CELL PRINT METAD VOLUME MATHEVAL ENERGY | bias generic function colvar |
| 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 | Gabriella Heller | GYRATION PBMETAD PARABETARMSD ENSEMBLE METAINFERENCE CS2BACKBONE FLUSH COORDINATION COMBINE ENDPLUMED ALPHARMSD INCLUDE PRINT MOLINFO TORSION GROUP ANTIBETARMSD DIHCOR STATS WHOLEMOLECULES | secondarystructure multicolvar isdb colvar bias generic function core |
| 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 | Francesco Gervasio | UPPER_WALLS LOWER_WALLS BIASVALUE CONTACTMAP MOLINFO FUNCPATHGENERAL GROUP INCLUDE PRINT METAD LOAD DISTANCE MATHEVAL PROJECTION_ON_AXIS CONSTANT WHOLEMOLECULES COM | vatom setup colvar bias generic function core |
| 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 | Pablo Piaggi | ONES CONVERT_TO_FES VOLUME KDE Q6 TD_WELLTEMPERED OPT_AVERAGED_SGD TD_MULTITHERMAL_MULTIBARIC BF_LEGENDRE RESTART OPT_DUMMY LOWER_WALLS COMBINE VES_LINEAR_EXPANSION PRINT ACCUMULATE DUMPGRID MATHEVAL UPPER_WALLS CUSTOM HISTOGRAM REWEIGHT_BIAS CELL READ REWEIGHT_TEMP_PRESS LOAD ENERGY | setup ves colvar bias symfunc generic function gridtools |
| 19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Giovanni Bussi | COORDINATION MAXENT MOLINFO TORSION INCLUDE PRINT METAD DISTANCE MATHEVAL FLUSH SORT WHOLEMOLECULES COM | vatom colvar bias generic function |
| 19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | UPPER_WALLS GYRATION MOLINFO PRINT METAD DISTANCE ENERGY COM | vatom bias generic colvar |
| 19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Jim Pfaendtner | GYRATION PRINT METAD ENERGY WHOLEMOLECULES | bias generic colvar |
| 19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Kim Jelfs | CUSTOM ANGLE SUM DISTANCES INPLANEDISTANCES GROUP RESTART CENTER PRINT DISTANCE FLUSH MOVINGRESTRAINT COM | vatom multicolvar setup colvar bias generic function core |
| 19.055 | Flying Gaussian method | methods | flying Gaussians, alanine dipeptide, peptide bond, Met-enkephalin | Vojtech Spiwok | COMBINE TORSION PRINT METAD DISTANCE MATHEVAL | bias generic function colvar |
| 19.049 | Determining the sizes of solid/liquid clusters in MD trajectories of nucleation | methods | nucleation, metadynamics, clustering, Steinhardt order parameters | Gareth Tribello | ONES CLUSTER_PROPERTIES CLUSTER_DISTRIBUTION Q6 MORE_THAN DFSCLUSTERING OUTER_PRODUCT METAD MATRIX_VECTOR_PRODUCT COORDINATIONNUMBER CLUSTER_NATOMS MEAN SMAC SUM DISTANCES CONTACT_MATRIX PRINT CUSTOM GROUP CLUSTER_WEIGHTS OUTPUT_CLUSTER LOCAL_Q6 | multicolvar clusters bias symfunc generic matrixtools function core adjmat |
| 19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Carlo Camilloni | ALPHABETA PBMETAD RESTART CS2BACKBONE CONSTANT SECONDARY_STRUCTURE_RMSD FLUSH LOWER_WALLS BIASVALUE SUM COMBINE ENDPLUMED PRINT LESS_THAN UPPER_WALLS CUSTOM MOLINFO TORSION GROUP ANTIBETARMSD WHOLEMOLECULES | secondarystructure multicolvar setup isdb colvar bias generic function core |
| 19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Pratyush Tiwary | CUSTOM COMMITTOR ALPHABETA SUM COMBINE TORSION RESTART EXTERNAL PRINT DISTANCE CONSTANT WHOLEMOLECULES COM | vatom multicolvar setup colvar bias generic function |
| 19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Kresten Lindorff-Larsen | CUSTOM ALPHABETA SUM COMMITTOR MOLINFO TORSION COMBINE PRINT METAD CONSTANT FLUSH | multicolvar colvar bias generic function |
| 19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Giovanni Bussi | UPPER_WALLS ANGLE LOWER_WALLS ERMSD DISTANCES MOLINFO COMBINE GROUP INCLUDE CENTER PRINT METAD DISTANCE RANDOM_EXCHANGES LOWEST FLUSH | vatom multicolvar colvar bias generic function core |
| 24.016 | Cryo-EM guided simulations of ribozyme | bio | metainference, cryo-EM | Giovanni Bussi | GROUP BIASVALUE MOLINFO WHOLEMOLECULES EMMIVOX PRINT ERMSD RESTRAINT INCLUDE | core isdb bias colvar generic |
| 23.040 | Supramolecular capsules assembly dynamics | chemistry | Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics | Riccardo Capelli | GROUP SUM DISTANCES FLUSH COM WHOLEMOLECULES BETWEEN UNITS CUSTOM PRINT LESS_THAN METAD CENTER DISTANCE POSITION | core vatom bias colvar function multicolvar generic setup |
| 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 | Timothy Clark | MOLINFO WHOLEMOLECULES RMSD PRINT METAD DISTANCE MATHEVAL | function bias generic colvar |
| 23.026 | Machine Learning Nucleation Collective Variables with Graph Neural Networks | chemistry | Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks | Florian Dietrich | MATRIX_PRODUCT MEAN SUM LOCAL_Q6 VSTACK SPHERICAL_HARMONIC OUTER_PRODUCT MFILTER_MORE CUSTOM PRINT LOWER_WALLS MATRIX_VECTOR_PRODUCT Q6 ONES MOVINGRESTRAINT CONTACT_MATRIX GROUP COMBINE COORDINATIONNUMBER TRANSPOSE MORE_THAN METAD | core symfunc bias adjmat function multicolvar generic valtools matrixtools |
| 23.001 | Quantum phase diagram of water | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn-Løland Bore | GROUP MATRIX_VECTOR_PRODUCT SUM RESTART UPPER_WALLS ECV_UMBRELLAS_LINE DISTANCE_MATRIX LOWER_WALLS PRINT ONES CUSTOM MORE_THAN INCLUDE ENVIRONMENTSIMILARITY MEAN OPES_EXPANDED | core bias adjmat function setup opes generic matrixtools envsim |
| 23.000 | Atomistic simulations of RNA tetraloop folding via PTWTE-WTM | bio | parallel tempering, well-tempered metadynamics, well-tempered ensemble, RNA, Tetraloop, Folding | Gül Zerze | WHOLEMOLECULES UPPER_WALLS LOWER_WALLS PRINT ENERGY METAD CONTACTMAP | bias generic colvar |
| 22.019 | Exploring aspartic protease inhibitor binding to design selective antimalarials | bio | ligand binding, loop opening, path CV, funnel metadynamics, drug development | Raitis Bobrovs | PATHMSD COM WHOLEMOLECULES FUNNEL_PS UPPER_WALLS LOWER_WALLS PRINT FUNNEL METAD DISTANCE | vatom funnel bias colvar generic |
| 22.014 | Quasi Liquid Layer Order Parameters | materials | Quasi-Liquid Layer, Steinhardt Order Parameter, Entropy Fingerprint | Jihong Shi | DUMPGRID LOCAL_Q6 LOAD LOCAL_Q3 Q6 DUMPMULTICOLVAR Q3 HISTOGRAM PAIRENTROPIES LOCAL_AVERAGE Q4 LOCAL_Q4 ENDPLUMED UNITS | gridtools symfunc multicolvar generic setup |
| 22.008 | Ab initio metadynamics determination of temperature-dependent free-energy landscape in ultrasmall silver clusters | materials | Well tempered metadynamics, ab-initio, ase | Daniel Sucerquia | COMBINE GROUP CONTACT_MATRIX MATRIX_VECTOR_PRODUCT FLUSH COORDINATIONNUMBER COM UPPER_WALLS GYRATION LOWER_WALLS ONES CUSTOM METAD MEAN DISTANCE UNITS COORDINATION | core vatom symfunc bias adjmat colvar function generic setup matrixtools |
| 21.047 | Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations | materials | pair entropy, metadynamics, ves, solids, crystallization | Pablo Piaggi | COMBINE VOLUME BF_LEGENDRE RESTART VES_LINEAR_EXPANSION PAIRENTROPY TD_WELLTEMPERED OPT_AVERAGED_SGD LOAD PRINT ENERGY METAD | gridtools bias ves colvar function setup generic |
| 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 | Denis Maag | COMBINE GROUP CONTACT_MATRIX MATRIX_VECTOR_PRODUCT COORDINATIONNUMBER UPPER_WALLS LOWER_WALLS PRINT ONES METAD MEAN DISTANCE COORDINATION | core symfunc bias adjmat colvar function generic matrixtools |
| 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 | Huixia Lu | FIT_TO_TEMPLATE PRINT METAD FIXEDATOM TORSION | colvar bias generic vatom |
| 21.034 | Efficient sampling of high-dimensional free energy landscapes using adaptive reinforced dynamics | bio | reinforced dynamics, bias-exchange metadynamics, parallel-bias metadynamics | Dongdong Wang | PBMETAD PRINT RANDOM_EXCHANGES METAD INCLUDE ENDPLUMED TORSION | generic bias colvar |
| 21.028 | From Enhanced Sampling to Reaction Profiles | methods | collective variables, multi-state, machine learning, Deep-TDA | Enrico Trizio | WHOLEMOLECULES FIXEDATOM CENTER ENDPLUMED TORSION DISTANCES LOWER_WALLS PRINT OPES_METAD LOAD FIT_TO_TEMPLATE GROUP PYTORCH_MODEL UPPER_WALLS ANGLE DISTANCE UNITS MATHEVAL COORDINATION | core vatom pytorch bias colvar function multicolvar generic opes setup |
| 21.014 | how to determine statistically accurate conformational ensembles | bio | metadynamics, metainference, errors, cv, SAXS, ensemble determination | Cristina Paissoni | WHOLEMOLECULES CENTER TORSION SUM SAXS CONSTANT CUSTOM SECONDARY_STRUCTURE_RMSD PRINT CONTACTMAP ALPHABETA PBMETAD LESS_THAN COMBINE BIASVALUE MOLINFO STATS GYRATION ENSEMBLE METAD ANTIBETARMSD | vatom isdb bias colvar function multicolvar generic secondarystructure |
| 21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Adriana Pietropaolo | BIASVALUE RESTART WHOLEMOLECULES PBMETAD CONSTANT PRINT MATHEVAL TORSION | bias colvar function generic setup |
| 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 | Dorothea Gobbo | PATHMSD RESTART WHOLEMOLECULES UPPER_WALLS LOWER_WALLS PRINT METAD | generic bias setup colvar |
| 21.000 | Uremic toxin time scale dynamics | bio | uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs) | Jim Pfaendtner | GROUP COM WHOLEMOLECULES PRINT DISTANCE | colvar core generic vatom |
| 20.026 | Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor | bio | Metadynamics, Umbrella sampling | Brandon Peters | COMBINE DUMPGRID MULTI_RMSD ACCUMULATE WHOLEMOLECULES CONCATENATE CONSTANT RMSD_VECTOR CUSTOM PRINT HISTOGRAM ONES RESTRAINT METAD KDE CONVERT_TO_FES POSITION REWEIGHT_METAD | gridtools bias colvar function generic valtools |
| 20.018 | Free energy barriers from biased molecular dynamics simulations | methods | kinetics, free energy barriers, chemical reactions, nucleation, metadynamics | Kristof Bal | SPRINT HISTOGRAM LOCAL_AVERAGE CENTER REWEIGHT_METAD LOWER_WALLS PRINT REWEIGHT_BIAS DENSITY VOLUME FLUSH LOAD Q6 ENERGY COMBINE DUMPGRID CONTACT_MATRIX COORDINATIONNUMBER PAIRENTROPY UPPER_WALLS METAD CONVERT_TO_FES DISTANCE UNITS COORDINATION | gridtools vatom symfunc bias volumes colvar adjmat function generic setup sprint |
| 20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Jim Pfaendtner | GROUP SUM DISTANCES RESTART WHOLEMOLECULES CUSTOM PRINT CENTER DISTANCE COORDINATION | core vatom colvar function multicolvar setup generic |
| 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 | Carlo Camilloni | WHOLEMOLECULES CS2BACKBONE ENDPLUMED TORSION SUM CONSTANT CUSTOM SECONDARY_STRUCTURE_RMSD LOWER_WALLS PRINT ALPHABETA FLUSH PBMETAD LESS_THAN COMBINE GROUP BIASVALUE MOLINFO UPPER_WALLS ANTIBETARMSD | core isdb bias colvar function multicolvar generic secondarystructure |
| 20.000 | Muscarinic M2 receptor-ligand funnel metadynamics | bio | multiple walker metadynamics, well-tempered metadynamics, funnel metadynamics, MC-HLDA, GPCR, receptor, Adiabatic Bias MD | Riccardo Capelli | COM ABMD HISTOGRAM ENDPLUMED LOWER_WALLS PRINT CUSTOM KDE READ ONES COMBINE DUMPGRID ACCUMULATE UPPER_WALLS METAD CONVERT_TO_FES DISTANCE MATHEVAL REWEIGHT_METAD | gridtools vatom bias colvar function generic |
| 19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | MOLINFO COM UPPER_WALLS GYRATION PRINT ENERGY METAD DISTANCE | colvar bias generic vatom |
| 19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Michele Invernizzi | EXTERNAL POSITION PRINT METAD OPES_METAD ENDPLUMED UNITS TORSION | bias colvar generic opes setup |
| 19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Jakub Rydzewski | PATHMSD RESTART UPPER_WALLS LOWER_WALLS PRINT METAD UNITS | generic bias setup colvar |
| 19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Kim E. Jelfs | GROUP RESTART COM UPPER_WALLS LOWER_WALLS PRINT METAD CENTER DISTANCE | core vatom bias colvar generic setup |
| 19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Matteo Salvalaglio | COMBINE VOLUME UPPER_WALLS CELL PRINT LOWER_WALLS ENERGY METAD ENDPLUMED MATHEVAL TORSION | function bias colvar generic |
| 19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Matteo Salvalaglio | UPPER_WALLS LOWER_WALLS PRINT COMMITTOR METAD CENTER DISTANCE TORSION | generic bias vatom colvar |
| 19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Carlo Camilloni | GROUP ENDPLUMED BIASVALUE INCLUDE MOLINFO WHOLEMOLECULES RMSD UPPER_WALLS SAXS STATS PRINT RESTRAINT CENTER DISTANCE | core vatom isdb bias colvar function generic |
| 19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Carlo Camilloni | DIHEDRAL_CORRELATION DIHCOR WHOLEMOLECULES METAINFERENCE CENTER ENDPLUMED TORSION SUM CONSTANT DHENERGY CUSTOM PRINT RDC ALPHABETA PBMETAD RESTRAINT COMBINE GROUP MOLINFO UPPER_WALLS STATS ENSEMBLE DISTANCE | core vatom isdb bias colvar function multicolvar generic |
| 19.004 | MI Ubiquitin | bio | metainference, NMR | Max Bonomi | GROUP MOLINFO WHOLEMOLECULES CS2BACKBONE METAINFERENCE PRINT RDC | core isdb generic |
| 24.007 | SWISH-X | bio | swish-x, SWISH-X, swish, expanded SWISH | Alberto Borsatto | ENERGY MOLINFO UPPER_WALLS PRINT CONTACTMAP OPES_EXPANDED WHOLEMOLECULES ECV_MULTITHERMAL INCLUDE | generic bias colvar opes |
| 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 | Federico Ballabio | BIASVALUE MOLINFO UPPER_WALLS PRINT GROUP STATS ENSEMBLE CENTER DISTANCE SAXS WRAPAROUND RMSD | core generic colvar vatom function isdb bias |
| 23.019 | Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors | bio | binding pathway, binding energy, sketch-map, drug development | Raitis Bobrovs | COM VSTACK PATHMSD COLLECT_FRAMES UPPER_WALLS METAD PRINT CUSTOM SKETCHMAP_PROJECTION LANDMARK_SELECT_FPS SKETCHMAP WHOLEMOLECULES DISTANCE DISSIMILARITIES TRANSPOSE VORONOI | generic colvar vatom valtools function bias dimred landmarks matrixtools |
| 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 | Istvan Kolossvary | TIME UNITS BIASVALUE PATHMSD CUSTOM DRR METAD UPPER_WALLS PRINT LOWER_WALLS FLUSH | generic setup colvar function drr bias |
| 23.012 | JAK2 2D meta-eABF PMF with statistical analysis | bio | 2D meta-eABF, path CV, PMF | Istvan Kolossvary | BIASVALUE PATHMSD CUSTOM METAD DRR UPPER_WALLS PRINT LOWER_WALLS FLUSH | generic colvar function drr bias |
| 23.011 | OneOPES, a combined enhanced sampling method to rule them all | bio | OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding | Valerio Rizzi | ENERGY MOLINFO ENDPLUMED METAD PRINT TORSION OPES_EXPANDED OPES_METAD_EXPLORE DISTANCE ECV_MULTITHERMAL | generic bias colvar opes |
| 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 | Dhiman Ray | MOLINFO CONTACTMAP GROUP PYTORCH_MODEL INCLUDE OPES_METAD WHOLEMOLECULES COMBINE MATHEVAL ENDPLUMED UPPER_WALLS CUSTOM PRINT FIT_TO_TEMPLATE CENTER ANGLE RMSD COORDINATION COMMITTOR FIXEDATOM ENERGY LOWER_WALLS DISTANCE | core generic colvar vatom function pytorch bias opes |
| 22.043 | Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES | bio | OPES, RNA, Tetraloop, Folding | Gül Zerze | ENERGY ECV_UMBRELLAS_LINE PRINT CONTACTMAP OPES_EXPANDED WHOLEMOLECULES ECV_MULTITHERMAL | generic colvar opes |
| 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 | Max Bonomi | PRINT RMSD | generic colvar |
| 22.024 | Conformational Entropy as a Potential Liability of Computationally Designed Antibodies | bio | metadynamics, conformational entropy, antibody, nanobody | Thomas Löhr | LESS_THAN COM MOLINFO CUSTOM PBMETAD PRINT TORSION SECONDARY_STRUCTURE_RMSD RESTART ALPHARMSD ANTIBETARMSD WHOLEMOLECULES COMBINE ALPHABETA CONSTANT SUM | multicolvar generic setup colvar vatom function secondarystructure bias |
| 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 | Vojtech Spiwok | PRINT LOAD WHOLEMOLECULES METAD | generic bias setup |
| 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 | Benjamin Pampel | UNITS BF_GAUSSIANS BF_LEGENDRE BF_CUBIC_B_SPLINES BF_WAVELETS TD_UNIFORM INCLUDE TD_WELLTEMPERED OPT_AVERAGED_SGD OPT_ADAM VES_LINEAR_EXPANSION UPPER_WALLS PRINT POSITION FLUSH BF_CHEBYSHEV COORDINATION ENERGY METAD DISTANCE VES_OUTPUT_BASISFUNCTIONS | generic setup colvar ves bias |
| 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 | Matej Badin | CUSTOM METAD VOLUME PRINT ENDPLUMED COMBINE COORDINATION | function generic bias colvar |
| 21.037 | Molecular Dynamics simulations of RBD/hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain | Max Bonomi | PRINT RMSD DISTANCE | generic colvar |
| 21.025 | Computational and biochemical analysis of type IV pilus dynamics and stability | bio | molecular dynamics, calcium binding, Type IV pilus | Yasaman Karami | LOWER_WALLS PRINT DISTANCE UPPER_WALLS | generic bias colvar |
| 21.022 | Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly | materials | parallel bias metadynamics, adsorption, peptide | Xin Qi | COM ENERGY MOLINFO UPPER_WALLS PBMETAD PRINT LOWER_WALLS DISTANCE GYRATION | generic bias colvar vatom |
| 21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Kresten Lindorff-Larsen | EEFSOLV BIASVALUE MOLINFO PRINT PBMETAD GROUP ALPHARMSD FLUSH WHOLEMOLECULES CENTER SAXS GYRATION METAINFERENCE | core generic colvar vatom isdb secondarystructure bias |
| 20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Cristina Paissoni | BIASVALUE MOLINFO PRINT RESTRAINT GROUP STATS ENSEMBLE CENTER WHOLEMOLECULES DISTANCE SAXS INCLUDE | core generic colvar vatom function isdb bias |
| 20.013 | Improving accuracy of biased Alchemistic simulations | methods | flying Gaussian method, Alchemistic simulations, thermodynamic integration, reweighting | Vojtech Spiwok | PRINT TORSION METAD | generic bias colvar |
| 20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Luigi Bonati | COM UNITS MATHEVAL ENDPLUMED UPPER_WALLS PRINT TORSION OPES_METAD GROUP LOWER_WALLS FLUSH DISTANCE LOAD PYTORCH_MODEL | core generic setup colvar vatom function pytorch bias opes |
| 20.003 | Enhanced sampling of transition states | methods | Variationally Enhanced Sampling, Target distribution, Transition state, Enhanced Sampling, Nucleation, chemical reaction | Jayashrita Debnath | ENERGY UNITS OPT_AVERAGED_SGD PRINT POSITION BF_LEGENDRE VES_LINEAR_EXPANSION LOAD | generic setup ves colvar |
| 19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Valerio Rizzi | COORDINATIONNUMBER UNITS EXTERNAL CUSTOM METAD ENDPLUMED PRINT GROUP ONES RESTART CONTACT_MATRIX FLUSH COMBINE MATRIX_VECTOR_PRODUCT MEAN SUM | core setup generic symfunc function bias adjmat matrixtools |
| 19.075 | PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python | other | Python, automatic differentiation | Toni Giorgino | DUMPDERIVATIVES CUSTOM ENDPLUMED PRINT RESTRAINT TORSION GROUP DISTANCE CENTER COMBINE ANGLE | core generic colvar vatom function bias |
| 19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Wei Chen | COM POSITION RESTRAINT COMBINE ANN | colvar vatom function annfunc bias |
| 19.050 | Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes | chemistry | metadynamics, membranes, Willard Chandler surface | Gareth Tribello | CONVERT_TO_FES CUSTOM METAD HISTOGRAM ACCUMULATE UPPER_WALLS PRINT ONES REWEIGHT_BIAS RESTART READ KDE COMBINE DUMPGRID DISTANCE_FROM_CONTOUR | generic setup function contour bias gridtools |
| 19.035 | Dimerization of GPCRs from coarse-grained umbrella sampling | bio | Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization | Davide Provasi | COM PRINT RESTRAINT TORSION GROUP DISTANCE | core generic colvar vatom bias |
| 19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Silvio Pipolo | UPPER_WALLS METAD PRINT LOWER_WALLS FUNCPATHMSD CELL PIV | piv generic colvar function bias |
| 19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Adriana Pietropaolo | MATHEVAL BIASVALUE METAD PRINT TORSION WHOLEMOLECULES CONSTANT | function generic bias colvar |
| 24.012 | Molecular simulations to investigate the impact of N6-methylation in RNA recognition | bio | metadynamics, alchemistry, RNA modification, RNA:protein interactions | Giovanni Bussi | DEBUG COMBINE COORDINATION METAD COM GHBFIX DISTANCE UPPER_WALLS PRINT LOWER_WALLS GROUP MOLINFO BIASVALUE CENTER | function generic bias core vatom colvar |
| 23.036 | Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? | bio | NaCl, nucleation, metadynamics | Ruiyu Wang | SPHERICAL_HARMONIC Q6 ONES CONTACT_MATRIX COMBINE MEAN METAD VOLUME CUSTOM ENERGY MATRIX_VECTOR_PRODUCT MATHEVAL Q4 SUM GROUP MORE_THAN COORDINATIONNUMBER PRINT | function matrixtools generic bias core symfunc adjmat colvar |
| 23.022 | A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar | methods | collective variables, machine learning, toy model | Enrico Trizio | UNITS ENDPLUMED POSITION CUSTOM PYTORCH_MODEL UPPER_WALLS PRINT LOWER_WALLS OPES_METAD BIASVALUE | function setup generic bias pytorch opes colvar |
| 23.018 | Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention | materials | metadynamics, surface binding, peptide adsorption | Kaylyn Torkelson | GYRATION COM DISTANCE UPPER_WALLS PBMETAD PRINT | generic bias colvar vatom |
| 23.007 | Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains | bio | metadynamics, peptoids, parallel-bias metadynamics | Jim Pfaendtner | COORDINATION GYRATION COM RESTRAINT INCLUDE TORSION PBMETAD PRINT WHOLEMOLECULES | generic bias colvar vatom |
| 22.042 | Metadynamics of NSP10 and variants | bio | metadynamics, NSP10, crystal structure, variants | Shozeb Haider | TORSION METAD PRINT | generic bias colvar |
| 22.037 | Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site | chemistry | metadynamics, DNA, abasic | Mike Jones | MEAN METAD DISTANCES DISTANCE PRINT GROUP CENTER | function generic bias core vatom multicolvar colvar |
| 22.034 | Rationalising the difference in crystallisability of two Sulflowers using efficient in silico methods | materials | metadynamics, crystallizability, crystal structure prediction, sulflower, persulforated coronene | Matteo Salvalaglio | COMMITTOR METAD SUM CUSTOM CONSTANT DISTANCE MATHEVAL CELL UPPER_WALLS PRINT LOWER_WALLS DRMSD | generic bias function colvar |
| 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 | Weiwei He | METAD COM DISTANCE TORSION PRINT GROUP WHOLEMOLECULES | generic bias core vatom colvar |
| 21.042 | Peptoid-mediated Au nanocrystal growth | materials | parallel-bias metadynamics, peptoid, Au | Xin Qi | GYRATION COM DISTANCE UPPER_WALLS PBMETAD PRINT MOLINFO | generic bias colvar vatom |
| 21.032 | Metal-coupled folding mechanism to metallothionein | bio | parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination | Manuel-Peris Diaz | UNITS COORDINATION PBMETAD GROUP WHOLEMOLECULES | setup generic core bias colvar |
| 21.023 | Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling | methods | enhanced sampling, collective variables, machine learning | Jakub Rydzewski | UNITS METAD REWEIGHT_METAD CUSTOM CONSTANT ENERGY DISTANCE INCLUDE TORSION PRINT BIASVALUE | function setup generic bias colvar |
| 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 | Pablo Piaggi | ECV_MULTITHERMAL_MULTIBARIC SUM DISTANCE_MATRIX MEAN VES_LINEAR_EXPANSION VOLUME CUSTOM MATHEVAL OPT_AVERAGED_SGD RESTART BF_LEGENDRE Q6 ONES COMBINE ENVIRONMENTSIMILARITY GROUP MORE_THAN OPES_EXPANDED SPHERICAL_HARMONIC CONTACT_MATRIX TD_UNIFORM ENERGY MATRIX_VECTOR_PRODUCT UPPER_WALLS ECV_UMBRELLAS_LINE PRINT | function ves setup matrixtools generic core bias symfunc envsim opes adjmat colvar |
| 20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Glen Hocky | UNITS GYRATION ENERGY DISTANCE RESTRAINT MATHEVAL FISST PRINT GROUP BIASVALUE | function setup generic bias core fisst colvar |
| 20.016 | Predicting polymorphism in molecular crystals using orientational entropy | materials | metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy | Pablo Piaggi | METAD VOLUME INCLUDE UPPER_WALLS PRINT GROUP LOAD CENTER | setup generic bias core vatom colvar |
| 19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Valerio Rizzi | FLUSH SUM MEAN CUSTOM RESTART COMBINE ONES METAD GROUP COORDINATIONNUMBER CENTER UNITS CONTACT_MATRIX ENDPLUMED DISTANCES MATRIX_VECTOR_PRODUCT DISTANCE UPPER_WALLS PRINT | function setup matrixtools colvar generic core bias symfunc multicolvar adjmat vatom |
| 19.078 | Iterative unbiasing of quasi-equilibrium sampling | methods | metadynamics, reweighting | Federico Giberti | REWEIGHT_BIAS MEAN UNITS METAD CONTACT_MATRIX ONES COLLECT_FRAMES DISTANCE MATHEVAL DUMPATOMS MATRIX_VECTOR_PRODUCT PRINT GROUP COORDINATIONNUMBER BIASVALUE | function setup matrixtools generic bias core symfunc landmarks adjmat colvar |
| 19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Cristina Paissoni | COMBINE ENDPLUMED COORDINATION BIASVALUE ALPHABETA ANGLE INCLUDE MATHEVAL PBMETAD ENSEMBLE PRINT GROUP WHOLEMOLECULES MOLINFO STATS SAXS CENTER | function isdb generic bias core vatom multicolvar colvar |
| 19.045 | Adsorption free energy of Ca/CO3 ions on calcite steps in contact with water | materials | metadynamics, well-tempered, multiple walkers, LAMMPS | Marco De La Pierre | UNITS COORDINATION POSITION METAD UPPER_WALLS RESTART FLUSH PRINT LOWER_WALLS GROUP | setup generic bias core colvar |
| 19.044 | Multithermal-multibaric simulations using VES | methods | ves, Wang Landau, multicanonical, water, density anomaly | Pablo Piaggi | KDE AVERAGE HISTOGRAM REWEIGHT_TEMP_PRESS REWEIGHT_BIAS VES_LINEAR_EXPANSION VOLUME CUSTOM DUMPGRID RESTART OPT_AVERAGED_SGD BF_LEGENDRE CONVERT_TO_FES OPT_DUMMY COMBINE ONES TD_MULTITHERMAL_MULTIBARIC ACCUMULATE READ ENERGY PRINT | function ves gridtools setup generic bias colvar |
| 24.015 | nanocluster QM/MM | chemistry | nanocluster, QM/MM, pathCV, OPES, reaction modelling | Vikas Tiwari | COMMITTOR PRINT RESTRAINT FLUSH OPES_METAD UNITS CENTER LOWER_WALLS UPPER_WALLS DISTANCE | generic opes vatom colvar setup bias |
| 24.001 | A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations | bio | OPES, OPES-Flooding, QM/MM, Kinetics, Enzyme Catalysis | Dhiman Ray | TORSION COMMITTOR PRINT FLUSH OPES_METAD UNITS COMBINE CUSTOM LOWER_WALLS UPPER_WALLS DISTANCE | generic function opes colvar setup bias |
| 23.044 | Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition | materials | metadynamics, interlocked molecules | Luigi Leanza | KDE GROUP COORDINATION DUMPGRID COMMITTOR ACCUMULATE ENDPLUMED HISTOGRAM READ ONES CONVERT_TO_FES CUSTOM PRINT METAD | core gridtools generic function colvar bias |
| 22.028 | N-glycan conformer distributions in atomistic simulation | bio | REST2, RECT, N-glycan, pucker | Isabell Grothaus | TORSION DUMPGRID MOLINFO HISTOGRAM READ CONVERT_TO_FES PUCKERING PRINT METAD | generic gridtools colvar bias |
| 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 | Faidon Brotzakis | COM GROUP TORSION COORDINATION PRINT MOLINFO WHOLEMOLECULES RMSD EMMI PBMETAD BIASVALUE RESTART UPPER_WALLS | core generic isdb vatom colvar setup bias |
| 22.018 | Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations | bio | ligand binding, docking, EMMI, LAT1 | Max Bonomi | GROUP LOAD MOLINFO WHOLEMOLECULES EMMIVOX BIASVALUE PRINT | core generic isdb setup bias |
| 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 | Pablo Piaggi | MATRIX_VECTOR_PRODUCT KDE DISTANCE_MATRIX CUSTOM PRINT HISTOGRAM OPES_METAD VOLUME DUMPGRID MORE_THAN ACCUMULATE AROUND SUM UPPER_WALLS ONES ENVIRONMENTSIMILARITY GROUP ENERGY MEAN RESTART | core gridtools volumes generic matrixtools function opes envsim adjmat colvar setup bias |
| 22.015 | Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome | bio | photodynamics, bacteriophytochrome, variationally enhanced sampling | Jakub Rydzewski | TD_UNIFORM TORSION VES_LINEAR_EXPANSION OPT_AVERAGED_SGD BF_FOURIER PRINT | ves generic colvar |
| 22.012 | Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT | bio | contact maps, protein-protein interactions | Isabell-Louise Grothaus | CENTER CONTACTMAP PRINT DISTANCE | generic colvar vatom |
| 22.003 | Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling | methods | opes, metadynamics, reweighting, alanine, muller | Michele Invernizzi | LOWER_WALLS TORSION OPES_METAD_EXPLORE ENDPLUMED ECV_UMBRELLAS_FILE UPPER_WALLS OPES_METAD ENERGY UNITS POSITION PBMETAD BIASVALUE CUSTOM ECV_MULTITHERMAL OPES_EXPANDED PRINT METAD | generic opes function colvar setup bias |
| 21.033 | Multiple-path-metadynamics applied to DNA base-pairing transitions | bio | path-CV, metadynamics, multiple-walker, dna | Alberto Pérez-de-Alba-Ortíz | TORSION INCLUDE PRINT LOAD RESTRAINT WHOLEMOLECULES UNITS CONSTANT CENTER MOVINGRESTRAINT COMBINE METAD CUSTOM UPPER_WALLS DISTANCE | generic function vatom colvar setup bias |
| 21.029 | Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs | bio | metadynamics, small peptide, machine learning | Pratyush Tiwary | TORSION EXTERNAL MOLINFO FLUSH ENERGY RESTART PRINT | generic colvar setup bias |
| 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 | Gaston Courtade | COORDINATION REWEIGHT_BIAS RESTRAINT WHOLEMOLECULES POSITION CENTER MATHEVAL RESTART PRINT METAD | generic function vatom colvar setup bias |
| 21.011 | CmuMD simulations of NaCl(aq) at graphite | chemistry | CmuMD, DFS clustering | Aaron Finney | MATRIX_VECTOR_PRODUCT KDE COORDINATIONNUMBER CUSTOM PRINT MULTICOLVARDENS LOAD RESTRAINT CONTACT_MATRIX CLUSTER_DISTRIBUTION DENSITY HIGHEST DUMPGRID MFILTER_MORE MORE_THAN ACCUMULATE AROUND CLUSTER_WEIGHTS SUM DFSCLUSTERING DISTANCES ONES GROUP FIXEDATOM MEAN CLUSTER_NATOMS | core gridtools volumes multicolvar generic matrixtools function symfunc clusters vatom adjmat setup bias |
| 21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Kristof Bal | MATRIX_VECTOR_PRODUCT COORDINATIONNUMBER CONVERT_TO_FES PRINT LOAD HISTOGRAM CONTACT_MATRIX REWEIGHT_METAD DUMPGRID COMMITTOR MORE_THAN FLUSH SUM UNITS MOVINGRESTRAINT UPPER_WALLS METAD ONES GROUP MEAN | core gridtools generic matrixtools function symfunc adjmat setup bias |
| 21.007 | Sampling enhancement by metadynamics driven by machine learning and de novo protein modelling | bio | metadynamics, machine learning, protein folding | Vojtech Spiwok | LESS_THAN MOLINFO WHOLEMOLECULES ALPHARMSD POSITION SUM SECONDARY_STRUCTURE_RMSD MATHEVAL COMBINE FIT_TO_TEMPLATE | generic function colvar secondarystructure |
| 20.028 | Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane | bio | metadynamics, KRas-4B, anionic membrane | Huixia Lu | RESTART CENTER DISTANCE FIT_TO_TEMPLATE PRINT METAD | generic vatom colvar setup bias |
| 20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Valerio Rizzi | ANGLE GROUP COORDINATION PRINT FIXEDATOM ENDPLUMED WHOLEMOLECULES OPES_METAD ENERGY CENTER MATHEVAL PYTORCH_MODEL FIT_TO_TEMPLATE UPPER_WALLS DISTANCE | core generic pytorch opes function vatom colvar bias |
| 20.006 | Class B GPCR activation mechanism | bio | metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | PRINT MOLINFO WHOLEMOLECULES ENERGY RMSD CENTER MATHEVAL COMBINE DISTANCE LOWER_WALLS UPPER_WALLS METAD | generic function vatom colvar bias |
| 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 | Sarah Alamdari | COM GROUP PRINT MOLINFO GYRATION ENERGY METAD UPPER_WALLS DISTANCE | core generic vatom colvar bias |
| 19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Sandro Bottaro | TORSION MOLINFO ERMSD WHOLEMOLECULES RMSD METAD PRINT DISTANCE | generic colvar bias |
| 19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Mattia Bernetti | PATHMSD PRINT WHOLEMOLECULES LOWER_WALLS UPPER_WALLS METAD | generic colvar bias |
| 19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Gareth Tribello | MATRIX_VECTOR_PRODUCT KDE CENTER ARGS2VATOM CUSTOM MULTICOLVARDENS MASS FCCUBIC CONTACT_MATRIX FOURIER_TRANSFORM DUMPGRID MORE_THAN ACCUMULATE SUM UNITS DISTANCES ONES GROUP CHARGE POSITION FCCUBIC_FUNC FIND_CONTOUR_SURFACE | core gridtools multicolvar generic matrixtools contour function symfunc vatom fourier adjmat colvar setup |
| 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 | Jim Pfaendtner | COM PRINT ENERGY DISTANCE UPPER_WALLS METAD | generic colvar vatom bias |
| 19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Vittorio Limongelli | COM FUNNEL_PS PRINT FUNNEL WHOLEMOLECULES RMSD METAD LOWER_WALLS UPPER_WALLS DISTANCE | generic funnel vatom colvar bias |
| 19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Elena Papaleo | GROUP TORSION PRINT MOLINFO GYRATION WHOLEMOLECULES SUM CONSTANT COMBINE CUSTOM ALPHABETA LOWER_WALLS UPPER_WALLS METAD | core multicolvar generic function colvar bias |
| 19.009 | RNA tetraloops folding | bio | metadynamics, RNA, folding | Giovanni Bussi | MOLINFO ERMSD WHOLEMOLECULES ENDPLUMED RMSD PRINT METAD | generic colvar bias |
| 19.005 | Cmyc small molecule interaction | bio | metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP | Gabriella Heller | GROUP COORDINATION INCLUDE MOLINFO GYRATION WHOLEMOLECULES CS2BACKBONE CENTER METAINFERENCE PBMETAD ALPHABETA PRINT DISTANCE | core multicolvar generic isdb vatom colvar bias |