Browse the eggs in PLUMED-NEST
PLUMED-NEST provides all the data needed to reproduce the results of a PLUMED-enhanced molecular dynamics simulation or analysis contained in a published paper. Furthermore, PLUMED-NEST monitors the compatibility of the provided PLUMED input files with the current and development versions of the code and integrates links from these files to the PLUMED manual.
Here is the list of projects already deposited in PLUMED-NEST, while a complete bibliography can be found here.
| plumID | Name | Category | Keywords | Contributor | Actions | Modules |
|---|---|---|---|---|---|---|
| 25.005 | Mechanism of Nanocluster Formation from Machine-Learned Potential-based Simulations | chemistry | WT-metadynamics, metal nanoclusters, nucleation, neural network potential, deepMD | Vikas Tiwari, Tarak Karmakar | FIXEDATOM SUM ANGLE DISTANCE MATRIX_VECTOR_PRODUCT METAD DISTANCES COORDINATIONNUMBER ONES UPPER_WALLS FLUSH PRINT LOWER_WALLS COMBINE LOWEST MEAN COORDINATION CONTACT_MATRIX RESTRAINT COM UNITS CUSTOM GROUP | setup multicolvar core symfunc function matrixtools generic vatom bias colvar adjmat |
| 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 | DISTANCE INCLUDE READ RESTART CENTER GYRATION PRINT PBMETAD ENERGY VOLUME TORSION | setup vatom bias colvar generic |
| 25.002 | M3_PCV-ABMD | chemistry | Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor | Gian Marco Elisi | ABMD UPPER_WALLS ENDPLUMED PRINT PATHMSD UNITS | bias colvar generic setup |
| 24.028 | All-atom simulations of RNA-membrane interactions | bio | metadynamics, membrane, RNA | Giovanni Bussi | DISTANCE COMBINE LOWEST DISTANCES MATHEVAL UPPER_WALLS SORT GROUP CENTER GYRATION METAD MOLINFO PRINT LOWER_WALLS WHOLEMOLECULES PUCKERING GHOST POSITION | function core colvar vatom bias multicolvar generic |
| 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 | DISTANCE LOWEST FIXEDATOM OPES_METAD EUCLIDEAN_DISTANCE LOWER_WALLS PYTORCH_MODEL RESTART PATH WHOLEMOLECULES SUM CUSTOM FIT_TO_TEMPLATE COORDINATION GROUP CONSTANT COMBINE UPPER_WALLS CENTER PDB2CONSTANT TORSION | setup function core mapping refdist vatom opes bias colvar generic pytorch |
| 23.041 | Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference | methods | EMMIVox, cryo-EM, single-structure refinement, ensemble refinement, Bayesian inference, B-factors, structural ensembles | Samuel Hoff | DISTANCE EMMIVOX UPPER_WALLS INCLUDE GROUP MOLINFO WHOLEMOLECULES PRINT WRAPAROUND BIASVALUE | isdb core bias colvar generic |
| 23.024 | Permutationally Invariant Networks for Enhanced Sampling (PINES) | methods | collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent | Nicholas Herringer | PRINT PBMETAD LOAD | bias generic setup |
| 22.043 | Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES | bio | OPES, RNA, Tetraloop, Folding | Gül Zerze | CONTACTMAP ECV_MULTITHERMAL WHOLEMOLECULES OPES_EXPANDED PRINT ENERGY ECV_UMBRELLAS_LINE | opes colvar generic |
| 22.026 | Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification | materials | Peptoid, silica | Jim Pfaendtner | DISTANCE UPPER_WALLS COM GYRATION MOLINFO PRINT PBMETAD | vatom bias colvar generic |
| 21.052 | On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets | materials | Ibuprofen, unbinding, WTmetaD | Matteo Salvalaglio | DISTANCE MEAN ENDPLUMED CONTACT_MATRIX GROUP CENTER COORDINATIONNUMBER METAD PRINT COMMITTOR MATRIX_VECTOR_PRODUCT TORSION ONES | matrixtools function core symfunc vatom bias colvar generic adjmat |
| 21.032 | Metal-coupled folding mechanism to metallothionein | bio | parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination | Manuel-Peris Diaz | COORDINATION GROUP WHOLEMOLECULES PBMETAD UNITS | setup core bias colvar generic |
| 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 | DISTANCE COMBINE COORDINATION INCLUDE COM GYRATION METAD ALPHABETA SUM PBMETAD PRINT ENERGY CUSTOM TORSION CONSTANT | function multicolvar vatom bias colvar generic |
| 21.028 | From Enhanced Sampling to Reaction Profiles | methods | collective variables, multi-state, machine learning, Deep-TDA | Enrico Trizio | DISTANCE FIXEDATOM OPES_METAD LOWER_WALLS PYTORCH_MODEL ENDPLUMED ANGLE WHOLEMOLECULES UNITS MATHEVAL FIT_TO_TEMPLATE COORDINATION GROUP PRINT DISTANCES UPPER_WALLS CENTER LOAD TORSION | setup function core multicolvar vatom opes bias colvar generic pytorch |
| 21.025 | Computational and biochemical analysis of type IV pilus dynamics and stability | bio | molecular dynamics, calcium binding, Type IV pilus | Yasaman Karami | UPPER_WALLS DISTANCE PRINT LOWER_WALLS | bias colvar generic |
| 21.016 | MD SAXS GTPase associated center | bio | metadynamics, RNA, folding, SAXS | Giovanni Bussi | UPPER_WALLS INCLUDE ERMSD GROUP GYRATION LOWER_WALLS METAD MOLINFO WHOLEMOLECULES PRINT SAXS CUSTOM | isdb function core bias colvar generic |
| 21.010 | Step by Step Strecker Amino Acid Synthesis from Ab Initio Prebiotic Chemistry | chemistry | Strecker reaction, free energy landscape, ab initio molecular dynamics, glycine, prebiotic synthesis | Théo Magrino | generic | |
| 21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Kresten Lindorff-Larsen | EEFSOLV ALPHARMSD GROUP CENTER GYRATION METAINFERENCE MOLINFO WHOLEMOLECULES PRINT PBMETAD FLUSH BIASVALUE SAXS | isdb core secondarystructure vatom bias colvar generic |
| 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 | TD_UNIFORM SPHERICAL_HARMONIC ECV_UMBRELLAS_LINE ENVIRONMENTSIMILARITY OPT_AVERAGED_SGD CONTACT_MATRIX MORE_THAN RESTART SUM VES_LINEAR_EXPANSION VOLUME CUSTOM MATRIX_VECTOR_PRODUCT ECV_MULTITHERMAL_MULTIBARIC MATHEVAL ONES BF_LEGENDRE GROUP PRINT ENERGY Q6 COMBINE MEAN UPPER_WALLS OPES_EXPANDED DISTANCE_MATRIX | ves matrixtools envsim setup function core symfunc opes bias colvar generic adjmat |
| 20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Matteo Salvalaglio | UPPER_WALLS CELL LOWER_WALLS METAD PRINT ENERGY VOLUME MATHEVAL | bias colvar generic function |
| 20.010 | Phase equilibrium of liquid water and hexagonal ice from enhanced sampling molecular dynamics simulations | materials | water, ice, TIP4P, crystallization, EnvironmentSimilarity, RefCV, kernel, VES, variationally enhanced sampling | Pablo Piaggi | SPHERICAL_HARMONIC ENVIRONMENTSIMILARITY OPT_AVERAGED_SGD CONTACT_MATRIX MORE_THAN RESTART SUM TD_WELLTEMPERED VES_LINEAR_EXPANSION VOLUME CUSTOM OPT_DUMMY MATRIX_VECTOR_PRODUCT MATHEVAL ONES BF_LEGENDRE GROUP PRINT Q6 COMBINE MEAN UPPER_WALLS DISTANCE_MATRIX | ves matrixtools envsim setup function core symfunc bias colvar generic adjmat |
| 20.006 | Class B GPCR activation mechanism | bio | metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | DISTANCE COMBINE UPPER_WALLS CENTER LOWER_WALLS METAD MOLINFO WHOLEMOLECULES PRINT ENERGY RMSD MATHEVAL | function vatom bias colvar generic |
| 20.003 | Enhanced sampling of transition states | methods | Variationally Enhanced Sampling, Target distribution, Transition state, Enhanced Sampling, Nucleation, chemical reaction | Jayashrita Debnath | OPT_AVERAGED_SGD BF_LEGENDRE PRINT VES_LINEAR_EXPANSION LOAD ENERGY UNITS POSITION | ves colvar generic setup |
| 19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | DISTANCE UPPER_WALLS COM GYRATION METAD MOLINFO PRINT ENERGY | vatom bias colvar generic |
| 19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_SIMULATED_ANNEALING MAZE_LOSS PRINT MAZE_OPTIMIZER_BIAS UNITS POSITION | maze colvar generic setup |
| 19.048 | Understanding Ligand Binding Selectivity in a Prototypical GPCR Family | bio | metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | DISTANCE UPPER_WALLS COM LOWER_WALLS METAD WHOLEMOLECULES PRINT BIASVALUE CONSTANT MATHEVAL | function vatom bias colvar generic |
| 19.040 | Optimal Metric for Path Collective Variables | bio | metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path | Francesco Luigi Gervasio | ENDPLUMED METAD PRINT TORSION MATHEVAL | bias colvar generic function |
| 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 ENDPLUMED CS2BACKBONE GYRATION METAINFERENCE FLUSH JCOUPLING MOLINFO WHOLEMOLECULES PBMETAD PRINT STATS ENSEMBLE BIASVALUE TORSION | function isdb bias colvar generic |
| 19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Kresten Lindorff-Larsen | COMBINE FLUSH METAD MOLINFO ALPHABETA SUM PRINT COMMITTOR CUSTOM TORSION CONSTANT | function multicolvar bias colvar generic |
| 19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Adriana Pietropaolo | METAD WHOLEMOLECULES PRINT BIASVALUE TORSION CONSTANT MATHEVAL | bias colvar generic function |
| 19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Carlo Camilloni | DISTANCE RESTRAINT ENDPLUMED UPPER_WALLS INCLUDE GROUP CENTER STATS MOLINFO WHOLEMOLECULES PRINT BIASVALUE SAXS RMSD | function isdb core vatom bias colvar generic |
| 19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Carlo Camilloni | DISTANCE RESTRAINT METAINFERENCE STATS MOLINFO ALPHABETA RDC ENDPLUMED DHENERGY DIHCOR WHOLEMOLECULES SUM CUSTOM GROUP PRINT PBMETAD CONSTANT COMBINE UPPER_WALLS CENTER DIHEDRAL_CORRELATION ENSEMBLE TORSION | function isdb core multicolvar vatom bias colvar generic |
| 19.008 | anncolvar | methods | neural network, dimensionality reduction | Vojtech Spiwok | COMBINE FIT_TO_TEMPLATE ALPHARMSD LESS_THAN METAD WHOLEMOLECULES PRINT MOLINFO SUM SECONDARY_STRUCTURE_RMSD MATHEVAL POSITION | function secondarystructure bias colvar generic |
| 19.005 | Cmyc small molecule interaction | bio | metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP | Gabriella Heller | DISTANCE COORDINATION CS2BACKBONE INCLUDE GROUP GYRATION METAINFERENCE CENTER MOLINFO WHOLEMOLECULES ALPHABETA PBMETAD PRINT | isdb core multicolvar vatom bias colvar generic |
| 24.029 | Combination of OPES and OPES-Explore | methods | OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin | Dhiman Ray | OPES_METAD FIT_TO_TEMPLATE ENDPLUMED PYTORCH_MODEL ENERGY OPES_METAD_EXPLORE UPPER_WALLS PRINT FLUSH METAD MATHEVAL BIASVALUE COORDINATION CUSTOM POSITION MOLINFO RMSD CENTER FIXEDATOM GROUP COMBINE INCLUDE WHOLEMOLECULES DISTANCE CONTACTMAP LOWER_WALLS UNITS | setup function core generic colvar pytorch vatom opes bias |
| 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 | COMBINE TORSION ECV_MULTITHERMAL DISTANCE RESTART OPES_EXPANDED ENERGY COORDINATION OPES_METAD_EXPLORE CUSTOM GROUP PRINT | function core generic colvar opes setup |
| 24.020 | Graph Neural Network-State Predictive Information Bottleneck (GNN-SPIB) approach for learning molecular thermodynamics and kinetics | bio | LJ7, alanine, well-tempered metadynamics, infrequent metadynamics, machine learning | Ziyue Zou, Dedi Wang, Pratyush Tiwary | TORSION LOAD METAD COMMITTOR GROUP PRINT | core generic colvar setup bias |
| 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 | COORDINATIONNUMBER TORSION FLUSH MOLINFO METAD DISTANCE RESTRAINT MATHEVAL BIASVALUE COMMITTOR RESTART ENERGY PRINT | function generic colvar symfunc setup bias |
| 24.005 | Learning Markovian Dynamics with Spectral Maps | methods | spectral map, collective variables, machine learning | Jakub Rydzewski | DISTANCE BIASVALUE UNITS CUSTOM PRINT | function generic colvar setup bias |
| 24.004 | Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables | materials | metadynamics, nucleation, machine learning | Ziyue Zou | INCLUDE LOAD METAD RESTART GROUP PRINT | core setup generic bias |
| 23.033 | DNA G-quadruplex and G-hairpin folding with ST-metaD protocol | bio | DNA, G4, GQ, quadruplex, hairpin, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | COMBINE MOLINFO WHOLEMOLECULES ERMSD METAD BIASVALUE GHBFIX COORDINATION PRINT | function colvar generic bias |
| 23.025 | Probing ion binding to G-quadruplexes and related events | chemistry | metadynamics, repulsive potential, nucleic acids, G-quadruplexes | Marcelo Poleto | POSITION FLUSH WHOLEMOLECULES FIT_TO_TEMPLATE COM DISTANCES DISTANCE LOWER_WALLS MATHEVAL METAD UNITS LOWEST DUMPATOMS RESTART UPPER_WALLS GROUP WRAPAROUND PRINT | multicolvar function core generic colvar vatom setup bias |
| 23.020 | FEP simulations of ATOX1 homodimer | chemistry | parallel bias metadynamics, FEP, free-energy of metal ion dissociation | Adriana Pietropaolo | WHOLEMOLECULES DISTANCE MATHEVAL ANGLE BIASVALUE PBMETAD CONSTANT PRINT | function colvar generic bias |
| 23.018 | Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention | materials | metadynamics, surface binding, peptide adsorption | Kaylyn Torkelson | COM DISTANCE PBMETAD UPPER_WALLS GYRATION PRINT | generic colvar vatom bias |
| 22.038 | Enhanced Sampling Aided Design of Molecular Photoswitches | chemistry | reaction discovery, OPES explore, graph CV | Umberto Raucci | UNITS PYTORCH_MODEL COORDINATION OPES_METAD_EXPLORE CUSTOM PRINT | setup function generic colvar pytorch opes |
| 22.034 | Rationalising the difference in crystallisability of two Sulflowers using efficient in silico methods | materials | metadynamics, crystallizability, crystal structure prediction, sulflower, persulforated coronene | Matteo Salvalaglio | METAD COMMITTOR LOWER_WALLS MATHEVAL DISTANCE DRMSD CELL CONSTANT SUM UPPER_WALLS CUSTOM PRINT | function colvar generic bias |
| 22.024 | Conformational Entropy as a Potential Liability of Computationally Designed Antibodies | bio | metadynamics, conformational entropy, antibody, nanobody | Thomas Löhr | ANTIBETARMSD TORSION COMBINE MOLINFO WHOLEMOLECULES ALPHARMSD COM ALPHABETA SECONDARY_STRUCTURE_RMSD RESTART LESS_THAN PBMETAD CONSTANT SUM CUSTOM PRINT | multicolvar function generic secondarystructure colvar vatom setup bias |
| 22.019 | Exploring aspartic protease inhibitor binding to design selective antimalarials | bio | ligand binding, loop opening, path CV, funnel metadynamics, drug development | Raitis Bobrovs | FUNNEL WHOLEMOLECULES COM METAD DISTANCE LOWER_WALLS PATHMSD FUNNEL_PS UPPER_WALLS PRINT | generic colvar funnel vatom bias |
| 22.015 | Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome | bio | photodynamics, bacteriophytochrome, variationally enhanced sampling | Jakub Rydzewski | TORSION TD_UNIFORM BF_FOURIER OPT_AVERAGED_SGD VES_LINEAR_EXPANSION PRINT | colvar ves generic |
| 22.011 | Accelerating all-atom simulations and gaining mechanistic understanding of biophysical systems through State Predictive Information Bottleneck | methods | metadynamics, membrane permeation, protein folding | Shams Mehdi | TORSION UPPER_WALLS PRINT YANGLES METAD MATHEVAL MEAN CUSTOM MOLINFO COM ALPHABETA SUM ZANGLES COMBINE WHOLEMOLECULES DISTANCE LOWER_WALLS CONSTANT XANGLES | multicolvar function generic colvar vatom bias |
| 22.009 | Glycosylation in calixarenes capsule | chemistry | Metadynamics, glycosylation, supramolecular catalysis | GiovanniMaria Piccini | FIT_TO_TEMPLATE UPPER_WALLS PRINT FLUSH METAD MATHEVAL BRIDGE_MATRIX MEAN COORDINATION BRIDGE ANGLE RMSD SUM GROUP COMBINE WHOLEMOLECULES DISTANCES DISTANCE LOWER_WALLS UNITS | multicolvar function core generic adjmat colvar setup bias |
| 21.047 | Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations | materials | pair entropy, metadynamics, ves, solids, crystallization | Pablo Piaggi | COMBINE PAIRENTROPY LOAD METAD VOLUME TD_WELLTEMPERED OPT_AVERAGED_SGD BF_LEGENDRE RESTART VES_LINEAR_EXPANSION ENERGY PRINT | function gridtools generic colvar ves setup bias |
| 21.035 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, interface | Aaron Finney | LOAD RESTRAINT DISTANCE GROUP FIXEDATOM PRINT | core generic colvar vatom setup bias |
| 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 INCLUDE RANDOM_EXCHANGES METAD ENDPLUMED PBMETAD PRINT | colvar generic bias |
| 21.031 | Photo-switchable sulfonulureas in KATP channel | bio | metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels | Katarzyna Walczewska-Szewc | WHOLEMOLECULES COM METAD DISTANCE LOWER_WALLS UNITS UPPER_WALLS PRINT | generic colvar vatom setup bias |
| 21.029 | Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs | bio | metadynamics, small peptide, machine learning | Pratyush Tiwary | TORSION MOLINFO FLUSH RESTART ENERGY EXTERNAL PRINT | colvar setup generic bias |
| 20.024 | Gaussian Mixture Based Enhanced Sampling (GAMBES) | methods | enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias | Jayashrita Debnath | TORSION COMBINE LOAD DISTANCES DISTANCE LOWER_WALLS UNITS ENERGY UPPER_WALLS GROUP PRINT | multicolvar function core generic colvar setup bias |
| 20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Vojtech Spiwok | PRINT TORSION METAD | colvar generic bias |
| 20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Max Bonomi | TORSION COMBINE MOLINFO INCLUDE WHOLEMOLECULES ALPHABETA DIHEDRAL_CORRELATION DIHCOR PBMETAD COORDINATION CONSTANT SUM CUSTOM GYRATION PRINT | multicolvar function generic colvar bias |
| 19.078 | Iterative unbiasing of quasi-equilibrium sampling | methods | metadynamics, reweighting | Federico Giberti | COORDINATIONNUMBER CONTACT_MATRIX METAD DISTANCE REWEIGHT_BIAS MATHEVAL BIASVALUE COLLECT_FRAMES ONES MATRIX_VECTOR_PRODUCT UNITS DUMPATOMS MEAN GROUP PRINT | function core generic adjmat colvar symfunc landmarks matrixtools setup bias |
| 19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Sandro Bottaro | TORSION ERMSD MOLINFO WHOLEMOLECULES METAD DISTANCE RMSD PRINT | colvar generic bias |
| 19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Michele Invernizzi | TORSION OPES_METAD METAD ENDPLUMED UNITS EXTERNAL POSITION PRINT | generic colvar opes setup bias |
| 19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Wei Chen | COMBINE COM RESTRAINT POSITION ANN | function colvar vatom annfunc bias |
| 19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Jim Pfaendtner | WHOLEMOLECULES METAD ENERGY GYRATION PRINT | colvar generic bias |
| 19.027 | Multithermal-multibaric simulations using VES | methods | ves, Wang Landau, multicanonical, liquid sodium, density anomaly | Pablo Piaggi | BF_LEGENDRE ENERGY PRINT CONVERT_TO_FES ACCUMULATE REWEIGHT_TEMP_PRESS RESTART READ TD_MULTICANONICAL AVERAGE CUSTOM HISTOGRAM OPT_AVERAGED_SGD COMBINE REWEIGHT_BIAS UNITS DUMPGRID VES_LINEAR_EXPANSION OPT_DUMMY | function gridtools generic colvar ves setup bias |
| 19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Mattia Bernetti | ALPHARMSD MOLINFO WHOLEMOLECULES METAD ENDPLUMED SECONDARY_STRUCTURE_RMSD ENERGY LESS_THAN SUM GYRATION PRINT | function generic secondarystructure colvar bias |
| 19.011 | Automatic Gradient Computation for Collective Variables | other | gradient, differentiation, curvature | Toni Giorgino | ENDPLUMED | generic |
| 19.009 | RNA tetraloops folding | bio | metadynamics, RNA, folding | Giovanni Bussi | ERMSD MOLINFO WHOLEMOLECULES METAD ENDPLUMED RMSD PRINT | colvar generic bias |
| 19.003 | EMMI ClpP | bio | metainference, cryo-EM | Max Bonomi | MOLINFO EMMI BIASVALUE GROUP PRINT | core isdb generic bias |
| 19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Giovanni Bussi | COMBINE MOLINFO RANDOM_EXCHANGES FLUSH INCLUDE ERMSD DISTANCE LOWER_WALLS DISTANCES ANGLE METAD LOWEST UPPER_WALLS PRINT | multicolvar function generic colvar bias |
| 25.010 | Kinetic rates calculation with Ratchet&Pawl MD | methods | kinetics, ligand binding, ABMD, ratchet&pawl MD | Riccardo Capelli | DISTANCE COMMITTOR WHOLEMOLECULES FLUSH ABMD COM PRINT GROUP | colvar vatom core bias generic |
| 25.001 | RNA G-quadruplex folding with ST-metaD protocol | bio | RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | COMBINE MOLINFO ERMSD WHOLEMOLECULES METAD | function colvar bias generic |
| 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 | DISTANCE COMBINE COORDINATION TORSION GYRATION SUM ALPHARMSD MOLINFO OPES_METAD WHOLEMOLECULES CUSTOM SECONDARY_STRUCTURE_RMSD PRINT LESS_THAN | secondarystructure colvar function opes generic |
| 24.010 | Oxytocin metadynamics simulation | bio | metadynamics, oxytocin, peptide | Jan Beránek | TORSION RESTART METAD WHOLEMOLECULES FLUSH PRINT | setup bias colvar generic |
| 24.002 | Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes | chemistry | metadynamics, ligand design, solvent extraction | Xiaoyu Wang | TORSION RESTART METAD PRINT UNITS | setup bias colvar generic |
| 23.032 | Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics | bio | metadynamics, tSNE, neural network, machine learning, trp-cage, folding | Vojtech Spiwok | COMBINE ANN SUM POSITION ALPHARMSD FIT_TO_TEMPLATE MOLINFO WHOLEMOLECULES METAD SECONDARY_STRUCTURE_RMSD PRINT LESS_THAN | secondarystructure annfunc colvar function bias generic |
| 23.022 | A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar | methods | collective variables, machine learning, toy model | Enrico Trizio | UPPER_WALLS LOWER_WALLS POSITION OPES_METAD CUSTOM PRINT UNITS ENDPLUMED PYTORCH_MODEL BIASVALUE | colvar function opes bias pytorch setup generic |
| 23.008 | PBMetaD simulations of Histatin5 | bio | metadynamics, IDP, Rg, PPII | Francesco Pesce | TORSION GYRATION PBMETAD MOLINFO WHOLEMOLECULES PRINT GROUP | core bias colvar generic |
| 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 | UPPER_WALLS LOWER_WALLS ENERGY WHOLEMOLECULES METAD PRINT CONTACTMAP | bias colvar generic |
| 22.045 | Binding mode and mechanism of enzymatic polyethylene terephthalate degradation | bio | metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation | Francesco Colizzi | DISTANCE UPPER_WALLS LOWER_WALLS ANGLE MOVINGRESTRAINT METAD WHOLEMOLECULES PRINT COM | vatom bias colvar generic |
| 22.044 | Colloid Crystallisation Analyses | materials | Q4, Q6, Pair Entropy, DFS | Aaron Finney | MFILTER_LESS COMBINE Q4 DFSCLUSTERING LOCAL_Q4 CLUSTER_NATOMS LOCAL_Q6 COORDINATIONNUMBER CONTACT_MATRIX MFILTER_MORE PRINT GROUP Q6 LOCAL_AVERAGE | adjmat symfunc function core multicolvar clusters generic |
| 22.040 | From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure | bio | SARS-CoV-2, Spike, Omicron | Miłosz Wieczór | RMSD UPPER_WALLS PCAVARS COMBINE LOWER_WALLS SUM CONSTANT SELECT_COMPONENTS WHOLEMOLECULES CUSTOM METAD PRINT MATRIX_VECTOR_PRODUCT BIASVALUE | colvar mapping function bias generic valtools matrixtools |
| 22.018 | Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations | bio | ligand binding, docking, EMMI, LAT1 | Max Bonomi | EMMIVOX MOLINFO WHOLEMOLECULES PRINT LOAD GROUP BIASVALUE | bias core isdb setup generic |
| 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 | DISTANCE RMSD UPPER_WALLS COORDINATION LOWER_WALLS CENTER FIT_TO_TEMPLATE COMMITTOR OPES_METAD WHOLEMOLECULES CUSTOM FIXEDATOM PRINT GROUP PYTORCH_MODEL MATHEVAL | colvar function vatom opes bias core pytorch generic |
| 22.006 | Peptide framework for screening the effects of amino acids on assembly | bio | metadynamics, peptides | Andrew White | DISTANCE COMBINE GYRATION INCLUDE REWEIGHT_BIAS MEAN METAD HISTOGRAM CONVERT_TO_FES COM DUMPGRID GROUP PRINT DISTANCES | gridtools colvar function vatom bias core multicolvar 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 | VES_LINEAR_EXPANSION BF_LEGENDRE DISTANCE UPPER_WALLS COORDINATION TD_WELLTEMPERED BF_WAVELETS METAD PRINT UNITS BF_GAUSSIANS BF_CHEBYSHEV TD_UNIFORM POSITION OPT_AVERAGED_SGD INCLUDE BF_CUBIC_B_SPLINES ENERGY VES_OUTPUT_BASISFUNCTIONS OPT_ADAM FLUSH | colvar bias ves setup generic |
| 21.042 | Peptoid-mediated Au nanocrystal growth | materials | parallel-bias metadynamics, peptoid, Au | Xin Qi | DISTANCE UPPER_WALLS GYRATION PBMETAD MOLINFO COM PRINT | vatom bias colvar generic |
| 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 COORDINATION VOLUME METAD CUSTOM PRINT ENDPLUMED | function bias colvar generic |
| 21.027 | EGFR activating mutations mechanism | bio | metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA | Francesco Gervasio | DISTANCE UPPER_WALLS CONTACTMAP INCLUDE LOWER_WALLS SUM ALPHARMSD MOLINFO ENERGY WHOLEMOLECULES METAD SECONDARY_STRUCTURE_RMSD PRINT LESS_THAN MATHEVAL | secondarystructure colvar function bias generic |
| 21.015 | Coarse-grained metadynamics and umbrella sampling simulations to investigate interactions of carbohydrate-binding modules with chitin | bio | metadynamics, umbrella sampling, coarse-grained, MARTINI, chitin, carbohydrate-binding module | Gaston Courtade | COORDINATION POSITION CENTER RESTART REWEIGHT_BIAS RESTRAINT WHOLEMOLECULES METAD PRINT MATHEVAL | colvar function vatom bias setup generic |
| 21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Kristof Bal | COORDINATIONNUMBER REWEIGHT_METAD HISTOGRAM UPPER_WALLS ONES METAD DUMPGRID PRINT UNITS GROUP MOVINGRESTRAINT CONTACT_MATRIX MEAN CONVERT_TO_FES LOAD MATRIX_VECTOR_PRODUCT MORE_THAN SUM COMMITTOR FLUSH | adjmat gridtools symfunc function bias core setup generic matrixtools |
| 21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Tarak Karmakar | UPPER_WALLS LOWER_WALLS OPES_METAD FLUSH PRINT LOAD GROUP PYTORCH_MODEL MATHEVAL | function opes core bias pytorch setup generic |
| 20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Luigi Bonati | DISTANCE LOAD UPPER_WALLS TORSION LOWER_WALLS OPES_METAD FLUSH GROUP PRINT UNITS ENDPLUMED COM PYTORCH_MODEL MATHEVAL | colvar function vatom opes bias core pytorch setup generic |
| 19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Valerio Rizzi | DISTANCE COMBINE UPPER_WALLS SUM ENDPLUMED COORDINATIONNUMBER RESTART CONTACT_MATRIX ONES MEAN CUSTOM METAD PRINT UNITS GROUP FLUSH DISTANCES MATRIX_VECTOR_PRODUCT | adjmat symfunc colvar function bias core multicolvar setup generic matrixtools |
| 19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | DISTANCE UPPER_WALLS GYRATION MOLINFO ENERGY METAD COM PRINT | vatom bias colvar generic |
| 19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Cristina Paissoni | COMBINE STATS COORDINATION ALPHABETA INCLUDE ENDPLUMED ANGLE CENTER SAXS PBMETAD ENSEMBLE MOLINFO WHOLEMOLECULES PRINT GROUP MATHEVAL BIASVALUE | colvar function vatom bias core multicolvar isdb generic |
| 19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Gareth Tribello | LESS_THAN ENDPLUMED AROUND UPPER_WALLS LOWER_WALLS ONES METAD PRINT UNITS GROUP CONTACT_MATRIX MEAN FCCUBIC FCCUBIC_FUNC MATRIX_VECTOR_PRODUCT MORE_THAN SUM CUSTOM CELL | adjmat symfunc colvar function bias core setup generic volumes matrixtools |
| 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 UPPER_WALLS DISTANCE_FROM_CONTOUR REWEIGHT_BIAS RESTART READ HISTOGRAM DUMPGRID CONVERT_TO_FES METAD PRINT | gridtools function contour bias setup generic |
| 19.047 | Close Structure | methods | metadynamics, RMSD, path collective variables, property map | Vojtech Spiwok | PROPERTYMAP WHOLEMOLECULES METAD PRINT | bias colvar generic |
| 19.044 | Multithermal-multibaric simulations using VES | methods | ves, Wang Landau, multicanonical, water, density anomaly | Pablo Piaggi | VES_LINEAR_EXPANSION BF_LEGENDRE VOLUME HISTOGRAM AVERAGE DUMPGRID OPT_DUMMY PRINT REWEIGHT_TEMP_PRESS REWEIGHT_BIAS READ CONVERT_TO_FES TD_MULTITHERMAL_MULTIBARIC COMBINE OPT_AVERAGED_SGD ACCUMULATE RESTART ENERGY CUSTOM | gridtools colvar function bias ves setup generic |
| 19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Haochuan Chen | DRR TORSION PRINT | drr colvar generic |
| 19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Riccardo Capelli | UPPER_WALLS COORDINATION ENDPLUMED POSITION REWEIGHT_METAD FIT_TO_TEMPLATE READ WHOLEMOLECULES METAD FLUSH COM PRINT GROUP WRAPAROUND HISTOGRAM CONVERT_TO_FES MATHEVAL DUMPGRID | gridtools colvar function vatom core bias generic |
| 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 | ONES COMMITTOR DISTANCES FIXEDATOM MATRIX_VECTOR_PRODUCT ZDISTANCES FLUSH GROUP UNITS CUSTOM MEAN SUM CONTACT_MATRIX PRINT UPPER_WALLS DISTANCE OPES_METAD COORDINATIONNUMBER | core function setup generic bias colvar vatom adjmat opes symfunc matrixtools multicolvar |
| 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 | PARABETARMSD ALPHARMSD LESS_THAN DISTANCE WHOLEMOLECULES SECONDARY_STRUCTURE_RMSD BIASVALUE PBMETAD SUM UPPER_WALLS DUMPATOMS DUMPMASSCHARGE LOWEST COM GROUP MOLINFO RMSD CENTER EMMI PRINT COORDINATION | function core generic bias secondarystructure colvar vatom isdb |
| 24.012 | Molecular simulations to investigate the impact of N6-methylation in RNA recognition | bio | metadynamics, alchemistry, RNA modification, RNA:protein interactions | Giovanni Bussi | BIASVALUE DEBUG COMBINE LOWER_WALLS COM GHBFIX MOLINFO CENTER GROUP METAD DISTANCE PRINT UPPER_WALLS COORDINATION | function core generic bias colvar vatom |
| 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 | COMMITTOR COMBINE LOWER_WALLS TORSION FLUSH CUSTOM UNITS PRINT UPPER_WALLS DISTANCE OPES_METAD | function setup generic bias colvar opes |
| 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 FLUSH INCLUDE METAD SUM MATHEVAL TRANSPOSE PRINT | function generic valtools bias matrixtools |
| 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 | BIASVALUE LOWER_WALLS WHOLEMOLECULES METAD CENTER CONSTANT MATHEVAL PRINT UPPER_WALLS DISTANCE | function generic bias colvar vatom |
| 23.027 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, DFS, Q3, Pair Entropy | Aaron Finney | DENSITY HISTOGRAM LOCAL_AVERAGE DUMPGRID FIXEDATOM AROUND CLUSTER_DISTRIBUTION GROUP UNITS CLUSTER_NATOMS RESTRAINT DFSCLUSTERING LOAD CONTACT_MATRIX PRINT Q3 LOCAL_Q3 COORDINATIONNUMBER | core volumes setup clusters generic bias gridtools vatom symfunc adjmat |
| 23.026 | Machine Learning Nucleation Collective Variables with Graph Neural Networks | chemistry | Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks | Florian Dietrich | COMBINE LOWER_WALLS GROUP METAD LOCAL_Q6 Q6 PRINT MOVINGRESTRAINT COORDINATIONNUMBER MFILTER_MORE | core function generic bias symfunc multicolvar |
| 23.006 | Transcription factor unbinding | bio | metadynamics, DNA, conformational changes | Malin Lüking | ALPHARMSD COM MOLINFO METAD LESS_THAN DUMPFORCES SUM ANGLE CONTACTMAP PRINT SECONDARY_STRUCTURE_RMSD DISTANCE | function generic bias secondarystructure colvar vatom |
| 22.041 | Skipping the Replica Exchange Ladder with Normalizing Flows | methods | OPES, alanine, normalizing flows, replica exchange | Michele Invernizzi | ENERGY TORSION POSITION UNITS PRINT ENDPLUMED ECV_MULTITHERMAL OPES_EXPANDED OPES_METAD | colvar opes generic setup |
| 22.039 | Driving and characterizing nucleation of urea and glycine polymorphs in water | bio | metadynamics, nucleation, amino acids, polymorphism | Eric Beyerle | COMBINE CUSTOM SPHERICAL_HARMONIC MEAN ONES CONTACT_MATRIX MATRIX_VECTOR_PRODUCT METAD INCLUDE SUM MATHEVAL Q6 MORE_THAN COORDINATIONNUMBER Q4 GROUP CENTER PAIRENTROPY LOAD PRINT | function core setup generic bias vatom adjmat symfunc gridtools matrixtools |
| 22.036 | Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction | bio | Well-tempered MetaDynamics with Hamiltonian Replica Exchange | Miroslav Krepl | BIASVALUE COMBINE FLUSH GHBFIX MOLINFO GROUP CUSTOM METAD LOAD PRINT UPPER_WALLS COORDINATION | core function setup generic bias 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 | TORSION PBMETAD WHOLEMOLECULES MOLINFO GYRATION | colvar generic bias |
| 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 | ONES GYRATION COMBINE LOWER_WALLS MATRIX_VECTOR_PRODUCT FLUSH COM METAD UNITS GROUP CONTACT_MATRIX MEAN CUSTOM DISTANCE UPPER_WALLS COORDINATION COORDINATIONNUMBER | function core setup generic bias colvar vatom adjmat symfunc matrixtools |
| 21.049 | Multiple-path-metadynamics and PathMaps | methods | path-CV, metadynamics, multiple-walker, multiple paths, pathmap | Alberto Pérez-de-Alba-Ortíz | COMBINE LOWER_WALLS TORSION METAD UNITS CUSTOM RESTRAINT CONSTANT LOAD ENSEMBLE PRINT UPPER_WALLS MOVINGRESTRAINT | function setup generic bias colvar |
| 21.044 | NaCl nucleation | chemistry | metadynamics, DFS clustering | Aaron Finney | COMBINE FIXEDATOM CUSTOM MEAN DFSCLUSTERING ONES CONTACT_MATRIX DUMPGRID MATRIX_VECTOR_PRODUCT METAD HISTOGRAM SUM Q6 CLUSTER_DISTRIBUTION MORE_THAN MFILTER_MORE COORDINATIONNUMBER INSPHERE GROUP CLUSTER_NATOMS LOCAL_Q6 PRINT | function core volumes clusters generic bias vatom adjmat gridtools symfunc matrixtools multicolvar |
| 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 | FIXEDATOM TORSION FIT_TO_TEMPLATE METAD PRINT | colvar vatom generic bias |
| 21.020 | Reweighted Jarzynski sampling | methods | free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions | Kristof Bal | COMBINE BF_CHEBYSHEV CUSTOM UNITS MEAN CONSTANT ONES CONTACT_MATRIX CONVERT_TO_FES DISTANCE REWEIGHT_METAD DUMPGRID ANN MATRIX_VECTOR_PRODUCT FLUSH METAD MOVINGRESTRAINT BIASVALUE HISTOGRAM REWEIGHT_BIAS OPT_AVERAGED_SGD SUM UPPER_WALLS OPES_METAD MORE_THAN COORDINATIONNUMBER GROUP RESTRAINT VES_LINEAR_EXPANSION LOAD TD_WELLTEMPERED PRINT | function core setup ves annfunc generic bias colvar gridtools adjmat opes symfunc matrixtools |
| 21.013 | Role of vibrational excitation in heterogeneous catalysis | chemistry | catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption | Kristof Bal | TD_GRID COMBINE BF_CHEBYSHEV CUSTOM UNITS MEAN CONTACT_MATRIX ONES CONVERT_TO_FES REWEIGHT_METAD DISTANCE ANGLES DUMPGRID DISTANCES MATRIX_VECTOR_PRODUCT FLUSH EXTERNAL METAD UWALLS HISTOGRAM COORD_ANGLES REWEIGHT_BIAS OPT_AVERAGED_SGD UPPER_WALLS COORDINATIONNUMBER LOWER_WALLS GROUP RESTRAINT VES_LINEAR_EXPANSION LOAD PRINT COORDINATION | function core setup ves generic bias colvar gridtools adjmat symfunc matrixtools multicolvar |
| 20.028 | Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane | bio | metadynamics, KRas-4B, anionic membrane | Huixia Lu | FIT_TO_TEMPLATE METAD CENTER RESTART PRINT DISTANCE | setup generic bias colvar vatom |
| 20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Glen Hocky | BIASVALUE ENERGY FISST GROUP UNITS RESTRAINT MATHEVAL PRINT GYRATION DISTANCE | core function setup fisst generic bias colvar |
| 20.015 | Rational design of ASCT2 inhibitors using an integrated experimental-computational approach | bio | ASCT2 transporter, small-molecules, cryo-EM, metainference | Max Bonomi | BIASVALUE DUMPATOMS WHOLEMOLECULES GROUP MOLINFO PRINT LOAD EMMIVOX | core setup generic bias isdb |
| 20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Carlo Camilloni | METAINFERENCE STATS COMBINE SAXS TORSION ALPHABETA FLUSH PBMETAD WHOLEMOLECULES MOLINFO CUSTOM CENTER SUM CONSTANT ENSEMBLE PRINT GYRATION DISTANCE | function generic bias colvar vatom isdb multicolvar |
| 20.008 | Simulating solvation and acidity in complex mixtures with first-principles accuracy. The case of CH3SO3H and H2O2 in phenol | chemistry | proton trasfer, metadynamics | Kevin Rossi | DISTANCES CUSTOM UNITS METAD SUM DISTANCE PRINT COORDINATION | function setup generic bias colvar multicolvar |
| 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 | READ COMBINE HISTOGRAM LOWER_WALLS DUMPGRID COM METAD REWEIGHT_METAD ENDPLUMED MATHEVAL ABMD PRINT UPPER_WALLS DISTANCE CONVERT_TO_FES | function generic bias colvar gridtools vatom |
| 19.080 | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | methods | ves, variationally enhanced sampling, vibrational excitation, chemical reactions | Kristof Bal | TD_GRID HISTOGRAM COMBINE DUMPGRID LOWER_WALLS COORDINATION BF_CHEBYSHEV OPT_AVERAGED_SGD EXTERNAL FLUSH UNITS VES_LINEAR_EXPANSION ANGLE TD_WELLTEMPERED PRINT UPPER_WALLS DISTANCE CONVERT_TO_FES | function ves setup generic bias colvar gridtools |
| 19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Kim E. Jelfs | LOWER_WALLS COM GROUP METAD CENTER RESTART PRINT UPPER_WALLS DISTANCE | core setup generic bias colvar vatom |
| 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 | LOWER_WALLS FLUSH GROUP UNITS METAD PRINT RESTART POSITION UPPER_WALLS COORDINATION | core setup generic bias colvar |
| 19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | COMBINE DISTANCES FLUSH METAD UNITS RESTART PRINT UPPER_WALLS DISTANCE | function setup generic bias colvar multicolvar |
| 19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Vittorio Limongelli | LOWER_WALLS COM WHOLEMOLECULES METAD RMSD FUNNEL PRINT UPPER_WALLS DISTANCE FUNNEL_PS | funnel generic bias colvar vatom |
| 19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Silvio Pipolo | PIV LOWER_WALLS FUNCPATHMSD METAD PRINT CELL UPPER_WALLS | function generic bias colvar piv |
| 19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Matteo Salvalaglio | ENERGY COMBINE LOWER_WALLS TORSION CELL METAD VOLUME ENDPLUMED MATHEVAL PRINT UPPER_WALLS | colvar function generic bias |
| 19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Max Bonomi | BIASVALUE WHOLEMOLECULES GROUP MOLINFO EMMI PRINT | core isdb generic bias |
| 19.006 | Flying Gaussian proof | methods | flying Gaussians, alanine dipeptide | Vojtech Spiwok | PRINT METAD TORSION | colvar generic bias |
| 19.004 | MI Ubiquitin | bio | metainference, NMR | Max Bonomi | WHOLEMOLECULES GROUP MOLINFO RDC PRINT METAINFERENCE CS2BACKBONE | core isdb generic |
| 19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Max Bonomi | BIASVALUE GROUP MOLINFO EMMI PRINT | core isdb generic bias |
| 25.003 | Surrogate Model CV | methods | Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding | Sompriya Chatterjee | ENDPLUMED COMMITTOR MOLINFO PYTORCH_MODEL TORSION OPES_METAD CUSTOM WHOLEMOLECULES GROUP DISTANCE ENERGY PRINT COMBINE MATHEVAL | core generic colvar function opes pytorch |
| 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 | CONVERT_TO_FES WHOLEMOLECULES TORSION GROUP DUMPGRID DISTANCE COORDINATION PRINT ANGLE HISTOGRAM | gridtools core colvar generic |
| 24.011 | Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble | methods | committor, machine learning | Peilin Kang | LOWER_WALLS WHOLEMOLECULES POSITION PRINT MATHEVAL INCLUDE TORSION CELL ENDPLUMED UPPER_WALLS LOAD MOLINFO UNITS DISTANCE BIASVALUE GROUP CUSTOM COORDINATION ENERGY RMSD | bias core generic colvar function setup |
| 24.006 | Water vapor condensation | chemistry | metadynamics, homogeneous condensation, chemical potential | Shenghui Zhong | METAD UPPER_WALLS CLUSTER_PROPERTIES ONES GROUP UNITS MEAN SUM LESS_THAN PRINT CLUSTER_NATOMS COORDINATIONNUMBER CONTACT_MATRIX MATRIX_VECTOR_PRODUCT DFSCLUSTERING | bias symfunc clusters adjmat core generic matrixtools function setup |
| 23.046 | Lasso Peptides - HLDA CV | bio | metadynamics, protein folding, HLDA, harmonic | Gabriel da Hora | METAD WHOLEMOLECULES UNITS DISTANCE PRINT COMBINE | bias generic colvar function setup |
| 23.045 | Minute-timescale simulations of G Protein Coupled Receptor A2A activation mechanism reveal a receptor pseudo-active state | bio | Path CVs Metadynamics, GPCRs activation transition | Vittorio Limongelli | INCLUDE METAD SECONDARY_STRUCTURE_RMSD UPPER_WALLS LOWER_WALLS MOLINFO ALPHARMSD DISTANCE SUM LESS_THAN PRINT FUNCPATHMSD CONTACTMAP PATHMSD | bias secondarystructure generic colvar function |
| 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 MATRIX_VECTOR_PRODUCT SPHERICAL_HARMONIC VOLUME MORE_THAN ONES Q4 GROUP CUSTOM MEAN SUM ENERGY PRINT COORDINATIONNUMBER CONTACT_MATRIX Q6 MATHEVAL | bias symfunc adjmat core generic matrixtools colvar function |
| 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 | UPPER_WALLS SAXS MOLINFO ENSEMBLE GROUP DISTANCE BIASVALUE PRINT STATS WRAPAROUND CENTER RMSD | bias isdb core generic vatom colvar function |
| 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 | FIT_TO_TEMPLATE LOWER_WALLS WHOLEMOLECULES SUM PRINT COMBINE CENTER PDB2CONSTANT FIXEDATOM OPES_METAD_EXPLORE PYTORCH_MODEL TORSION CONSTANT UPPER_WALLS LOWEST UNITS DISTANCE PATH EUCLIDEAN_DISTANCE GROUP CUSTOM COORDINATION OPES_METAD | mapping bias refdist core generic vatom colvar function opes pytorch setup |
| 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 | METAD FLUSH UPPER_WALLS LOWER_WALLS DRR TIME UNITS CUSTOM BIASVALUE PRINT PATHMSD | bias generic colvar function drr setup |
| 23.007 | Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains | bio | metadynamics, peptoids, parallel-bias metadynamics | Jim Pfaendtner | COM INCLUDE PBMETAD RESTRAINT WHOLEMOLECULES TORSION GYRATION COORDINATION PRINT | vatom bias colvar generic |
| 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 | METAD READ EXTRACV TORSION PRINT PUT | bias core colvar generic |
| 23.002 | Critical comparison of general-purpose collective variables for crystal nucleation | methods | metadynamics, umbrella sampling, commitor, entropy, PIV | Julien Lam | METAD UPPER_WALLS VOLUME RESTRAINT LOCAL_AVERAGE Q4 UNITS CUSTOM PIV ENERGY PRINT FUNCPATHMSD Q6 PAIRENTROPY | bias symfunc piv generic gridtools colvar function setup |
| 22.042 | Metadynamics of NSP10 and variants | bio | metadynamics, NSP10, crystal structure, variants | Shozeb Haider | METAD TORSION PRINT | bias colvar 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 GROUP DISTANCE PRINT MEAN DISTANCES CENTER | bias multicolvar core generic vatom colvar function |
| 22.028 | N-glycan conformer distributions in atomistic simulation | bio | REST2, RECT, N-glycan, pucker | Isabell Grothaus | METAD CONVERT_TO_FES READ MOLINFO TORSION DUMPGRID PRINT PUCKERING HISTOGRAM | bias gridtools colvar generic |
| 22.004 | Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques | chemistry | reaction discovery, OPES, collective variables | Umberto Raucci | COM UPPER_WALLS OPES_METAD_EXPLORE LOAD LOWER_WALLS PYTORCH_MODEL GROUP UNITS CUSTOM DISTANCE COORDINATION PRINT OPES_METAD MATHEVAL | bias core generic vatom colvar function opes pytorch setup |
| 21.051 | Automatic learning of hydrogen-bond fixes in an AMBER RNA force field | methods | force field, RNA | Giovanni Bussi | METAD ERMSD MOLINFO WHOLEMOLECULES BIASVALUE COORDINATION PRINT COMBINE | bias function colvar generic |
| 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 | COM UPPER_WALLS MOLINFO WHOLEMOLECULES GROUP RESTART DISTANCE BIASVALUE PRINT EMMI | bias isdb core generic vatom colvar setup |
| 21.039 | Deep learning the slow modes for rare events sampling | methods | collective variables, machine learning, slow modes, deep-tica, opes | Luigi Bonati | SPHERICAL_HARMONIC MORE_THAN ONES WHOLEMOLECULES DISTANCE_MATRIX ECV_MULTITHERMAL PRINT SUM COMBINE MATRIX_VECTOR_PRODUCT INCLUDE FLUSH PYTORCH_MODEL TORSION CONTACT_MATRIX Q6 ENDPLUMED LOAD MOLINFO UNITS DISTANCE ENVIRONMENTSIMILARITY CONTACTMAP MEAN VOLUME GROUP CUSTOM OPES_EXPANDED ENERGY OPES_METAD RMSD | symfunc envsim adjmat core generic matrixtools colvar function opes pytorch setup |
| 21.038 | Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics | materials | metadynamics, SGOOP, nucleation, urea | Ziyue Zou | INCLUDE METAD LOAD VOLUME ONES GROUP CONTACT_MATRIX MEAN PRINT ENERGY COORDINATIONNUMBER COMBINE CENTER MATRIX_VECTOR_PRODUCT | bias symfunc adjmat core generic vatom matrixtools colvar function setup |
| 21.017 | All-atom simulations of the Vav1 AD construct | bio | metadynamics, parallel-bias, well-tempered | Simone Orioli | ALPHABETA PBMETAD REWEIGHT_BIAS SECONDARY_STRUCTURE_RMSD METAD MOLINFO WHOLEMOLECULES GROUP RESTART TORSION CONSTANT CUSTOM ALPHARMSD SUM LESS_THAN PRINT COMBINE CONTACTMAP | multicolvar bias core generic colvar function secondarystructure setup |
| 21.007 | Sampling enhancement by metadynamics driven by machine learning and de novo protein modelling | bio | metadynamics, machine learning, protein folding | Vojtech Spiwok | SECONDARY_STRUCTURE_RMSD FIT_TO_TEMPLATE MOLINFO WHOLEMOLECULES POSITION ALPHARMSD SUM LESS_THAN COMBINE MATHEVAL | function secondarystructure colvar generic |
| 21.004 | Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy | bio | machine learning, well-tempered metadynamics, path collective variable, potential of mean force, standard binding free energy calculations, host-guest, protein-ligand unbinding | Dorothea Gobbo | METAD UPPER_WALLS LOWER_WALLS WHOLEMOLECULES RESTART PRINT PATHMSD | setup bias colvar generic |
| 20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Faidon Brotzakis | CONVERT_TO_FES READ EMMI MOLINFO WHOLEMOLECULES GROUP DUMPGRID BIASVALUE PRINT DISTANCES RMSD HISTOGRAM | bias multicolvar isdb core generic gridtools colvar |
| 20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Michele Invernizzi | SPHERICAL_HARMONIC MORE_THAN ECV_LINEAR ONES WHOLEMOLECULES POSITION DISTANCE_MATRIX ECV_MULTITHERMAL PRINT SUM COMBINE MATRIX_VECTOR_PRODUCT MATHEVAL ECV_MULTITHERMAL_MULTIBARIC ECV_UMBRELLAS_LINE TORSION CONTACT_MATRIX Q6 ENDPLUMED UPPER_WALLS LOAD MOLINFO UNITS ENVIRONMENTSIMILARITY MEAN VOLUME GROUP CUSTOM OPES_EXPANDED ENERGY RMSD | bias symfunc envsim adjmat core generic matrixtools colvar function opes setup |
| 20.018 | Free energy barriers from biased molecular dynamics simulations | methods | kinetics, free energy barriers, chemical reactions, nucleation, metadynamics | Kristof Bal | DENSITY SPRINT LOWER_WALLS DUMPGRID REWEIGHT_METAD PRINT COMBINE CENTER PAIRENTROPY METAD REWEIGHT_BIAS CONVERT_TO_FES FLUSH CONTACT_MATRIX Q6 UPPER_WALLS LOAD UNITS DISTANCE COORDINATIONNUMBER HISTOGRAM VOLUME LOCAL_AVERAGE COORDINATION ENERGY | bias symfunc adjmat generic vatom gridtools sprint colvar volumes function setup |
| 20.013 | Improving accuracy of biased Alchemistic simulations | methods | flying Gaussian method, Alchemistic simulations, thermodynamic integration, reweighting | Vojtech Spiwok | METAD TORSION PRINT | bias colvar generic |
| 19.079 | Impact of Glutamate Carboxylation in the Adsorption of the alpha-1 Domain of Osteocalcin to Hydroxyapatite and Titania | bio | metadynamics, peptide adsorption, parallel tempering, well-tempered ensemble | Sarah Alamdari | COM METAD UPPER_WALLS MOLINFO GROUP GYRATION DISTANCE ENERGY PRINT | bias core generic vatom colvar |
| 19.075 | PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python | other | Python, automatic differentiation | Toni Giorgino | ENDPLUMED RESTRAINT GROUP TORSION CUSTOM DISTANCE PRINT COMBINE ANGLE CENTER DUMPDERIVATIVES | bias core generic vatom colvar function |
| 19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Giovanni Bussi | INCLUDE COM MAXENT METAD FLUSH MOLINFO WHOLEMOLECULES TORSION DISTANCE COORDINATION PRINT SORT MATHEVAL | bias generic vatom colvar function |
| 19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Matteo Salvalaglio | METAD REWEIGHT_BIAS CONVERT_TO_FES COMMITTOR READ TORSION DISTANCE BIASVALUE EXTERNAL PRINT DUMPGRID REWEIGHT_METAD MATHEVAL HISTOGRAM | bias generic gridtools colvar function |
| 19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Gareth Tribello | MORE_THAN ONES POSITION DUMPGRID SUM KDE DISTANCES CHARGE CENTER MATRIX_VECTOR_PRODUCT FIND_CONTOUR_SURFACE ACCUMULATE MULTICOLVARDENS CONTACT_MATRIX FOURIER_TRANSFORM FCCUBIC MASS UNITS ARGS2VATOM GROUP CUSTOM FCCUBIC_FUNC | multicolvar symfunc contour adjmat core generic vatom matrixtools fourier gridtools colvar function setup |
| 19.035 | Dimerization of GPCRs from coarse-grained umbrella sampling | bio | Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization | Davide Provasi | COM RESTRAINT TORSION GROUP DISTANCE PRINT | bias core generic vatom colvar |
| 19.032 | Chemical reaction in solution using path collective variables based on coordination patterns | chemistry | chemical reactions, solutions, metadynamics, coordination patterns | Fabio Pietrucci | METAD FLUSH PATH UPPER_WALLS RESTART PRINT DISTANCES | mapping bias multicolvar generic setup |
| 19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Pratyush Tiwary | COM ALPHABETA COMMITTOR WHOLEMOLECULES RESTART TORSION CONSTANT CUSTOM DISTANCE SUM EXTERNAL PRINT COMBINE | multicolvar bias generic vatom colvar function setup |
| 19.023 | RECT | methods | metadynamics, replica exchange | Giovanni Bussi | METAD WHOLEMOLECULES GYRATION TORSION PRINT | bias colvar generic |
| 24.032 | DeepLNE++ | methods | PATHCV, OPES | Thorben Fröhlking | GROUP LOAD COORDINATION DISTANCE PRINT ENERGY TORSION COMBINE CUSTOM OPES_METAD | setup function core colvar generic opes |
| 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 | COORDINATION DISTANCE PRINT ENERGY OPES_METAD UPPER_WALLS | opes generic colvar bias |
| 24.018 | A new route to the prebiotic synthesis of glycine via ab initio-based machine learning calculations | chemistry | prebiotic chemistry, glycine, Strecker synthesis, ab initio calculations, machine learning | Léon HUET | DISTANCE PRINT | generic colvar |
| 24.007 | SWISH-X | bio | swish-x, SWISH-X, swish, expanded SWISH | Alberto Borsatto | ECV_MULTITHERMAL CONTACTMAP PRINT ENERGY INCLUDE WHOLEMOLECULES OPES_EXPANDED MOLINFO UPPER_WALLS | opes colvar generic bias |
| 24.000 | Ammonia Decomposition on Non-stoichiometric Lithium Imide | chemistry | ammonia decomposition, non-stoichiometric lithium imide, machine learning interatomic potentials, enhanced sampling, heterogeneous catalysis | Francesco Mambretti | UNITS ONES GROUP FLUSH DISTANCE CUSTOM MEAN SUM FIXEDATOM ZDISTANCES PRINT CONTACT_MATRIX MATRIX_VECTOR_PRODUCT COORDINATIONNUMBER OPES_METAD UPPER_WALLS | setup bias function core colvar symfunc generic vatom matrixtools opes adjmat multicolvar |
| 23.034 | Urea nucleation in water: do long-range forces matter? | materials | LMF theory, Metadynamics, Nucleation | Ziyue Zou | ONES GROUP LOAD MORE_THAN CUSTOM MEAN SUM PRINT INCLUDE CONTACT_MATRIX METAD CENTER MATRIX_VECTOR_PRODUCT COORDINATIONNUMBER | setup bias function core symfunc generic vatom matrixtools adjmat |
| 23.021 | Into the Dynamics of Rotaxanes at Atomistic Resolution | materials | metadynamics, rotaxanes, molecular shuttles, molecular machines | Luigi Leanza | MATHEVAL DISTANCE FIXEDATOM PRINT TORSION METAD CENTER CUSTOM UPPER_WALLS | bias function colvar generic vatom |
| 23.016 | Activation/deactivation free-energy profiles for the β2-adrenergic receptor: Ligand modes of action | bio | G protein coupled receptor, beta-adrenergic, receptor activation, partial agonism, metadynamics | Timothy Clark | MATHEVAL DISTANCE REWEIGHT_METAD WHOLEMOLECULES PRINT HISTOGRAM CONVERT_TO_FES READ METAD RMSD DUMPGRID MOLINFO | bias function colvar generic gridtools |
| 23.014 | Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 | bio | metadynamics, oligomerization, chemokine receptors, GPCR, membrane | Vittorio Limongelli | FLUSH DISTANCE WHOLEMOLECULES COM PRINT TORSION METAD COMBINE UPPER_WALLS | bias function colvar generic vatom |
| 23.005 | A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs | bio | metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A | Timothy Clark | MATHEVAL DISTANCE REWEIGHT_METAD WHOLEMOLECULES PRINT HISTOGRAM CONVERT_TO_FES READ METAD RMSD DUMPGRID MOLINFO | bias function colvar generic gridtools |
| 22.029 | Angiotensin-1-7_Metadynamics | bio | Metadynamics, Angiotensin-(1-7), peptide | L.-América Chi | GROUP FLUSH COORDINATION WHOLEMOLECULES PRINT METAD LOWER_WALLS GYRATION UPPER_WALLS | generic core colvar bias |
| 22.027 | Molecular Dynamics simulations of BANAL-236 RBD-hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, BANAL-236, receptor-binding domain | Max Bonomi | PRINT RMSD | generic colvar |
| 22.025 | Bubble nucleation rate predictions in a Lennard-Jones fluid | materials | free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation | Kristof Bal | GROUP FLUSH LESS_THAN MEAN RESTRAINT LOAD MOVINGRESTRAINT CONVERT_TO_FES HISTOGRAM BIASVALUE COORDINATIONNUMBER ANN COMMITTOR VOLUME PRINT CONTACT_MATRIX MATRIX_VECTOR_PRODUCT DUMPGRID UNITS ONES SUM REWEIGHT_BIAS CUSTOM UPPER_WALLS | setup bias function annfunc core colvar symfunc generic gridtools matrixtools adjmat |
| 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 | GROUP DISTANCE COM PRINT TORSION METAD WHOLEMOLECULES | bias core colvar generic vatom |
| 22.013 | Ligand dissociation from PreQ1 riboswitch | bio | ligand, RNA, metadynamics, pRAVE | Yihang Wang | ONES GROUP COMMITTOR DISTANCE CUSTOM MEAN SUM PRINT COM RMSD METAD WHOLEMOLECULES CONTACT_MATRIX MATRIX_VECTOR_PRODUCT COORDINATIONNUMBER MOLINFO COMBINE | bias function core colvar symfunc generic vatom matrixtools adjmat |
| 22.005 | Collective Variable for Metadynamics Derived from AlphaFold Output | bio | AlphaFold, protein folding, protein structure prediction, metadynamics, deep learning, free energy simulation, collective variable | Vojtech Spiwok | PRINT LOAD METAD WHOLEMOLECULES | setup generic bias |
| 22.003 | Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling | methods | opes, metadynamics, reweighting, alanine, muller | Michele Invernizzi | PBMETAD UNITS ECV_MULTITHERMAL CUSTOM ECV_UMBRELLAS_FILE PRINT ENDPLUMED TORSION OPES_METAD_EXPLORE ENERGY METAD LOWER_WALLS OPES_EXPANDED BIASVALUE OPES_METAD POSITION UPPER_WALLS | setup bias function colvar generic opes |
| 21.050 | N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity | methods | bio | Isabell Louise Grothaus | DISTANCE PRINT CENTER | generic colvar vatom |
| 21.037 | Molecular Dynamics simulations of RBD/hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain | Max Bonomi | DISTANCE PRINT RMSD | generic 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 DISTANCE REWEIGHT_METAD CONSTANT PRINT INCLUDE ENERGY TORSION METAD CUSTOM BIASVALUE | setup bias function colvar generic |
| 21.022 | Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly | materials | parallel bias metadynamics, adsorption, peptide | Xin Qi | PBMETAD DISTANCE COM ENERGY PRINT LOWER_WALLS GYRATION MOLINFO UPPER_WALLS | bias colvar vatom generic |
| 21.012 | NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition | bio | funnel metadynamics | Jim Pfaendtner | FUNNEL DISTANCE COM PRINT METAD LOWER_WALLS FUNNEL_PS UPPER_WALLS | bias colvar generic vatom funnel |
| 21.011 | CmuMD simulations of NaCl(aq) at graphite | chemistry | CmuMD, DFS clustering | Aaron Finney | MULTICOLVARDENS GROUP LOAD RESTRAINT FIXEDATOM MFILTER_MORE PRINT CONTACT_MATRIX DFSCLUSTERING CLUSTER_NATOMS AROUND DUMPGRID COORDINATIONNUMBER CLUSTER_DISTRIBUTION DENSITY | setup bias volumes core symfunc generic gridtools vatom clusters adjmat multicolvar |
| 21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Adriana Pietropaolo | PBMETAD MATHEVAL RESTART CONSTANT PRINT TORSION WHOLEMOLECULES BIASVALUE | setup bias function colvar 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 | COORDINATION RESTRAINT STATS WHOLEMOLECULES PRINT COMBINE MOLINFO | bias colvar generic function |
| 20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Valerio Rizzi | MATHEVAL GROUP COORDINATION DISTANCE FIXEDATOM FIT_TO_TEMPLATE ANGLE PRINT ENERGY ENDPLUMED PYTORCH_MODEL WHOLEMOLECULES CENTER OPES_METAD UPPER_WALLS | bias function core colvar pytorch generic vatom opes |
| 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 | PROJECTION_ON_AXIS MATHEVAL GROUP FUNCPATHGENERAL LOAD LOWER_WALLS DISTANCE CONTACTMAP COM CONSTANT INCLUDE PRINT METAD WHOLEMOLECULES BIASVALUE MOLINFO UPPER_WALLS | setup bias function colvar core generic vatom |
| 19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Valerio Rizzi | UNITS ONES GROUP FLUSH CUSTOM MEAN SUM RESTART PRINT ENDPLUMED EXTERNAL METAD COMBINE CONTACT_MATRIX MATRIX_VECTOR_PRODUCT COORDINATIONNUMBER | setup bias function core symfunc generic matrixtools adjmat |
| 19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Kim Jelfs | INPLANEDISTANCES FLUSH MOVINGRESTRAINT DISTANCE SUM ANGLE RESTART COM PRINT DISTANCES CUSTOM | setup bias function colvar generic vatom multicolvar |
| 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 | FUNNEL COMBINE LOWER_WALLS GROUP DISTANCE DISTANCES REWEIGHT_METAD ALPHABETA COM PRINT RMSD TORSION METAD WHOLEMOLECULES BRIDGE MOLINFO UPPER_WALLS | bias function colvar core generic vatom funnel adjmat multicolvar |
| 19.030 | Coarse-Grained MetaDynamics (CG-MetaD) | bio | Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy | Vittorio Limongelli | LOWER_WALLS DISTANCE COM PRINT METAD WHOLEMOLECULES UPPER_WALLS | bias colvar vatom generic |
| 19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Matteo Salvalaglio | DISTANCE PRINT TORSION METAD LOWER_WALLS CENTER COMMITTOR UPPER_WALLS | generic colvar vatom bias |
| 19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Matteo Salvalaglio | ONES GROUP MORE_THAN DISTANCE SUM MEAN RESTART PRINT ENDPLUMED LOWEST METAD DISTANCES CONTACT_MATRIX MATRIX_VECTOR_PRODUCT COORDINATIONNUMBER GYRATION | setup bias function core colvar symfunc generic matrixtools adjmat multicolvar |
| 19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Michele Invernizzi | UNITS LOAD RESTART PRINT ENDPLUMED TORSION ENERGY METAD POSITION VES_DELTA_F | setup bias ves colvar generic |
| 25.007 | Shaping the glycan landscape. Hidden relationships between linkage and ring distortion induced by carbohydrate-active enzmyes | bio | REST-RECT, REST2, glycan, enzyme, CAZyme, steered | Isabell Grothaus | RESTART DISTANCE MOLINFO PUCKERING TORSION MOVINGRESTRAINT METAD PRINT RESTRAINT | generic setup bias colvar |
| 25.000 | Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer | bio | metadynamics, pathCV | Sahithya Sridharan Iyer | UPPER_WALLS RESTART DISTANCE GROUP WHOLEMOLECULES MOLINFO FUNCPATHGENERAL METAD PRINT COM | core vatom setup function colvar generic bias |
| 24.035 | Data efficient machine learning potentials for modeling catalytic reactivity via active learning and enhanced sampling | chemistry | opes, catalysis, ammonia, machine learning potentials | Luigi Bonati | COMMITTOR UPPER_WALLS DISTANCE RESTART GROUP UNITS LOWER_WALLS PRINT CUSTOM COORDINATION OPES_METAD | core setup function colvar generic bias opes |
| 24.027 | Proline cis and trans subensembles of a disordered peptide | bio | intrinsically disordered proteins, proline cis trans isomerisation, metadynamics, collective variables | Alice Pettitt | DISTANCE DIHCOR ALPHARMSD GROUP PARABETARMSD WHOLEMOLECULES FLUSH PBMETAD MOLINFO TORSION ANTIBETARMSD INCLUDE COMBINE GYRATION PRINT COORDINATION ENDPLUMED | core function multicolvar colvar generic secondarystructure bias |
| 23.044 | Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition | materials | metadynamics, interlocked molecules | Luigi Leanza | COMMITTOR DUMPGRID GROUP HISTOGRAM METAD CONVERT_TO_FES PRINT COORDINATION ENDPLUMED READ | core gridtools colvar generic bias |
| 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 | DISTANCE WHOLEMOLECULES MATHEVAL RMSD MOLINFO METAD PRINT | generic function bias 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 | UPPER_WALLS DISTANCE GROUP FIT_TO_TEMPLATE WHOLEMOLECULES DISTANCES MOLINFO METAD PRINT CUSTOM CENTER POSITION WRAPAROUND SHADOW SUM | core vatom function isdb multicolvar colvar generic bias |
| 22.032 | Reciprocal barrier restraint. Application to path-meta-eABF | methods | restraint, upper wall, lower wall, path colvar, meta-eABF, metadynamics, DRR, protein conformational transition, PROTAC | Istvan Kolossvary | PATHMSD BIASVALUE FLUSH METAD DRR PRINT CUSTOM | function drr colvar generic bias |
| 22.031 | Rare Event Kinetics from Adaptive Bias Enhanced Sampling | methods | OPES Flooding, Kinetics, Rate, OPES, Machine Learning | Dhiman Ray | RMSD POSITION DISTANCE CONSTANT BIASVALUE ENERGY GROUP MOLINFO CUSTOM PYTORCH_MODEL COMMITTOR WHOLEMOLECULES INCLUDE CONTACTMAP OPES_METAD UNITS TORSION PRINT COMBINE ENDPLUMED | core pytorch function setup colvar generic bias opes |
| 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 RESTART ONES DUMPGRID GROUP MATRIX_VECTOR_PRODUCT ENERGY VOLUME OPES_METAD MORE_THAN AROUND HISTOGRAM PRINT CUSTOM MEAN ENVIRONMENTSIMILARITY SUM DISTANCE_MATRIX | adjmat core colvar envsim setup function matrixtools volumes gridtools generic bias opes |
| 22.007 | Characterization of a natural variant of human NDP52 and its functional consequences on mitophagy | bio | metadynamics, well-tempered, protein-protein interactions, disordered proteins, mutations autophagy | Elena Papaleo | UPPER_WALLS DISTANCE ALPHABETA ALPHARMSD CONSTANT WHOLEMOLECULES FLUSH MOLINFO LESS_THAN TORSION METAD COMBINE CUSTOM PRINT COORDINATION SECONDARY_STRUCTURE_RMSD SUM ANGLE | secondarystructure function multicolvar colvar generic bias |
| 22.000 | Amyloid precursor protein processing by human γ-secretase | bio | Bias Exchange Metadynamics, Helix unfolding, coupled binding | Xiaoli Lu | RANDOM_EXCHANGES DISTANCE ALPHARMSD UNITS MOLINFO LESS_THAN ANTIBETARMSD METAD INCLUDE PRINT CONTACTMAP CENTER COORDINATION SECONDARY_STRUCTURE_RMSD SUM | vatom setup function colvar generic secondarystructure bias |
| 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 | UPPER_WALLS DISTANCE UNITS LOWER_WALLS TORSION METAD PRINT CUSTOM COM | vatom setup function colvar generic bias |
| 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 | UPPER_WALLS ALPHABETA GROUP CONSTANT WHOLEMOLECULES LOWER_WALLS TORSION METAD GYRATION COMBINE CUSTOM PRINT ENDPLUMED SUM | core function multicolvar colvar generic bias |
| 21.018 | Localized Volume-based Metadynamics | bio | LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification | Riccardo Capelli | REWEIGHT_METAD RMSD POSITION DISTANCE GROUP HISTOGRAM METAD CONVERT_TO_FES FIXEDATOM COM UPPER_WALLS WHOLEMOLECULES FLUSH READ DUMPGRID MATHEVAL PRINT COORDINATION ENDPLUMED | core colvar vatom function gridtools generic bias |
| 21.006 | OPES, On-the-fly Probability Enhanced Sampling Method | methods | opes, alanine dipeptide, well-tempered, multithermal, multiumbrella | Michele Invernizzi | ECV_MULTITHERMAL ENERGY ECV_UMBRELLAS_LINE TORSION PRINT ENDPLUMED OPES_EXPANDED OPES_METAD | generic opes colvar |
| 20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Adriana Pietropaolo | WHOLEMOLECULES PBMETAD PRINT CENTER COORDINATION | generic bias vatom colvar |
| 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 | DISTANCE METAD PRINT TORSION | generic bias colvar |
| 20.016 | Predicting polymorphism in molecular crystals using orientational entropy | materials | metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy | Pablo Piaggi | UPPER_WALLS GROUP VOLUME METAD INCLUDE LOAD PRINT CENTER | core vatom setup colvar generic bias |
| 19.076 | Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones | bio | molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics | Salvatore Assenza | UNITS MOVINGRESTRAINT PRINT GYRATION ENDPLUMED | bias setup generic colvar |
| 19.073 | On the role of enthalpic and entropic contributions on the conformational free energy landscape of MIL-101(Cr) building units | materials | metadynamics, MOF, MIL101Cr, conformational | Matteo Salvalaglio | UPPER_WALLS DISTANCE COORDINATIONNUMBER ONES SUM GROUP MATRIX_VECTOR_PRODUCT ENERGY LOWER_WALLS DISTANCES MORE_THAN CONTACT_MATRIX LOWEST METAD PRINT GYRATION ENDPLUMED MEAN | adjmat core function symfunc matrixtools multicolvar colvar generic bias |
| 19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Matteo Salvalaglio | DISTANCE GROUP INCLUDE PRINT CENTER ENDPLUMED | generic vatom core 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 | RANDOM_EXCHANGES TORSION METAD INCLUDE PRINT | generic bias colvar |
| 19.055 | Flying Gaussian method | methods | flying Gaussians, alanine dipeptide, peptide bond, Met-enkephalin | Vojtech Spiwok | DISTANCE MATHEVAL TORSION METAD PRINT COMBINE | bias function generic colvar |
| 19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | GiovanniMaria Piccini | UPPER_WALLS DISTANCE UNITS ENERGY LOWER_WALLS FLUSH METAD COMBINE PRINT | setup function colvar generic bias |
| 19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | UPPER_WALLS DISTANCE UNITS ENERGY FLUSH METAD COMBINE PRINT | setup function colvar generic bias |
| 19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Davide Provasi | FUNCPATHMSD DISTANCE WHOLEMOLECULES RMSD METAD PRINT CONTACTMAP COM ENDPLUMED | vatom function colvar generic bias |
| 19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Jim Pfaendtner | GROUP EXTERNAL ENERGY METAD COORDINATION | bias core colvar |
| 19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Glen Hocky | DISTANCE EDS TORSION PRINT COMBINE RESTRAINT | eds function colvar generic bias |
| 19.013 | RNA FF FITTING | methods | force field, RNA | Giovanni Bussi | CONSTANT BIASVALUE MATHEVAL MOLINFO PUCKERING TORSION INCLUDE | generic bias function colvar |
| 24.034 | Umbrella sampling of ion in transporter SLC26A7 | bio | umbrella sampling, transporter, ions | Xiaoli Lu | PRINT UNITS POSITION RESTRAINT | bias colvar setup generic |
| 24.026 | Constant pH metadynamics of RNA oligomers | bio | metadynamics, pH, RNA | Giovanni Bussi | PUCKERING PRINT RESTART TORSION MOLINFO METAD | bias colvar setup generic |
| 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 | UPPER_WALLS OPES_METAD_EXPLORE COORDINATION ANGLE PRINT MATHEVAL DISTANCE TORSION ECV_MULTITHERMAL OPES_EXPANDED LOWER_WALLS GROUP WHOLEMOLECULES CENTER FIT_TO_TEMPLATE ENDPLUMED ENERGY FIXEDATOM | function generic core vatom colvar opes bias |
| 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 | COORDINATION OPES_METAD CONTACTMAP ENDPLUMED TORSION COMBINE MOLINFO GROUP FIT_TO_TEMPLATE FIXEDATOM DISTANCE CENTER COMMITTOR UPPER_WALLS ANGLE PRINT MATHEVAL CUSTOM WHOLEMOLECULES METAD RMSD | core function generic vatom colvar opes bias |
| 24.016 | Cryo-EM guided simulations of ribozyme | bio | metainference, cryo-EM | Giovanni Bussi | INCLUDE ERMSD PRINT BIASVALUE MOLINFO GROUP WHOLEMOLECULES EMMIVOX RESTRAINT | core generic colvar isdb bias |
| 24.009 | Weighted Shape Gaussian Mixture Models | bio | metadynamics, clustering | Glen Hocky | PRINT TORSION GROUP UNITS METAD | core generic colvar setup bias |
| 24.008 | yCD Metadynamics | bio | volume-based MetaD, path CVs, infrequent MetaD, product release | James McCarty | INCLUDE COORDINATION CONTACTMAP ENDPLUMED COMBINE GPATH MOLINFO GROUP PATH FIT_TO_TEMPLATE FLUSH FIXEDATOM CONVERT_TO_FES DISTANCE REWEIGHT_METAD COMMITTOR UPPER_WALLS DUMPGRID PRINT MATHEVAL COM WRAPAROUND WHOLEMOLECULES HISTOGRAM READ METAD RMSD | core generic function vatom colvar mapping bias gridtools |
| 24.003 | Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations | chemistry | steered molecular dynamics, foldamers, peptoids, bio-inspired | Kaylyn Torkelson | INCLUDE MOVINGRESTRAINT COORDINATION PRINT GYRATION DISTANCE TORSION COM WHOLEMOLECULES ALPHABETA | generic multicolvar vatom colvar bias |
| 23.040 | Supramolecular capsules assembly dynamics | chemistry | Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics | Riccardo Capelli | SUM BETWEEN PRINT DISTANCE CUSTOM POSITION COM GROUP WHOLEMOLECULES CENTER UNITS LESS_THAN FLUSH METAD DISTANCES | generic core function vatom multicolvar colvar setup bias |
| 23.037 | Estimating binding free energy of solid binding peptides without extensive sampling | bio | metadynamics, solid binding peptides | Xin Qi | UPPER_WALLS PRINT GYRATION DISTANCE MOLINFO COM LOWER_WALLS PBMETAD | bias colvar generic vatom |
| 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 | COORDINATION BIASVALUE POSITION OPES_METAD ENDPLUMED TORSION MOLINFO GROUP FIT_TO_TEMPLATE FLUSH ENERGY DISTANCE CENTER COMMITTOR UPPER_WALLS OPES_METAD_EXPLORE PRINT MATHEVAL CUSTOM COM LOWER_WALLS WRAPAROUND WHOLEMOLECULES UNITS | core generic vatom function colvar setup opes bias |
| 23.015 | MPCs aggregation | bio | opes_explore, dimerization, MPCs, self-assembly | Vikas Tiwari | UPPER_WALLS OPES_METAD_EXPLORE COORDINATION PRINT DISTANCE CUSTOM COM LOWER_WALLS GROUP WHOLEMOLECULES CENTER METAD | function generic vatom core colvar opes bias |
| 23.001 | Quantum phase diagram of water | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn-Løland Bore | INCLUDE UPPER_WALLS SUM ONES PRINT RESTART CUSTOM MEAN OPES_EXPANDED LOWER_WALLS DISTANCE_MATRIX GROUP MATRIX_VECTOR_PRODUCT MORE_THAN ECV_UMBRELLAS_LINE ENVIRONMENTSIMILARITY | matrixtools generic function core adjmat setup envsim opes bias |
| 22.030 | Mixing physics across temperatures with generative artificial intelligence | methods | REMD, Generative AI, DDPM | Yihang Wang | TORSION WHOLEMOLECULES PRINT | colvar generic |
| 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 | UPPER_WALLS COORDINATION PRINT RESTART TORSION EMMI MOLINFO COM BIASVALUE GROUP WHOLEMOLECULES PBMETAD RMSD | generic core vatom colvar setup isdb bias |
| 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 UPPER_WALLS SUM PRINT CUSTOM MEAN OPES_EXPANDED LOWER_WALLS DISTANCE_MATRIX GROUP MATRIX_VECTOR_PRODUCT ECV_UMBRELLAS_LINE MORE_THAN ONES ENVIRONMENTSIMILARITY | matrixtools generic function core adjmat envsim opes bias |
| 22.002 | GAMBES_SAMPL5_RATES | other | GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding | Jayashrita Debnath | UPPER_WALLS COORDINATION ANGLE PRINT LOAD DISTANCE MATHEVAL GROUP WHOLEMOLECULES CENTER FIT_TO_TEMPLATE ENDPLUMED FLUSH ENERGY COMMITTOR PYTORCH_MODEL FIXEDATOM | generic function core vatom colvar setup bias pytorch |
| 21.045 | QM/MM metadynamics of thiol-disulfide exchange between methylthiolate and dimethyldisulfide in water with an imposed external electrostatic potential (ESP) | chemistry | metadynamics, QM/MM, electrostatic potential, thiol-disulfide exchange | Denis Maag | UPPER_WALLS COORDINATION PRINT DISTANCE COMBINE MEAN LOWER_WALLS COORDINATIONNUMBER GROUP MATRIX_VECTOR_PRODUCT ONES METAD CONTACT_MATRIX | matrixtools generic function core adjmat colvar symfunc bias |
| 21.036 | Modelling the structure and interactions of intrinsically disordered peptides with multiple-replica, metadynamics-based sampling methods and force-field combinations | bio | Bias Exchange Metadynamics, PTWTE-metaD | Matteo Salvalaglio | RANDOM_EXCHANGES COORDINATION SECONDARY_STRUCTURE_RMSD PARABETARMSD ALPHARMSD ANTIBETARMSD GYRATION MOLINFO DIHEDRAL_CORRELATION DIHCOR GROUP ENERGY LOWEST UPPER_WALLS SUM PRINT LOWER_WALLS WHOLEMOLECULES LESS_THAN METAD | core generic multicolvar function colvar bias secondarystructure |
| 21.026 | Probing allosteric regulations with coevolution-driven molecular simulations | bio | metadynamics, coevolution, allostery, adenylate cyclase | Francesco Colizzi | UPPER_WALLS PATHMSD PRINT DISTANCE COM UNITS WHOLEMOLECULES METAD | generic vatom colvar setup bias |
| 21.024 | Property map collective variable as a useful tool for force field correction | chemistry | molecular mechanics | Vojtech Spiwok | PRINT BIASVALUE TORSION WHOLEMOLECULES PROPERTYMAP METAD | bias colvar generic |
| 21.021 | ATLAS | methods | Machine Learning, Metadynamics | Federico Giberti | COORDINATION PRINT GYRATION MATHEVAL DISTANCE BIASVALUE TORSION MEAN COORDINATIONNUMBER GROUP UNITS MATRIX_VECTOR_PRODUCT WHOLEMOLECULES DUMPATOMS ONES METAD CONTACT_MATRIX | matrixtools generic function core adjmat colvar symfunc setup bias |
| 21.014 | how to determine statistically accurate conformational ensembles | bio | metadynamics, metainference, errors, cv, SAXS, ensemble determination | Cristina Paissoni | BIASVALUE SECONDARY_STRUCTURE_RMSD SAXS CONTACTMAP ANTIBETARMSD ENSEMBLE GYRATION TORSION COMBINE MOLINFO STATS CENTER PBMETAD SUM PRINT CUSTOM CONSTANT WHOLEMOLECULES ALPHABETA LESS_THAN METAD | function generic vatom multicolvar colvar isdb bias secondarystructure |
| 21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Tarsis Ferreira | UPPER_WALLS INCLUDE RANDOM_EXCHANGES DUMPGRID PUCKERING COORDINATION PRINT DISTANCE MOLINFO LOWER_WALLS GROUP WHOLEMOLECULES HISTOGRAM ENERGY METAD REWEIGHT_METAD | core generic colvar bias gridtools |
| 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 | ERMSD PRINT RESTART DISTANCE TORSION MOLINFO CENTER ABMD | generic vatom colvar setup bias |
| 20.026 | Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor | bio | Metadynamics, Umbrella sampling | Brandon Peters | MULTI_RMSD DUMPGRID RESTRAINT PRINT CONVERT_TO_FES CONCATENATE COMBINE CUSTOM POSITION CONSTANT WHOLEMOLECULES HISTOGRAM RMSD_VECTOR METAD REWEIGHT_METAD | generic function colvar bias gridtools valtools |
| 20.021 | Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins. | bio | phi-values, restrained MD, transition-state, protein folding, disordered proteins, protein evolution | Cristina Paissoni | COORDINATION PRINT STATS MOLINFO WHOLEMOLECULES RESTRAINT | bias colvar generic function |
| 20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Jim Pfaendtner | SUM COORDINATION PRINT RESTART DISTANCE CUSTOM GROUP WHOLEMOLECULES CENTER DISTANCES | core function generic vatom multicolvar colvar setup |
| 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 | BIASVALUE SECONDARY_STRUCTURE_RMSD ENDPLUMED ANTIBETARMSD TORSION COMBINE MOLINFO GROUP FLUSH PBMETAD UPPER_WALLS SUM PRINT CUSTOM CONSTANT LOWER_WALLS WHOLEMOLECULES LESS_THAN ALPHABETA CS2BACKBONE | generic function core multicolvar colvar isdb bias secondarystructure |
| 19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Giovanni Bussi | COORDINATION DISTANCE LOWER_WALLS WHOLEMOLECULES RESTRAINT ENDPLUMED | bias colvar generic |
| 19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Jakub Rydzewski | UPPER_WALLS PATHMSD PRINT RESTART LOWER_WALLS UNITS METAD | bias colvar setup generic |
| 19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Mattia Bernetti | UPPER_WALLS PATHMSD PRINT LOWER_WALLS WHOLEMOLECULES METAD | bias colvar generic |
| 19.056 | maze | methods | maze, ligand unbinding | Jakub Rydzewski | PRINT MAZE_SIMULATED_ANNEALING POSITION UNITS MAZE_LOSS MAZE_OPTIMIZER_BIAS | colvar setup generic maze |
| 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 | UPPER_WALLS PRINT DISTANCE COM ENERGY METAD | bias colvar generic vatom |
| 19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Carlo Camilloni | RESTART BIASVALUE SECONDARY_STRUCTURE_RMSD ENDPLUMED ANTIBETARMSD TORSION COMBINE MOLINFO GROUP FLUSH PBMETAD UPPER_WALLS SUM PRINT CUSTOM CONSTANT LOWER_WALLS WHOLEMOLECULES LESS_THAN ALPHABETA CS2BACKBONE | generic function core multicolvar colvar setup isdb bias secondarystructure |
| 19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Elena Papaleo | UPPER_WALLS SUM PRINT GYRATION TORSION COMBINE MOLINFO CONSTANT CUSTOM LOWER_WALLS GROUP WHOLEMOLECULES ALPHABETA METAD | generic core function multicolvar colvar bias |
| 25.009 | Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water | chemistry | metadynamics, nitrate photolysis | Kam-Tung Chan | UPPER_WALLS READ REWEIGHT_METAD DUMPGRID DISTANCE HISTOGRAM PRINT RESTART CUSTOM METAD FLUSH COORDINATION GROUP | setup gridtools function generic core colvar bias |
| 25.008 | Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting | methods | metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting | Dhiman Ray | MOLINFO UPPER_WALLS PYTORCH_MODEL POSITION ENDPLUMED BIASVALUE OPES_METAD DISTANCE PRINT RMSD METAD ENERGY CUSTOM UNITS TORSION LOWER_WALLS WHOLEMOLECULES GROUP | setup pytorch opes function generic core colvar bias |
| 24.031 | DeepLNE | methods | PATHCV, OPES, OneOPES | Thorben Fröhlking | MOLINFO COORDINATION COMBINE PYTORCH_MODEL OPES_EXPANDED PRINT ERMSD ENERGY OPES_METAD_EXPLORE RESTART VOLUME ECV_MULTITHERMAL | setup pytorch opes function generic colvar |
| 24.030 | NMR guided simulation of dsRBD | bio | Metainference, NMR, protein dynamics | Debadutta Patra | STATS MOLINFO COMBINE METAINFERENCE SUM TORSION ENSEMBLE DISTANCE CONSTANT PRINT CUSTOM RDC FLUSH ALPHABETA WHOLEMOLECULES GROUP | multicolvar core function generic isdb 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 | WRAPAROUND CONSTANT GROUP UPPER_WALLS MATHEVAL OPES_EXPANDED RMSD PRINT ENERGY PROJECTION_ON_AXIS TORSION WHOLEMOLECULES INCLUDE METAD CUSTOM OPES_METAD_EXPLORE CONTACTMAP COORDINATION RESTART LOWER_WALLS MOLINFO COM BIASVALUE ECV_MULTITHERMAL | setup opes function generic core vatom colvar bias |
| 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 | UPPER_WALLS MOLINFO PYTORCH_MODEL RMSD PRINT METAD FLUSH DRR COORDINATION LOWER_WALLS WHOLEMOLECULES | pytorch drr generic colvar bias |
| 23.039 | Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation | chemistry | metadynamics, ligand dissociation | Eric Beyerle | MOLINFO CENTER UPPER_WALLS COMBINE RESTRAINT DUMPMASSCHARGE DISTANCE PRINT METAD FIXEDATOM | function generic vatom colvar bias |
| 23.028 | Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process | chemistry | Ammonia decomposition; Dynamics;OPES; Neural Network potential | Manyi Yang | MEAN OPES_METAD DISTANCE COMMITTOR ONES FLUSH DISTANCES COORDINATIONNUMBER FIXEDATOM GROUP UPPER_WALLS MATHEVAL PRINT ENERGY MATRIX_VECTOR_PRODUCT UNITS CONTACT_MATRIX SUM CUSTOM LOWER_WALLS ZDISTANCES COM LESS_THAN | multicolvar setup adjmat opes function generic core matrixtools vatom symfunc colvar bias |
| 23.023 | Rational design of novel biomimetic sequence-defined polymers for mineralization applications | methods | metadynamics, surface binding, biomimetic mineralization | Kaylyn Torkelson | UPPER_WALLS COM PBMETAD DISTANCE PRINT GYRATION COORDINATION | colvar vatom generic bias |
| 23.019 | Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors | bio | binding pathway, binding energy, sketch-map, drug development | Raitis Bobrovs | TRANSPOSE EUCLIDEAN_DISTANCE DISTANCE CONSTANT MORE_THAN VSTACK UPPER_WALLS PDB2CONSTANT PROJECT_POINTS PRINT DISSIMILARITIES WHOLEMOLECULES SKETCHMAP SKETCHMAP_PROJECTION SUM VORONOI METAD CUSTOM COLLECT_FRAMES COM PATHMSD LANDMARK_SELECT_FPS | valtools vatom function generic matrixtools refdist dimred landmarks colvar bias |
| 23.012 | JAK2 2D meta-eABF PMF with statistical analysis | bio | 2D meta-eABF, path CV, PMF | Istvan Kolossvary | UPPER_WALLS BIASVALUE PATHMSD PRINT METAD CUSTOM FLUSH DRR LOWER_WALLS | drr function generic colvar bias |
| 23.011 | OneOPES, a combined enhanced sampling method to rule them all | bio | OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding | Valerio Rizzi | MOLINFO ENDPLUMED OPES_EXPANDED DISTANCE PRINT METAD ENERGY OPES_METAD_EXPLORE TORSION ECV_MULTITHERMAL | opes colvar generic bias |
| 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 | UPPER_WALLS MATHEVAL BIASVALUE DISTANCE PRINT METAD CONSTANT LOWER_WALLS WHOLEMOLECULES | function colvar generic bias |
| 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 | CENTER OPES_METAD DISTANCE COMMITTOR FIXEDATOM GROUP UPPER_WALLS MATHEVAL PYTORCH_MODEL COMBINE RMSD PRINT ENERGY WHOLEMOLECULES INCLUDE CUSTOM CONTACTMAP COORDINATION LOWER_WALLS MOLINFO FIT_TO_TEMPLATE ENDPLUMED ANGLE | pytorch opes function generic core colvar vatom bias |
| 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 | DISTANCE_MATRIX UPPER_WALLS ECV_UMBRELLAS_LINE SUM OPES_EXPANDED ENVIRONMENTSIMILARITY DUMPGRID PRINT HISTOGRAM ONES CUSTOM MATRIX_VECTOR_PRODUCT RESTART LOWER_WALLS MORE_THAN GROUP | setup core envsim adjmat opes gridtools function generic matrixtools bias |
| 22.033 | Reciprocal barrier restraint. Application to PROTAC passive permeability prediction | methods | PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR | Istvan Kolossvary | COM BIASVALUE DISTANCE PRINT METAD CUSTOM FLUSH DRR UNITS | setup drr function generic vatom colvar bias |
| 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 |
| 22.012 | 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 DISTANCE PRINT CONTACTMAP | vatom generic colvar |
| 21.033 | Multiple-path-metadynamics applied to DNA base-pairing transitions | bio | path-CV, metadynamics, multiple-walker, dna | Alberto Pérez-de-Alba-Ortíz | UPPER_WALLS RESTRAINT COMBINE INCLUDE PRINT METAD MOVINGRESTRAINT CONSTANT | function generic bias |
| 21.019 | Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations | materials | Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen | Matteo Salvalaglio | KDE MATHEVAL COM DISTANCE PRINT TORSIONS | multicolvar gridtools function generic colvar vatom |
| 21.000 | Uremic toxin time scale dynamics | bio | uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs) | Jim Pfaendtner | COM DISTANCE PRINT WHOLEMOLECULES GROUP | core vatom generic colvar |
| 20.032 | Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil | materials | clustering, conformational isomers | Matteo Salvalaglio | TORSION PRINT ENDPLUMED | colvar generic |
| 20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Cristina Paissoni | STATS MOLINFO CENTER RESTRAINT SAXS BIASVALUE INCLUDE ENSEMBLE DISTANCE PRINT WHOLEMOLECULES GROUP | core function isdb generic colvar vatom bias |
| 20.014 | amyloid beta small molecule interaction | bio | intrinsically disordered proteins, disordered proteins, IDPs, fuzzy binding, small molecule, drugs, entropy, binding, Alzheimer’s disease, amyloid beta | Gabriella Heller | METAINFERENCE PARABETARMSD FLUSH GROUP CS2BACKBONE COMBINE PRINT TORSION WHOLEMOLECULES ENSEMBLE INCLUDE DIHCOR PBMETAD COORDINATION ALPHARMSD STATS MOLINFO ENDPLUMED GYRATION ANTIBETARMSD | multicolvar core secondarystructure function generic isdb colvar bias |
| 20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Pratyush Tiwary | UPPER_WALLS MOLINFO COMBINE RMSD DISTANCE PRINT METAD RESTART TORSION WHOLEMOLECULES | setup function generic colvar bias |
| 20.005 | Muscarinic M2 receptor/ligand Frequency-Adaptive Metadynamics and QM/MM calculations | bio | Frequency-adaptive metadynamics, multiple-walkers metadynamics, well-tempered metadynamics, GPCR, receptor, Adiabatic Bias MD | Riccardo Capelli | REWEIGHT_METAD DISTANCE ABMD FLUSH UPPER_WALLS COMBINE FUNCPATHMSD PRINT CONVERT_TO_FES WHOLEMOLECULES READ HISTOGRAM METAD CONTACTMAP LOWER_WALLS MOLINFO ENDPLUMED COM DUMPGRID | gridtools function generic vatom colvar bias |
| 20.002 | Exploring conformational dynamics of the extracellular Venus flytrap domain of the GABAB receptor, a path-metadynamics study | bio | Metadynamics, path CVs | Riccardo Ocello | MOLINFO UPPER_WALLS PATHMSD PRINT METAD RESTART WHOLEMOLECULES GROUP | setup generic core colvar 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 | Q6 LOAD VOLUME UPPER_WALLS MATHEVAL COMBINE TD_MULTITHERMAL_MULTIBARIC PRINT ENERGY CONVERT_TO_FES REWEIGHT_BIAS TD_WELLTEMPERED VES_LINEAR_EXPANSION READ HISTOGRAM RESTART LOWER_WALLS OPT_DUMMY DUMPGRID BF_LEGENDRE OPT_AVERAGED_SGD CELL REWEIGHT_TEMP_PRESS | setup ves gridtools function generic symfunc colvar bias |
| 19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Luigi Bonati | POSITION ENDPLUMED Q6 ENVIRONMENTSIMILARITY LOAD PRINT ENERGY UNITS TORSION | setup envsim generic symfunc colvar |
| 19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Gareth Tribello | UPPER_WALLS FCCUBIC_FUNC MEAN CONTACT_MATRIX SUM ENDPLUMED FCCUBIC PRINT CUSTOM ONES METAD MATRIX_VECTOR_PRODUCT UNITS CELL MORE_THAN GROUP | setup core adjmat function generic matrixtools symfunc colvar bias |
| 19.049 | Determining the sizes of solid/liquid clusters in MD trajectories of nucleation | methods | nucleation, metadynamics, clustering, Steinhardt order parameters | Gareth Tribello | CLUSTER_PROPERTIES CONTACT_MATRIX SMAC DFSCLUSTERING Q6 COORDINATIONNUMBER PRINT CLUSTER_DISTRIBUTION OUTER_PRODUCT CLUSTER_NATOMS CUSTOM LOCAL_Q6 ONES METAD MATRIX_VECTOR_PRODUCT DISTANCES OUTPUT_CLUSTER MORE_THAN | multicolvar adjmat function generic matrixtools clusters symfunc bias |
| 19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Paolo Raiteri | UPPER_WALLS MATHEVAL DISTANCE PRINT METAD FLUSH RESTART UNITS | setup function generic colvar bias |
| 19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Gabriele Cesare Sosso | CONTACT_MATRIX DFSCLUSTERING ENDPLUMED Q6 CLUSTER_WITHSURFACE COMMITTOR MFILTER_MORE LOCAL_Q6 FLUSH OUTPUT_CLUSTER CLUSTER_NATOMS | multicolvar adjmat generic clusters symfunc |