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 |
|---|---|---|---|---|---|---|
| 26.007 | Metadynamics Simulations Reveal the Protonation-Dependent Conformational Landscape of GSK-3β Dual Inhibitors | chemistry | metadynamics, ligand unbinding, path CVs, funnel metadynamics | Gian Marco Elisi | ANGLE COMBINE MOLINFO METAD RMSD WHOLEMOLECULES DISTANCE MATHEVAL ENDPLUMED COM UNITS UPPER_WALLS FUNNEL_PS PATHMSD LOWER_WALLS FUNNEL PRINT | generic funnel colvar function setup vatom bias |
| 26.002 | A Transferable and Robust Computational Framework for Class A GPCR Activation Free Energies | bio | OneOPES, GPCR, ADRB1, activation, euclidean path, microswitches, conformational changes, allostery | Valerio Rizzi | PATH RMSD CENTER DISTANCE CUSTOM ECV_MULTITHERMAL OPES_EXPANDED PATHMSD OPES_METAD_EXPLORE ENERGY UPPER_WALLS GROUP VOLUME COORDINATION LOWER_WALLS PRINT | generic mapping colvar function opes core vatom bias |
| 25.027 | Enhanced-sampling MD simulations of a protein-peptide complex integrating SAXS and XL-MS experimental information | bio | steered MD, metadynamics, SAXS, XL-MS, ensemble reconstruction | Mattia Bernetti | MOVINGRESTRAINT SAXS MOLINFO METAD WHOLEMOLECULES DISTANCE INCLUDE CENTER GYRATION UPPER_WALLS GROUP PRINT | generic colvar core vatom bias isdb |
| 25.014 | Atomic resolution ensembles of intrinsically disordered proteins with Alphafold | bio | bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement | Vincent Schnapka | GROUP BIASVALUE BAIES PRINT | generic bias core isdb |
| 24.030 | NMR guided simulation of dsRBD | bio | Metainference, NMR, protein dynamics | Debadutta Patra | MOLINFO WHOLEMOLECULES DISTANCE ENSEMBLE STATS FLUSH RDC ALPHABETA METAINFERENCE GROUP PRINT | generic colvar function core multicolvar isdb |
| 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 | DISTANCE OPES_METAD ENERGY UPPER_WALLS COORDINATION PRINT | colvar bias opes generic |
| 24.012 | Molecular simulations to investigate the impact of N6-methylation in RNA recognition | bio | metadynamics, alchemistry, RNA modification, RNA:protein interactions | Giovanni Bussi | COMBINE MOLINFO METAD GHBFIX CENTER BIASVALUE DISTANCE UPPER_WALLS GROUP COM COORDINATION LOWER_WALLS DEBUG PRINT | generic colvar function core vatom 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 | DISTANCE OPES_METAD FIXEDATOM COORDINATIONNUMBER UNITS FLUSH ZDISTANCES UPPER_WALLS GROUP PRINT | symfunc generic colvar opes setup core vatom bias multicolvar |
| 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 | SELECT_COMPONENTS TRANSPOSE METAD INCLUDE MATHEVAL FLUSH SUM PRINT | generic valtools function matrixtools 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 METAD MATHEVAL Q4 COORDINATIONNUMBER ENERGY Q6 VOLUME PRINT | symfunc generic colvar function bias |
| 23.034 | Urea nucleation in water: do long-range forces matter? | materials | LMF theory, Metadynamics, Nucleation | Ziyue Zou | METAD INCLUDE CENTER LOAD COORDINATIONNUMBER GROUP PRINT | symfunc generic setup core vatom bias |
| 23.015 | MPCs aggregation | bio | opes_explore, dimerization, MPCs, self-assembly | Vikas Tiwari | METAD WHOLEMOLECULES CENTER DISTANCE CUSTOM OPES_METAD_EXPLORE COM UPPER_WALLS GROUP LOWER_WALLS COORDINATION PRINT | generic colvar function opes core vatom bias |
| 23.012 | JAK2 2D meta-eABF PMF with statistical analysis | bio | 2D meta-eABF, path CV, PMF | Istvan Kolossvary | DRR METAD BIASVALUE CUSTOM UPPER_WALLS FLUSH LOWER_WALLS PATHMSD PRINT | generic drr colvar function bias |
| 23.007 | Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains | bio | metadynamics, peptoids, parallel-bias metadynamics | Jim Pfaendtner | TORSION WHOLEMOLECULES INCLUDE PBMETAD GYRATION COM COORDINATION RESTRAINT PRINT | colvar bias generic vatom |
| 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 VOLUME DUMPGRID BIASVALUE LOAD HISTOGRAM CUSTOM RESTRAINT COMMITTOR REWEIGHT_BIAS COORDINATIONNUMBER UNITS FLUSH CONVERT_TO_FES UPPER_WALLS PRINT | generic symfunc gridtools colvar function setup bias annfunc |
| 21.042 | Peptoid-mediated Au nanocrystal growth | materials | parallel-bias metadynamics, peptoid, Au | Xin Qi | MOLINFO DISTANCE PBMETAD GYRATION UPPER_WALLS COM PRINT | generic bias colvar vatom |
| 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 | COMBINE METAD ENDPLUMED CUSTOM VOLUME COORDINATION PRINT | generic function bias colvar |
| 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 | MOLINFO EMMI WHOLEMOLECULES DISTANCE BIASVALUE RESTART UPPER_WALLS GROUP COM PRINT | generic colvar setup core vatom bias isdb |
| 21.039 | Deep learning the slow modes for rare events sampling | methods | collective variables, machine learning, slow modes, deep-tica, opes | Luigi Bonati | TORSION MOLINFO RMSD INCLUDE OPES_METAD OPES_EXPANDED PRINT ECV_MULTITHERMAL COMBINE ENDPLUMED LOAD ENVIRONMENTSIMILARITY UNITS CONTACTMAP FLUSH GROUP Q6 DISTANCE ENERGY WHOLEMOLECULES PYTORCH_MODEL VOLUME | generic symfunc colvar function opes setup core pytorch envsim |
| 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 | TORSION METAD ENDPLUMED INCLUDE PBMETAD RANDOM_EXCHANGES PRINT | colvar bias generic |
| 21.032 | Metal-coupled folding mechanism to metallothionein | bio | parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination | Manuel-Peris Diaz | WHOLEMOLECULES PBMETAD UNITS GROUP COORDINATION | generic colvar setup core bias |
| 21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Kristof Bal | MOVINGRESTRAINT METAD REWEIGHT_METAD DUMPGRID LOAD HISTOGRAM COMMITTOR CONVERT_TO_FES UNITS COORDINATIONNUMBER FLUSH UPPER_WALLS PRINT | symfunc generic gridtools setup bias |
| 21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Adriana Pietropaolo | TORSION WHOLEMOLECULES MATHEVAL BIASVALUE RESTART PBMETAD CONSTANT PRINT | generic colvar function setup bias |
| 21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Tarak Karmakar | MATHEVAL PYTORCH_MODEL LOAD OPES_METAD UPPER_WALLS FLUSH LOWER_WALLS GROUP PRINT | generic function opes setup core pytorch bias |
| 20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Valerio Rizzi | ANGLE ENDPLUMED WHOLEMOLECULES CENTER DISTANCE MATHEVAL PYTORCH_MODEL OPES_METAD FIT_TO_TEMPLATE FIXEDATOM ENERGY UPPER_WALLS GROUP COORDINATION PRINT | generic colvar function opes core pytorch vatom bias |
| 20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Michele Invernizzi | TORSION MOLINFO RMSD MATHEVAL OPES_EXPANDED UPPER_WALLS ECV_LINEAR PRINT ECV_MULTITHERMAL ENDPLUMED LOAD CUSTOM ENVIRONMENTSIMILARITY UNITS POSITION Q6 ECV_UMBRELLAS_LINE ECV_MULTITHERMAL_MULTIBARIC ENERGY WHOLEMOLECULES VOLUME | generic symfunc colvar function opes setup envsim bias |
| 20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Glen Hocky | MATHEVAL DISTANCE BIASVALUE GYRATION UNITS ENERGY GROUP RESTRAINT FISST PRINT | generic colvar function fisst setup core 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 | MOLINFO METAD INCLUDE DISTANCE LOAD WHOLEMOLECULES MATHEVAL FUNCPATHGENERAL BIASVALUE CONTACTMAP CONSTANT COM UPPER_WALLS GROUP LOWER_WALLS PROJECTION_ON_AXIS PRINT | generic colvar function setup core vatom 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 | CS2BACKBONE MOLINFO ENDPLUMED WHOLEMOLECULES BIASVALUE FLUSH PBMETAD UPPER_WALLS ANTIBETARMSD LOWER_WALLS ALPHABETA GROUP PRINT | generic secondarystructure core bias multicolvar isdb |
| 19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Jim Pfaendtner | METAD WHOLEMOLECULES GYRATION ENERGY PRINT | generic bias colvar |
| 19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Kim E. Jelfs | METAD DISTANCE CENTER RESTART UPPER_WALLS GROUP COM LOWER_WALLS PRINT | generic colvar setup core vatom bias |
| 19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Kim Jelfs | MOVINGRESTRAINT DISTANCES RESTART INPLANEDISTANCES FLUSH COM PRINT | generic setup vatom bias multicolvar |
| 19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Cristina Paissoni | ANGLE COMBINE SAXS MOLINFO ENDPLUMED WHOLEMOLECULES CENTER INCLUDE MATHEVAL BIASVALUE PBMETAD ENSEMBLE STATS GROUP COORDINATION ALPHABETA PRINT | generic colvar function core vatom bias multicolvar isdb |
| 19.056 | maze | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_LOSS MAZE_SIMULATED_ANNEALING UNITS POSITION MAZE_OPTIMIZER_BIAS PRINT | maze colvar setup generic |
| 19.050 | Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes | chemistry | metadynamics, membranes, Willard Chandler surface | Gareth Tribello | COMBINE READ METAD DUMPGRID HISTOGRAM RESTART REWEIGHT_BIAS CONVERT_TO_FES UPPER_WALLS DISTANCE_FROM_CONTOUR PRINT | generic gridtools function setup contour bias |
| 19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Paolo Raiteri | METAD MATHEVAL DISTANCE RESTART UNITS UPPER_WALLS FLUSH PRINT | generic colvar function setup bias |
| 19.030 | Coarse-Grained MetaDynamics (CG-MetaD) | bio | Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy | Vittorio Limongelli | METAD WHOLEMOLECULES DISTANCE UPPER_WALLS COM LOWER_WALLS PRINT | generic bias colvar vatom |
| 19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Matteo Salvalaglio | COMBINE TORSION METAD ENDPLUMED MATHEVAL ENERGY UPPER_WALLS VOLUME LOWER_WALLS CELL PRINT | colvar function bias generic |
| 19.013 | RNA FF FITTING | methods | force field, RNA | Giovanni Bussi | MOLINFO TORSION INCLUDE MATHEVAL BIASVALUE PUCKERING CONSTANT | generic function bias colvar |
| 26.009 | Exploring the Conformational Landscape of HIV-1 TAR RNA by PT-WTE | bio | RNA, PT-WTE, HIV-1 TAR | Stefano Bosio | PRINT ENERGY GROUP WHOLEMOLECULES METAD MOLINFO | colvar generic bias core |
| 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 | GROUP BAIES PRINT BIASVALUE | generic core isdb 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 | DISTANCE COORDINATION COMBINE RESTRAINT PRINT UPPER_WALLS COM ANGLE COORDINATIONNUMBER FIXEDATOM UNITS GROUP METAD FLUSH DISTANCES LOWER_WALLS | core symfunc colvar bias vatom setup multicolvar generic function |
| 24.008 | yCD Metadynamics | bio | volume-based MetaD, path CVs, infrequent MetaD, product release | James McCarty | ENDPLUMED UPPER_WALLS CONTACTMAP FLUSH HISTOGRAM PRINT FIT_TO_TEMPLATE WRAPAROUND DUMPGRID COORDINATION COM INCLUDE FIXEDATOM GROUP MATHEVAL READ WHOLEMOLECULES MOLINFO METAD DISTANCE PATH REWEIGHT_METAD RMSD COMMITTOR CONVERT_TO_FES | core colvar gridtools bias mapping vatom generic function |
| 23.027 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, DFS, Q3, Pair Entropy | Aaron Finney | AROUND LOCAL_AVERAGE CLUSTER_NATOMS RESTRAINT PRINT DFSCLUSTERING Q3 CONTACT_MATRIX CLUSTER_DISTRIBUTION LOAD COORDINATIONNUMBER FIXEDATOM UNITS LOCAL_Q3 GROUP DENSITY DUMPGRID HISTOGRAM | core clusters symfunc gridtools adjmat bias vatom setup generic volumes |
| 23.025 | Probing ion binding to G-quadruplexes and related events | chemistry | metadynamics, repulsive potential, nucleic acids, G-quadruplexes | Marcelo Poleto | DISTANCE RESTART POSITION PRINT UPPER_WALLS COM WRAPAROUND UNITS GROUP LOWER_WALLS MATHEVAL FIT_TO_TEMPLATE WHOLEMOLECULES FLUSH DISTANCES DUMPATOMS METAD | core colvar bias vatom setup multicolvar generic function |
| 22.045 | Binding mode and mechanism of enzymatic polyethylene terephthalate degradation | bio | metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation | Francesco Colizzi | DISTANCE PRINT UPPER_WALLS MOVINGRESTRAINT COM ANGLE LOWER_WALLS WHOLEMOLECULES METAD | colvar generic bias vatom |
| 22.015 | Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome | bio | photodynamics, bacteriophytochrome, variationally enhanced sampling | Jakub Rydzewski | VES_LINEAR_EXPANSION PRINT TORSION BF_FOURIER TD_UNIFORM OPT_AVERAGED_SGD | colvar generic ves |
| 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 | COORDINATION GYRATION DISTANCE COMBINE UPPER_WALLS COM COORDINATIONNUMBER UNITS LOWER_WALLS FLUSH METAD | symfunc colvar bias vatom setup generic function |
| 21.050 | N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity | methods | bio | Isabell Louise Grothaus | DISTANCE CENTER PRINT | colvar generic vatom |
| 21.016 | MD SAXS GTPase associated center | bio | metadynamics, RNA, folding, SAXS | Giovanni Bussi | GYRATION PRINT UPPER_WALLS ERMSD MOLINFO CUSTOM INCLUDE SAXS GROUP WHOLEMOLECULES METAD LOWER_WALLS | core colvar bias generic isdb function |
| 21.010 | Step by Step Strecker Amino Acid Synthesis from Ab Initio Prebiotic Chemistry | chemistry | Strecker reaction, free energy landscape, ab initio molecular dynamics, glycine, prebiotic synthesis | Théo Magrino | generic | |
| 20.030 | Converging experimental and computational views of the knotting mechanism of the smallest knotted protein | bio | phi-values, transition state, knotted proteins | Cristina Paissoni | STATS COORDINATION COMBINE RESTRAINT PRINT WHOLEMOLECULES MOLINFO | colvar generic bias function |
| 19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | GiovanniMaria Piccini | DISTANCE COMBINE PRINT UPPER_WALLS ENERGY UNITS LOWER_WALLS FLUSH METAD | colvar bias setup generic function |
| 19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Gabriele Cesare Sosso | ENDPLUMED CLUSTER_NATOMS DFSCLUSTERING COMMITTOR CONTACT_MATRIX LOCAL_Q6 CLUSTER_WITHSURFACE MFILTER_MORE Q6 OUTPUT_CLUSTER FLUSH | clusters symfunc adjmat multicolvar generic |
| 19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Jim Pfaendtner | COORDINATION EXTERNAL ENERGY GROUP METAD | colvar core bias |
| 19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Riccardo Capelli | HISTOGRAM COORDINATION ENDPLUMED POSITION PRINT UPPER_WALLS COM REWEIGHT_METAD WRAPAROUND GROUP CONVERT_TO_FES MATHEVAL FIT_TO_TEMPLATE WHOLEMOLECULES READ FLUSH DUMPGRID METAD | core colvar gridtools bias vatom generic function |
| 25.030 | Committor Regularization | methods | metadynamics, enhanced sampling, mlcvs, committor, machine learning | Florian Dietrich | UNITS PRINT METAD MOVINGRESTRAINT | bias setup generic |
| 25.029 | Energetic Constraints in the Enzymatic Depolymerization of Crystalline PET from enhanced molecular simulations | bio | HREX-Metadynamics, PETase, crystalline PET, amorphous PET, conformational ensembles, substrate binding, chain detachment | Ania Di Pede-Mattatelli and Francesco Colizzi | HISTOGRAM COM WHOLEMOLECULES CONVERT_TO_FES LOWER_WALLS MOLINFO UPPER_WALLS FIXEDATOM DUMPGRID DISTANCE METAD REWEIGHT_BIAS PRINT | gridtools vatom generic bias colvar |
| 25.026 | Deciphering the Molecular Mechanisms of Startle Disease - the Role of the Asn46Lys Mutation in the Glycine Receptor | bio | metadynamics, glycine receptors, funnel metadynamics | Jacob Adam Clark | COM FUNNEL_PS LOWER_WALLS FUNNEL UPPER_WALLS METAD PRINT | vatom bias funnel generic |
| 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 | WHOLEMOLECULES EMMIVOX MOLINFO GROUP BIASVALUE PRINT | core isdb bias generic |
| 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 | UNITS COMBINE CELL COORDINATION OPES_METAD MATHEVAL INCLUDE POSITION ENERGY CUSTOM TORSION FLUSH DISTANCE BIASVALUE PRINT LOAD | function opes setup generic bias colvar |
| 25.009 | Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water | chemistry | metadynamics, nitrate photolysis | Kam-Tung Chan | HISTOGRAM REWEIGHT_METAD COORDINATION READ UPPER_WALLS CUSTOM DUMPGRID GROUP FLUSH DISTANCE METAD PRINT RESTART | function gridtools setup generic bias core colvar |
| 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 | MOVINGRESTRAINT MOLINFO TORSION PUCKERING RESTRAINT DISTANCE METAD PRINT RESTART | colvar bias setup generic |
| 24.034 | Umbrella sampling of ion in transporter SLC26A7 | bio | umbrella sampling, transporter, ions | Xiaoli Lu | UNITS POSITION RESTRAINT PRINT | colvar bias setup 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 MATHEVAL GROUP PRINT WHOLEMOLECULES CUSTOM CONTACTMAP FIXEDATOM RMSD METAD COMMITTOR COORDINATION OPES_METAD CENTER MOLINFO FIT_TO_TEMPLATE UPPER_WALLS TORSION DISTANCE ANGLE | function opes vatom generic bias core colvar |
| 24.004 | Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables | materials | metadynamics, nucleation, machine learning | Ziyue Zou | INCLUDE GROUP LOAD METAD PRINT RESTART | core bias setup generic |
| 23.046 | Lasso Peptides - HLDA CV | bio | metadynamics, protein folding, HLDA, harmonic | Gabriel da Hora | UNITS WHOLEMOLECULES COMBINE DISTANCE METAD PRINT | function setup generic bias colvar |
| 23.044 | Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition | materials | metadynamics, interlocked molecules | Luigi Leanza | HISTOGRAM ENDPLUMED CONVERT_TO_FES COORDINATION READ DUMPGRID GROUP METAD PRINT COMMITTOR | gridtools generic bias core colvar |
| 23.040 | Supramolecular capsules assembly dynamics | chemistry | Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics | Riccardo Capelli | UNITS WHOLEMOLECULES COM CENTER DISTANCES POSITION CUSTOM GROUP FLUSH DISTANCE METAD PRINT | function vatom setup generic multicolvar bias core colvar |
| 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 | WHOLEMOLECULES CONSTANT LOWER_WALLS CENTER UPPER_WALLS MATHEVAL DISTANCE METAD BIASVALUE PRINT | function vatom generic bias colvar |
| 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 | COMBINE WHOLEMOLECULES GHBFIX COORDINATION MOLINFO BIASVALUE METAD ERMSD PRINT | colvar function bias generic |
| 23.023 | Rational design of novel biomimetic sequence-defined polymers for mineralization applications | methods | metadynamics, surface binding, biomimetic mineralization | Kaylyn Torkelson | COM COORDINATION UPPER_WALLS GYRATION DISTANCE PBMETAD PRINT | colvar vatom bias generic |
| 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 | PYTORCH_MODEL UNITS WHOLEMOLECULES PATH COORDINATION OPES_METAD LOWER_WALLS CENTER OPES_METAD_EXPLORE FIT_TO_TEMPLATE UPPER_WALLS FIXEDATOM CUSTOM TORSION GROUP DISTANCE PRINT | pytorch function mapping opes vatom setup generic bias core colvar |
| 23.001 | Quantum phase diagram of water | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn-Løland Bore | ECV_UMBRELLAS_LINE LOWER_WALLS UPPER_WALLS ENVIRONMENTSIMILARITY INCLUDE OPES_EXPANDED PRINT RESTART | opes setup generic envsim bias |
| 22.038 | Enhanced Sampling Aided Design of Molecular Photoswitches | chemistry | reaction discovery, OPES explore, graph CV | Umberto Raucci | PYTORCH_MODEL UNITS COORDINATION OPES_METAD_EXPLORE CUSTOM PRINT | pytorch function opes setup generic colvar |
| 22.034 | Rationalising the difference in crystallisability of two Sulflowers using efficient in silico methods | materials | metadynamics, crystallizability, crystal structure prediction, sulflower, persulforated coronene | Matteo Salvalaglio | CELL LOWER_WALLS DRMSD UPPER_WALLS MATHEVAL CUSTOM METAD PRINT COMMITTOR | colvar function bias generic |
| 22.031 | Rare Event Kinetics from Adaptive Bias Enhanced Sampling | methods | OPES Flooding, Kinetics, Rate, OPES, Machine Learning | Dhiman Ray | PYTORCH_MODEL COMBINE ENDPLUMED CONSTANT POSITION ENERGY GROUP PRINT UNITS WHOLEMOLECULES CUSTOM BIASVALUE CONTACTMAP RMSD COMMITTOR OPES_METAD MOLINFO INCLUDE TORSION DISTANCE | pytorch function opes setup generic bias core colvar |
| 22.030 | Mixing physics across temperatures with generative artificial intelligence | methods | REMD, Generative AI, DDPM | Yihang Wang | WHOLEMOLECULES TORSION PRINT | colvar generic |
| 22.022 | Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir | bio | RMSD, protein-ligand interactions | Isabell Grothaus | RMSD PRINT | colvar generic |
| 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 WHOLEMOLECULES FUNNEL_PS LOWER_WALLS FUNNEL UPPER_WALLS PATHMSD DISTANCE METAD PRINT | funnel vatom generic bias colvar |
| 21.051 | Automatic learning of hydrogen-bond fixes in an AMBER RNA force field | methods | force field, RNA | Giovanni Bussi | COMBINE WHOLEMOLECULES COORDINATION MOLINFO BIASVALUE METAD ERMSD PRINT | colvar function bias generic |
| 21.049 | Multiple-path-metadynamics and PathMaps | methods | path-CV, metadynamics, multiple-walker, multiple paths, pathmap | Alberto Pérez-de-Alba-Ortíz | UNITS COMBINE ENSEMBLE CONSTANT MOVINGRESTRAINT LOWER_WALLS UPPER_WALLS TORSION CUSTOM RESTRAINT LOAD METAD PRINT | function setup generic bias colvar |
| 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 | colvar vatom bias generic |
| 21.028 | From Enhanced Sampling to Reaction Profiles | methods | collective variables, multi-state, machine learning, Deep-TDA | Enrico Trizio | PYTORCH_MODEL ENDPLUMED MATHEVAL GROUP PRINT UNITS WHOLEMOLECULES LOWER_WALLS DISTANCES FIXEDATOM COORDINATION OPES_METAD CENTER FIT_TO_TEMPLATE UPPER_WALLS TORSION LOAD DISTANCE ANGLE | pytorch function opes vatom setup generic multicolvar bias 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 | CONTACTMAP WHOLEMOLECULES ALPHARMSD LOWER_WALLS MOLINFO UPPER_WALLS MATHEVAL INCLUDE ENERGY DISTANCE METAD PRINT | function generic bias colvar secondarystructure |
| 21.026 | Probing allosteric regulations with coevolution-driven molecular simulations | bio | metadynamics, coevolution, allostery, adenylate cyclase | Francesco Colizzi | UNITS WHOLEMOLECULES COM UPPER_WALLS PATHMSD DISTANCE METAD PRINT | vatom setup generic bias colvar |
| 21.023 | Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling | methods | enhanced sampling, collective variables, machine learning | Jakub Rydzewski | UNITS REWEIGHT_METAD CONSTANT INCLUDE CUSTOM ENERGY TORSION DISTANCE METAD BIASVALUE PRINT | function setup generic bias colvar |
| 21.014 | how to determine statistically accurate conformational ensembles | bio | metadynamics, metainference, errors, cv, SAXS, ensemble determination | Cristina Paissoni | WHOLEMOLECULES CONTACTMAP ENSEMBLE MOLINFO CENTER ALPHABETA ANTIBETARMSD SAXS BIASVALUE STATS TORSION GYRATION METAD PBMETAD PRINT | function isdb vatom generic multicolvar bias colvar secondarystructure |
| 20.028 | Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane | bio | metadynamics, KRas-4B, anionic membrane | Huixia Lu | CENTER FIT_TO_TEMPLATE DISTANCE METAD PRINT RESTART | vatom setup generic bias colvar |
| 20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Matteo Salvalaglio | CELL LOWER_WALLS UPPER_WALLS MATHEVAL ENERGY VOLUME METAD PRINT | colvar function bias generic |
| 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 COORDINATION DISTANCES CUSTOM METAD PRINT | function setup generic multicolvar bias colvar |
| 19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Giovanni Bussi | WHOLEMOLECULES ENDPLUMED COORDINATION LOWER_WALLS RESTRAINT DISTANCE | colvar bias generic |
| 19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Wei Chen | COM COMBINE POSITION RESTRAINT ANN | function vatom annfunc bias colvar |
| 19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Gareth Tribello | UNITS MORE_THAN FIND_CONTOUR_SURFACE FOURIER_TRANSFORM FCCUBIC CENTER MULTICOLVARDENS DUMPGRID GROUP | contour function gridtools vatom setup symfunc core fourier |
| 19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Gareth Tribello | UNITS ENDPLUMED CELL AROUND FCCUBIC LOWER_WALLS UPPER_WALLS METAD PRINT | setup generic symfunc bias colvar volumes |
| 19.048 | Understanding Ligand Binding Selectivity in a Prototypical GPCR Family | bio | metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | COM WHOLEMOLECULES CONSTANT LOWER_WALLS UPPER_WALLS MATHEVAL DISTANCE METAD BIASVALUE PRINT | function vatom generic bias colvar |
| 19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | UNITS COMBINE DISTANCES UPPER_WALLS FLUSH DISTANCE METAD PRINT RESTART | function setup generic multicolvar bias colvar |
| 19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Vittorio Limongelli | COM WHOLEMOLECULES RMSD FUNNEL_PS LOWER_WALLS FUNNEL UPPER_WALLS DISTANCE METAD PRINT | funnel vatom generic bias colvar |
| 19.025 | Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide | bio | metainference, NMR, protein dynamics, force-fields | Carlo Camilloni | RDC WHOLEMOLECULES ENDPLUMED ENSEMBLE CS2BACKBONE MOLINFO METAINFERENCE PBMETAD STATS TORSION FLUSH BIASVALUE PRINT JCOUPLING GYRATION | function isdb generic bias colvar |
| 19.023 | RECT | methods | metadynamics, replica exchange | Giovanni Bussi | WHOLEMOLECULES TORSION GYRATION METAD PRINT | colvar bias generic |
| 19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Haochuan Chen | DRR PRINT TORSION | drr colvar generic |
| 19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Adriana Pietropaolo | WHOLEMOLECULES CONSTANT MATHEVAL TORSION METAD BIASVALUE PRINT | colvar function bias generic |
| 19.011 | Automatic Gradient Computation for Collective Variables | other | gradient, differentiation, curvature | Toni Giorgino | ENDPLUMED | generic |
| 26.010 | Solvation-Mediated Ammonia Synthesis in a Nanoheterogeneous Liquid Alloy | materials | OPES, Catalysis, Ammonia Synthesis | Axel Tosello Gardini | GROUP INCLUDE OPES_METAD_EXPLORE OPES_METAD CUSTOM UNITS COORDINATIONNUMBER PRINT FLUSH COORDINATION UPPER_WALLS DISTANCES DISTANCE | opes symfunc core colvar multicolvar function generic setup bias |
| 25.021 | All You Need Is Water. Converging Ligand Binding Simulations with Hydration Collective Variables | bio | OPES Explore, ligand binding, binding free energy, water, hydration CVs, SAMPL challenge, host-guest | Valerio Rizzi | FIXEDATOM GROUP OPES_METAD_EXPLORE CENTER WHOLEMOLECULES FIT_TO_TEMPLATE MATHEVAL COORDINATION ANGLE PRINT UPPER_WALLS ENERGY DISTANCE | opes vatom core colvar function generic bias |
| 25.020 | Revealing Water-Mediated Activation Mechanisms in the Beta 1-Adrenergic Receptor via OneOPES-Enhanced Free Energy Landscapes | bio | OneOPES, GPCR, ADRB1, activation, microswitches, conformational changes, allostery | Valerio Rizzi | ECV_MULTITHERMAL GROUP OPES_METAD_EXPLORE CENTER CUSTOM DISTANCES GHOST PRINT COORDINATION LOWER_WALLS RMSD PATHMSD ENERGY UPPER_WALLS OPES_EXPANDED DISTANCE | opes vatom core multicolvar colvar function generic bias |
| 24.029 | Combination of OPES and OPES-Explore | methods | OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin | Dhiman Ray | FIXEDATOM GROUP FLUSH RMSD ENERGY COMBINE METAD PYTORCH_MODEL CENTER LOWER_WALLS DISTANCE ENDPLUMED INCLUDE MOLINFO CONTACTMAP PRINT COORDINATION POSITION UPPER_WALLS BIASVALUE OPES_METAD_EXPLORE OPES_METAD CUSTOM WHOLEMOLECULES UNITS FIT_TO_TEMPLATE MATHEVAL | opes pytorch vatom core colvar function generic setup bias |
| 24.006 | Water vapor condensation | chemistry | metadynamics, homogeneous condensation, chemical potential | Shenghui Zhong | DFSCLUSTERING CLUSTER_NATOMS UNITS COORDINATIONNUMBER PRINT CONTACT_MATRIX UPPER_WALLS METAD CLUSTER_PROPERTIES | symfunc adjmat clusters generic setup bias |
| 24.003 | Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations | chemistry | steered molecular dynamics, foldamers, peptoids, bio-inspired | Kaylyn Torkelson | MOVINGRESTRAINT INCLUDE COM WHOLEMOLECULES PRINT COORDINATION ALPHABETA GYRATION DISTANCE TORSION | vatom colvar multicolvar generic bias |
| 24.002 | Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes | chemistry | metadynamics, ligand design, solvent extraction | Xiaoyu Wang | UNITS PRINT METAD RESTART TORSION | setup bias generic colvar |
| 23.020 | FEP simulations of ATOX1 homodimer | chemistry | parallel bias metadynamics, FEP, free-energy of metal ion dissociation | Adriana Pietropaolo | PBMETAD BIASVALUE WHOLEMOLECULES PRINT MATHEVAL ANGLE CONSTANT DISTANCE | function bias generic colvar |
| 23.008 | PBMetaD simulations of Histatin5 | bio | metadynamics, IDP, Rg, PPII | Francesco Pesce | PBMETAD GROUP MOLINFO WHOLEMOLECULES PRINT GYRATION TORSION | core bias generic colvar |
| 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 | ECV_UMBRELLAS_LINE HISTOGRAM PRINT LOWER_WALLS OPES_EXPANDED ENVIRONMENTSIMILARITY UPPER_WALLS DUMPGRID RESTART | opes envsim generic setup bias gridtools |
| 22.043 | Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES | bio | OPES, RNA, Tetraloop, Folding | Gül Zerze | ECV_MULTITHERMAL WHOLEMOLECULES ECV_UMBRELLAS_LINE PRINT CONTACTMAP ENERGY OPES_EXPANDED | opes generic colvar |
| 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 MOLINFO WHOLEMOLECULES GYRATION TORSION | bias generic colvar |
| 22.033 | Reciprocal barrier restraint. Application to PROTAC passive permeability prediction | methods | PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR | Istvan Kolossvary | BIASVALUE COM CUSTOM UNITS PRINT FLUSH DRR METAD DISTANCE | drr vatom colvar function generic setup bias |
| 21.047 | Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations | materials | pair entropy, metadynamics, ves, solids, crystallization | Pablo Piaggi | PAIRENTROPY BF_LEGENDRE VOLUME VES_LINEAR_EXPANSION PRINT TD_WELLTEMPERED OPT_AVERAGED_SGD ENERGY METAD RESTART COMBINE LOAD | ves colvar function generic setup bias gridtools |
| 21.031 | Photo-switchable sulfonulureas in KATP channel | bio | metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels | Katarzyna Walczewska-Szewc | COM WHOLEMOLECULES UNITS PRINT LOWER_WALLS UPPER_WALLS METAD DISTANCE | vatom colvar generic setup bias |
| 21.025 | Computational and biochemical analysis of type IV pilus dynamics and stability | bio | molecular dynamics, calcium binding, Type IV pilus | Yasaman Karami | LOWER_WALLS DISTANCE UPPER_WALLS PRINT | bias generic colvar |
| 21.006 | OPES, On-the-fly Probability Enhanced Sampling Method | methods | opes, alanine dipeptide, well-tempered, multithermal, multiumbrella | Michele Invernizzi | ECV_MULTITHERMAL ENDPLUMED OPES_METAD ECV_UMBRELLAS_LINE PRINT ENERGY OPES_EXPANDED TORSION | opes generic 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 | BF_LEGENDRE ECV_MULTITHERMAL_MULTIBARIC TD_UNIFORM VOLUME VES_LINEAR_EXPANSION ECV_UMBRELLAS_LINE PRINT MATHEVAL OPT_AVERAGED_SGD ENVIRONMENTSIMILARITY UPPER_WALLS ENERGY OPES_EXPANDED RESTART Q6 | opes symfunc ves colvar envsim function generic setup bias |
| 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 | CONVERT_TO_FES REWEIGHT_METAD ENDPLUMED COM ABMD HISTOGRAM PRINT MATHEVAL LOWER_WALLS UPPER_WALLS COMBINE METAD DUMPGRID READ DISTANCE | vatom colvar function generic bias gridtools |
| 19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Valerio Rizzi | GROUP ENDPLUMED RESTART UNITS COORDINATIONNUMBER PRINT FLUSH UPPER_WALLS METAD DISTANCES COMBINE | symfunc core multicolvar function generic setup bias |
| 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 | HISTOGRAM OPT_AVERAGED_SGD ENERGY COMBINE VES_LINEAR_EXPANSION REWEIGHT_BIAS LOWER_WALLS DUMPGRID BF_LEGENDRE OPT_DUMMY VOLUME PRINT TD_WELLTEMPERED UPPER_WALLS READ Q6 TD_MULTITHERMAL_MULTIBARIC CONVERT_TO_FES CELL MATHEVAL REWEIGHT_TEMP_PRESS RESTART LOAD | symfunc ves colvar function generic setup bias gridtools |
| 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 | ENDPLUMED COORDINATIONNUMBER PRINT LOWER_WALLS UPPER_WALLS ENERGY METAD GYRATION DISTANCES | symfunc multicolvar colvar generic bias |
| 19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Giovanni Bussi | TORSION INCLUDE COM MAXENT MOLINFO WHOLEMOLECULES PRINT MATHEVAL COORDINATION FLUSH SORT METAD DISTANCE | vatom colvar function generic bias |
| 19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Michele Invernizzi | ENDPLUMED OPES_METAD UNITS PRINT POSITION METAD EXTERNAL TORSION | opes colvar generic setup bias |
| 19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Carlo Camilloni | DHENERGY PBMETAD ENSEMBLE GROUP RDC ENDPLUMED DISTANCE CENTER METAINFERENCE MOLINFO WHOLEMOLECULES RESTRAINT PRINT STATS UPPER_WALLS ALPHABETA DIHCOR TORSION | vatom core isdb colvar function multicolvar generic bias |
| 25.028 | Designing transferable transition state guided collective variable via interpretable machine learning model for enhanced sampling. A case study on polymer collapse transition | bio | metadynamics, polymer collapse transition, transferable CV,interpretable ML-model | Saikat Dhibar and Biman Jana | GROUP MATHEVAL COORDINATION LOWER_WALLS COMBINE CENTER WHOLEMOLECULES DISTANCE METAD UPPER_WALLS GYRATION PRINT | colvar core vatom bias generic function |
| 25.024 | Sampling glycan-glycan interactions for B22 calculations | bio | B22, glycan, carbohydrates, distance, REST2, metadynamics, RECT, replica exchange | Isabell Louise Grothaus | RESTRAINT COM COMBINE METAD DISTANCE POSITION PRINT | colvar bias vatom generic function |
| 25.019 | The Arch from the Stones. Understanding Protein Folding Energy Landscapes via Bio-inspired Collective Variables | bio | protein folding, OPES, OneOPES, binding free energy | Valerio Rizzi | ENERGY OPES_EXPANDED GROUP ECV_MULTITHERMAL COORDINATION RMSD MOLINFO COMBINE CENTER GHOST OPES_METAD_EXPLORE DISTANCE CUSTOM PRINT | colvar core opes vatom generic function |
| 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 TORSIONS DUMPMULTICOLVAR SMAC PRINT | generic symfunc multicolvar |
| 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 | GROUP UNITS COMMITTOR DISTANCES FIXEDATOM ZDISTANCES DISTANCE UPPER_WALLS OPES_METAD COORDINATIONNUMBER CUSTOM FLUSH PRINT | colvar symfunc opes setup multicolvar vatom bias generic function core |
| 25.001 | RNA G-quadruplex folding with ST-metaD protocol | bio | RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | MOLINFO COMBINE WHOLEMOLECULES METAD ERMSD | bias generic colvar 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 | TORSION GROUP PATH PYTORCH_MODEL COORDINATION FIT_TO_TEMPLATE LOWER_WALLS CENTER WHOLEMOLECULES FIXEDATOM RESTART DISTANCE UPPER_WALLS OPES_METAD CUSTOM PRINT | colvar core opes setup pytorch bias vatom generic function mapping |
| 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 | PRINT DISTANCE | generic 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 | GROUP MOLINFO WRAPAROUND WHOLEMOLECULES DISTANCE EMMIVOX UPPER_WALLS BIASVALUE PRINT INCLUDE | colvar core bias generic isdb |
| 23.037 | Estimating binding free energy of solid binding peptides without extensive sampling | bio | metadynamics, solid binding peptides | Xin Qi | PBMETAD COM LOWER_WALLS MOLINFO DISTANCE UPPER_WALLS GYRATION PRINT | bias vatom generic colvar |
| 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 COMBINE ANN WHOLEMOLECULES MOLINFO ALPHARMSD METAD POSITION PRINT | colvar bias secondarystructure generic annfunc function |
| 23.028 | Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process | chemistry | Ammonia decomposition; Dynamics;OPES; Neural Network potential | Manyi Yang | ENERGY GROUP MATHEVAL COM LOWER_WALLS UNITS DISTANCES COMMITTOR FIXEDATOM DISTANCE UPPER_WALLS ZDISTANCES OPES_METAD COORDINATIONNUMBER CUSTOM FLUSH PRINT | colvar core symfunc opes setup multicolvar vatom bias generic function |
| 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 LOWER_WALLS UNITS UPPER_WALLS BIASVALUE OPES_METAD CUSTOM POSITION PRINT ENDPLUMED | colvar opes setup pytorch bias generic function |
| 23.019 | Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors | bio | binding pathway, binding energy, sketch-map, drug development | Raitis Bobrovs | SKETCHMAP VORONOI DISSIMILARITIES LANDMARK_SELECT_FPS COM WHOLEMOLECULES PATHMSD VSTACK METAD UPPER_WALLS DISTANCE COLLECT_FRAMES CUSTOM SKETCHMAP_PROJECTION TRANSPOSE PRINT | landmarks matrixtools valtools colvar vatom bias generic dimred function |
| 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 | DRR LOWER_WALLS UNITS PATHMSD METAD TIME UPPER_WALLS BIASVALUE CUSTOM FLUSH PRINT | drr colvar setup bias generic function |
| 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 | ENERGY LOWER_WALLS WHOLEMOLECULES CONTACTMAP METAD UPPER_WALLS PRINT | bias generic colvar |
| 22.041 | Skipping the Replica Exchange Ladder with Normalizing Flows | methods | OPES, alanine, normalizing flows, replica exchange | Michele Invernizzi | ENERGY TORSION OPES_EXPANDED ECV_MULTITHERMAL UNITS OPES_METAD POSITION PRINT ENDPLUMED | generic opes setup colvar |
| 22.026 | Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification | materials | Peptoid, silica | Jim Pfaendtner | PBMETAD COM MOLINFO DISTANCE UPPER_WALLS GYRATION PRINT | bias vatom generic colvar |
| 22.012 | Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT | bio | contact maps, protein-protein interactions | Isabell-Louise Grothaus | CENTER PRINT DISTANCE CONTACTMAP | vatom 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 | ALPHABETA TORSION COORDINATION MOLINFO ALPHARMSD WHOLEMOLECULES DISTANCE UPPER_WALLS METAD FLUSH PRINT ANGLE | colvar multicolvar bias secondarystructure generic |
| 22.004 | Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques | chemistry | reaction discovery, OPES, collective variables | Umberto Raucci | PYTORCH_MODEL GROUP MATHEVAL COORDINATION COM LOWER_WALLS UNITS OPES_METAD_EXPLORE DISTANCE UPPER_WALLS LOAD OPES_METAD CUSTOM PRINT | colvar core opes setup pytorch vatom bias generic function |
| 21.017 | All-atom simulations of the Vav1 AD construct | bio | metadynamics, parallel-bias, well-tempered | Simone Orioli | PBMETAD ALPHABETA GROUP REWEIGHT_BIAS MOLINFO ALPHARMSD WHOLEMOLECULES CONTACTMAP RESTART METAD PRINT | colvar setup multicolvar bias secondarystructure generic core |
| 20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Faidon Brotzakis | CONVERT_TO_FES GROUP EMMI RMSD MOLINFO DISTANCES WHOLEMOLECULES READ BIASVALUE HISTOGRAM PRINT DUMPGRID | colvar core multicolvar bias generic gridtools isdb |
| 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 PRINT DISTANCE METAD | bias generic colvar |
| 20.018 | Free energy barriers from biased molecular dynamics simulations | methods | kinetics, free energy barriers, chemical reactions, nucleation, metadynamics | Kristof Bal | ENERGY UNITS COMBINE CENTER DISTANCE PAIRENTROPY COORDINATION SPRINT PRINT DUMPGRID VOLUME CONVERT_TO_FES REWEIGHT_BIAS UPPER_WALLS FLUSH DENSITY LOWER_WALLS LOCAL_AVERAGE METAD CONTACT_MATRIX LOAD REWEIGHT_METAD HISTOGRAM COORDINATIONNUMBER Q6 | adjmat colvar symfunc setup vatom bias generic sprint volumes gridtools function |
| 20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Luigi Bonati | PYTORCH_MODEL TORSION GROUP MATHEVAL COM LOWER_WALLS UNITS DISTANCE UPPER_WALLS OPES_METAD LOAD FLUSH PRINT ENDPLUMED | colvar core opes setup pytorch vatom bias generic function |
| 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 | GROUP MOLINFO WHOLEMOLECULES PATHMSD METAD RESTART UPPER_WALLS PRINT | colvar setup bias generic core |
| 19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Valerio Rizzi | GROUP UNITS COMBINE RESTART METAD COORDINATIONNUMBER EXTERNAL FLUSH PRINT ENDPLUMED | symfunc core setup bias generic function |
| 19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Jakub Rydzewski | LOWER_WALLS UNITS PATHMSD UPPER_WALLS METAD RESTART PRINT | bias generic setup colvar |
| 19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Luigi Bonati | ENERGY TORSION Q6 ENVIRONMENTSIMILARITY UNITS LOAD POSITION PRINT ENDPLUMED | symfunc colvar setup generic envsim |
| 19.032 | Chemical reaction in solution using path collective variables based on coordination patterns | chemistry | chemical reactions, solutions, metadynamics, coordination patterns | Fabio Pietrucci | PATH DISTANCES RESTART METAD UPPER_WALLS FLUSH PRINT | setup multicolvar bias generic mapping |
| 19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Silvio Pipolo | CELL LOWER_WALLS FUNCPATHMSD PIV UPPER_WALLS METAD PRINT | colvar bias generic piv function |
| 19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Carlo Camilloni | RESTRAINT GROUP RMSD MOLINFO CENTER WHOLEMOLECULES DISTANCE UPPER_WALLS SAXS BIASVALUE STATS PRINT ENDPLUMED INCLUDE | colvar bias vatom isdb generic function core |
| 19.003 | EMMI ClpP | bio | metainference, cryo-EM | Max Bonomi | GROUP EMMI MOLINFO BIASVALUE PRINT | bias isdb generic core |
| 19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Giovanni Bussi | LOWER_WALLS MOLINFO COMBINE DISTANCES DISTANCE UPPER_WALLS METAD RANDOM_EXCHANGES ERMSD FLUSH PRINT INCLUDE ANGLE | colvar multicolvar bias generic function |
| 26.004 | Resolving the ambiguous binding site of quercetin at the calcineurin subunit junction using funnel metadynamics with deep learning collective variables | bio | metadynamics, funnel metadynamics, DeepTICA | Jason Loo | MATHEVAL COM ENERGY FUNNEL WHOLEMOLECULES GROUP DISTANCE COORDINATION METAD WRAPAROUND PYTORCH_MODEL UPPER_WALLS FUNNEL_PS LOWER_WALLS PRINT RMSD | function pytorch vatom core bias generic colvar funnel |
| 26.000 | OPES simulations of disordered proteins | bio | OPES, IDPs | Julian Streit | RESTART OPES_EXPANDED ECV_MULTITHERMAL PRINT ENERGY | generic colvar opes setup |
| 25.022 | Imidazole Diffusion in SALEM-2 MOF | materials | OPES, Diffusion, Ring opening, MOFs, Machine Learning Potentials | Sudheesh Kumar Ethirajan | DISTANCES WHOLEMOLECULES GROUP PROJECTION_ON_AXIS DISTANCE UNITS MOLINFO CENTER OPES_METAD ENDPLUMED PRINT | vatom core multicolvar generic colvar opes setup |
| 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 | HISTOGRAM WHOLEMOLECULES GROUP DISTANCE COORDINATION CONVERT_TO_FES TORSION DUMPGRID ANGLE PRINT | generic gridtools colvar 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 | BIASVALUE RMSD WHOLEMOLECULES GROUP UPPER_WALLS DISTANCE COORDINATION MOLINFO PBMETAD EMMI DUMPATOMS PARABETARMSD CENTER DUMPMASSCHARGE COM PRINT ALPHARMSD | vatom isdb core bias generic colvar secondarystructure |
| 24.026 | Constant pH metadynamics of RNA oligomers | bio | metadynamics, pH, RNA | Giovanni Bussi | PUCKERING MOLINFO METAD RESTART TORSION PRINT | bias generic colvar setup |
| 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 | MATHEVAL ECV_MULTITHERMAL WHOLEMOLECULES GROUP DISTANCE COORDINATION OPES_METAD_EXPLORE CENTER FIT_TO_TEMPLATE TORSION ENDPLUMED UPPER_WALLS OPES_EXPANDED FIXEDATOM ANGLE LOWER_WALLS PRINT ENERGY | function vatom core bias generic colvar opes |
| 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 | CUSTOM GROUP DISTANCE COMBINE COORDINATION OPES_METAD_EXPLORE RESTART TORSION OPES_EXPANDED ECV_MULTITHERMAL PRINT ENERGY | function core generic colvar opes setup |
| 24.005 | Learning Markovian Dynamics with Spectral Maps | methods | spectral map, collective variables, machine learning | Jakub Rydzewski | BIASVALUE CUSTOM DISTANCE UNITS PRINT | function bias generic colvar setup |
| 23.030 | Data Driven Classification of Ligand Unbinding Pathways | bio | OPES Explore, OPES Flooding, Benzene T4 Lysozyme, Ligand unbinding, Pathway classification, Kinetics, Residence time | Dhiman Ray | MATHEVAL CUSTOM MOLINFO FLUSH COORDINATION CENTER POSITION WRAPAROUND COM COMMITTOR UPPER_WALLS WHOLEMOLECULES ENDPLUMED LOWER_WALLS OPES_METAD_EXPLORE PRINT BIASVALUE GROUP DISTANCE UNITS OPES_METAD FIT_TO_TEMPLATE TORSION ENERGY | function vatom core bias generic colvar opes setup |
| 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 | MATHEVAL CUSTOM MOLINFO PYTORCH_MODEL ANGLE CONTACTMAP COMBINE COORDINATION CENTER UPPER_WALLS COMMITTOR RMSD WHOLEMOLECULES ENDPLUMED INCLUDE LOWER_WALLS PRINT GROUP DISTANCE OPES_METAD FIT_TO_TEMPLATE FIXEDATOM ENERGY | function pytorch vatom core bias generic colvar opes |
| 23.002 | Critical comparison of general-purpose collective variables for crystal nucleation | methods | metadynamics, umbrella sampling, commitor, entropy, PIV | Julien Lam | LOCAL_AVERAGE CUSTOM Q6 PAIRENTROPY RESTRAINT UNITS METAD PIV Q4 UPPER_WALLS VOLUME FUNCPATHMSD PRINT ENERGY | function symfunc gridtools bias generic colvar piv setup |
| 22.044 | Colloid Crystallisation Analyses | materials | Q4, Q6, Pair Entropy, DFS | Aaron Finney | LOCAL_AVERAGE MFILTER_MORE Q6 GROUP COORDINATIONNUMBER COMBINE LOCAL_Q6 CONTACT_MATRIX Q4 CLUSTER_NATOMS MFILTER_LESS DFSCLUSTERING LOCAL_Q4 PRINT | function symfunc core multicolvar generic clusters adjmat |
| 22.042 | Metadynamics of NSP10 and variants | bio | metadynamics, NSP10, crystal structure, variants | Shozeb Haider | TORSION PRINT METAD | 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 | BIASVALUE CUSTOM FLUSH METAD DRR PATHMSD PRINT | function drr bias generic colvar |
| 22.020 | Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix–Junction–Helix RNA | bio | RNA force field, Helix-Junction-Helix RNA, SAXS, Well tempered metadynamics | Weiwei He | WHOLEMOLECULES GROUP DISTANCE METAD TORSION COM PRINT | vatom core bias generic colvar |
| 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 | MATHEVAL CUSTOM COMMITTOR WHOLEMOLECULES GROUP DISTANCE COORDINATION CENTER OPES_METAD FIT_TO_TEMPLATE PYTORCH_MODEL UPPER_WALLS FIXEDATOM LOWER_WALLS PRINT RMSD | function pytorch vatom core bias generic colvar opes |
| 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 | MATHEVAL ZANGLES CUSTOM YANGLES WHOLEMOLECULES UPPER_WALLS ALPHABETA DISTANCE COMBINE MOLINFO METAD TORSION COM XANGLES LOWER_WALLS PRINT | function vatom multicolvar bias generic 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 | COM CUSTOM DISTANCE UNITS METAD TORSION UPPER_WALLS LOWER_WALLS PRINT | function vatom bias generic colvar setup |
| 21.033 | Multiple-path-metadynamics applied to DNA base-pairing transitions | bio | path-CV, metadynamics, multiple-walker, dna | Alberto Pérez-de-Alba-Ortíz | RESTRAINT CONSTANT COMBINE METAD UPPER_WALLS INCLUDE MOVINGRESTRAINT PRINT | bias generic function |
| 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 | ALPHABETA GYRATION DISTANCE COORDINATION METAD PBMETAD TORSION COM INCLUDE PRINT ENERGY | vatom multicolvar generic colvar bias |
| 20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Cristina Paissoni | BIASVALUE WHOLEMOLECULES GROUP RESTRAINT DISTANCE ENSEMBLE MOLINFO CENTER STATS SAXS INCLUDE PRINT | function vatom core isdb bias generic colvar |
| 20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Vojtech Spiwok | TORSION PRINT METAD | bias generic colvar |
| 20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Max Bonomi | ALPHABETA DIHCOR WHOLEMOLECULES GYRATION COORDINATION MOLINFO PBMETAD INCLUDE PRINT | multicolvar generic colvar bias |
| 20.016 | Predicting polymorphism in molecular crystals using orientational entropy | materials | metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy | Pablo Piaggi | GROUP LOAD METAD CENTER UPPER_WALLS VOLUME INCLUDE PRINT | vatom core bias generic colvar setup |
| 20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Pratyush Tiwary | WHOLEMOLECULES DISTANCE COMBINE METAD MOLINFO RESTART TORSION UPPER_WALLS PRINT RMSD | function bias generic colvar setup |
| 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 | MOLINFO CONVERT_TO_FES DUMPGRID REWEIGHT_METAD CONTACTMAP FLUSH COMBINE UPPER_WALLS COM HISTOGRAM READ WHOLEMOLECULES ENDPLUMED FUNCPATHMSD LOWER_WALLS PRINT ABMD DISTANCE METAD | function gridtools vatom bias generic colvar |
| 19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Mattia Bernetti | WHOLEMOLECULES METAD UPPER_WALLS PATHMSD LOWER_WALLS PRINT | bias generic colvar |
| 19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Michele Invernizzi | UNITS LOAD METAD RESTART VES_DELTA_F TORSION ENDPLUMED POSITION PRINT ENERGY | bias generic colvar setup ves |
| 26.008 | Ensemble Dynamics | methods | State Exploration, Protein Folding, Drug Binding, Phase Transition | Florian M. Dietrich | CELL DISTANCE BIASVALUE POSITION LOAD OPES_METAD_EXPLORE CUSTOM GROUP TORSION PRINT UNITS | function core setup bias generic opes colvar |
| 25.023 | Molecular simulations of Tau-protein oligomers | bio | metadynamics, proteins, aggregation | Giovanni Bussi | RESTRAINT CONTACTMAP REWEIGHT_BIAS METAD RMSD CONVERT_TO_FES FLUSH HISTOGRAM CUSTOM PRINT RESTART DUMPGRID | function setup bias generic gridtools colvar |
| 25.011 | Chiral perovskite nucleation | chemistry | metadynamics, chiral perovskites, nucleation | Adriana Pietropaolo | MULTI_RMSD LOWER_WALLS DISTANCE UPPER_WALLS PBMETAD MATHEVAL PRINT RESTART UNITS | function setup bias generic colvar |
| 25.010 | Kinetic rates calculation with Ratchet&Pawl MD | methods | kinetics, ligand binding, ABMD, ratchet&pawl MD | Riccardo Capelli | COMMITTOR WHOLEMOLECULES DISTANCE FLUSH ABMD GROUP COM PRINT | core bias vatom generic colvar |
| 25.008 | Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting | methods | metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting | Dhiman Ray | MOLINFO WHOLEMOLECULES LOWER_WALLS DISTANCE BIASVALUE CUSTOM METAD OPES_METAD RMSD POSITION UPPER_WALLS ENDPLUMED PYTORCH_MODEL PRINT TORSION GROUP ENERGY UNITS | function core setup bias generic opes pytorch colvar |
| 25.002 | M3_PCV-ABMD | chemistry | Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor | Gian Marco Elisi | UPPER_WALLS ENDPLUMED ABMD PRINT UNITS PATHMSD | setup generic bias colvar |
| 24.031 | DeepLNE | methods | PATHCV, OPES, OneOPES | Thorben Fröhlking | MOLINFO COORDINATION OPES_EXPANDED ERMSD COMBINE OPES_METAD_EXPLORE VOLUME ECV_MULTITHERMAL PYTORCH_MODEL PRINT RESTART ENERGY | function setup generic opes pytorch colvar |
| 24.028 | All-atom simulations of RNA-membrane interactions | bio | metadynamics, membrane, RNA | Giovanni Bussi | MOLINFO SORT LOWER_WALLS WHOLEMOLECULES DISTANCE GYRATION GHOST METAD POSITION UPPER_WALLS COMBINE CENTER DISTANCES MATHEVAL PUCKERING GROUP PRINT | function core bias vatom generic multicolvar 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 | MOLINFO COORDINATION WHOLEMOLECULES ANTIBETARMSD GYRATION DISTANCE DIHCOR INCLUDE ALPHARMSD PARABETARMSD COMBINE PBMETAD ENDPLUMED FLUSH GROUP TORSION PRINT | function core bias generic multicolvar secondarystructure colvar |
| 24.017 | Absolute Binding Free Energies with OneOPES | methods | protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy | Francesco Gervasio | WHOLEMOLECULES CONTACTMAP LOWER_WALLS UPPER_WALLS INCLUDE METAD ECV_MULTITHERMAL COORDINATION OPES_EXPANDED BIASVALUE PROJECTION_ON_AXIS RMSD ENERGY MOLINFO WRAPAROUND OPES_METAD_EXPLORE MATHEVAL CUSTOM GROUP COM PRINT RESTART TORSION CONSTANT | function core setup bias vatom generic opes colvar |
| 24.016 | Cryo-EM guided simulations of ribozyme | bio | metainference, cryo-EM | Giovanni Bussi | MOLINFO WHOLEMOLECULES RESTRAINT BIASVALUE INCLUDE ERMSD EMMIVOX GROUP PRINT | isdb core bias generic colvar |
| 24.009 | Weighted Shape Gaussian Mixture Models | bio | metadynamics, clustering | Glen Hocky | TORSION METAD GROUP UNITS PRINT | core setup bias generic 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 CONTACTMAP LOWER_WALLS DISTANCE INCLUDE METAD ALPHARMSD UPPER_WALLS PRINT FUNCPATHMSD PATHMSD | function bias generic secondarystructure colvar |
| 23.010 | An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G‑Protein-Coupled Receptor Ligands | bio | GPCR, binding free energy, free energy surface | Timothy Clark | WHOLEMOLECULES LOWER_WALLS DISTANCE BIASVALUE UPPER_WALLS METAD MATHEVAL PRINT CONSTANT | generic function bias colvar |
| 22.040 | From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure | bio | SARS-CoV-2, Spike, Omicron | Miłosz Wieczór | WHOLEMOLECULES LOWER_WALLS METAD UPPER_WALLS PCAVARS PRINT | generic bias mapping |
| 22.036 | Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction | bio | Well-tempered MetaDynamics with Hamiltonian Replica Exchange | Miroslav Krepl | MOLINFO COORDINATION BIASVALUE UPPER_WALLS METAD COMBINE GHBFIX LOAD FLUSH CUSTOM GROUP PRINT | function core setup bias generic colvar |
| 22.024 | Conformational Entropy as a Potential Liability of Computationally Designed Antibodies | bio | metadynamics, conformational entropy, antibody, nanobody | Thomas Löhr | MOLINFO WHOLEMOLECULES ANTIBETARMSD COM ALPHARMSD PBMETAD PRINT ALPHABETA TORSION RESTART | setup bias vatom generic multicolvar secondarystructure colvar |
| 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 | MOLINFO COORDINATION WHOLEMOLECULES TORSION EMMI BIASVALUE UPPER_WALLS RMSD PBMETAD GROUP RESTART COM PRINT | isdb core setup bias vatom generic colvar |
| 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 | UPPER_WALLS OPES_METAD ENVIRONMENTSIMILARITY VOLUME HISTOGRAM CUSTOM PRINT RESTART AROUND DUMPGRID ENERGY | volumes function envsim setup bias generic opes gridtools colvar |
| 22.013 | Ligand dissociation from PreQ1 riboswitch | bio | ligand, RNA, metadynamics, pRAVE | Yihang Wang | COMMITTOR MOLINFO WHOLEMOLECULES DISTANCE METAD RMSD COMBINE COORDINATIONNUMBER PRINT COM | function colvar bias vatom generic symfunc |
| 22.006 | Peptide framework for screening the effects of amino acids on assembly | bio | metadynamics, peptides | Andrew White | REWEIGHT_BIAS GYRATION INCLUDE METAD COMBINE CONVERT_TO_FES DISTANCES HISTOGRAM GROUP COM DUMPGRID PRINT | function core bias vatom generic gridtools multicolvar colvar |
| 22.003 | Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling | methods | opes, metadynamics, reweighting, alanine, muller | Michele Invernizzi | ECV_UMBRELLAS_FILE LOWER_WALLS OPES_EXPANDED BIASVALUE METAD OPES_METAD POSITION UPPER_WALLS PBMETAD OPES_METAD_EXPLORE ENDPLUMED ECV_MULTITHERMAL CUSTOM PRINT TORSION ENERGY UNITS | function setup bias generic opes colvar |
| 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 | WHOLEMOLECULES LOWER_WALLS GYRATION UPPER_WALLS METAD ENDPLUMED GROUP ALPHABETA PRINT | core bias generic multicolvar colvar |
| 21.037 | Molecular Dynamics simulations of RBD/hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain | Max Bonomi | PRINT RMSD DISTANCE | generic colvar |
| 21.036 | 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 | MOLINFO COORDINATION LOWER_WALLS WHOLEMOLECULES DIHCOR ANTIBETARMSD GYRATION UPPER_WALLS METAD ALPHARMSD PARABETARMSD GROUP RANDOM_EXCHANGES PRINT ENERGY | core bias generic multicolvar secondarystructure colvar |
| 21.020 | Reweighted Jarzynski sampling | methods | free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions | Kristof Bal | UPPER_WALLS ANN METAD OPES_METAD CONVERT_TO_FES REWEIGHT_METAD DUMPGRID RESTRAINT BIASVALUE MOVINGRESTRAINT BF_CHEBYSHEV VES_LINEAR_EXPANSION UNITS COMBINE LOAD COORDINATIONNUMBER CUSTOM OPT_AVERAGED_SGD TD_WELLTEMPERED REWEIGHT_BIAS DISTANCE FLUSH HISTOGRAM PRINT CONSTANT | function annfunc setup colvar bias generic opes gridtools ves symfunc |
| 21.018 | Localized Volume-based Metadynamics | bio | LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification | Riccardo Capelli | WHOLEMOLECULES FIXEDATOM READ UPPER_WALLS METAD CONVERT_TO_FES ENDPLUMED REWEIGHT_METAD DUMPGRID COORDINATION RMSD MATHEVAL GROUP COM DISTANCE POSITION FLUSH HISTOGRAM PRINT | function core bias vatom generic gridtools 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 | WHOLEMOLECULES COORDINATION RESTRAINT REWEIGHT_BIAS POSITION METAD CENTER MATHEVAL PRINT RESTART | function setup bias vatom generic colvar |
| 21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Tarsis Ferreira | MOLINFO WHOLEMOLECULES LOWER_WALLS COORDINATION DISTANCE METAD UPPER_WALLS INCLUDE HISTOGRAM REWEIGHT_METAD PUCKERING GROUP RANDOM_EXCHANGES DUMPGRID PRINT ENERGY | core bias generic gridtools colvar |
| 20.024 | Gaussian Mixture Based Enhanced Sampling (GAMBES) | methods | enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias | Jayashrita Debnath | LOWER_WALLS DISTANCE UPPER_WALLS COMBINE LOAD DISTANCES PRINT TORSION GROUP ENERGY UNITS | function core setup bias generic multicolvar colvar |
| 20.006 | Class B GPCR activation mechanism | bio | metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | MOLINFO WHOLEMOLECULES LOWER_WALLS DISTANCE UPPER_WALLS METAD RMSD COMBINE CENTER MATHEVAL PRINT ENERGY | function bias vatom generic colvar |
| 19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | MOLINFO GYRATION DISTANCE UPPER_WALLS METAD PRINT COM ENERGY | vatom generic bias colvar |
| 19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | MOLINFO GYRATION DISTANCE METAD UPPER_WALLS PRINT COM ENERGY | vatom generic bias colvar |
| 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 | BRIDGE MOLINFO WHOLEMOLECULES LOWER_WALLS DISTANCE COM UPPER_WALLS METAD RMSD COMBINE FUNNEL DISTANCES REWEIGHT_METAD GROUP ALPHABETA TORSION PRINT | function core bias vatom generic multicolvar funnel adjmat colvar |
| 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 | DISTANCE UPPER_WALLS METAD PRINT COM ENERGY | vatom generic bias 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 | RESTRAINT DISTANCE COM GROUP TORSION PRINT | core bias vatom generic colvar |
| 19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Matteo Salvalaglio | GYRATION METAD ENDPLUMED DISTANCES COORDINATIONNUMBER PRINT RESTART | setup colvar bias generic multicolvar symfunc |
| 26.006 | Metadynamics simulations of buried phosphorylation sites and proline isomerisation | bio | metadynamics | Julian Streit | METAD COORDINATION TORSION WHOLEMOLECULES MOLINFO PRINT | bias generic colvar |
| 25.025 | Enhanced Sampling of Ligand Binding Coupled to RNA Conformational Dynamics | bio | OPES, OPES Flooding , Metadynamics, RNA, Ligand binding, Free Energy, Kinetics, Funnel | Revanth Elangovan and Dhiman Ray | FUNNEL RMSD LOWER_WALLS COMMITTOR CUSTOM FUNNEL_PS PRINT COORDINATION METAD WRAPAROUND COM GROUP TORSION ENDPLUMED WHOLEMOLECULES MATHEVAL OPES_METAD UPPER_WALLS DISTANCE CENTER | generic funnel function vatom opes core colvar bias |
| 25.013 | Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices | bio | umbrella sampling, temperature ramping | Alexander Berlaga | RESTRAINT PYTORCH_MODEL DISTANCE GYRATION PRINT | pytorch bias generic colvar |
| 24.032 | DeepLNE++ | methods | PATHCV, OPES | Thorben Fröhlking | ENERGY GROUP DISTANCE TORSION LOAD COMBINE CUSTOM COORDINATION OPES_METAD PRINT | generic setup function opes core colvar |
| 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 | METAD GROUP TORSION COMMITTOR LOAD PRINT | generic setup core colvar bias |
| 24.010 | Oxytocin metadynamics simulation | bio | metadynamics, oxytocin, peptide | Jan Beránek | METAD FLUSH TORSION RESTART WHOLEMOLECULES PRINT | bias setup generic colvar |
| 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 | METAD RMSD WHOLEMOLECULES DISTANCE MATHEVAL MOLINFO PRINT | function bias generic colvar |
| 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 | SHADOW METAD DISTANCES WRAPAROUND POSITION GROUP UPPER_WALLS CENTER WHOLEMOLECULES MOLINFO FIT_TO_TEMPLATE PRINT | generic vatom core colvar multicolvar bias isdb |
| 23.024 | Permutationally Invariant Networks for Enhanced Sampling (PINES) | methods | collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent | Nicholas Herringer | LOAD PRINT PBMETAD | bias generic setup |
| 23.018 | Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention | materials | metadynamics, surface binding, peptide adsorption | Kaylyn Torkelson | COM UPPER_WALLS DISTANCE PBMETAD GYRATION PRINT | bias vatom generic colvar |
| 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 | bias generic setup |
| 22.000 | Amyloid precursor protein processing by human γ-secretase | bio | Bias Exchange Metadynamics, Helix unfolding, coupled binding | Xiaoli Lu | ALPHARMSD METAD ANTIBETARMSD COORDINATION RANDOM_EXCHANGES DISTANCE CENTER MOLINFO UNITS CONTACTMAP INCLUDE PRINT | generic setup vatom colvar bias secondarystructure |
| 21.044 | NaCl nucleation | chemistry | metadynamics, DFS clustering | Aaron Finney | METAD DUMPGRID COORDINATIONNUMBER CLUSTER_NATOMS GROUP CONTACT_MATRIX INSPHERE HISTOGRAM COMBINE LOCAL_Q6 DFSCLUSTERING MFILTER_MORE FIXEDATOM CLUSTER_DISTRIBUTION PRINT Q6 | gridtools generic function vatom volumes adjmat core symfunc multicolvar bias clusters |
| 21.029 | Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs | bio | metadynamics, small peptide, machine learning | Pratyush Tiwary | ENERGY FLUSH EXTERNAL TORSION RESTART MOLINFO PRINT | generic colvar bias setup |
| 21.013 | Role of vibrational excitation in heterogeneous catalysis | chemistry | catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption | Kristof Bal | FLUSH CONVERT_TO_FES REWEIGHT_METAD REWEIGHT_BIAS HISTOGRAM LOAD BF_CHEBYSHEV DUMPGRID RESTRAINT LOWER_WALLS UNITS COORDINATION PRINT OPT_AVERAGED_SGD METAD COORDINATIONNUMBER UWALLS COMBINE VES_LINEAR_EXPANSION DISTANCES EXTERNAL UPPER_WALLS DISTANCE ANGLES TD_GRID | ves gridtools generic setup function colvar symfunc multicolvar bias |
| 21.012 | NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition | bio | funnel metadynamics | Jim Pfaendtner | FUNNEL METAD LOWER_WALLS COM UPPER_WALLS DISTANCE FUNNEL_PS PRINT | generic funnel vatom colvar bias |
| 21.004 | Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy | bio | machine learning, well-tempered metadynamics, path collective variable, potential of mean force, standard binding free energy calculations, host-guest, protein-ligand unbinding | Dorothea Gobbo | PATHMSD METAD LOWER_WALLS UPPER_WALLS RESTART WHOLEMOLECULES PRINT | bias generic colvar setup |
| 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 ERMSD DISTANCE CENTER RESTART TORSION MOLINFO PRINT | generic setup vatom colvar bias |
| 19.080 | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | methods | ves, variationally enhanced sampling, vibrational excitation, chemical reactions | Kristof Bal | OPT_AVERAGED_SGD DUMPGRID LOWER_WALLS VES_LINEAR_EXPANSION FLUSH CONVERT_TO_FES EXTERNAL UPPER_WALLS DISTANCE HISTOGRAM COMBINE BF_CHEBYSHEV COORDINATION UNITS TD_WELLTEMPERED TD_GRID ANGLE PRINT | ves generic gridtools setup function colvar bias |
| 19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Matteo Salvalaglio | METAD BIASVALUE READ DUMPGRID CONVERT_TO_FES REWEIGHT_METAD EXTERNAL DISTANCE TORSION COMMITTOR REWEIGHT_BIAS HISTOGRAM MATHEVAL PRINT | gridtools generic function colvar bias |
| 19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Matteo Salvalaglio | GROUP DISTANCE CENTER ENDPLUMED INCLUDE PRINT | core generic vatom colvar |
| 19.059 | cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide | bio | bias-exchange metadynamics, cis-trans isomerization | Fabrizio Marinelli | METAD RANDOM_EXCHANGES TORSION INCLUDE PRINT | bias generic colvar |
| 19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Glen Hocky | RESTRAINT EDS DISTANCE TORSION COMBINE PRINT | generic function colvar bias eds |
| 19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Matteo Salvalaglio | METAD LOWER_WALLS UPPER_WALLS DISTANCE TORSION CENTER COMMITTOR PRINT | bias vatom generic colvar |
| 19.009 | RNA tetraloops folding | bio | metadynamics, RNA, folding | Giovanni Bussi | METAD ERMSD RMSD ENDPLUMED WHOLEMOLECULES MOLINFO PRINT | bias generic colvar |
| 19.004 | MI Ubiquitin | bio | metainference, NMR | Max Bonomi | CS2BACKBONE RDC GROUP METAINFERENCE WHOLEMOLECULES MOLINFO PRINT | core generic isdb |
| 26.005 | Cryptic pocket discovery in Alzheimer disease risk proteins BIN1, PICALM, and CD2AP via well-tempered metadynamics | methods | cryptic pockets, Alzheimer disease, BIN1, PICALM, CD2AP, well-tempered metadynamics, endocytosis, clathrin-mediated trafficking, virtual screening | Cagrı Ozkurt | WHOLEMOLECULES DISTANCE PRINT METAD ANGLE | colvar bias generic |
| 26.001 | Molecular simulations Alx riboswitch | bio | RNA, riboswitch | Giovanni Bussi | RESTRAINT MOLINFO MOVINGRESTRAINT DISTANCE ERMSD PRINT MATHEVAL | function bias colvar generic |
| 25.003 | Surrogate Model CV | methods | Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding | Sompriya Chatterjee | ENDPLUMED MOLINFO WHOLEMOLECULES DISTANCE COMBINE TORSION CUSTOM COMMITTOR GROUP PRINT ENERGY OPES_METAD MATHEVAL PYTORCH_MODEL | function colvar core opes pytorch generic |
| 25.000 | Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer | bio | metadynamics, pathCV | Sahithya Sridharan Iyer | RESTART MOLINFO WHOLEMOLECULES UPPER_WALLS DISTANCE COM PRINT METAD GROUP FUNCPATHGENERAL | function colvar setup core bias vatom generic |
| 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 | RESTART LOWER_WALLS COORDINATION UPPER_WALLS DISTANCE CUSTOM COMMITTOR UNITS PRINT GROUP OPES_METAD | function colvar setup core opes bias generic |
| 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 | LOWER_WALLS UPPER_WALLS DISTANCE CUSTOM COMBINE COMMITTOR TORSION UNITS PRINT FLUSH OPES_METAD | function colvar setup opes bias generic |
| 23.039 | Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation | chemistry | metadynamics, ligand dissociation | Eric Beyerle | RESTRAINT DUMPMASSCHARGE MOLINFO UPPER_WALLS DISTANCE COMBINE FIXEDATOM PRINT METAD CENTER | function colvar bias vatom generic |
| 23.021 | Into the Dynamics of Rotaxanes at Atomistic Resolution | materials | metadynamics, rotaxanes, molecular shuttles, molecular machines | Luigi Leanza | UPPER_WALLS DISTANCE TORSION FIXEDATOM PRINT METAD CENTER MATHEVAL CUSTOM | function colvar bias vatom generic |
| 23.016 | Activation/deactivation free-energy profiles for the β2-adrenergic receptor: Ligand modes of action | bio | G protein coupled receptor, beta-adrenergic, receptor activation, partial agonism, metadynamics | Timothy Clark | READ MOLINFO REWEIGHT_METAD HISTOGRAM WHOLEMOLECULES DISTANCE RMSD PRINT METAD CONVERT_TO_FES DUMPGRID MATHEVAL | function colvar gridtools bias generic |
| 23.014 | Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 | bio | metadynamics, oligomerization, chemokine receptors, GPCR, membrane | Vittorio Limongelli | WHOLEMOLECULES UPPER_WALLS DISTANCE COMBINE TORSION COM PRINT METAD FLUSH | function colvar bias vatom generic |
| 23.011 | OneOPES, a combined enhanced sampling method to rule them all | bio | OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding | Valerio Rizzi | ENDPLUMED MOLINFO ECV_MULTITHERMAL DISTANCE TORSION OPES_EXPANDED PRINT METAD ENERGY OPES_METAD_EXPLORE | opes colvar bias generic |
| 23.006 | Transcription factor unbinding | bio | metadynamics, DNA, conformational changes | Malin Lüking | MOLINFO CONTACTMAP DISTANCE COM ALPHARMSD DUMPFORCES PRINT METAD ANGLE | colvar secondarystructure bias vatom generic |
| 22.039 | Driving and characterizing nucleation of urea and glycine polymorphs in water | bio | metadynamics, nucleation, amino acids, polymorphism | Eric Beyerle | PAIRENTROPY INCLUDE Q6 COMBINE COORDINATIONNUMBER LOAD Q4 PRINT METAD CENTER GROUP MATHEVAL | function setup core symfunc gridtools bias vatom generic |
| 22.037 | Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site | chemistry | metadynamics, DNA, abasic | Mike Jones | METAD DISTANCES DISTANCE PRINT | multicolvar bias colvar generic |
| 22.029 | Angiotensin-1-7_Metadynamics | bio | Metadynamics, Angiotensin-(1-7), peptide | L.-América Chi | LOWER_WALLS WHOLEMOLECULES COORDINATION UPPER_WALLS GYRATION GROUP PRINT METAD FLUSH | core bias colvar generic |
| 22.028 | N-glycan conformer distributions in atomistic simulation | bio | REST2, RECT, N-glycan, pucker | Isabell Grothaus | READ MOLINFO HISTOGRAM TORSION PRINT METAD CONVERT_TO_FES DUMPGRID PUCKERING | gridtools colvar 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 | RMSD PRINT | colvar generic |
| 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 | UPPER_WALLS UNITS METAD FLUSH OPT_ADAM POSITION INCLUDE BF_LEGENDRE BF_CHEBYSHEV PRINT ENERGY VES_OUTPUT_BASISFUNCTIONS TD_UNIFORM DISTANCE BF_GAUSSIANS OPT_AVERAGED_SGD TD_WELLTEMPERED BF_WAVELETS VES_LINEAR_EXPANSION COORDINATION BF_CUBIC_B_SPLINES | colvar setup bias ves generic |
| 21.035 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, interface | Aaron Finney | RESTRAINT DISTANCE FIXEDATOM LOAD PRINT GROUP | colvar core generic bias vatom setup |
| 21.022 | Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly | materials | parallel bias metadynamics, adsorption, peptide | Xin Qi | MOLINFO LOWER_WALLS PBMETAD UPPER_WALLS GYRATION DISTANCE COM PRINT ENERGY | bias colvar vatom generic |
| 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 WHOLEMOLECULES COORDINATION STATS PRINT | function bias colvar generic |
| 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 | MOLINFO DIHCOR WHOLEMOLECULES STATS TORSION PARABETARMSD FLUSH ENDPLUMED INCLUDE PBMETAD METAINFERENCE PRINT GYRATION COMBINE COORDINATION CS2BACKBONE ENSEMBLE ANTIBETARMSD ALPHARMSD GROUP | function colvar core isdb multicolvar secondarystructure bias generic |
| 20.010 | Phase equilibrium of liquid water and hexagonal ice from enhanced sampling molecular dynamics simulations | materials | water, ice, TIP4P, crystallization, EnvironmentSimilarity, RefCV, kernel, VES, variationally enhanced sampling | Pablo Piaggi | RESTART ENVIRONMENTSIMILARITY VES_LINEAR_EXPANSION OPT_DUMMY BF_LEGENDRE VOLUME Q6 UPPER_WALLS OPT_AVERAGED_SGD PRINT TD_WELLTEMPERED MATHEVAL | function colvar envsim symfunc generic bias ves setup |
| 20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Carlo Camilloni | MOLINFO PBMETAD WHOLEMOLECULES GYRATION DISTANCE TORSION STATS ENSEMBLE ALPHABETA METAINFERENCE PRINT CENTER SAXS FLUSH | function colvar isdb multicolvar bias vatom generic |
| 19.076 | Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones | bio | molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics | Salvatore Assenza | ENDPLUMED MOVINGRESTRAINT GYRATION UNITS PRINT | bias colvar generic setup |
| 19.075 | PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python | other | Python, automatic differentiation | Toni Giorgino | RESTRAINT ENDPLUMED DUMPDERIVATIVES COMBINE DISTANCE TORSION PRINT CENTER GROUP ANGLE CUSTOM | function colvar core bias vatom generic |
| 19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Sandro Bottaro | MOLINFO WHOLEMOLECULES DISTANCE RMSD ERMSD TORSION PRINT METAD | colvar bias generic |
| 19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Gareth Tribello | ENDPLUMED FCCUBIC PRINT UPPER_WALLS UNITS METAD CELL | colvar setup symfunc bias generic |
| 19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | PRINT UPPER_WALLS DISTANCE COMBINE UNITS METAD ENERGY FLUSH | function colvar setup bias generic |
| 19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Mattia Bernetti | ENDPLUMED MOLINFO WHOLEMOLECULES GYRATION ALPHARMSD PRINT METAD ENERGY | bias colvar secondarystructure generic |
| 19.005 | Cmyc small molecule interaction | bio | metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP | Gabriella Heller | INCLUDE MOLINFO PBMETAD WHOLEMOLECULES COORDINATION GYRATION CS2BACKBONE DISTANCE ALPHABETA METAINFERENCE PRINT CENTER GROUP | colvar core isdb multicolvar bias vatom generic |
| 19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Max Bonomi | BIASVALUE MOLINFO EMMI PRINT GROUP | bias core generic isdb |
| 25.018 | Metainference simulation for dimerization of RNA binding protein | bio | Metainference, Metadynamics, SAXS, protein dimer | Debadutta Patra | SAXS CENTER MOLINFO GYRATION STATS DISTANCE UPPER_WALLS METAINFERENCE PBMETAD TORSION FLUSH WHOLEMOLECULES PRINT ENSEMBLE | bias vatom isdb function generic colvar |
| 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 | INCLUDE CENTER MOLINFO GYRATION VOLUME DISTANCE ENERGY READ DUMPATOMS RESTART PBMETAD TORSION UPDATE_IF WHOLEMOLECULES PRINT | bias vatom setup generic colvar |
| 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 COMBINE MOLINFO GYRATION OPES_METAD DISTANCE TORSION CUSTOM ALPHARMSD WHOLEMOLECULES PRINT | secondarystructure function generic colvar opes |
| 24.014 | Learning Collective Variables with Synthetic Data Augmentation through Physics-inspired Geodesic Interpolation | methods | data augmentation, geodesic interpolation, collective variables, protein folding | Juno Nam | COORDINATION MOLINFO LOWER_WALLS METAD UPPER_WALLS PYTORCH_MODEL DRR FLUSH WHOLEMOLECULES RMSD PRINT | bias drr pytorch generic 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 | RESTRAINT MOLINFO DISTANCE METAD ENERGY COORDINATIONNUMBER COMMITTOR BIASVALUE RESTART TORSION MATHEVAL FLUSH PRINT | symfunc bias function setup generic colvar |
| 24.011 | Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble | methods | committor, machine learning | Peilin Kang | MOLINFO UNITS UPPER_WALLS CELL RMSD POSITION LOWER_WALLS PRINT GROUP INCLUDE COORDINATION ENDPLUMED ENERGY BIASVALUE LOAD MATHEVAL WHOLEMOLECULES DISTANCE TORSION CUSTOM | bias core function setup generic colvar |
| 24.007 | SWISH-X | bio | swish-x, SWISH-X, swish, expanded SWISH | Alberto Borsatto | INCLUDE ECV_MULTITHERMAL MOLINFO ENERGY UPPER_WALLS OPES_EXPANDED CONTACTMAP WHOLEMOLECULES PRINT | bias generic colvar opes |
| 23.029 | An accurate and efficient SAXS/SANS implementation including solvation layer effects suitable for restrained Molecular Dynamics simulations | bio | SAXS, SANS, SAS, metainference, proteins, nucleic-acid | Federico Ballabio | SAXS GROUP CENTER MOLINFO STATS DISTANCE UPPER_WALLS BIASVALUE WRAPAROUND RMSD PRINT ENSEMBLE | bias core vatom isdb function generic colvar |
| 23.026 | Machine Learning Nucleation Collective Variables with Graph Neural Networks | chemistry | Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks | Florian Dietrich | GROUP LOCAL_Q6 COMBINE MOVINGRESTRAINT LOWER_WALLS COORDINATIONNUMBER METAD MFILTER_MORE Q6 PRINT | symfunc bias core generic multicolvar function |
| 23.005 | A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs | bio | metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A | Timothy Clark | MOLINFO DISTANCE METAD HISTOGRAM READ CONVERT_TO_FES MATHEVAL REWEIGHT_METAD WHOLEMOLECULES RMSD PRINT DUMPGRID | bias gridtools generic function colvar |
| 23.003 | Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations | methods | metadynamics, alchemical variable, alchemical free energy calculations | Wei-Tse Hsu | EXTRACV METAD READ TORSION PRINT | bias 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 | INCLUDE ECV_UMBRELLAS_LINE ENVIRONMENTSIMILARITY LOWER_WALLS UPPER_WALLS OPES_EXPANDED PRINT | bias envsim generic opes |
| 22.018 | Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations | bio | ligand binding, docking, EMMI, LAT1 | Max Bonomi | GROUP MOLINFO BIASVALUE EMMIVOX LOAD WHOLEMOLECULES PRINT | bias core isdb setup generic |
| 22.009 | Glycosylation in calixarenes capsule | chemistry | Metadynamics, glycosylation, supramolecular catalysis | GiovanniMaria Piccini | GROUP COMBINE COORDINATION UNITS DISTANCE UPPER_WALLS LOWER_WALLS FIT_TO_TEMPLATE DISTANCES METAD ANGLE BRIDGE MATHEVAL FLUSH WHOLEMOLECULES RMSD PRINT | bias core adjmat generic setup multicolvar function colvar |
| 22.002 | GAMBES_SAMPL5_RATES | other | GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding | Jayashrita Debnath | GROUP CENTER COORDINATION ENDPLUMED DISTANCE UPPER_WALLS PYTORCH_MODEL FIT_TO_TEMPLATE ENERGY COMMITTOR ANGLE FIXEDATOM LOAD MATHEVAL FLUSH WHOLEMOLECULES PRINT | bias core vatom function setup pytorch generic colvar |
| 21.052 | On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets | materials | Ibuprofen, unbinding, WTmetaD | Matteo Salvalaglio | CENTER ENDPLUMED DISTANCE METAD COORDINATIONNUMBER COMMITTOR TORSION PRINT | symfunc bias vatom generic colvar |
| 21.038 | Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics | materials | metadynamics, SGOOP, nucleation, urea | Ziyue Zou | INCLUDE GROUP CENTER COMBINE VOLUME ENERGY METAD COORDINATIONNUMBER LOAD PRINT | symfunc bias core vatom function setup generic colvar |
| 21.019 | Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations | materials | Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen | Matteo Salvalaglio | COM TORSIONS KDE DISTANCE MATHEVAL PRINT | vatom gridtools generic multicolvar function colvar |
| 21.011 | CmuMD simulations of NaCl(aq) at graphite | chemistry | CmuMD, DFS clustering | Aaron Finney | AROUND GROUP RESTRAINT DFSCLUSTERING DENSITY COORDINATIONNUMBER CONTACT_MATRIX MULTICOLVARDENS MFILTER_MORE FIXEDATOM CLUSTER_DISTRIBUTION LOAD CLUSTER_NATOMS PRINT DUMPGRID | symfunc bias clusters core vatom volumes adjmat gridtools setup multicolvar generic |
| 21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Kresten Lindorff-Larsen | GROUP SAXS EEFSOLV CENTER MOLINFO GYRATION METAINFERENCE BIASVALUE PBMETAD FLUSH ALPHARMSD WHOLEMOLECULES PRINT | bias core vatom isdb secondarystructure generic colvar |
| 21.000 | Uremic toxin time scale dynamics | bio | uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs) | Jim Pfaendtner | GROUP COM DISTANCE WHOLEMOLECULES PRINT | vatom generic colvar core |
| 20.032 | Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil | materials | clustering, conformational isomers | Matteo Salvalaglio | ENDPLUMED PRINT TORSION | generic colvar |
| 20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Adriana Pietropaolo | CENTER COORDINATION PBMETAD WHOLEMOLECULES PRINT | bias generic colvar vatom |
| 20.026 | Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor | bio | Metadynamics, Umbrella sampling | Brandon Peters | RESTRAINT MULTI_RMSD METAD HISTOGRAM CONVERT_TO_FES REWEIGHT_METAD PRINT DUMPGRID | bias generic gridtools colvar |
| 20.015 | Rational design of ASCT2 inhibitors using an integrated experimental-computational approach | bio | ASCT2 transporter, small-molecules, cryo-EM, metainference | Max Bonomi | GROUP MOLINFO BIASVALUE EMMIVOX DUMPATOMS LOAD WHOLEMOLECULES PRINT | bias core isdb setup generic |
| 20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Jim Pfaendtner | GROUP CENTER COORDINATION DISTANCE DISTANCES RESTART WHOLEMOLECULES PRINT | core vatom setup multicolvar generic colvar |
| 19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Jakub Rydzewski | POSITION UNITS MAZE_OPTIMIZER_BIAS MAZE_SIMULATED_ANNEALING MAZE_LOSS PRINT | maze setup generic colvar |
| 19.049 | Determining the sizes of solid/liquid clusters in MD trajectories of nucleation | methods | nucleation, metadynamics, clustering, Steinhardt order parameters | Gareth Tribello | LOCAL_Q6 MORE_THAN CLUSTER_PROPERTIES DFSCLUSTERING SMAC CONTACT_MATRIX ONES METAD COORDINATIONNUMBER DISTANCES Q6 CLUSTER_DISTRIBUTION MATRIX_VECTOR_PRODUCT CUSTOM CLUSTER_NATOMS OUTER_PRODUCT PRINT OUTPUT_CLUSTER | symfunc bias clusters matrixtools adjmat generic multicolvar function |
| 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 | GROUP POSITION COORDINATION UNITS LOWER_WALLS UPPER_WALLS METAD RESTART FLUSH PRINT | bias core setup generic colvar |
| 19.040 | Optimal Metric for Path Collective Variables | bio | metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path | Francesco Luigi Gervasio | ENDPLUMED METAD TORSION MATHEVAL PRINT | bias generic colvar function |
| 19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Carlo Camilloni | GROUP MOLINFO ANTIBETARMSD ALPHABETA ENDPLUMED LOWER_WALLS UPPER_WALLS BIASVALUE RESTART PBMETAD FLUSH WHOLEMOLECULES PRINT CS2BACKBONE | bias core isdb secondarystructure setup multicolvar generic |
| 19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Davide Provasi | COM FUNCPATHMSD ENDPLUMED DISTANCE METAD CONTACTMAP WHOLEMOLECULES RMSD PRINT | bias vatom generic function colvar |
| 19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Elena Papaleo | GROUP MOLINFO ALPHABETA GYRATION LOWER_WALLS UPPER_WALLS METAD WHOLEMOLECULES PRINT | bias core multicolvar generic colvar |
| 19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Pratyush Tiwary | COM COMBINE ALPHABETA DISTANCE COMMITTOR RESTART TORSION EXTERNAL WHOLEMOLECULES PRINT | bias vatom function setup multicolvar generic colvar |
| 19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Kresten Lindorff-Larsen | COMBINE MOLINFO ALPHABETA METAD COMMITTOR FLUSH PRINT | bias multicolvar function generic |
| 19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Max Bonomi | GROUP MOLINFO EMMI BIASVALUE WHOLEMOLECULES PRINT | bias isdb generic core |