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 |
|---|---|---|---|---|---|---|
| 25.015 | Assessment of Force Fields for Describing Conformational Polymorphic Crystals of ROY | materials | Molecular crystal, Force Field, Collective Variable | Pradip Si and Omar Valsson | DISTANCES PRINT TORSIONS SMAC DUMPMULTICOLVAR | symfunc generic multicolvar |
| 25.009 | Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water | chemistry | metadynamics, nitrate photolysis | Kam-Tung Chan | REWEIGHT_METAD METAD DUMPGRID HISTOGRAM PRINT COORDINATION FLUSH READ DISTANCE CUSTOM RESTART GROUP UPPER_WALLS | core gridtools setup colvar function bias generic |
| 25.007 | Shaping the glycan landscape. Hidden relationships between linkage and ring distortion induced by carbohydrate-active enzmyes | bio | REST-RECT, REST2, glycan, enzyme, CAZyme, steered | Isabell Grothaus | METAD TORSION MOVINGRESTRAINT PRINT MOLINFO RESTART DISTANCE RESTRAINT PUCKERING | bias colvar generic setup |
| 24.021 | Ab initio machine learning simulation of calcium carbonate from aqueous solutions to the solid state | chemistry | ion pairing, caco3, opes, proton transfer, crystallization | Pablo Piaggi | PRINT COORDINATION DISTANCE ENERGY OPES_METAD UPPER_WALLS | opes colvar generic bias |
| 24.020 | Graph Neural Network-State Predictive Information Bottleneck (GNN-SPIB) approach for learning molecular thermodynamics and kinetics | bio | LJ7, alanine, well-tempered metadynamics, infrequent metadynamics, machine learning | Ziyue Zou, Dedi Wang, Pratyush Tiwary | TORSION METAD COMMITTOR PRINT LOAD GROUP | core setup colvar bias generic |
| 23.037 | Estimating binding free energy of solid binding peptides without extensive sampling | bio | metadynamics, solid binding peptides | Xin Qi | MOLINFO PRINT DISTANCE LOWER_WALLS GYRATION COM UPPER_WALLS PBMETAD | bias colvar generic vatom |
| 23.012 | JAK2 2D meta-eABF PMF with statistical analysis | bio | 2D meta-eABF, path CV, PMF | Istvan Kolossvary | METAD DRR PRINT FLUSH BIASVALUE PATHMSD CUSTOM LOWER_WALLS UPPER_WALLS | colvar drr function bias generic |
| 23.011 | OneOPES, a combined enhanced sampling method to rule them all | bio | OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding | Valerio Rizzi | TORSION METAD MOLINFO OPES_METAD_EXPLORE PRINT ECV_MULTITHERMAL DISTANCE ENERGY ENDPLUMED OPES_EXPANDED | bias colvar opes generic |
| 23.008 | PBMetaD simulations of Histatin5 | bio | metadynamics, IDP, Rg, PPII | Francesco Pesce | TORSION WHOLEMOLECULES MOLINFO PRINT GROUP GYRATION PBMETAD | bias colvar core generic |
| 23.002 | Critical comparison of general-purpose collective variables for crystal nucleation | methods | metadynamics, umbrella sampling, commitor, entropy, PIV | Julien Lam | Q4 METAD LOCAL_AVERAGE PIV PRINT FUNCPATHMSD CUSTOM RESTRAINT ENERGY UNITS Q6 PAIRENTROPY UPPER_WALLS VOLUME | gridtools setup colvar function bias symfunc generic piv |
| 23.001 | Quantum phase diagram of water | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn-Løland Bore | INCLUDE ENVIRONMENTSIMILARITY PRINT RESTART LOWER_WALLS OPES_EXPANDED UPPER_WALLS ECV_UMBRELLAS_LINE | opes envsim bias setup generic |
| 22.040 | From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure | bio | SARS-CoV-2, Spike, Omicron | Miłosz Wieczór | METAD WHOLEMOLECULES PRINT LOWER_WALLS PCAVARS UPPER_WALLS | bias generic mapping |
| 22.038 | Enhanced Sampling Aided Design of Molecular Photoswitches | chemistry | reaction discovery, OPES explore, graph CV | Umberto Raucci | OPES_METAD_EXPLORE COORDINATION PRINT CUSTOM PYTORCH_MODEL UNITS | opes colvar pytorch function setup generic |
| 22.031 | Rare Event Kinetics from Adaptive Bias Enhanced Sampling | methods | OPES Flooding, Kinetics, Rate, OPES, Machine Learning | Dhiman Ray | TORSION PRINT ENERGY OPES_METAD POSITION WHOLEMOLECULES INCLUDE CONTACTMAP COMMITTOR MOLINFO BIASVALUE CONSTANT CUSTOM RMSD GROUP UNITS COMBINE DISTANCE PYTORCH_MODEL ENDPLUMED | opes core setup colvar pytorch function bias generic |
| 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 | colvar generic |
| 22.025 | Bubble nucleation rate predictions in a Lennard-Jones fluid | materials | free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation | Kristof Bal | MOVINGRESTRAINT ANN HISTOGRAM BIASVALUE LOAD CONVERT_TO_FES CUSTOM DUMPGRID FLUSH PRINT RESTRAINT COMMITTOR COORDINATIONNUMBER UNITS REWEIGHT_BIAS UPPER_WALLS VOLUME | gridtools setup colvar annfunc function bias symfunc generic |
| 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 | TORSION METAD WHOLEMOLECULES PRINT DISTANCE GROUP COM | core colvar bias vatom generic |
| 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 | ENVIRONMENTSIMILARITY AROUND PRINT DUMPGRID HISTOGRAM RESTART CUSTOM ENERGY OPES_METAD UPPER_WALLS VOLUME | opes bias envsim gridtools colvar volumes function setup generic |
| 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 | COMBINE METAD TORSION ZANGLES WHOLEMOLECULES MOLINFO PRINT DISTANCE LOWER_WALLS YANGLES CUSTOM ALPHABETA MATHEVAL COM UPPER_WALLS XANGLES | multicolvar colvar function bias vatom generic |
| 21.051 | Automatic learning of hydrogen-bond fixes in an AMBER RNA force field | methods | force field, RNA | Giovanni Bussi | COMBINE METAD WHOLEMOLECULES MOLINFO COORDINATION BIASVALUE PRINT ERMSD | bias colvar generic function |
| 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 | METAD WHOLEMOLECULES PRINT LOWER_WALLS ALPHABETA GROUP ENDPLUMED GYRATION UPPER_WALLS | core multicolvar colvar bias generic |
| 21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Kristof Bal | REWEIGHT_METAD MOVINGRESTRAINT METAD COMMITTOR PRINT FLUSH DUMPGRID HISTOGRAM LOAD CONVERT_TO_FES COORDINATIONNUMBER UNITS UPPER_WALLS | gridtools setup bias symfunc generic |
| 21.006 | OPES, On-the-fly Probability Enhanced Sampling Method | methods | opes, alanine dipeptide, well-tempered, multithermal, multiumbrella | Michele Invernizzi | OPES_METAD TORSION PRINT ECV_MULTITHERMAL ENERGY ENDPLUMED OPES_EXPANDED ECV_UMBRELLAS_LINE | opes colvar generic |
| 20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Valerio Rizzi | OPES_METAD FIT_TO_TEMPLATE WHOLEMOLECULES CENTER FIXEDATOM COORDINATION PRINT DISTANCE ENERGY GROUP PYTORCH_MODEL ENDPLUMED ANGLE MATHEVAL UPPER_WALLS | opes core colvar pytorch function bias vatom generic |
| 20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Jim Pfaendtner | DISTANCES WHOLEMOLECULES CENTER PRINT COORDINATION RESTART DISTANCE GROUP | core multicolvar colvar setup vatom generic |
| 20.006 | Class B GPCR activation mechanism | bio | metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | COMBINE METAD WHOLEMOLECULES CENTER MOLINFO PRINT DISTANCE RMSD LOWER_WALLS ENERGY MATHEVAL UPPER_WALLS | colvar function bias vatom generic |
| 19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Valerio Rizzi | COMBINE METAD DISTANCES PRINT FLUSH RESTART COORDINATIONNUMBER GROUP ENDPLUMED UNITS UPPER_WALLS | core multicolvar setup function bias symfunc generic |
| 19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Matteo Salvalaglio | REWEIGHT_METAD METAD TORSION PRINT COMMITTOR BIASVALUE DUMPGRID DISTANCE READ HISTOGRAM CONVERT_TO_FES EXTERNAL MATHEVAL REWEIGHT_BIAS | gridtools colvar function bias generic |
| 19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Wei Chen | COMBINE ANN RESTRAINT COM POSITION | colvar annfunc function bias vatom |
| 19.049 | Determining the sizes of solid/liquid clusters in MD trajectories of nucleation | methods | nucleation, metadynamics, clustering, Steinhardt order parameters | Gareth Tribello | METAD OUTER_PRODUCT CLUSTER_NATOMS DISTANCES MATRIX_VECTOR_PRODUCT PRINT SMAC CLUSTER_PROPERTIES CUSTOM OUTPUT_CLUSTER DFSCLUSTERING COORDINATIONNUMBER CLUSTER_DISTRIBUTION ONES MORE_THAN Q6 LOCAL_Q6 CONTACT_MATRIX | multicolvar adjmat matrixtools function clusters bias symfunc generic |
| 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 | REWEIGHT_METAD TORSION COMBINE DISTANCES METAD WHOLEMOLECULES BRIDGE MOLINFO PRINT LOWER_WALLS RMSD DISTANCE ALPHABETA UPPER_WALLS GROUP COM FUNNEL | core multicolvar adjmat colvar funnel function bias vatom generic |
| 19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Vittorio Limongelli | METAD WHOLEMOLECULES PRINT FUNNEL DISTANCE RMSD LOWER_WALLS FUNNEL_PS COM UPPER_WALLS | colvar funnel bias vatom generic |
| 19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Paolo Raiteri | METAD PRINT FLUSH RESTART DISTANCE UNITS MATHEVAL UPPER_WALLS | setup colvar function bias generic |
| 19.023 | RECT | methods | metadynamics, replica exchange | Giovanni Bussi | TORSION METAD WHOLEMOLECULES PRINT GYRATION | bias colvar generic |
| 19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Mattia Bernetti | METAD WHOLEMOLECULES MOLINFO PRINT ENERGY ALPHARMSD ENDPLUMED GYRATION | bias colvar generic secondarystructure |
| 19.011 | Automatic Gradient Computation for Collective Variables | other | gradient, differentiation, curvature | Toni Giorgino | ENDPLUMED | generic |
| 19.008 | anncolvar | methods | neural network, dimensionality reduction | Vojtech Spiwok | COMBINE FIT_TO_TEMPLATE METAD WHOLEMOLECULES PRINT MOLINFO ALPHARMSD MATHEVAL POSITION | colvar function bias generic secondarystructure |
| 25.011 | Chiral perovskite nucleation | chemistry | metadynamics, chiral perovskites, nucleation | Adriana Pietropaolo | MATHEVAL DISTANCE PBMETAD RESTART UNITS LOWER_WALLS UPPER_WALLS PRINT MULTI_RMSD | generic bias function setup colvar |
| 24.007 | SWISH-X | bio | swish-x, SWISH-X, swish, expanded SWISH | Alberto Borsatto | CONTACTMAP MOLINFO ECV_MULTITHERMAL UPPER_WALLS OPES_EXPANDED PRINT ENERGY INCLUDE WHOLEMOLECULES | bias opes generic colvar |
| 24.003 | Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations | chemistry | steered molecular dynamics, foldamers, peptoids, bio-inspired | Kaylyn Torkelson | GYRATION DISTANCE COORDINATION MOVINGRESTRAINT ALPHABETA COM PRINT TORSION WHOLEMOLECULES INCLUDE | vatom generic multicolvar bias colvar |
| 23.046 | Lasso Peptides - HLDA CV | bio | metadynamics, protein folding, HLDA, harmonic | Gabriel da Hora | DISTANCE METAD COMBINE UNITS PRINT WHOLEMOLECULES | generic bias function setup colvar |
| 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 | DISTANCE WRAPAROUND MOLINFO GROUP BIASVALUE UPPER_WALLS PRINT INCLUDE EMMIVOX WHOLEMOLECULES | generic core isdb bias colvar |
| 23.034 | Urea nucleation in water: do long-range forces matter? | materials | LMF theory, Metadynamics, Nucleation | Ziyue Zou | LOAD METAD CENTER GROUP PRINT COORDINATIONNUMBER INCLUDE | vatom generic core bias setup symfunc |
| 23.022 | A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar | methods | collective variables, machine learning, toy model | Enrico Trizio | PYTORCH_MODEL OPES_METAD CUSTOM UNITS LOWER_WALLS BIASVALUE UPPER_WALLS POSITION ENDPLUMED PRINT | generic opes pytorch bias setup colvar function |
| 23.018 | Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention | materials | metadynamics, surface binding, peptide adsorption | Kaylyn Torkelson | GYRATION PBMETAD DISTANCE COM UPPER_WALLS PRINT | bias vatom generic colvar |
| 23.014 | Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 | bio | metadynamics, oligomerization, chemokine receptors, GPCR, membrane | Vittorio Limongelli | FLUSH DISTANCE METAD COMBINE COM UPPER_WALLS PRINT TORSION WHOLEMOLECULES | vatom generic bias function colvar |
| 22.042 | Metadynamics of NSP10 and variants | bio | metadynamics, NSP10, crystal structure, variants | Shozeb Haider | TORSION METAD PRINT | bias generic colvar |
| 22.037 | Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site | chemistry | metadynamics, DNA, abasic | Mike Jones | DISTANCES DISTANCE METAD PRINT | bias generic colvar multicolvar |
| 22.026 | Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification | materials | Peptoid, silica | Jim Pfaendtner | GYRATION PBMETAD DISTANCE MOLINFO COM UPPER_WALLS PRINT | bias vatom generic colvar |
| 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 | ENVIRONMENTSIMILARITY ECV_UMBRELLAS_LINE LOWER_WALLS UPPER_WALLS OPES_EXPANDED PRINT INCLUDE | bias generic opes envsim |
| 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 | GYRATION FLUSH DISTANCE METAD COMBINE COORDINATION UNITS LOWER_WALLS COM UPPER_WALLS COORDINATIONNUMBER | vatom generic bias function setup symfunc colvar |
| 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 | GYRATION RANDOM_EXCHANGES METAD COORDINATION MOLINFO ALPHARMSD GROUP PARABETARMSD LOWER_WALLS UPPER_WALLS PRINT ENERGY ANTIBETARMSD DIHCOR WHOLEMOLECULES | generic core multicolvar bias secondarystructure colvar |
| 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 | GYRATION PBMETAD DISTANCE METAD COORDINATION ALPHABETA COM PRINT ENERGY TORSION INCLUDE | vatom generic multicolvar bias colvar |
| 21.018 | Localized Volume-based Metadynamics | bio | LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification | Riccardo Capelli | COORDINATION HISTOGRAM ENDPLUMED CONVERT_TO_FES WHOLEMOLECULES FIXEDATOM GROUP COM UPPER_WALLS RMSD FLUSH MATHEVAL DISTANCE POSITION PRINT METAD DUMPGRID READ REWEIGHT_METAD | vatom generic core bias function gridtools colvar |
| 21.016 | MD SAXS GTPase associated center | bio | metadynamics, RNA, folding, SAXS | Giovanni Bussi | GYRATION METAD MOLINFO GROUP CUSTOM LOWER_WALLS ERMSD UPPER_WALLS SAXS PRINT WHOLEMOLECULES INCLUDE | generic core isdb bias colvar function |
| 21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Adriana Pietropaolo | MATHEVAL PBMETAD CONSTANT RESTART BIASVALUE PRINT TORSION WHOLEMOLECULES | generic bias function setup colvar |
| 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 | METAD PATHMSD RESTART LOWER_WALLS UPPER_WALLS PRINT WHOLEMOLECULES | bias generic colvar setup |
| 20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Faidon Brotzakis | EMMI MOLINFO HISTOGRAM GROUP DUMPGRID DISTANCES READ BIASVALUE PRINT CONVERT_TO_FES RMSD WHOLEMOLECULES | generic core isdb multicolvar bias gridtools colvar |
| 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 | RESTRAINT MOLINFO COORDINATION PRINT STATS WHOLEMOLECULES | bias generic colvar function |
| 20.016 | Predicting polymorphism in molecular crystals using orientational entropy | materials | metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy | Pablo Piaggi | LOAD METAD CENTER GROUP VOLUME UPPER_WALLS PRINT INCLUDE | vatom generic core bias setup colvar |
| 20.013 | Improving accuracy of biased Alchemistic simulations | methods | flying Gaussian method, Alchemistic simulations, thermodynamic integration, reweighting | Vojtech Spiwok | TORSION METAD PRINT | bias generic colvar |
| 19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Luigi Bonati | LOAD ENVIRONMENTSIMILARITY Q6 UNITS POSITION ENDPLUMED PRINT ENERGY TORSION | generic envsim setup symfunc colvar |
| 19.055 | Flying Gaussian method | methods | flying Gaussians, alanine dipeptide, peptide bond, Met-enkephalin | Vojtech Spiwok | MATHEVAL DISTANCE METAD COMBINE PRINT TORSION | colvar generic function bias |
| 19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Gareth Tribello | METAD CELL UNITS LOWER_WALLS AROUND UPPER_WALLS ENDPLUMED PRINT FCCUBIC | generic volumes bias setup symfunc 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 | FLUSH METAD COORDINATION RESTART GROUP UNITS LOWER_WALLS UPPER_WALLS POSITION PRINT | generic core bias setup colvar |
| 19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Davide Provasi | DISTANCE METAD CONTACTMAP COM ENDPLUMED PRINT RMSD FUNCPATHMSD WHOLEMOLECULES | vatom generic bias function colvar |
| 19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Silvio Pipolo | METAD CELL PIV LOWER_WALLS UPPER_WALLS PRINT FUNCPATHMSD | generic bias colvar piv function |
| 19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Pratyush Tiwary | DISTANCE COMMITTOR COMBINE RESTART ALPHABETA COM EXTERNAL PRINT TORSION WHOLEMOLECULES | vatom generic multicolvar bias function setup colvar |
| 19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Matteo Salvalaglio | MATHEVAL METAD COMBINE CELL LOWER_WALLS VOLUME UPPER_WALLS ENDPLUMED PRINT ENERGY TORSION | bias colvar generic function |
| 19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Matteo Salvalaglio | GYRATION METAD RESTART DISTANCES ENDPLUMED PRINT COORDINATIONNUMBER | generic multicolvar bias setup symfunc colvar |
| 19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Max Bonomi | EMMI MOLINFO GROUP BIASVALUE PRINT WHOLEMOLECULES | bias generic core isdb |
| 19.004 | MI Ubiquitin | bio | metainference, NMR | Max Bonomi | MOLINFO GROUP CS2BACKBONE PRINT METAINFERENCE RDC WHOLEMOLECULES | generic core isdb |
| 19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Giovanni Bussi | FLUSH RANDOM_EXCHANGES DISTANCE METAD COMBINE MOLINFO DISTANCES LOWER_WALLS ERMSD UPPER_WALLS ANGLE PRINT INCLUDE | generic multicolvar bias function colvar |
| 25.017 | Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity | bio | EMMIVox, cryo-EM, allostery, decamer, filament, ensemble refinement, glutamine synthetase | Samuel Hoff | PRINT EMMIVOX GROUP MOLINFO BIASVALUE WHOLEMOLECULES | bias generic isdb core |
| 24.033 | Transient interactions between the fuzzy coat and the cross-b core of brain-derived Ab42 filaments | bio | CryoEM, MEMMI, Metadynamics, Metainference, Ab42 Fibrils, structural ensemble | Maria Milanesi | DISTANCE PRINT CENTER DUMPATOMS GROUP UPPER_WALLS COORDINATION DUMPMASSCHARGE MOLINFO PARABETARMSD COM BIASVALUE WHOLEMOLECULES RMSD PBMETAD ALPHARMSD EMMI | bias generic isdb core vatom secondarystructure colvar |
| 24.016 | Cryo-EM guided simulations of ribozyme | bio | metainference, cryo-EM | Giovanni Bussi | INCLUDE PRINT EMMIVOX GROUP MOLINFO BIASVALUE WHOLEMOLECULES RESTRAINT ERMSD | bias generic isdb core colvar |
| 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 | DISTANCE PRINT TORSION MATHEVAL METAD COORDINATIONNUMBER MOLINFO BIASVALUE COMMITTOR RESTART RESTRAINT ENERGY FLUSH | bias generic symfunc setup function colvar |
| 23.044 | Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition | materials | metadynamics, interlocked molecules | Luigi Leanza | PRINT ENDPLUMED READ GROUP METAD COMMITTOR CONVERT_TO_FES HISTOGRAM COORDINATION DUMPGRID | bias generic core gridtools colvar |
| 23.039 | Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation | chemistry | metadynamics, ligand dissociation | Eric Beyerle | CENTER DISTANCE PRINT COMBINE UPPER_WALLS METAD DUMPMASSCHARGE MOLINFO FIXEDATOM RESTRAINT | bias generic vatom function colvar |
| 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 | DISTANCE PRINT MATHEVAL READ METAD MOLINFO WHOLEMOLECULES RMSD CONVERT_TO_FES HISTOGRAM REWEIGHT_METAD DUMPGRID | bias generic gridtools function colvar |
| 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 | PRINT DRR TIME METAD UPPER_WALLS LOWER_WALLS UNITS BIASVALUE PATHMSD CUSTOM FLUSH | bias generic drr setup function colvar |
| 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 | PRINT METAD LOWER_WALLS UPPER_WALLS CONTACTMAP WHOLEMOLECULES ENERGY | bias generic colvar |
| 22.039 | Driving and characterizing nucleation of urea and glycine polymorphs in water | bio | metadynamics, nucleation, amino acids, polymorphism | Eric Beyerle | INCLUDE PRINT CENTER MATHEVAL GROUP COMBINE METAD COORDINATIONNUMBER LOAD Q4 Q6 PAIRENTROPY | bias generic core vatom gridtools symfunc setup function |
| 22.024 | Conformational Entropy as a Potential Liability of Computationally Designed Antibodies | bio | metadynamics, conformational entropy, antibody, nanobody | Thomas Löhr | PRINT TORSION ALPHABETA ANTIBETARMSD MOLINFO COM RESTART WHOLEMOLECULES PBMETAD ALPHARMSD | bias generic vatom secondarystructure multicolvar setup colvar |
| 22.009 | Glycosylation in calixarenes capsule | chemistry | Metadynamics, glycosylation, supramolecular catalysis | GiovanniMaria Piccini | DISTANCE PRINT MATHEVAL BRIDGE GROUP COMBINE FIT_TO_TEMPLATE UPPER_WALLS LOWER_WALLS UNITS METAD COORDINATION ANGLE WHOLEMOLECULES RMSD DISTANCES FLUSH | adjmat generic bias core multicolvar setup function colvar |
| 22.006 | Peptide framework for screening the effects of amino acids on assembly | bio | metadynamics, peptides | Andrew White | INCLUDE PRINT METAD COMBINE GROUP REWEIGHT_BIAS COM DISTANCES CONVERT_TO_FES GYRATION HISTOGRAM DUMPGRID | bias generic core vatom gridtools multicolvar function colvar |
| 22.000 | Amyloid precursor protein processing by human γ-secretase | bio | Bias Exchange Metadynamics, Helix unfolding, coupled binding | Xiaoli Lu | INCLUDE DISTANCE CENTER PRINT ANTIBETARMSD METAD RANDOM_EXCHANGES CONTACTMAP UNITS MOLINFO ALPHARMSD COORDINATION | bias generic vatom secondarystructure setup colvar |
| 21.052 | On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets | materials | Ibuprofen, unbinding, WTmetaD | Matteo Salvalaglio | CENTER DISTANCE PRINT TORSION METAD COORDINATIONNUMBER COMMITTOR ENDPLUMED | bias generic vatom symfunc 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 PRINT TORSION METAD UPPER_WALLS LOWER_WALLS UNITS COM CUSTOM | bias generic vatom setup function colvar |
| 21.019 | Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations | materials | Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen | Matteo Salvalaglio | DISTANCE PRINT TORSIONS MATHEVAL KDE COM | generic vatom gridtools multicolvar function colvar |
| 21.007 | Sampling enhancement by metadynamics driven by machine learning and de novo protein modelling | bio | metadynamics, machine learning, protein folding | Vojtech Spiwok | MATHEVAL COMBINE FIT_TO_TEMPLATE MOLINFO WHOLEMOLECULES POSITION ALPHARMSD | generic colvar secondarystructure function |
| 21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Tarak Karmakar | PRINT OPES_METAD MATHEVAL GROUP UPPER_WALLS LOWER_WALLS LOAD PYTORCH_MODEL FLUSH | bias generic pytorch core setup function opes |
| 20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Adriana Pietropaolo | CENTER PRINT WHOLEMOLECULES PBMETAD COORDINATION | bias generic colvar vatom |
| 19.080 | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | methods | ves, variationally enhanced sampling, vibrational excitation, chemical reactions | Kristof Bal | DISTANCE PRINT BF_CHEBYSHEV EXTERNAL COMBINE UPPER_WALLS TD_GRID COORDINATION LOWER_WALLS UNITS TD_WELLTEMPERED OPT_AVERAGED_SGD ANGLE VES_LINEAR_EXPANSION CONVERT_TO_FES HISTOGRAM FLUSH DUMPGRID | bias generic gridtools setup function colvar ves |
| 19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Giovanni Bussi | DISTANCE LOWER_WALLS WHOLEMOLECULES RESTRAINT ENDPLUMED COORDINATION | bias generic colvar |
| 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 | PRINT METAD LOWER_WALLS UPPER_WALLS COORDINATIONNUMBER GYRATION ENDPLUMED ENERGY DISTANCES | bias generic multicolvar symfunc colvar |
| 19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Mattia Bernetti | PRINT METAD LOWER_WALLS UPPER_WALLS WHOLEMOLECULES PATHMSD | bias generic colvar |
| 19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Kim E. Jelfs | DISTANCE PRINT CENTER GROUP LOWER_WALLS UPPER_WALLS METAD COM RESTART | bias generic core vatom setup colvar |
| 19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Gareth Tribello | CENTER GROUP UNITS FOURIER_TRANSFORM FIND_CONTOUR_SURFACE MORE_THAN FCCUBIC MULTICOLVARDENS DUMPGRID | core vatom fourier gridtools setup symfunc function contour |
| 19.048 | Understanding Ligand Binding Selectivity in a Prototypical GPCR Family | bio | metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | DISTANCE PRINT MATHEVAL METAD UPPER_WALLS LOWER_WALLS BIASVALUE COM WHOLEMOLECULES CONSTANT | bias generic vatom function colvar |
| 19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Carlo Camilloni | INCLUDE DISTANCE CENTER PRINT GROUP UPPER_WALLS MOLINFO BIASVALUE WHOLEMOLECULES RMSD RESTRAINT STATS ENDPLUMED SAXS | bias generic isdb core vatom function colvar |
| 19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Michele Invernizzi | PRINT TORSION METAD VES_DELTA_F UNITS LOAD RESTART POSITION ENDPLUMED ENERGY | bias generic setup colvar ves |
| 25.012 | A Machine Learning-Driven, Probability-Based Approach to Enzyme Catalysis | bio | enzyme catalysis, transition state, structure-activity relationship, free energy surface, reaction mechanism, water, alpha-amylase, sugar, QM/MM MD, OPES, committor function, machine learning | Sudip Das | COMBINE PRINT COORDINATION OPES_METAD ENERGY MATHEVAL LOAD POSITION DISTANCE CUSTOM FLUSH INCLUDE TORSION CELL UNITS BIASVALUE | opes function setup colvar generic bias |
| 24.035 | Data efficient machine learning potentials for modeling catalytic reactivity via active learning and enhanced sampling | chemistry | opes, catalysis, ammonia, machine learning potentials | Luigi Bonati | PRINT COORDINATION OPES_METAD DISTANCE GROUP CUSTOM COMMITTOR RESTART UNITS LOWER_WALLS UPPER_WALLS | core function opes colvar setup generic bias |
| 24.032 | DeepLNE++ | methods | PATHCV, OPES | Thorben Fröhlking | COMBINE PRINT COORDINATION OPES_METAD ENERGY LOAD DISTANCE CUSTOM GROUP TORSION | core opes function setup colvar generic |
| 24.029 | Combination of OPES and OPES-Explore | methods | OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin | Dhiman Ray | COMBINE PRINT FIT_TO_TEMPLATE DISTANCE POSITION CUSTOM INCLUDE PYTORCH_MODEL COORDINATION OPES_METAD GROUP METAD OPES_METAD_EXPLORE FIXEDATOM UNITS CONTACTMAP UPPER_WALLS CENTER MATHEVAL ENERGY FLUSH WHOLEMOLECULES MOLINFO BIASVALUE LOWER_WALLS RMSD ENDPLUMED | pytorch core opes function colvar setup generic vatom bias |
| 24.011 | Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble | methods | committor, machine learning | Peilin Kang | PRINT POSITION DISTANCE CUSTOM INCLUDE COORDINATION GROUP TORSION UNITS UPPER_WALLS MATHEVAL ENERGY CELL WHOLEMOLECULES MOLINFO LOAD BIASVALUE LOWER_WALLS RMSD ENDPLUMED | core function colvar setup generic bias |
| 24.004 | Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables | materials | metadynamics, nucleation, machine learning | Ziyue Zou | PRINT LOAD GROUP METAD INCLUDE RESTART | setup bias generic core |
| 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 | PRINT COMBINE OPES_METAD DISTANCE CUSTOM FLUSH COMMITTOR TORSION UNITS LOWER_WALLS UPPER_WALLS | opes function setup colvar generic bias |
| 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 | PRINT OPES_METAD DISTANCE COORDINATIONNUMBER GROUP FLUSH FIXEDATOM ZDISTANCES UNITS UPPER_WALLS | core symfunc opes colvar multicolvar setup generic vatom bias |
| 23.036 | Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? | bio | NaCl, nucleation, metadynamics | Ruiyu Wang | COMBINE Q6 PRINT MATHEVAL ENERGY COORDINATIONNUMBER METAD VOLUME Q4 | symfunc function colvar generic bias |
| 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 | PRINT CENTER MATHEVAL DISTANCE METAD LOWER_WALLS BIASVALUE CONSTANT UPPER_WALLS WHOLEMOLECULES | function colvar generic vatom bias |
| 23.027 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, DFS, Q3, Pair Entropy | Aaron Finney | HISTOGRAM PRINT DUMPGRID CONTACT_MATRIX Q3 LOAD DFSCLUSTERING COORDINATIONNUMBER GROUP DENSITY FIXEDATOM LOCAL_Q3 CLUSTER_NATOMS UNITS RESTRAINT CLUSTER_DISTRIBUTION LOCAL_AVERAGE AROUND | core symfunc volumes adjmat gridtools setup generic vatom clusters bias |
| 23.024 | Permutationally Invariant Networks for Enhanced Sampling (PINES) | methods | collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent | Nicholas Herringer | PRINT LOAD PBMETAD | setup bias 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 | HISTOGRAM PRINT DUMPGRID OPES_EXPANDED ECV_UMBRELLAS_LINE RESTART LOWER_WALLS ENVIRONMENTSIMILARITY UPPER_WALLS | opes gridtools setup generic envsim bias |
| 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 | PRINT METAD TORSION READ EXTRACV | bias generic colvar |
| 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 | PRINT DRR PATHMSD CUSTOM METAD FLUSH BIASVALUE | function colvar drr generic bias |
| 22.029 | Angiotensin-1-7_Metadynamics | bio | Metadynamics, Angiotensin-(1-7), peptide | L.-América Chi | PRINT COORDINATION GYRATION GROUP METAD FLUSH LOWER_WALLS UPPER_WALLS WHOLEMOLECULES | core 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 | COM PRINT DISTANCE PATHMSD METAD FUNNEL FUNNEL_PS LOWER_WALLS UPPER_WALLS WHOLEMOLECULES | funnel colvar generic vatom bias |
| 22.004 | Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques | chemistry | reaction discovery, OPES, collective variables | Umberto Raucci | COM PRINT COORDINATION MATHEVAL OPES_METAD LOAD DISTANCE CUSTOM GROUP OPES_METAD_EXPLORE PYTORCH_MODEL UNITS LOWER_WALLS UPPER_WALLS | core pytorch function opes colvar setup generic vatom bias |
| 21.042 | Peptoid-mediated Au nanocrystal growth | materials | parallel-bias metadynamics, peptoid, Au | Xin Qi | COM PRINT MOLINFO PBMETAD DISTANCE GYRATION UPPER_WALLS | bias generic vatom colvar |
| 21.039 | Deep learning the slow modes for rare events sampling | methods | collective variables, machine learning, slow modes, deep-tica, opes | Luigi Bonati | PRINT COMBINE DISTANCE VOLUME INCLUDE PYTORCH_MODEL OPES_METAD GROUP TORSION UNITS CONTACTMAP OPES_EXPANDED ENERGY FLUSH WHOLEMOLECULES Q6 MOLINFO LOAD ECV_MULTITHERMAL ENVIRONMENTSIMILARITY RMSD ENDPLUMED | pytorch core symfunc opes function colvar setup generic envsim |
| 21.021 | ATLAS | methods | Machine Learning, Metadynamics | Federico Giberti | PRINT COORDINATION MATHEVAL DUMPATOMS DISTANCE COORDINATIONNUMBER METAD GYRATION GROUP TORSION BIASVALUE WHOLEMOLECULES UNITS | core symfunc function colvar setup generic bias |
| 21.014 | how to determine statistically accurate conformational ensembles | bio | metadynamics, metainference, errors, cv, SAXS, ensemble determination | Cristina Paissoni | PRINT CENTER SAXS MOLINFO ANTIBETARMSD PBMETAD ALPHABETA GYRATION METAD TORSION STATS ENSEMBLE BIASVALUE CONTACTMAP WHOLEMOLECULES | multicolvar colvar function secondarystructure generic vatom isdb bias |
| 21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Tarsis Ferreira | HISTOGRAM PRINT DUMPGRID COORDINATION MOLINFO ENERGY RANDOM_EXCHANGES PUCKERING REWEIGHT_METAD DISTANCE GROUP METAD INCLUDE LOWER_WALLS UPPER_WALLS WHOLEMOLECULES | core colvar gridtools generic bias |
| 20.026 | Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor | bio | Metadynamics, Umbrella sampling | Brandon Peters | HISTOGRAM PRINT DUMPGRID REWEIGHT_METAD METAD CONVERT_TO_FES RESTRAINT MULTI_RMSD | colvar bias generic gridtools |
| 20.015 | Rational design of ASCT2 inhibitors using an integrated experimental-computational approach | bio | ASCT2 transporter, small-molecules, cryo-EM, metainference | Max Bonomi | PRINT MOLINFO LOAD DUMPATOMS GROUP EMMIVOX BIASVALUE WHOLEMOLECULES | core setup generic isdb bias |
| 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 | PARABETARMSD COMBINE PRINT INCLUDE ALPHARMSD COORDINATION DIHCOR GROUP TORSION ANTIBETARMSD FLUSH ENSEMBLE WHOLEMOLECULES MOLINFO PBMETAD GYRATION CS2BACKBONE METAINFERENCE STATS ENDPLUMED | core multicolvar function colvar secondarystructure generic isdb bias |
| 20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Luigi Bonati | PRINT COM OPES_METAD MATHEVAL LOAD DISTANCE GROUP FLUSH TORSION PYTORCH_MODEL UNITS LOWER_WALLS UPPER_WALLS ENDPLUMED | core pytorch function opes setup colvar generic vatom 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 PRINT ENERGY MOLINFO DISTANCE GYRATION GROUP METAD UPPER_WALLS | core colvar generic vatom bias |
| 19.078 | Iterative unbiasing of quasi-equilibrium sampling | methods | metadynamics, reweighting | Federico Giberti | PRINT REWEIGHT_BIAS MATHEVAL DUMPATOMS DISTANCE COORDINATIONNUMBER METAD COLLECT_FRAMES BIASVALUE UNITS | symfunc function colvar setup generic bias landmarks |
| 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 METAD UPPER_WALLS | bias generic vatom colvar |
| 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 DISTANCE GROUP TORSION RESTRAINT | core colvar generic vatom bias |
| 19.027 | Multithermal-multibaric simulations using VES | methods | ves, Wang Landau, multicanonical, liquid sodium, density anomaly | Pablo Piaggi | HISTOGRAM COMBINE REWEIGHT_BIAS PRINT DUMPGRID VES_LINEAR_EXPANSION ENERGY OPT_AVERAGED_SGD REWEIGHT_TEMP_PRESS OPT_DUMMY AVERAGE CONVERT_TO_FES RESTART READ TD_MULTICANONICAL BF_LEGENDRE UNITS | function gridtools colvar setup generic ves bias |
| 19.025 | Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide | bio | metainference, NMR, protein dynamics, force-fields | Carlo Camilloni | PRINT WHOLEMOLECULES MOLINFO BIASVALUE PBMETAD GYRATION CS2BACKBONE METAINFERENCE FLUSH TORSION STATS ENSEMBLE RDC JCOUPLING ENDPLUMED | function colvar generic isdb bias |
| 19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Haochuan Chen | PRINT DRR TORSION | drr generic colvar |
| 19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Kresten Lindorff-Larsen | COMBINE PRINT MOLINFO ALPHABETA METAD FLUSH COMMITTOR | multicolvar generic bias function |
| 19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Matteo Salvalaglio | PRINT CENTER DISTANCE METAD COMMITTOR TORSION LOWER_WALLS UPPER_WALLS | bias generic vatom colvar |
| 19.013 | RNA FF FITTING | methods | force field, RNA | Giovanni Bussi | MATHEVAL MOLINFO PUCKERING INCLUDE TORSION BIASVALUE CONSTANT | bias generic function colvar |
| 19.006 | Flying Gaussian proof | methods | flying Gaussians, alanine dipeptide | Vojtech Spiwok | METAD PRINT TORSION | bias generic colvar |
| 25.000 | Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer | bio | metadynamics, pathCV | Sahithya Sridharan Iyer | MOLINFO DISTANCE COM PRINT METAD FUNCPATHGENERAL RESTART WHOLEMOLECULES GROUP UPPER_WALLS | bias setup vatom generic function core colvar |
| 24.030 | NMR guided simulation of dsRBD | bio | Metainference, NMR, protein dynamics | Debadutta Patra | ENSEMBLE MOLINFO DISTANCE FLUSH PRINT ALPHABETA RDC METAINFERENCE WHOLEMOLECULES GROUP STATS | generic function multicolvar isdb core colvar |
| 24.027 | Proline cis and trans subensembles of a disordered peptide | bio | intrinsically disordered proteins, proline cis trans isomerisation, metadynamics, collective variables | Alice Pettitt | GYRATION MOLINFO DISTANCE FLUSH PBMETAD PARABETARMSD PRINT ANTIBETARMSD ENDPLUMED TORSION COMBINE INCLUDE ALPHARMSD COORDINATION DIHCOR WHOLEMOLECULES GROUP | secondarystructure bias generic function multicolvar core colvar |
| 24.024 | Host-Guest binding free energies à la carte, an automated OneOPES protocol | bio | OneOPES, ligand binding, binding free energy,SAMPL challenge, host-guest | Valerio Rizzi | OPES_METAD_EXPLORE ANGLE FIXEDATOM DISTANCE ECV_MULTITHERMAL LOWER_WALLS CENTER PRINT OPES_EXPANDED MATHEVAL TORSION ENDPLUMED COORDINATION ENERGY FIT_TO_TEMPLATE WHOLEMOLECULES GROUP UPPER_WALLS | bias vatom generic function core colvar opes |
| 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 |
| 24.012 | Molecular simulations to investigate the impact of N6-methylation in RNA recognition | bio | metadynamics, alchemistry, RNA modification, RNA:protein interactions | Giovanni Bussi | GHBFIX MOLINFO DISTANCE COM BIASVALUE LOWER_WALLS CENTER PRINT DEBUG COMBINE COORDINATION METAD GROUP UPPER_WALLS | bias vatom generic function core colvar |
| 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 | MOLINFO FUNCPATHMSD DISTANCE PATHMSD LOWER_WALLS PRINT CONTACTMAP METAD INCLUDE ALPHARMSD UPPER_WALLS | secondarystructure bias generic function colvar |
| 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 | MOLINFO DISTANCE PRINT COMMITTOR OPES_METAD WRAPAROUND MATHEVAL POSITION ENERGY WHOLEMOLECULES BIASVALUE OPES_METAD_EXPLORE COM LOWER_WALLS CENTER UNITS UPPER_WALLS FLUSH CUSTOM ENDPLUMED TORSION COORDINATION FIT_TO_TEMPLATE GROUP | bias setup vatom generic function core colvar opes |
| 23.028 | Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process | chemistry | Ammonia decomposition; Dynamics;OPES; Neural Network potential | Manyi Yang | DISTANCES FIXEDATOM DISTANCE FLUSH COORDINATIONNUMBER OPES_METAD COM PRINT ZDISTANCES LOWER_WALLS CUSTOM MATHEVAL UNITS ENERGY COMMITTOR GROUP UPPER_WALLS | bias setup vatom generic function multicolvar core colvar opes symfunc |
| 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 DISTANCE PRINT COMBINE COMMITTOR FIXEDATOM ANGLE OPES_METAD PYTORCH_MODEL MATHEVAL ENERGY WHOLEMOLECULES RMSD LOWER_WALLS CENTER UPPER_WALLS CONTACTMAP CUSTOM ENDPLUMED COORDINATION INCLUDE FIT_TO_TEMPLATE GROUP | bias vatom generic function pytorch core colvar opes |
| 22.028 | N-glycan conformer distributions in atomistic simulation | bio | REST2, RECT, N-glycan, pucker | Isabell Grothaus | MOLINFO READ CONVERT_TO_FES PRINT DUMPGRID TORSION PUCKERING HISTOGRAM METAD | generic gridtools bias colvar |
| 22.022 | Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir | bio | RMSD, protein-ligand interactions | Isabell Grothaus | PRINT RMSD | 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 | UPPER_WALLS MOLINFO ANGLE DISTANCE FLUSH PRINT ALPHABETA TORSION COORDINATION ALPHARMSD WHOLEMOLECULES METAD | secondarystructure bias generic multicolvar colvar |
| 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 | UPPER_WALLS DISTANCE COORDINATIONNUMBER LOWER_WALLS PRINT COORDINATION COMBINE METAD | bias generic function colvar symfunc |
| 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 | UPPER_WALLS MOLINFO DISTANCE COM PRINT EMMI RESTART WHOLEMOLECULES GROUP BIASVALUE | bias setup vatom generic isdb core colvar |
| 21.027 | EGFR activating mutations mechanism | bio | metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA | Francesco Gervasio | UPPER_WALLS MOLINFO DISTANCE LOWER_WALLS PRINT CONTACTMAP MATHEVAL INCLUDE ALPHARMSD ENERGY WHOLEMOLECULES METAD | secondarystructure bias generic function colvar |
| 21.025 | Computational and biochemical analysis of type IV pilus dynamics and stability | bio | molecular dynamics, calcium binding, Type IV pilus | Yasaman Karami | UPPER_WALLS DISTANCE LOWER_WALLS PRINT | generic colvar bias |
| 21.017 | All-atom simulations of the Vav1 AD construct | bio | metadynamics, parallel-bias, well-tempered | Simone Orioli | MOLINFO PBMETAD REWEIGHT_BIAS PRINT CONTACTMAP ALPHABETA ALPHARMSD RESTART WHOLEMOLECULES GROUP METAD | secondarystructure bias setup generic multicolvar core colvar |
| 21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Kresten Lindorff-Larsen | EEFSOLV GYRATION MOLINFO FLUSH PBMETAD SAXS PRINT CENTER ALPHARMSD METAINFERENCE WHOLEMOLECULES GROUP BIASVALUE | secondarystructure bias vatom generic isdb core 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_UMBRELLAS_LINE VOLUME ECV_MULTITHERMAL_MULTIBARIC OPT_AVERAGED_SGD PRINT Q6 OPES_EXPANDED MATHEVAL ENERGY TD_UNIFORM ENVIRONMENTSIMILARITY BF_LEGENDRE RESTART VES_LINEAR_EXPANSION UPPER_WALLS | ves bias setup generic function colvar opes symfunc envsim |
| 20.032 | Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil | materials | clustering, conformational isomers | Matteo Salvalaglio | ENDPLUMED TORSION PRINT | generic colvar |
| 20.028 | Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane | bio | metadynamics, KRas-4B, anionic membrane | Huixia Lu | DISTANCE PRINT CENTER FIT_TO_TEMPLATE RESTART METAD | bias setup vatom generic colvar |
| 20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Vojtech Spiwok | TORSION PRINT METAD | generic colvar bias |
| 20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Max Bonomi | GYRATION MOLINFO PBMETAD PRINT ALPHABETA COORDINATION INCLUDE DIHCOR WHOLEMOLECULES | generic colvar bias multicolvar |
| 20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Carlo Camilloni | ENSEMBLE GYRATION MOLINFO DISTANCE FLUSH PBMETAD SAXS PRINT CENTER TORSION ALPHABETA METAINFERENCE WHOLEMOLECULES STATS | bias vatom generic function multicolvar isdb colvar |
| 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 | MOLINFO PATHMSD PRINT METAD RESTART WHOLEMOLECULES GROUP UPPER_WALLS | bias setup generic core colvar |
| 19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Matteo Salvalaglio | DISTANCE PRINT CENTER ENDPLUMED INCLUDE GROUP | core generic colvar vatom |
| 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 PRINT TORSION INCLUDE METAD | generic colvar 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 | READ REWEIGHT_BIAS DISTANCE_FROM_CONTOUR CONVERT_TO_FES PRINT DUMPGRID METAD COMBINE RESTART HISTOGRAM UPPER_WALLS | bias setup generic contour function gridtools |
| 19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Carlo Camilloni | UPPER_WALLS MOLINFO FLUSH PBMETAD CS2BACKBONE LOWER_WALLS PRINT ANTIBETARMSD ENDPLUMED ALPHABETA RESTART WHOLEMOLECULES GROUP BIASVALUE | secondarystructure bias setup generic multicolvar isdb core |
| 19.032 | Chemical reaction in solution using path collective variables based on coordination patterns | chemistry | chemical reactions, solutions, metadynamics, coordination patterns | Fabio Pietrucci | DISTANCES UPPER_WALLS FLUSH PRINT PATH RESTART METAD | bias mapping setup generic multicolvar |
| 19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Glen Hocky | DISTANCE EDS PRINT TORSION COMBINE RESTRAINT | bias eds generic function colvar |
| 19.009 | RNA tetraloops folding | bio | metadynamics, RNA, folding | Giovanni Bussi | ERMSD MOLINFO PRINT ENDPLUMED METAD WHOLEMOLECULES RMSD | generic colvar bias |
| 19.005 | Cmyc small molecule interaction | bio | metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP | Gabriella Heller | GYRATION MOLINFO DISTANCE PBMETAD CS2BACKBONE PRINT CENTER ALPHABETA COORDINATION INCLUDE METAINFERENCE WHOLEMOLECULES GROUP | bias vatom generic multicolvar isdb core colvar |
| 25.014 | Atomic resolution ensembles of intrinsically disordered and multi-domain proteins with Alphafold | bio | bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement | Vincent Schnapka | BAIES GROUP BIASVALUE PRINT | generic isdb bias core |
| 25.010 | Kinetic rates calculation with Ratchet&Pawl MD | methods | kinetics, ligand binding, ABMD, ratchet&pawl MD | Riccardo Capelli | COMMITTOR GROUP WHOLEMOLECULES ABMD COM FLUSH PRINT DISTANCE | vatom colvar generic bias core |
| 25.008 | Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting | methods | metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting | Dhiman Ray | CUSTOM MOLINFO GROUP PYTORCH_MODEL ENDPLUMED WHOLEMOLECULES ENERGY RMSD TORSION UNITS METAD UPPER_WALLS PRINT LOWER_WALLS POSITION OPES_METAD BIASVALUE DISTANCE | opes pytorch function colvar generic setup bias core |
| 24.028 | All-atom simulations of RNA-membrane interactions | bio | metadynamics, membrane, RNA | Giovanni Bussi | GHOST COMBINE PUCKERING CENTER DISTANCES MOLINFO GROUP GYRATION SORT WHOLEMOLECULES METAD MATHEVAL PRINT UPPER_WALLS LOWER_WALLS POSITION DISTANCE | vatom multicolvar function colvar generic bias core |
| 24.026 | Constant pH metadynamics of RNA oligomers | bio | metadynamics, pH, RNA | Giovanni Bussi | PUCKERING MOLINFO RESTART TORSION METAD PRINT | setup bias colvar generic |
| 24.022 | Integrating Path Sampling with Enhanced Sampling for Rare-event Kinetics | methods | OPES Flooding, Weighted Ensemble, Metadynamics, Kinetics, Infrequent Metadynamics, Integrated Sampling | Dhiman Ray | COMBINE ENDPLUMED WHOLEMOLECULES PRINT CUSTOM FIXEDATOM TORSION OPES_METAD DISTANCE FIT_TO_TEMPLATE MOLINFO UPPER_WALLS CENTER GROUP COMMITTOR COORDINATION RMSD METAD CONTACTMAP MATHEVAL ANGLE | vatom opes function colvar generic bias core |
| 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 | MOLINFO COORDINATION PYTORCH_MODEL WHOLEMOLECULES RMSD METAD DRR UPPER_WALLS PRINT FLUSH LOWER_WALLS | pytorch drr colvar generic bias |
| 24.010 | Oxytocin metadynamics simulation | bio | metadynamics, oxytocin, peptide | Jan Beránek | RESTART WHOLEMOLECULES TORSION METAD FLUSH PRINT | bias colvar setup generic |
| 24.009 | Weighted Shape Gaussian Mixture Models | bio | metadynamics, clustering | Glen Hocky | GROUP UNITS TORSION METAD PRINT | colvar generic setup bias core |
| 24.006 | Water vapor condensation | chemistry | metadynamics, homogeneous condensation, chemical potential | Shenghui Zhong | CLUSTER_PROPERTIES CLUSTER_NATOMS DFSCLUSTERING UNITS METAD COORDINATIONNUMBER UPPER_WALLS PRINT CONTACT_MATRIX | symfunc clusters setup generic bias adjmat |
| 24.005 | Learning Markovian Dynamics with Spectral Maps | methods | spectral map, collective variables, machine learning | Jakub Rydzewski | UNITS PRINT DISTANCE BIASVALUE CUSTOM | generic function colvar setup bias |
| 23.040 | Supramolecular capsules assembly dynamics | chemistry | Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics | Riccardo Capelli | CENTER DISTANCES GROUP WHOLEMOLECULES COM UNITS METAD FLUSH PRINT POSITION DISTANCE CUSTOM | vatom multicolvar function setup generic colvar bias core |
| 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 | SAXS CENTER MOLINFO ENSEMBLE GROUP RMSD DISTANCE UPPER_WALLS PRINT WRAPAROUND BIASVALUE STATS | vatom isdb function colvar generic bias core |
| 23.023 | Rational design of novel biomimetic sequence-defined polymers for mineralization applications | methods | metadynamics, surface binding, biomimetic mineralization | Kaylyn Torkelson | COORDINATION COM UPPER_WALLS PRINT GYRATION PBMETAD DISTANCE | bias vatom colvar generic |
| 23.020 | FEP simulations of ATOX1 homodimer | chemistry | parallel bias metadynamics, FEP, free-energy of metal ion dissociation | Adriana Pietropaolo | WHOLEMOLECULES PBMETAD CONSTANT MATHEVAL PRINT ANGLE BIASVALUE DISTANCE | bias function colvar generic |
| 23.015 | MPCs aggregation | bio | opes_explore, dimerization, MPCs, self-assembly | Vikas Tiwari | CENTER GROUP COORDINATION WHOLEMOLECULES OPES_METAD_EXPLORE COM METAD UPPER_WALLS PRINT LOWER_WALLS DISTANCE CUSTOM | vatom opes function colvar generic bias core |
| 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 | WHOLEMOLECULES CONSTANT METAD MATHEVAL UPPER_WALLS PRINT LOWER_WALLS BIASVALUE DISTANCE | bias function colvar generic |
| 23.007 | Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains | bio | metadynamics, peptoids, parallel-bias metadynamics | Jim Pfaendtner | RESTRAINT INCLUDE COORDINATION WHOLEMOLECULES COM TORSION PRINT GYRATION PBMETAD | bias vatom colvar generic |
| 22.036 | Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction | bio | Well-tempered MetaDynamics with Hamiltonian Replica Exchange | Miroslav Krepl | COMBINE GHBFIX MOLINFO GROUP COORDINATION LOAD METAD FLUSH UPPER_WALLS PRINT BIASVALUE CUSTOM | generic function setup colvar bias core |
| 22.030 | Mixing physics across temperatures with generative artificial intelligence | methods | REMD, Generative AI, DDPM | Yihang Wang | TORSION WHOLEMOLECULES PRINT | colvar generic |
| 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 DISTANCE PRINT | vatom colvar generic |
| 21.050 | N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity | methods | bio | Isabell Louise Grothaus | CENTER DISTANCE PRINT | vatom colvar generic |
| 21.049 | Multiple-path-metadynamics and PathMaps | methods | path-CV, metadynamics, multiple-walker, multiple paths, pathmap | Alberto Pérez-de-Alba-Ortíz | COMBINE MOVINGRESTRAINT RESTRAINT ENSEMBLE LOAD UNITS TORSION CONSTANT METAD UPPER_WALLS PRINT LOWER_WALLS CUSTOM | generic function colvar setup bias |
| 21.044 | NaCl nucleation | chemistry | metadynamics, DFS clustering | Aaron Finney | COMBINE HISTOGRAM Q6 GROUP MFILTER_MORE CLUSTER_NATOMS DUMPGRID CLUSTER_DISTRIBUTION DFSCLUSTERING LOCAL_Q6 INSPHERE FIXEDATOM METAD COORDINATIONNUMBER CONTACT_MATRIX PRINT | vatom symfunc gridtools volumes multicolvar clusters function generic bias adjmat core |
| 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 FIXEDATOM TORSION METAD PRINT | bias vatom colvar generic |
| 21.038 | Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics | materials | metadynamics, SGOOP, nucleation, urea | Ziyue Zou | COMBINE VOLUME CENTER GROUP INCLUDE ENERGY LOAD METAD COORDINATIONNUMBER PRINT | vatom symfunc function colvar generic setup bias core |
| 21.035 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, interface | Aaron Finney | RESTRAINT GROUP LOAD FIXEDATOM PRINT DISTANCE | vatom setup generic colvar bias core |
| 21.033 | Multiple-path-metadynamics applied to DNA base-pairing transitions | bio | path-CV, metadynamics, multiple-walker, dna | Alberto Pérez-de-Alba-Ortíz | COMBINE MOVINGRESTRAINT RESTRAINT INCLUDE CONSTANT METAD UPPER_WALLS PRINT | bias function generic |
| 21.011 | CmuMD simulations of NaCl(aq) at graphite | chemistry | CmuMD, DFS clustering | Aaron Finney | RESTRAINT GROUP CLUSTER_NATOMS MFILTER_MORE MULTICOLVARDENS CLUSTER_DISTRIBUTION DUMPGRID DFSCLUSTERING LOAD FIXEDATOM AROUND COORDINATIONNUMBER CONTACT_MATRIX PRINT DENSITY | vatom symfunc gridtools volumes multicolvar clusters setup generic bias adjmat 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 DISTANCE PRINT | bias colvar generic |
| 20.024 | Gaussian Mixture Based Enhanced Sampling (GAMBES) | methods | enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias | Jayashrita Debnath | COMBINE DISTANCES GROUP ENERGY LOAD TORSION UNITS UPPER_WALLS PRINT LOWER_WALLS DISTANCE | generic multicolvar function setup colvar bias core |
| 20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Glen Hocky | RESTRAINT GROUP ENERGY UNITS MATHEVAL PRINT GYRATION FISST BIASVALUE DISTANCE | generic function setup colvar bias fisst core |
| 20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Pratyush Tiwary | COMBINE MOLINFO RESTART WHOLEMOLECULES RMSD TORSION METAD UPPER_WALLS PRINT DISTANCE | generic function colvar setup bias |
| 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 | COMBINE ENDPLUMED WHOLEMOLECULES PRINT HISTOGRAM CONVERT_TO_FES FUNCPATHMSD DISTANCE MOLINFO DUMPGRID UPPER_WALLS FLUSH REWEIGHT_METAD ABMD COM READ METAD CONTACTMAP LOWER_WALLS | vatom gridtools function colvar generic bias |
| 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 | MOLINFO GROUP ANTIBETARMSD ENDPLUMED WHOLEMOLECULES ALPHABETA PBMETAD UPPER_WALLS PRINT FLUSH LOWER_WALLS CS2BACKBONE BIASVALUE | isdb secondarystructure multicolvar generic bias core |
| 19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Valerio Rizzi | COMBINE GROUP ENDPLUMED RESTART UNITS METAD COORDINATIONNUMBER FLUSH PRINT EXTERNAL | symfunc function setup generic bias core |
| 19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | MOLINFO ENERGY COM METAD UPPER_WALLS PRINT GYRATION DISTANCE | bias vatom colvar generic |
| 19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Sandro Bottaro | MOLINFO WHOLEMOLECULES RMSD TORSION METAD ERMSD PRINT DISTANCE | bias colvar generic |
| 19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Kim Jelfs | MOVINGRESTRAINT DISTANCES RESTART COM FLUSH PRINT INPLANEDISTANCES | vatom multicolvar setup generic bias |
| 19.044 | Multithermal-multibaric simulations using VES | methods | ves, Wang Landau, multicanonical, water, density anomaly | Pablo Piaggi | COMBINE HISTOGRAM CONVERT_TO_FES AVERAGE VOLUME BF_LEGENDRE VES_LINEAR_EXPANSION DUMPGRID RESTART ENERGY READ TD_MULTITHERMAL_MULTIBARIC REWEIGHT_BIAS PRINT OPT_DUMMY REWEIGHT_TEMP_PRESS OPT_AVERAGED_SGD | gridtools function colvar generic setup bias ves |
| 19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | COMBINE ENERGY UNITS METAD UPPER_WALLS FLUSH PRINT DISTANCE | generic function setup colvar bias |
| 19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Adriana Pietropaolo | WHOLEMOLECULES TORSION CONSTANT METAD MATHEVAL PRINT BIASVALUE | bias function colvar generic |
| 19.003 | EMMI ClpP | bio | metainference, cryo-EM | Max Bonomi | MOLINFO GROUP PRINT EMMI BIASVALUE | isdb bias core generic |
| 25.006 | Characterizing the conformational ensemble of PROTAC degraders in solutions via atomistic simulations | methods | Enhanced sampling, Atomistic simulations, Conformational ensemble, PROTACs, Targeted Protein Degradation, Chamelonic molecules | Shikshya Bhusal, Omar Valsson | RESTART PBMETAD DISTANCE VOLUME PRINT GYRATION CENTER INCLUDE ENERGY READ TORSION | generic vatom colvar setup bias |
| 25.001 | RNA G-quadruplex folding with ST-metaD protocol | bio | RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | MOLINFO ERMSD METAD COMBINE WHOLEMOLECULES | colvar generic function bias |
| 24.036 | Leveraging cryptic ligand envelopes through enhanced molecular simulations | bio | HREX, conformational heterogeneity, drug discovery, ligand binding, plitidepsin, aplidin, ligand-target complexes, cryptic ligand envelope | Francesco Colizzi | DISTANCE DUMPGRID PRINT CONVERT_TO_FES ANGLE GROUP COORDINATION HISTOGRAM TORSION WHOLEMOLECULES | colvar core generic gridtools |
| 24.023 | Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21. A Machine-Learning-Aided Enhanced Sampling Study | bio | RNA, miRNA, OneOPES, ligand binding, conformational changes | Valerio Rizzi | RESTART DISTANCE PRINT COMBINE CUSTOM GROUP ENERGY COORDINATION OPES_EXPANDED OPES_METAD_EXPLORE ECV_MULTITHERMAL TORSION | generic function opes colvar setup core |
| 24.002 | Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes | chemistry | metadynamics, ligand design, solvent extraction | Xiaoyu Wang | RESTART PRINT UNITS METAD TORSION | setup colvar generic bias |
| 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 | PRINT BIASVALUE MOLINFO GHBFIX COORDINATION ERMSD METAD COMBINE WHOLEMOLECULES | colvar generic function bias |
| 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 | LOWER_WALLS DISTANCE PRINT UNITS CENTER CUSTOM GROUP PYTORCH_MODEL COORDINATION FIT_TO_TEMPLATE PATH OPES_METAD_EXPLORE OPES_METAD TORSION UPPER_WALLS FIXEDATOM WHOLEMOLECULES | generic function vatom pytorch colvar opes mapping setup core bias |
| 23.006 | Transcription factor unbinding | bio | metadynamics, DNA, conformational changes | Malin Lüking | DISTANCE PRINT ALPHARMSD COM MOLINFO CONTACTMAP METAD DUMPFORCES ANGLE | secondarystructure generic vatom colvar bias |
| 23.005 | A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs | bio | metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A | Timothy Clark | RMSD DISTANCE DUMPGRID PRINT CONVERT_TO_FES MOLINFO MATHEVAL READ METAD HISTOGRAM REWEIGHT_METAD WHOLEMOLECULES | generic function colvar bias gridtools |
| 22.041 | Skipping the Replica Exchange Ladder with Normalizing Flows | methods | OPES, alanine, normalizing flows, replica exchange | Michele Invernizzi | PRINT UNITS ENERGY OPES_EXPANDED OPES_METAD ECV_MULTITHERMAL POSITION TORSION ENDPLUMED | setup colvar generic opes |
| 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 | LOWER_WALLS DRMSD PRINT CELL COMMITTOR MATHEVAL CUSTOM UPPER_WALLS METAD | colvar generic function bias |
| 22.015 | Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome | bio | photodynamics, bacteriophytochrome, variationally enhanced sampling | Jakub Rydzewski | PRINT TD_UNIFORM TORSION OPT_AVERAGED_SGD VES_LINEAR_EXPANSION BF_FOURIER | colvar generic ves |
| 22.013 | Ligand dissociation from PreQ1 riboswitch | bio | ligand, RNA, metadynamics, pRAVE | Yihang Wang | RMSD DISTANCE PRINT COMMITTOR COM MOLINFO METAD COORDINATIONNUMBER COMBINE WHOLEMOLECULES | symfunc generic function vatom colvar 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 | METAD LOAD PRINT WHOLEMOLECULES | setup generic bias |
| 22.003 | Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling | methods | opes, metadynamics, reweighting, alanine, muller | Michele Invernizzi | ECV_UMBRELLAS_FILE LOWER_WALLS PBMETAD PRINT UNITS BIASVALUE CUSTOM ENERGY METAD UPPER_WALLS OPES_EXPANDED OPES_METAD_EXPLORE OPES_METAD ECV_MULTITHERMAL POSITION TORSION ENDPLUMED | generic function opes colvar setup bias |
| 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 INCLUDE BF_CUBIC_B_SPLINES OPT_AVERAGED_SGD POSITION BF_CHEBYSHEV BF_WAVELETS PRINT OPT_ADAM VES_OUTPUT_BASISFUNCTIONS COORDINATION METAD VES_LINEAR_EXPANSION DISTANCE BF_GAUSSIANS TD_WELLTEMPERED TD_UNIFORM ENERGY FLUSH UPPER_WALLS BF_LEGENDRE | generic colvar setup bias ves |
| 21.037 | Molecular Dynamics simulations of RBD/hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain | Max Bonomi | RMSD DISTANCE PRINT | colvar generic |
| 21.032 | Metal-coupled folding mechanism to metallothionein | bio | parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination | Manuel-Peris Diaz | PBMETAD UNITS GROUP COORDINATION WHOLEMOLECULES | generic colvar setup core bias |
| 21.029 | Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs | bio | metadynamics, small peptide, machine learning | Pratyush Tiwary | RESTART PRINT MOLINFO EXTERNAL ENERGY FLUSH TORSION | setup colvar generic bias |
| 21.026 | Probing allosteric regulations with coevolution-driven molecular simulations | bio | metadynamics, coevolution, allostery, adenylate cyclase | Francesco Colizzi | DISTANCE PRINT UNITS COM UPPER_WALLS METAD PATHMSD WHOLEMOLECULES | generic vatom colvar setup bias |
| 21.023 | Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling | methods | enhanced sampling, collective variables, machine learning | Jakub Rydzewski | DISTANCE CONSTANT PRINT UNITS BIASVALUE INCLUDE CUSTOM ENERGY METAD TORSION REWEIGHT_METAD | generic function colvar setup bias |
| 21.022 | Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly | materials | parallel bias metadynamics, adsorption, peptide | Xin Qi | LOWER_WALLS DISTANCE PBMETAD PRINT GYRATION COM MOLINFO ENERGY UPPER_WALLS | colvar vatom generic bias |
| 20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Matteo Salvalaglio | LOWER_WALLS PRINT CELL MATHEVAL ENERGY UPPER_WALLS METAD VOLUME | colvar generic function bias |
| 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 | LOWER_WALLS DISTANCE CONSTANT PRINT COM BIASVALUE PROJECTION_ON_AXIS MOLINFO INCLUDE GROUP MATHEVAL FUNCPATHGENERAL CONTACTMAP UPPER_WALLS METAD LOAD WHOLEMOLECULES | generic function vatom colvar setup core bias |
| 19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Jakub Rydzewski | LOWER_WALLS RESTART PRINT UNITS UPPER_WALLS METAD PATHMSD | setup colvar generic bias |
| 19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | DISTANCE PRINT GYRATION COM MOLINFO ENERGY UPPER_WALLS METAD | colvar generic bias vatom |
| 19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Cristina Paissoni | PBMETAD PRINT STATS ENSEMBLE CENTER MOLINFO BIASVALUE INCLUDE GROUP MATHEVAL COORDINATION SAXS ANGLE COMBINE ENDPLUMED WHOLEMOLECULES ALPHABETA | multicolvar generic function vatom colvar isdb core bias |
| 19.056 | maze | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_SIMULATED_ANNEALING PRINT MAZE_OPTIMIZER_BIAS UNITS MAZE_LOSS POSITION | setup maze generic colvar |
| 19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Gareth Tribello | PRINT CELL UNITS UPPER_WALLS METAD ENDPLUMED FCCUBIC | symfunc generic colvar setup bias |
| 19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | DISTANCE RESTART DISTANCES PRINT UNITS FLUSH UPPER_WALLS METAD COMBINE | multicolvar generic function colvar setup bias |
| 19.040 | Optimal Metric for Path Collective Variables | bio | metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path | Francesco Luigi Gervasio | PRINT MATHEVAL METAD TORSION ENDPLUMED | colvar generic function bias |
| 19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Elena Papaleo | LOWER_WALLS PRINT ALPHABETA GYRATION MOLINFO GROUP UPPER_WALLS METAD WHOLEMOLECULES | multicolvar generic colvar core bias |
| 19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Carlo Camilloni | DISTANCE PBMETAD PRINT WHOLEMOLECULES RDC ENSEMBLE CENTER MOLINFO ALPHABETA GROUP DIHCOR METAINFERENCE RESTRAINT UPPER_WALLS TORSION ENDPLUMED DHENERGY STATS | multicolvar generic function vatom colvar isdb core bias |
| 25.005 | Mechanism of Nanocluster Formation from Machine-Learned Potential-based Simulations | chemistry | WT-metadynamics, metal nanoclusters, nucleation, neural network potential, deepMD | Vikas Tiwari, Tarak Karmakar | COORDINATION LOWER_WALLS DISTANCE METAD RESTRAINT GROUP DISTANCES COMBINE ANGLE COM PRINT UPPER_WALLS COORDINATIONNUMBER UNITS FIXEDATOM FLUSH | vatom multicolvar core bias setup colvar symfunc function generic |
| 25.018 | Metainference simulation for dimerization of RNA binding protein | bio | Metainference, Metadynamics, SAXS, protein dimer | Debadutta Patra | WHOLEMOLECULES PBMETAD STATS PRINT CENTER UPPER_WALLS SAXS ENSEMBLE GYRATION DISTANCE FLUSH TORSION METAINFERENCE MOLINFO | bias function generic isdb colvar vatom |
| 25.004 | Machine Learning-Driven Molecular Dynamics Unveil a Bulk Phase Transformation Driving Ammonia Synthesis on Barium Hydride | chemistry | OPES, OPES flooding, Catalysis, Ammonia Synthesis | Axel Tosello Gardini | ZDISTANCES COORDINATIONNUMBER UNITS CUSTOM OPES_METAD PRINT UPPER_WALLS DISTANCES COMMITTOR DISTANCE FLUSH FIXEDATOM GROUP | bias function multicolvar opes generic colvar symfunc vatom core setup |
| 25.003 | Surrogate Model CV | methods | Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding | Sompriya Chatterjee | WHOLEMOLECULES ENERGY MATHEVAL CUSTOM COMBINE OPES_METAD ENDPLUMED PRINT GROUP PYTORCH_MODEL COMMITTOR TORSION DISTANCE MOLINFO | pytorch function opes generic core colvar |
| 24.034 | Umbrella sampling of ion in transporter SLC26A7 | bio | umbrella sampling, transporter, ions | Xiaoli Lu | POSITION PRINT UNITS RESTRAINT | generic bias colvar setup |
| 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 | WHOLEMOLECULES METAD PRINT CENTER UPPER_WALLS FIT_TO_TEMPLATE DISTANCES SHADOW WRAPAROUND POSITION GROUP MOLINFO | bias multicolvar generic isdb colvar core vatom |
| 23.026 | Machine Learning Nucleation Collective Variables with Graph Neural Networks | chemistry | Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks | Florian Dietrich | LOWER_WALLS MFILTER_MORE COORDINATIONNUMBER METAD COMBINE PRINT Q6 LOCAL_Q6 MOVINGRESTRAINT GROUP | bias function multicolvar generic core symfunc |
| 23.025 | Probing ion binding to G-quadruplexes and related events | chemistry | metadynamics, repulsive potential, nucleic acids, G-quadruplexes | Marcelo Poleto | LOWER_WALLS WHOLEMOLECULES MATHEVAL UNITS METAD RESTART PRINT DUMPATOMS COM FIT_TO_TEMPLATE UPPER_WALLS DISTANCES GROUP WRAPAROUND POSITION FLUSH DISTANCE | bias function multicolvar generic core colvar vatom setup |
| 22.045 | Binding mode and mechanism of enzymatic polyethylene terephthalate degradation | bio | metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation | Francesco Colizzi | LOWER_WALLS WHOLEMOLECULES METAD PRINT UPPER_WALLS COM MOVINGRESTRAINT DISTANCE ANGLE | vatom generic bias colvar |
| 22.044 | Colloid Crystallisation Analyses | materials | Q4, Q6, Pair Entropy, DFS | Aaron Finney | LOCAL_AVERAGE MFILTER_LESS COORDINATIONNUMBER MFILTER_MORE LOCAL_Q4 COMBINE CLUSTER_NATOMS PRINT Q6 DFSCLUSTERING GROUP LOCAL_Q6 Q4 CONTACT_MATRIX | function multicolvar adjmat clusters generic core symfunc |
| 22.043 | Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES | bio | OPES, RNA, Tetraloop, Folding | Gül Zerze | ECV_MULTITHERMAL WHOLEMOLECULES ENERGY CONTACTMAP ECV_UMBRELLAS_LINE PRINT OPES_EXPANDED | generic colvar opes |
| 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 | WHOLEMOLECULES PBMETAD RESTART PRINT UPPER_WALLS COORDINATION COM EMMI BIASVALUE RMSD TORSION GROUP MOLINFO | bias generic isdb colvar core vatom setup |
| 22.002 | GAMBES_SAMPL5_RATES | other | GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding | Jayashrita Debnath | WHOLEMOLECULES ENERGY MATHEVAL LOAD PRINT CENTER ENDPLUMED COORDINATION FIT_TO_TEMPLATE PYTORCH_MODEL UPPER_WALLS GROUP COMMITTOR FLUSH FIXEDATOM DISTANCE ANGLE | bias function generic colvar pytorch vatom core setup |
| 21.047 | Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations | materials | pair entropy, metadynamics, ves, solids, crystallization | Pablo Piaggi | ENERGY OPT_AVERAGED_SGD VOLUME COMBINE RESTART LOAD METAD PRINT BF_LEGENDRE VES_LINEAR_EXPANSION TD_WELLTEMPERED PAIRENTROPY | bias function ves gridtools generic colvar setup |
| 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 | RANDOM_EXCHANGES METAD PBMETAD ENDPLUMED PRINT INCLUDE TORSION | generic bias colvar |
| 21.020 | Reweighted Jarzynski sampling | methods | free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions | Kristof Bal | REWEIGHT_BIAS CUSTOM COMBINE VES_LINEAR_EXPANSION OPES_METAD TD_WELLTEMPERED FLUSH DUMPGRID UNITS ANN UPPER_WALLS MOVINGRESTRAINT BIASVALUE CONVERT_TO_FES DISTANCE COORDINATIONNUMBER LOAD RESTRAINT REWEIGHT_METAD CONSTANT OPT_AVERAGED_SGD METAD PRINT BF_CHEBYSHEV HISTOGRAM | bias function ves gridtools opes annfunc generic colvar symfunc setup |
| 21.013 | Role of vibrational excitation in heterogeneous catalysis | chemistry | catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption | Kristof Bal | REWEIGHT_BIAS LOWER_WALLS COMBINE VES_LINEAR_EXPANSION FLUSH DUMPGRID UNITS UPPER_WALLS CONVERT_TO_FES TD_GRID DISTANCE COORDINATIONNUMBER LOAD RESTRAINT REWEIGHT_METAD COORDINATION EXTERNAL ANGLES UWALLS OPT_AVERAGED_SGD METAD PRINT BF_CHEBYSHEV HISTOGRAM DISTANCES | bias function ves multicolvar gridtools generic colvar symfunc setup |
| 21.012 | NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition | bio | funnel metadynamics | Jim Pfaendtner | LOWER_WALLS FUNNEL_PS FUNNEL METAD PRINT COM UPPER_WALLS DISTANCE | bias funnel generic colvar vatom |
| 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 | |
| 21.000 | Uremic toxin time scale dynamics | bio | uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs) | Jim Pfaendtner | WHOLEMOLECULES PRINT GROUP COM DISTANCE | vatom generic colvar core |
| 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 | ABMD RESTART PRINT CENTER TORSION ERMSD DISTANCE MOLINFO | bias generic colvar vatom setup |
| 20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Cristina Paissoni | WHOLEMOLECULES STATS PRINT CENTER RESTRAINT GROUP SAXS ENSEMBLE BIASVALUE INCLUDE DISTANCE MOLINFO | bias function generic isdb core colvar vatom |
| 20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Michele Invernizzi | CUSTOM ENVIRONMENTSIMILARITY MOLINFO ENERGY UNITS ECV_UMBRELLAS_LINE ENDPLUMED UPPER_WALLS ECV_MULTITHERMAL WHOLEMOLECULES LOAD Q6 OPES_EXPANDED POSITION MATHEVAL ECV_MULTITHERMAL_MULTIBARIC VOLUME PRINT ECV_LINEAR RMSD TORSION | bias function opes generic colvar symfunc setup envsim |
| 20.018 | Free energy barriers from biased molecular dynamics simulations | methods | kinetics, free energy barriers, chemical reactions, nucleation, metadynamics | Kristof Bal | REWEIGHT_BIAS LOWER_WALLS COMBINE DENSITY FLUSH DUMPGRID ENERGY UNITS LOCAL_AVERAGE UPPER_WALLS PAIRENTROPY CONVERT_TO_FES CONTACT_MATRIX DISTANCE COORDINATIONNUMBER LOAD SPRINT REWEIGHT_METAD Q6 COORDINATION METAD VOLUME PRINT CENTER HISTOGRAM | bias function adjmat gridtools sprint generic colvar symfunc vatom setup volumes |
| 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 | UNITS CUSTOM METAD PRINT COORDINATION DISTANCES | bias function multicolvar generic colvar setup |
| 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 BF_LEGENDRE VES_LINEAR_EXPANSION LOAD PRINT POSITION | setup ves colvar generic |
| 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 | LOWER_WALLS REWEIGHT_BIAS VES_LINEAR_EXPANSION RESTART COMBINE TD_WELLTEMPERED CELL OPT_DUMMY ENERGY DUMPGRID UPPER_WALLS REWEIGHT_TEMP_PRESS READ CONVERT_TO_FES BF_LEGENDRE LOAD Q6 MATHEVAL OPT_AVERAGED_SGD VOLUME PRINT HISTOGRAM TD_MULTITHERMAL_MULTIBARIC | bias function ves gridtools generic colvar symfunc setup |
| 19.076 | Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones | bio | molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics | Salvatore Assenza | UNITS ENDPLUMED PRINT MOVINGRESTRAINT GYRATION | setup bias colvar generic |
| 19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Giovanni Bussi | WHOLEMOLECULES MATHEVAL METAD SORT PRINT COM COORDINATION MAXENT FLUSH TORSION INCLUDE DISTANCE MOLINFO | bias function generic colvar vatom |
| 19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Michele Invernizzi | UNITS METAD OPES_METAD ENDPLUMED PRINT POSITION TORSION EXTERNAL | bias opes generic colvar setup |
| 19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | GiovanniMaria Piccini | LOWER_WALLS ENERGY UNITS METAD COMBINE PRINT UPPER_WALLS FLUSH DISTANCE | bias function generic colvar setup |
| 19.030 | Coarse-Grained MetaDynamics (CG-MetaD) | bio | Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy | Vittorio Limongelli | LOWER_WALLS WHOLEMOLECULES METAD PRINT UPPER_WALLS COM DISTANCE | vatom generic bias colvar |
| 19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Jim Pfaendtner | ENERGY METAD COORDINATION EXTERNAL GROUP | core bias colvar |
| 19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Riccardo Capelli | WHOLEMOLECULES MATHEVAL DUMPGRID METAD ENDPLUMED PRINT REWEIGHT_METAD COM FIT_TO_TEMPLATE UPPER_WALLS COORDINATION HISTOGRAM READ WRAPAROUND POSITION FLUSH CONVERT_TO_FES GROUP | bias function gridtools generic colvar core vatom |
| 25.016 | Advancing in silico drug design with Bayesian refinement of AlphaFold models | bio | bAIes, AlphaFold, Bayesian refinement, virtual screening, docking, small-molecule, enrichment | Samiran Sen | BIASVALUE GROUP BAIES PRINT | generic isdb bias core |
| 25.013 | Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices | bio | umbrella sampling, temperature ramping | Alexander Berlaga | GYRATION PRINT DISTANCE RESTRAINT PYTORCH_MODEL | pytorch generic bias colvar |
| 25.002 | M3_PCV-ABMD | chemistry | Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor | Gian Marco Elisi | UNITS UPPER_WALLS PATHMSD ENDPLUMED PRINT ABMD | generic setup colvar bias |
| 24.031 | DeepLNE | methods | PATHCV, OPES, OneOPES | Thorben Fröhlking | COORDINATION ECV_MULTITHERMAL PRINT RESTART OPES_EXPANDED ENERGY ERMSD VOLUME OPES_METAD_EXPLORE MOLINFO COMBINE PYTORCH_MODEL | opes colvar generic setup pytorch function |
| 24.025 | Correlating Enzymatic Reactivity for Different Substrates using Transferable Data-Driven Collective Variables | bio | enzymatic reactivity, k_cat, transfer learning, data-driven CVs, catalysis, ligand-binding modes, water, alpha-amylase, sugar, classical MD, OPES, machine learning, Deep TDA CV, path CV | Sudip Das | COORDINATION GROUP FIT_TO_TEMPLATE TORSION WHOLEMOLECULES DISTANCE RESTART UPPER_WALLS OPES_METAD PRINT CUSTOM LOWER_WALLS PATH CENTER FIXEDATOM PYTORCH_MODEL | opes vatom colvar core generic setup pytorch bias function mapping |
| 24.019 | Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning | bio | OPES, machine learning, protein folding, adaptive sampling | Mingyuan Zhang | COORDINATION TORSION PRINT GYRATION DISTANCE OPES_METAD CUSTOM ALPHARMSD MOLINFO WHOLEMOLECULES COMBINE | opes secondarystructure colvar generic function |
| 24.017 | Absolute Binding Free Energies with OneOPES | methods | protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy | Francesco Gervasio | COORDINATION MATHEVAL OPES_EXPANDED LOWER_WALLS RMSD INCLUDE TORSION METAD CUSTOM COM OPES_METAD_EXPLORE ECV_MULTITHERMAL RESTART BIASVALUE PROJECTION_ON_AXIS GROUP WRAPAROUND UPPER_WALLS PRINT ENERGY CONTACTMAP CONSTANT MOLINFO WHOLEMOLECULES | opes vatom colvar core generic setup bias function |
| 24.008 | yCD Metadynamics | bio | volume-based MetaD, path CVs, infrequent MetaD, product release | James McCarty | COORDINATION READ MATHEVAL RMSD INCLUDE FIT_TO_TEMPLATE METAD ENDPLUMED COMMITTOR COM REWEIGHT_METAD HISTOGRAM CONVERT_TO_FES GROUP FLUSH WRAPAROUND DISTANCE UPPER_WALLS PRINT DUMPGRID CONTACTMAP MOLINFO PATH WHOLEMOLECULES FIXEDATOM | colvar function core generic gridtools bias vatom mapping |
| 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 | INCLUDE TRANSPOSE SELECT_COMPONENTS FLUSH MATHEVAL PRINT METAD SUM | generic valtools bias matrixtools function |
| 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 | WHOLEMOLECULES METAD DISTANCE PRINT MATHEVAL MOLINFO RMSD | generic colvar function 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 | FIT_TO_TEMPLATE PRINT METAD POSITION ALPHARMSD MOLINFO WHOLEMOLECULES ANN COMBINE | secondarystructure colvar annfunc generic bias function |
| 23.021 | Into the Dynamics of Rotaxanes at Atomistic Resolution | materials | metadynamics, rotaxanes, molecular shuttles, molecular machines | Luigi Leanza | TORSION METAD DISTANCE MATHEVAL PRINT UPPER_WALLS CUSTOM CENTER FIXEDATOM | colvar function generic bias vatom |
| 23.019 | Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors | bio | binding pathway, binding energy, sketch-map, drug development | Raitis Bobrovs | TRANSPOSE SKETCHMAP METAD PATHMSD PRINT UPPER_WALLS DISTANCE DISSIMILARITIES LANDMARK_SELECT_FPS VSTACK CUSTOM COLLECT_FRAMES COM SKETCHMAP_PROJECTION WHOLEMOLECULES VORONOI | vatom colvar generic valtools landmarks bias dimred matrixtools function |
| 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 | PBMETAD TORSION GYRATION MOLINFO WHOLEMOLECULES | generic colvar bias |
| 22.033 | Reciprocal barrier restraint. Application to PROTAC passive permeability prediction | methods | PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR | Istvan Kolossvary | UNITS DRR FLUSH DISTANCE METAD BIASVALUE PRINT CUSTOM COM | vatom colvar drr generic setup bias function |
| 22.018 | Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations | bio | ligand binding, docking, EMMI, LAT1 | Max Bonomi | GROUP PRINT EMMIVOX BIASVALUE LOAD MOLINFO WHOLEMOLECULES | core generic setup bias isdb |
| 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 | COORDINATION CENTER GROUP FIT_TO_TEMPLATE MATHEVAL DISTANCE UPPER_WALLS OPES_METAD PRINT CUSTOM COMMITTOR LOWER_WALLS RMSD WHOLEMOLECULES FIXEDATOM PYTORCH_MODEL | vatom opes colvar core generic pytorch bias function |
| 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 | COORDINATION ENDPLUMED PRINT METAD CUSTOM VOLUME COMBINE | generic bias colvar function |
| 21.031 | Photo-switchable sulfonulureas in KATP channel | bio | metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels | Katarzyna Walczewska-Szewc | UNITS DISTANCE METAD PRINT UPPER_WALLS LOWER_WALLS COM WHOLEMOLECULES | colvar generic setup bias vatom |
| 21.028 | From Enhanced Sampling to Reaction Profiles | methods | collective variables, multi-state, machine learning, Deep-TDA | Enrico Trizio | COORDINATION UNITS MATHEVAL OPES_METAD LOWER_WALLS FIT_TO_TEMPLATE TORSION WHOLEMOLECULES ENDPLUMED DISTANCES LOAD ANGLE GROUP DISTANCE UPPER_WALLS PRINT CENTER FIXEDATOM PYTORCH_MODEL | opes vatom colvar core generic setup pytorch multicolvar bias function |
| 21.024 | Property map collective variable as a useful tool for force field correction | chemistry | molecular mechanics | Vojtech Spiwok | TORSION PROPERTYMAP PRINT METAD BIASVALUE WHOLEMOLECULES | generic bias colvar |
| 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 CENTER MATHEVAL RESTART PRINT METAD POSITION RESTRAINT REWEIGHT_BIAS WHOLEMOLECULES | colvar function generic setup bias 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 | COORDINATION PRINT RESTRAINT STATS MOLINFO WHOLEMOLECULES COMBINE | generic bias colvar function |
| 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 | OPT_AVERAGED_SGD Q6 UPPER_WALLS RESTART ENVIRONMENTSIMILARITY MATHEVAL TD_WELLTEMPERED PRINT VOLUME OPT_DUMMY VES_LINEAR_EXPANSION BF_LEGENDRE | ves colvar generic symfunc setup envsim bias function |
| 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 | HISTOGRAM READ DISTANCE ENDPLUMED PRINT UPPER_WALLS MATHEVAL METAD DUMPGRID ABMD LOWER_WALLS COM CONVERT_TO_FES REWEIGHT_METAD COMBINE | vatom colvar gridtools generic bias function |
| 19.075 | PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python | other | Python, automatic differentiation | Toni Giorgino | GROUP TORSION DISTANCE PRINT ENDPLUMED ANGLE RESTRAINT DUMPDERIVATIVES CUSTOM CENTER COMBINE | vatom colvar core generic bias function |
| 19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Jakub Rydzewski | UNITS PRINT MAZE_SIMULATED_ANNEALING POSITION MAZE_OPTIMIZER_BIAS MAZE_LOSS | generic setup maze colvar |
| 19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Jim Pfaendtner | METAD GYRATION PRINT ENERGY WHOLEMOLECULES | generic colvar bias |
| 19.047 | Close Structure | methods | metadynamics, RMSD, path collective variables, property map | Vojtech Spiwok | METAD WHOLEMOLECULES PROPERTYMAP PRINT | generic colvar bias |
| 19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Gabriele Cesare Sosso | FLUSH Q6 ENDPLUMED LOCAL_Q6 COMMITTOR DFSCLUSTERING CONTACT_MATRIX CLUSTER_NATOMS OUTPUT_CLUSTER CLUSTER_WITHSURFACE MFILTER_MORE | generic symfunc multicolvar clusters adjmat |
| 19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Max Bonomi | EMMI GROUP PRINT BIASVALUE MOLINFO | generic isdb core bias |