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 | CONTACT_MATRIX GROUP RESTRAINT ONES FIXEDATOM MEAN UPPER_WALLS MATRIX_VECTOR_PRODUCT COM COORDINATIONNUMBER PRINT SUM DISTANCE FLUSH CUSTOM LOWER_WALLS COMBINE DISTANCES ANGLE UNITS METAD COORDINATION LOWEST | generic symfunc core multicolvar setup matrixtools colvar vatom bias adjmat function |
| 25.006 | Characterizing the conformational ensemble of PROTAC degraders in solutions via atomistic simulations | methods | Enhanced sampling, Atomistic simulations, Conformational ensemble, PROTACs, Targeted Protein Degradation, Chamelonic molecules | Shikshya Bhusal, Omar Valsson | RESTART DISTANCE READ PBMETAD INCLUDE VOLUME PRINT CENTER TORSION GYRATION ENERGY | generic colvar setup vatom bias |
| 25.002 | M3_PCV-ABMD | chemistry | Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor | Gian Marco Elisi | PATHMSD ENDPLUMED UNITS UPPER_WALLS PRINT ABMD | setup generic colvar bias |
| 24.028 | All-atom simulations of RNA-membrane interactions | bio | metadynamics, membrane, RNA | Giovanni Bussi | DISTANCE MOLINFO MATHEVAL PUCKERING COMBINE LOWER_WALLS GHOST SORT CENTER DISTANCES PRINT UPPER_WALLS METAD LOWEST WHOLEMOLECULES POSITION GROUP GYRATION | generic core multicolvar colvar vatom bias function |
| 24.025 | Correlating Enzymatic Reactivity for Different Substrates using Transferable Data-Driven Collective Variables | bio | enzymatic reactivity, k_cat, transfer learning, data-driven CVs, catalysis, ligand-binding modes, water, alpha-amylase, sugar, classical MD, OPES, machine learning, Deep TDA CV, path CV | Sudip Das | LOWER_WALLS WHOLEMOLECULES CONSTANT OPES_METAD PYTORCH_MODEL COMBINE PDB2CONSTANT UPPER_WALLS FIT_TO_TEMPLATE LOWEST SUM RESTART DISTANCE PATH FIXEDATOM CENTER TORSION COORDINATION EUCLIDEAN_DISTANCE CUSTOM GROUP | generic pytorch mapping core colvar setup opes refdist vatom bias function |
| 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 MOLINFO WRAPAROUND BIASVALUE EMMIVOX INCLUDE PRINT UPPER_WALLS WHOLEMOLECULES GROUP | generic core colvar isdb bias |
| 23.024 | Permutationally Invariant Networks for Enhanced Sampling (PINES) | methods | collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent | Nicholas Herringer | PRINT PBMETAD LOAD | setup generic bias |
| 22.043 | Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES | bio | OPES, RNA, Tetraloop, Folding | Gül Zerze | CONTACTMAP OPES_EXPANDED ECV_UMBRELLAS_LINE PRINT ECV_MULTITHERMAL WHOLEMOLECULES ENERGY | generic opes colvar |
| 22.026 | Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification | materials | Peptoid, silica | Jim Pfaendtner | DISTANCE MOLINFO PBMETAD UPPER_WALLS PRINT COM GYRATION | generic vatom colvar bias |
| 21.052 | On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets | materials | Ibuprofen, unbinding, WTmetaD | Matteo Salvalaglio | DISTANCE ONES COMMITTOR COORDINATIONNUMBER MEAN CONTACT_MATRIX ENDPLUMED CENTER TORSION PRINT METAD GROUP MATRIX_VECTOR_PRODUCT | bias generic core matrixtools adjmat colvar vatom symfunc function |
| 21.032 | Metal-coupled folding mechanism to metallothionein | bio | parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination | Manuel-Peris Diaz | PBMETAD UNITS COORDINATION WHOLEMOLECULES GROUP | generic core colvar setup bias |
| 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 ALPHABETA PBMETAD COMBINE INCLUDE TORSION COORDINATION PRINT COM ENERGY METAD CONSTANT CUSTOM SUM GYRATION | generic multicolvar colvar vatom bias function |
| 21.028 | From Enhanced Sampling to Reaction Profiles | methods | collective variables, multi-state, machine learning, Deep-TDA | Enrico Trizio | MATHEVAL LOWER_WALLS DISTANCES WHOLEMOLECULES OPES_METAD PYTORCH_MODEL LOAD PRINT ANGLE UPPER_WALLS FIT_TO_TEMPLATE DISTANCE ENDPLUMED FIXEDATOM UNITS CENTER TORSION COORDINATION GROUP | generic pytorch core multicolvar colvar setup opes vatom bias function |
| 21.025 | Computational and biochemical analysis of type IV pilus dynamics and stability | bio | molecular dynamics, calcium binding, Type IV pilus | Yasaman Karami | DISTANCE UPPER_WALLS LOWER_WALLS PRINT | generic colvar bias |
| 21.016 | MD SAXS GTPase associated center | bio | metadynamics, RNA, folding, SAXS | Giovanni Bussi | MOLINFO SAXS LOWER_WALLS INCLUDE UPPER_WALLS PRINT METAD WHOLEMOLECULES ERMSD CUSTOM GROUP GYRATION | generic core colvar isdb bias function |
| 21.010 | Step by Step Strecker Amino Acid Synthesis from Ab Initio Prebiotic Chemistry | chemistry | Strecker reaction, free energy landscape, ab initio molecular dynamics, glycine, prebiotic synthesis | Théo Magrino | generic | |
| 21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Kresten Lindorff-Larsen | MOLINFO SAXS BIASVALUE PBMETAD METAINFERENCE EEFSOLV CENTER PRINT ALPHARMSD WHOLEMOLECULES FLUSH GROUP GYRATION | generic core colvar isdb secondarystructure vatom bias |
| 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 | MATHEVAL VES_LINEAR_EXPANSION ECV_MULTITHERMAL_MULTIBARIC CONTACT_MATRIX OPT_AVERAGED_SGD TD_UNIFORM PRINT MEAN MATRIX_VECTOR_PRODUCT OPES_EXPANDED COMBINE SPHERICAL_HARMONIC ENVIRONMENTSIMILARITY VOLUME ECV_UMBRELLAS_LINE UPPER_WALLS SUM ENERGY RESTART MORE_THAN ONES DISTANCE_MATRIX Q6 CUSTOM GROUP BF_LEGENDRE | bias generic core matrixtools adjmat colvar ves envsim setup opes symfunc function |
| 20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Matteo Salvalaglio | MATHEVAL LOWER_WALLS VOLUME UPPER_WALLS PRINT METAD CELL ENERGY | generic colvar bias 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 | MATHEVAL VES_LINEAR_EXPANSION CONTACT_MATRIX OPT_AVERAGED_SGD OPT_DUMMY PRINT MEAN MATRIX_VECTOR_PRODUCT COMBINE SPHERICAL_HARMONIC VOLUME ENVIRONMENTSIMILARITY UPPER_WALLS TD_WELLTEMPERED SUM RESTART MORE_THAN ONES DISTANCE_MATRIX Q6 CUSTOM GROUP BF_LEGENDRE | bias generic core matrixtools adjmat colvar ves envsim setup symfunc function |
| 20.006 | Class B GPCR activation mechanism | bio | metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | DISTANCE MOLINFO MATHEVAL COMBINE LOWER_WALLS CENTER UPPER_WALLS PRINT METAD WHOLEMOLECULES RMSD ENERGY | generic colvar vatom bias function |
| 20.003 | Enhanced sampling of transition states | methods | Variationally Enhanced Sampling, Target distribution, Transition state, Enhanced Sampling, Nucleation, chemical reaction | Jayashrita Debnath | VES_LINEAR_EXPANSION UNITS OPT_AVERAGED_SGD PRINT ENERGY POSITION LOAD BF_LEGENDRE | setup generic colvar ves |
| 19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | DISTANCE MOLINFO UPPER_WALLS PRINT COM METAD GYRATION ENERGY | generic vatom colvar bias |
| 19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_LOSS UNITS PRINT MAZE_SIMULATED_ANNEALING POSITION MAZE_OPTIMIZER_BIAS | maze generic setup colvar |
| 19.048 | Understanding Ligand Binding Selectivity in a Prototypical GPCR Family | bio | metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | DISTANCE MATHEVAL BIASVALUE CONSTANT LOWER_WALLS UPPER_WALLS PRINT COM METAD WHOLEMOLECULES | generic colvar vatom bias function |
| 19.040 | Optimal Metric for Path Collective Variables | bio | metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path | Francesco Luigi Gervasio | MATHEVAL ENDPLUMED TORSION PRINT METAD | generic colvar bias 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 | MOLINFO PBMETAD BIASVALUE ENDPLUMED ENSEMBLE STATS METAINFERENCE CS2BACKBONE TORSION PRINT RDC JCOUPLING WHOLEMOLECULES FLUSH GYRATION | generic colvar isdb bias function |
| 19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Kresten Lindorff-Larsen | MOLINFO ALPHABETA CUSTOM COMMITTOR COMBINE TORSION PRINT METAD CONSTANT FLUSH SUM | generic multicolvar colvar bias function |
| 19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Adriana Pietropaolo | MATHEVAL BIASVALUE CONSTANT TORSION PRINT METAD WHOLEMOLECULES | generic colvar bias function |
| 19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Carlo Camilloni | DISTANCE MOLINFO SAXS BIASVALUE RESTRAINT ENDPLUMED STATS INCLUDE CENTER UPPER_WALLS PRINT WHOLEMOLECULES RMSD GROUP | generic core colvar isdb vatom bias function |
| 19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Carlo Camilloni | MOLINFO DIHCOR ENSEMBLE METAINFERENCE CONSTANT WHOLEMOLECULES ALPHABETA PBMETAD PRINT COMBINE UPPER_WALLS RESTRAINT SUM DISTANCE DIHEDRAL_CORRELATION ENDPLUMED STATS CENTER TORSION DHENERGY RDC CUSTOM GROUP | generic core multicolvar colvar isdb vatom bias function |
| 19.008 | anncolvar | methods | neural network, dimensionality reduction | Vojtech Spiwok | MATHEVAL MOLINFO COMBINE ALPHARMSD LESS_THAN PRINT SECONDARY_STRUCTURE_RMSD FIT_TO_TEMPLATE METAD WHOLEMOLECULES POSITION SUM | generic colvar secondarystructure bias function |
| 19.005 | Cmyc small molecule interaction | bio | metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP | Gabriella Heller | DISTANCE MOLINFO ALPHABETA PBMETAD METAINFERENCE INCLUDE CS2BACKBONE PRINT COORDINATION CENTER WHOLEMOLECULES GROUP GYRATION | generic core multicolvar colvar isdb vatom bias |
| 24.029 | Combination of OPES and OPES-Explore | methods | OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin | Dhiman Ray | OPES_METAD FIXEDATOM DISTANCE UPPER_WALLS UNITS OPES_METAD_EXPLORE FLUSH MOLINFO INCLUDE FIT_TO_TEMPLATE WHOLEMOLECULES CENTER COMBINE ENDPLUMED CONTACTMAP GROUP PYTORCH_MODEL ENERGY COORDINATION PRINT POSITION BIASVALUE RMSD LOWER_WALLS METAD MATHEVAL CUSTOM | function pytorch opes bias setup colvar vatom generic core |
| 24.023 | Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21. A Machine-Learning-Aided Enhanced Sampling Study | bio | RNA, miRNA, OneOPES, ligand binding, conformational changes | Valerio Rizzi | RESTART OPES_METAD_EXPLORE OPES_EXPANDED GROUP DISTANCE ECV_MULTITHERMAL PRINT ENERGY COORDINATION TORSION CUSTOM COMBINE | function opes setup colvar generic core |
| 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 | COMMITTOR LOAD GROUP METAD TORSION PRINT | setup bias colvar generic core |
| 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 | COMMITTOR RESTART BIASVALUE COORDINATIONNUMBER RESTRAINT FLUSH MOLINFO METAD MATHEVAL DISTANCE TORSION ENERGY PRINT | symfunc function setup bias colvar generic |
| 24.005 | Learning Markovian Dynamics with Spectral Maps | methods | spectral map, collective variables, machine learning | Jakub Rydzewski | BIASVALUE DISTANCE UNITS PRINT CUSTOM | function bias setup colvar generic |
| 24.004 | Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables | materials | metadynamics, nucleation, machine learning | Ziyue Zou | RESTART LOAD GROUP INCLUDE METAD PRINT | setup core 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 | BIASVALUE GHBFIX MOLINFO METAD ERMSD PRINT COORDINATION WHOLEMOLECULES COMBINE | bias function colvar generic |
| 23.025 | Probing ion binding to G-quadruplexes and related events | chemistry | metadynamics, repulsive potential, nucleic acids, G-quadruplexes | Marcelo Poleto | DUMPATOMS DISTANCES RESTART POSITION WRAPAROUND FLUSH LOWER_WALLS COM GROUP METAD MATHEVAL DISTANCE LOWEST UPPER_WALLS PRINT UNITS FIT_TO_TEMPLATE WHOLEMOLECULES | function setup bias colvar generic vatom core multicolvar |
| 23.020 | FEP simulations of ATOX1 homodimer | chemistry | parallel bias metadynamics, FEP, free-energy of metal ion dissociation | Adriana Pietropaolo | CONSTANT BIASVALUE MATHEVAL DISTANCE ANGLE PRINT PBMETAD WHOLEMOLECULES | bias function colvar generic |
| 23.018 | Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention | materials | metadynamics, surface binding, peptide adsorption | Kaylyn Torkelson | GYRATION COM DISTANCE UPPER_WALLS PBMETAD PRINT | colvar bias generic vatom |
| 22.038 | Enhanced Sampling Aided Design of Molecular Photoswitches | chemistry | reaction discovery, OPES explore, graph CV | Umberto Raucci | OPES_METAD_EXPLORE PYTORCH_MODEL UNITS COORDINATION PRINT CUSTOM | pytorch function opes setup colvar generic |
| 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 | DRMSD COMMITTOR CONSTANT SUM LOWER_WALLS METAD MATHEVAL DISTANCE CELL UPPER_WALLS PRINT CUSTOM | colvar function bias generic |
| 22.024 | Conformational Entropy as a Potential Liability of Computationally Designed Antibodies | bio | metadynamics, conformational entropy, antibody, nanobody | Thomas Löhr | LESS_THAN PRINT RESTART CONSTANT SUM MOLINFO ALPHARMSD CUSTOM COM PBMETAD ANTIBETARMSD SECONDARY_STRUCTURE_RMSD WHOLEMOLECULES TORSION ALPHABETA COMBINE | function setup bias secondarystructure colvar vatom generic multicolvar |
| 22.019 | Exploring aspartic protease inhibitor binding to design selective antimalarials | bio | ligand binding, loop opening, path CV, funnel metadynamics, drug development | Raitis Bobrovs | PATHMSD FUNNEL LOWER_WALLS COM METAD DISTANCE UPPER_WALLS PRINT WHOLEMOLECULES FUNNEL_PS | bias colvar funnel generic vatom |
| 22.015 | Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome | bio | photodynamics, bacteriophytochrome, variationally enhanced sampling | Jakub Rydzewski | VES_LINEAR_EXPANSION TD_UNIFORM BF_FOURIER PRINT OPT_AVERAGED_SGD TORSION | colvar generic ves |
| 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 | CONSTANT YANGLES DISTANCE XANGLES UPPER_WALLS MOLINFO ZANGLES WHOLEMOLECULES ALPHABETA COMBINE MEAN COM TORSION PRINT SUM LOWER_WALLS METAD MATHEVAL CUSTOM | function bias colvar generic vatom multicolvar |
| 22.009 | Glycosylation in calixarenes capsule | chemistry | Metadynamics, glycosylation, supramolecular catalysis | GiovanniMaria Piccini | DISTANCE ANGLE UPPER_WALLS UNITS DISTANCES BRIDGE_MATRIX FLUSH FIT_TO_TEMPLATE WHOLEMOLECULES COMBINE MEAN GROUP COORDINATION PRINT BRIDGE RMSD SUM LOWER_WALLS METAD MATHEVAL | function bias setup colvar adjmat generic core multicolvar |
| 21.047 | Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations | materials | pair entropy, metadynamics, ves, solids, crystallization | Pablo Piaggi | VES_LINEAR_EXPANSION RESTART BF_LEGENDRE LOAD METAD TD_WELLTEMPERED PAIRENTROPY VOLUME OPT_AVERAGED_SGD ENERGY PRINT COMBINE | function setup bias ves colvar generic gridtools |
| 21.035 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, interface | Aaron Finney | RESTRAINT LOAD FIXEDATOM GROUP DISTANCE PRINT | bias setup colvar vatom generic core |
| 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 | ENDPLUMED INCLUDE METAD TORSION PBMETAD RANDOM_EXCHANGES PRINT | bias colvar generic |
| 21.031 | Photo-switchable sulfonulureas in KATP channel | bio | metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels | Katarzyna Walczewska-Szewc | LOWER_WALLS COM METAD DISTANCE UPPER_WALLS PRINT UNITS WHOLEMOLECULES | bias setup colvar generic vatom |
| 21.029 | Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs | bio | metadynamics, small peptide, machine learning | Pratyush Tiwary | RESTART EXTERNAL FLUSH MOLINFO TORSION ENERGY PRINT | setup colvar bias generic |
| 20.024 | Gaussian Mixture Based Enhanced Sampling (GAMBES) | methods | enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias | Jayashrita Debnath | DISTANCES LOAD LOWER_WALLS GROUP DISTANCE TORSION ENERGY UPPER_WALLS UNITS PRINT COMBINE | function setup bias colvar generic core multicolvar |
| 20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Vojtech Spiwok | PRINT METAD TORSION | bias colvar generic |
| 20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Max Bonomi | GYRATION CONSTANT DIHCOR SUM MOLINFO CUSTOM INCLUDE TORSION DIHEDRAL_CORRELATION PRINT PBMETAD COORDINATION WHOLEMOLECULES ALPHABETA COMBINE | function bias colvar generic multicolvar |
| 19.078 | Iterative unbiasing of quasi-equilibrium sampling | methods | metadynamics, reweighting | Federico Giberti | DUMPATOMS BIASVALUE COORDINATIONNUMBER COLLECT_FRAMES CONTACT_MATRIX ONES MEAN GROUP METAD MATHEVAL DISTANCE MATRIX_VECTOR_PRODUCT UNITS PRINT REWEIGHT_BIAS | symfunc landmarks function matrixtools bias setup colvar adjmat generic core |
| 19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Sandro Bottaro | RMSD MOLINFO METAD ERMSD DISTANCE PRINT WHOLEMOLECULES TORSION | colvar bias generic |
| 19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Michele Invernizzi | EXTERNAL POSITION ENDPLUMED OPES_METAD METAD TORSION UNITS PRINT | opes bias setup colvar generic |
| 19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Wei Chen | POSITION RESTRAINT ANN COM COMBINE | function bias colvar annfunc vatom |
| 19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Jim Pfaendtner | GYRATION WHOLEMOLECULES METAD ENERGY PRINT | colvar bias generic |
| 19.027 | Multithermal-multibaric simulations using VES | methods | ves, Wang Landau, multicanonical, liquid sodium, density anomaly | Pablo Piaggi | CONVERT_TO_FES AVERAGE READ ACCUMULATE UNITS REWEIGHT_TEMP_PRESS TD_MULTICANONICAL DUMPGRID COMBINE REWEIGHT_BIAS RESTART HISTOGRAM ENERGY PRINT OPT_DUMMY VES_LINEAR_EXPANSION BF_LEGENDRE OPT_AVERAGED_SGD CUSTOM | function setup bias ves colvar generic gridtools |
| 19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Mattia Bernetti | LESS_THAN GYRATION ENDPLUMED SUM MOLINFO ALPHARMSD METAD PRINT SECONDARY_STRUCTURE_RMSD ENERGY WHOLEMOLECULES | function bias secondarystructure colvar generic |
| 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 | ENDPLUMED RMSD MOLINFO METAD ERMSD PRINT WHOLEMOLECULES | colvar bias generic |
| 19.003 | EMMI ClpP | bio | metainference, cryo-EM | Max Bonomi | BIASVALUE MOLINFO GROUP EMMI PRINT | bias core isdb generic |
| 19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Giovanni Bussi | FLUSH MOLINFO LOWER_WALLS INCLUDE METAD ERMSD DISTANCE LOWEST ANGLE UPPER_WALLS PRINT RANDOM_EXCHANGES DISTANCES COMBINE | function bias colvar generic multicolvar |
| 25.010 | Kinetic rates calculation with Ratchet&Pawl MD | methods | kinetics, ligand binding, ABMD, ratchet&pawl MD | Riccardo Capelli | DISTANCE ABMD COMMITTOR PRINT WHOLEMOLECULES FLUSH GROUP COM | vatom generic bias colvar core |
| 25.001 | RNA G-quadruplex folding with ST-metaD protocol | bio | RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | METAD ERMSD MOLINFO WHOLEMOLECULES COMBINE | colvar generic bias function |
| 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 MOLINFO GYRATION PRINT LESS_THAN TORSION WHOLEMOLECULES ALPHARMSD COORDINATION CUSTOM OPES_METAD SECONDARY_STRUCTURE_RMSD COMBINE SUM | opes generic colvar secondarystructure function |
| 24.010 | Oxytocin metadynamics simulation | bio | metadynamics, oxytocin, peptide | Jan Beránek | METAD PRINT RESTART TORSION WHOLEMOLECULES FLUSH | colvar generic bias setup |
| 24.002 | Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes | chemistry | metadynamics, ligand design, solvent extraction | Xiaoyu Wang | METAD PRINT RESTART TORSION UNITS | colvar generic bias setup |
| 23.032 | Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics | bio | metadynamics, tSNE, neural network, machine learning, trp-cage, folding | Vojtech Spiwok | METAD MOLINFO ANN PRINT LESS_THAN POSITION WHOLEMOLECULES ALPHARMSD FIT_TO_TEMPLATE SECONDARY_STRUCTURE_RMSD COMBINE SUM | annfunc generic colvar bias secondarystructure function |
| 23.022 | A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar | methods | collective variables, machine learning, toy model | Enrico Trizio | ENDPLUMED BIASVALUE PRINT POSITION UPPER_WALLS LOWER_WALLS UNITS CUSTOM OPES_METAD PYTORCH_MODEL | pytorch opes generic colvar bias setup function |
| 23.008 | PBMetaD simulations of Histatin5 | bio | metadynamics, IDP, Rg, PPII | Francesco Pesce | PBMETAD MOLINFO PRINT TORSION WHOLEMOLECULES GROUP GYRATION | colvar generic core bias |
| 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 | METAD PRINT UPPER_WALLS WHOLEMOLECULES CONTACTMAP LOWER_WALLS ENERGY | colvar generic bias |
| 22.045 | Binding mode and mechanism of enzymatic polyethylene terephthalate degradation | bio | metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation | Francesco Colizzi | DISTANCE METAD PRINT UPPER_WALLS MOVINGRESTRAINT WHOLEMOLECULES LOWER_WALLS ANGLE COM | vatom generic bias colvar |
| 22.044 | Colloid Crystallisation Analyses | materials | Q4, Q6, Pair Entropy, DFS | Aaron Finney | GROUP LOCAL_AVERAGE CONTACT_MATRIX COORDINATIONNUMBER PRINT CLUSTER_NATOMS DFSCLUSTERING Q6 LOCAL_Q4 MFILTER_LESS LOCAL_Q6 MFILTER_MORE Q4 COMBINE | adjmat multicolvar clusters generic symfunc core function |
| 22.040 | From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure | bio | SARS-CoV-2, Spike, Omicron | Miłosz Wieczór | CONSTANT RMSD SELECT_COMPONENTS METAD BIASVALUE PRINT UPPER_WALLS WHOLEMOLECULES LOWER_WALLS MATRIX_VECTOR_PRODUCT CUSTOM PCAVARS COMBINE SUM | valtools mapping generic bias colvar function matrixtools |
| 22.018 | Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations | bio | ligand binding, docking, EMMI, LAT1 | Max Bonomi | BIASVALUE MOLINFO PRINT WHOLEMOLECULES EMMIVOX LOAD GROUP | generic isdb bias setup core |
| 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 COMMITTOR PRINT MATHEVAL UPPER_WALLS FIXEDATOM WHOLEMOLECULES CENTER LOWER_WALLS FIT_TO_TEMPLATE COORDINATION CUSTOM OPES_METAD PYTORCH_MODEL GROUP | pytorch vatom opes generic bias colvar core function |
| 22.006 | Peptide framework for screening the effects of amino acids on assembly | bio | metadynamics, peptides | Andrew White | REWEIGHT_BIAS GROUP METAD DISTANCE INCLUDE COM PRINT HISTOGRAM DISTANCES MEAN DUMPGRID CONVERT_TO_FES COMBINE GYRATION | vatom multicolvar generic colvar bias gridtools core function |
| 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 | POSITION BF_LEGENDRE OPT_ADAM DISTANCE VES_OUTPUT_BASISFUNCTIONS UPPER_WALLS OPT_AVERAGED_SGD ENERGY BF_WAVELETS COORDINATION METAD TD_UNIFORM INCLUDE BF_GAUSSIANS PRINT BF_CUBIC_B_SPLINES UNITS VES_LINEAR_EXPANSION BF_CHEBYSHEV FLUSH TD_WELLTEMPERED | generic bias colvar setup ves |
| 21.042 | Peptoid-mediated Au nanocrystal growth | materials | parallel-bias metadynamics, peptoid, Au | Xin Qi | PBMETAD DISTANCE MOLINFO PRINT UPPER_WALLS GYRATION COM | vatom colvar generic bias |
| 21.041 | Nucleating a Different Coordination in a Crystal under Pressure. A Study of the B1−B2 Transition in NaCl by Metadynamics | methods | metadynamics, structural phase transitions, pressure-induced phase transition, martensitic transitions | Matej Badin | ENDPLUMED METAD VOLUME PRINT COORDINATION CUSTOM COMBINE | colvar generic bias function |
| 21.027 | EGFR activating mutations mechanism | bio | metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA | Francesco Gervasio | DISTANCE METAD INCLUDE MOLINFO PRINT MATHEVAL LESS_THAN UPPER_WALLS WHOLEMOLECULES CONTACTMAP LOWER_WALLS ALPHARMSD ENERGY SECONDARY_STRUCTURE_RMSD SUM | generic bias colvar secondarystructure function |
| 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 | METAD PRINT MATHEVAL POSITION RESTART WHOLEMOLECULES RESTRAINT CENTER COORDINATION REWEIGHT_BIAS | vatom generic colvar bias setup function |
| 21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Kristof Bal | COORDINATIONNUMBER MEAN MATRIX_VECTOR_PRODUCT LOAD GROUP CONTACT_MATRIX COMMITTOR UPPER_WALLS HISTOGRAM REWEIGHT_METAD DUMPGRID SUM METAD PRINT MOVINGRESTRAINT MORE_THAN UNITS ONES FLUSH CONVERT_TO_FES | adjmat generic symfunc bias gridtools setup core function matrixtools |
| 21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Tarak Karmakar | FLUSH PRINT MATHEVAL UPPER_WALLS LOWER_WALLS LOAD OPES_METAD PYTORCH_MODEL GROUP | pytorch opes generic bias setup core function |
| 20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Luigi Bonati | FLUSH ENDPLUMED DISTANCE PRINT MATHEVAL UPPER_WALLS TORSION LOWER_WALLS UNITS LOAD OPES_METAD PYTORCH_MODEL GROUP COM | pytorch vatom opes generic bias colvar setup core function |
| 19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Valerio Rizzi | ENDPLUMED DISTANCE METAD CONTACT_MATRIX COORDINATIONNUMBER PRINT UPPER_WALLS RESTART ONES DISTANCES MEAN COMBINE MATRIX_VECTOR_PRODUCT UNITS CUSTOM FLUSH GROUP SUM | adjmat multicolvar generic symfunc bias colvar setup core function matrixtools |
| 19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | DISTANCE METAD MOLINFO PRINT UPPER_WALLS ENERGY GYRATION COM | vatom generic bias colvar |
| 19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Cristina Paissoni | PBMETAD ENDPLUMED SAXS INCLUDE MOLINFO BIASVALUE ENSEMBLE MATHEVAL PRINT STATS WHOLEMOLECULES CENTER ANGLE COMBINE COORDINATION ALPHABETA GROUP | vatom multicolvar generic isdb bias colvar core function |
| 19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Gareth Tribello | ENDPLUMED MEAN LOWER_WALLS MATRIX_VECTOR_PRODUCT CELL GROUP CONTACT_MATRIX UPPER_WALLS CUSTOM AROUND LESS_THAN SUM METAD PRINT MORE_THAN UNITS FCCUBIC_FUNC FCCUBIC ONES | adjmat volumes generic colvar bias symfunc setup core function 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 | METAD DISTANCE_FROM_CONTOUR PRINT HISTOGRAM READ UPPER_WALLS RESTART COMBINE DUMPGRID CONVERT_TO_FES REWEIGHT_BIAS | generic bias contour gridtools setup function |
| 19.047 | Close Structure | methods | metadynamics, RMSD, path collective variables, property map | Vojtech Spiwok | PROPERTYMAP PRINT METAD WHOLEMOLECULES | generic bias colvar |
| 19.044 | Multithermal-multibaric simulations using VES | methods | ves, Wang Landau, multicanonical, water, density anomaly | Pablo Piaggi | REWEIGHT_BIAS VOLUME HISTOGRAM AVERAGE REWEIGHT_TEMP_PRESS DUMPGRID CUSTOM OPT_AVERAGED_SGD ENERGY COMBINE TD_MULTITHERMAL_MULTIBARIC PRINT ACCUMULATE VES_LINEAR_EXPANSION OPT_DUMMY READ RESTART BF_LEGENDRE CONVERT_TO_FES | ves generic colvar bias gridtools setup function |
| 19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Haochuan Chen | PRINT DRR TORSION | generic drr colvar |
| 19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Riccardo Capelli | ENDPLUMED METAD PRINT MATHEVAL POSITION UPPER_WALLS READ WHOLEMOLECULES HISTOGRAM REWEIGHT_METAD WRAPAROUND FIT_TO_TEMPLATE DUMPGRID COORDINATION FLUSH CONVERT_TO_FES GROUP COM | vatom generic colvar bias gridtools core function |
| 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 UNITS PRINT DISTANCES DISTANCE UPPER_WALLS ZDISTANCES GROUP COORDINATIONNUMBER MEAN FLUSH CONTACT_MATRIX FIXEDATOM COMMITTOR SUM CUSTOM OPES_METAD MATRIX_VECTOR_PRODUCT | core function adjmat colvar bias multicolvar opes vatom symfunc generic matrixtools setup |
| 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 | MOLINFO LOWEST CENTER PBMETAD RMSD SECONDARY_STRUCTURE_RMSD PARABETARMSD DUMPATOMS ALPHARMSD WHOLEMOLECULES BIASVALUE LESS_THAN PRINT COORDINATION GROUP DUMPMASSCHARGE DISTANCE UPPER_WALLS COM SUM EMMI | core function isdb colvar bias vatom generic secondarystructure |
| 24.012 | Molecular simulations to investigate the impact of N6-methylation in RNA recognition | bio | metadynamics, alchemistry, RNA modification, RNA:protein interactions | Giovanni Bussi | COMBINE PRINT DISTANCE METAD UPPER_WALLS COORDINATION BIASVALUE GROUP MOLINFO GHBFIX COM DEBUG CENTER LOWER_WALLS | core function colvar bias vatom generic |
| 24.001 | A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations | bio | OPES, OPES-Flooding, QM/MM, Kinetics, Enzyme Catalysis | Dhiman Ray | COMBINE UNITS PRINT DISTANCE UPPER_WALLS FLUSH COMMITTOR CUSTOM OPES_METAD LOWER_WALLS TORSION | function colvar bias opes generic setup |
| 23.043 | Modeling the ferroelectric phase transition in barium titanate with DFT accuracy and converged sampling | materials | Barium Titanate, ferroelectric phase transition, Machine Learning, polarization order parameters | Lorenzo Gigli | TRANSPOSE PRINT METAD INCLUDE SELECT_COMPONENTS FLUSH MATHEVAL SUM | function bias valtools generic 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 | PRINT DISTANCE METAD UPPER_WALLS WHOLEMOLECULES BIASVALUE CONSTANT MATHEVAL CENTER LOWER_WALLS | function colvar bias vatom generic |
| 23.027 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, DFS, Q3, Pair Entropy | Aaron Finney | LOCAL_AVERAGE Q3 AROUND UNITS LOCAL_Q3 DENSITY PRINT CLUSTER_DISTRIBUTION DUMPGRID GROUP COORDINATIONNUMBER CLUSTER_NATOMS RESTRAINT FIXEDATOM CONTACT_MATRIX LOAD HISTOGRAM DFSCLUSTERING | core adjmat gridtools bias vatom symfunc generic setup volumes clusters |
| 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 PRINT LOWER_WALLS METAD MOVINGRESTRAINT GROUP COORDINATIONNUMBER MFILTER_MORE LOCAL_Q6 Q6 | core function bias multicolvar symfunc generic |
| 23.006 | Transcription factor unbinding | bio | metadynamics, DNA, conformational changes | Malin Lüking | LESS_THAN CONTACTMAP PRINT DISTANCE ANGLE ALPHARMSD METAD DUMPFORCES MOLINFO COM SUM SECONDARY_STRUCTURE_RMSD | function colvar bias vatom generic secondarystructure |
| 22.041 | Skipping the Replica Exchange Ladder with Normalizing Flows | methods | OPES, alanine, normalizing flows, replica exchange | Michele Invernizzi | ECV_MULTITHERMAL UNITS ENERGY PRINT ENDPLUMED OPES_EXPANDED TORSION OPES_METAD POSITION | opes setup generic colvar |
| 22.039 | Driving and characterizing nucleation of urea and glycine polymorphs in water | bio | metadynamics, nucleation, amino acids, polymorphism | Eric Beyerle | MEAN COORDINATIONNUMBER CONTACT_MATRIX CENTER ONES MATHEVAL SPHERICAL_HARMONIC MATRIX_VECTOR_PRODUCT PAIRENTROPY MORE_THAN PRINT METAD GROUP Q4 LOAD COMBINE INCLUDE SUM CUSTOM Q6 | adjmat function core gridtools bias vatom symfunc generic matrixtools setup |
| 22.036 | Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction | bio | Well-tempered MetaDynamics with Hamiltonian Replica Exchange | Miroslav Krepl | COMBINE PRINT METAD UPPER_WALLS COORDINATION BIASVALUE GROUP MOLINFO FLUSH GHBFIX LOAD CUSTOM | core function colvar bias generic setup |
| 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 | WHOLEMOLECULES MOLINFO GYRATION TORSION PBMETAD | generic colvar 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 | COMBINE ONES UNITS DISTANCE METAD UPPER_WALLS COORDINATION GROUP COM GYRATION FLUSH COORDINATIONNUMBER CONTACT_MATRIX MEAN CUSTOM LOWER_WALLS MATRIX_VECTOR_PRODUCT | core function adjmat colvar bias vatom symfunc generic matrixtools setup |
| 21.049 | Multiple-path-metadynamics and PathMaps | methods | path-CV, metadynamics, multiple-walker, multiple paths, pathmap | Alberto Pérez-de-Alba-Ortíz | COMBINE UNITS PRINT MOVINGRESTRAINT METAD UPPER_WALLS RESTRAINT CONSTANT ENSEMBLE LOAD TORSION CUSTOM LOWER_WALLS | function colvar bias generic setup |
| 21.044 | NaCl nucleation | chemistry | metadynamics, DFS clustering | Aaron Finney | MEAN COORDINATIONNUMBER MFILTER_MORE CONTACT_MATRIX ONES DFSCLUSTERING MATRIX_VECTOR_PRODUCT MORE_THAN PRINT METAD CLUSTER_DISTRIBUTION GROUP FIXEDATOM LOCAL_Q6 COMBINE INSPHERE DUMPGRID CLUSTER_NATOMS SUM CUSTOM HISTOGRAM Q6 | adjmat function core gridtools bias multicolvar vatom symfunc generic matrixtools volumes clusters |
| 21.043 | Predicting the Conformational Variability of Oncogenic GTP-bound G12D Mutated KRas-4B Proteins at Cell Membranes | chemistry | well-tempered metadynamics, KRas-4B, anionic membrane, conformational variability | Huixia Lu | FIT_TO_TEMPLATE PRINT METAD FIXEDATOM TORSION | generic vatom colvar bias |
| 21.020 | Reweighted Jarzynski sampling | methods | free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions | Kristof Bal | BF_CHEBYSHEV UNITS MEAN COORDINATIONNUMBER ANN CONTACT_MATRIX TD_WELLTEMPERED ONES MOVINGRESTRAINT BIASVALUE FLUSH OPES_METAD MATRIX_VECTOR_PRODUCT MORE_THAN PRINT METAD CONVERT_TO_FES GROUP CONSTANT LOAD REWEIGHT_BIAS OPT_AVERAGED_SGD REWEIGHT_METAD COMBINE DISTANCE UPPER_WALLS RESTRAINT DUMPGRID SUM CUSTOM HISTOGRAM VES_LINEAR_EXPANSION | adjmat ves function core gridtools colvar bias opes symfunc generic annfunc matrixtools setup |
| 21.013 | Role of vibrational excitation in heterogeneous catalysis | chemistry | catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption | Kristof Bal | BF_CHEBYSHEV UNITS MEAN COORDINATIONNUMBER CONTACT_MATRIX UWALLS ONES DISTANCES FLUSH ANGLES LOWER_WALLS MATRIX_VECTOR_PRODUCT COORD_ANGLES PRINT METAD COORDINATION CONVERT_TO_FES EXTERNAL GROUP TD_GRID LOAD REWEIGHT_BIAS OPT_AVERAGED_SGD REWEIGHT_METAD COMBINE DISTANCE UPPER_WALLS DUMPGRID RESTRAINT CUSTOM HISTOGRAM VES_LINEAR_EXPANSION | adjmat ves function core colvar gridtools bias multicolvar symfunc generic matrixtools setup |
| 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 PRINT DISTANCE METAD RESTART CENTER | colvar bias vatom generic setup |
| 20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Glen Hocky | UNITS ENERGY PRINT DISTANCE FISST RESTRAINT GROUP BIASVALUE GYRATION MATHEVAL | core function colvar bias fisst generic setup |
| 20.015 | Rational design of ASCT2 inhibitors using an integrated experimental-computational approach | bio | ASCT2 transporter, small-molecules, cryo-EM, metainference | Max Bonomi | EMMIVOX DUMPATOMS PRINT WHOLEMOLECULES BIASVALUE GROUP MOLINFO LOAD | core isdb bias generic setup |
| 20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Carlo Camilloni | SAXS COMBINE PBMETAD ALPHABETA PRINT DISTANCE STATS WHOLEMOLECULES CONSTANT MOLINFO GYRATION METAINFERENCE ENSEMBLE FLUSH CENTER TORSION SUM CUSTOM | function isdb colvar bias multicolvar vatom generic |
| 20.008 | Simulating solvation and acidity in complex mixtures with first-principles accuracy. The case of CH3SO3H and H2O2 in phenol | chemistry | proton trasfer, metadynamics | Kevin Rossi | UNITS PRINT DISTANCES DISTANCE METAD COORDINATION SUM CUSTOM | function colvar bias multicolvar generic setup |
| 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 | REWEIGHT_METAD COMBINE ABMD PRINT DISTANCE METAD UPPER_WALLS ENDPLUMED READ CONVERT_TO_FES DUMPGRID COM MATHEVAL HISTOGRAM LOWER_WALLS | function colvar gridtools bias vatom generic |
| 19.080 | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | methods | ves, variationally enhanced sampling, vibrational excitation, chemical reactions | Kristof Bal | TD_WELLTEMPERED BF_CHEBYSHEV COMBINE UNITS PRINT DISTANCE ANGLE UPPER_WALLS COORDINATION CONVERT_TO_FES EXTERNAL DUMPGRID TD_GRID FLUSH LOWER_WALLS OPT_AVERAGED_SGD HISTOGRAM VES_LINEAR_EXPANSION | ves function colvar gridtools bias generic setup |
| 19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Kim E. Jelfs | PRINT DISTANCE METAD UPPER_WALLS GROUP COM RESTART CENTER LOWER_WALLS | core colvar bias vatom generic setup |
| 19.045 | Adsorption free energy of Ca/CO3 ions on calcite steps in contact with water | materials | metadynamics, well-tempered, multiple walkers, LAMMPS | Marco De La Pierre | UNITS LOWER_WALLS PRINT METAD UPPER_WALLS COORDINATION GROUP RESTART FLUSH POSITION | core colvar bias generic setup |
| 19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | COMBINE UNITS PRINT DISTANCES DISTANCE UPPER_WALLS METAD RESTART FLUSH | function colvar bias multicolvar generic setup |
| 19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Vittorio Limongelli | FUNNEL_PS FUNNEL LOWER_WALLS DISTANCE METAD UPPER_WALLS PRINT WHOLEMOLECULES COM RMSD | colvar bias vatom generic funnel |
| 19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Silvio Pipolo | PIV CELL PRINT METAD UPPER_WALLS FUNCPATHMSD LOWER_WALLS | function colvar piv bias generic |
| 19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Matteo Salvalaglio | VOLUME COMBINE ENERGY PRINT CELL METAD UPPER_WALLS ENDPLUMED MATHEVAL TORSION LOWER_WALLS | function generic colvar bias |
| 19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Max Bonomi | PRINT BIASVALUE WHOLEMOLECULES GROUP MOLINFO EMMI | core generic isdb bias |
| 19.006 | Flying Gaussian proof | methods | flying Gaussians, alanine dipeptide | Vojtech Spiwok | TORSION PRINT METAD | generic colvar bias |
| 19.004 | MI Ubiquitin | bio | metainference, NMR | Max Bonomi | PRINT CS2BACKBONE WHOLEMOLECULES GROUP MOLINFO METAINFERENCE RDC | isdb generic core |
| 19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Max Bonomi | PRINT BIASVALUE GROUP MOLINFO EMMI | core generic isdb bias |
| 25.003 | Surrogate Model CV | methods | Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding | Sompriya Chatterjee | DISTANCE MATHEVAL CUSTOM WHOLEMOLECULES PRINT MOLINFO PYTORCH_MODEL ENDPLUMED TORSION OPES_METAD COMBINE GROUP ENERGY COMMITTOR | opes generic core colvar pytorch function |
| 24.036 | Leveraging cryptic ligand envelopes through enhanced molecular simulations | bio | HREX, conformational heterogeneity, drug discovery, ligand binding, plitidepsin, aplidin, ligand-target complexes, cryptic ligand envelope | Francesco Colizzi | DISTANCE WHOLEMOLECULES PRINT HISTOGRAM TORSION CONVERT_TO_FES GROUP ANGLE DUMPGRID COORDINATION | core colvar gridtools generic |
| 24.011 | Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble | methods | committor, machine learning | Peilin Kang | CELL PRINT MOLINFO TORSION LOWER_WALLS UPPER_WALLS COORDINATION LOAD POSITION RMSD INCLUDE DISTANCE WHOLEMOLECULES UNITS ENERGY ENDPLUMED MATHEVAL CUSTOM GROUP BIASVALUE | setup generic core colvar bias function |
| 24.006 | Water vapor condensation | chemistry | metadynamics, homogeneous condensation, chemical potential | Shenghui Zhong | UNITS ONES PRINT DFSCLUSTERING LESS_THAN MEAN CLUSTER_NATOMS METAD SUM CLUSTER_PROPERTIES UPPER_WALLS MATRIX_VECTOR_PRODUCT COORDINATIONNUMBER GROUP CONTACT_MATRIX | adjmat setup generic matrixtools symfunc clusters core bias function |
| 23.046 | Lasso Peptides - HLDA CV | bio | metadynamics, protein folding, HLDA, harmonic | Gabriel da Hora | DISTANCE WHOLEMOLECULES UNITS PRINT METAD COMBINE | setup generic colvar bias function |
| 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 | DISTANCE PATHMSD ALPHARMSD FUNCPATHMSD PRINT MOLINFO LESS_THAN CONTACTMAP METAD SECONDARY_STRUCTURE_RMSD SUM LOWER_WALLS UPPER_WALLS INCLUDE | generic secondarystructure colvar bias function |
| 23.036 | Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? | bio | NaCl, nucleation, metadynamics | Ruiyu Wang | MATHEVAL CUSTOM VOLUME ONES PRINT SPHERICAL_HARMONIC MEAN Q4 Q6 METAD SUM COMBINE MATRIX_VECTOR_PRODUCT COORDINATIONNUMBER GROUP MORE_THAN CONTACT_MATRIX ENERGY | adjmat matrixtools generic symfunc core colvar bias 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 | DISTANCE PRINT MOLINFO SAXS ENSEMBLE STATS UPPER_WALLS RMSD CENTER GROUP BIASVALUE WRAPAROUND | vatom generic core colvar bias isdb 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 | PRINT FIXEDATOM TORSION SUM PATH CONSTANT OPES_METAD LOWER_WALLS UPPER_WALLS COORDINATION EUCLIDEAN_DISTANCE PDB2CONSTANT OPES_METAD_EXPLORE PYTORCH_MODEL DISTANCE WHOLEMOLECULES UNITS COMBINE CENTER LOWEST CUSTOM GROUP FIT_TO_TEMPLATE | vatom opes setup generic mapping core colvar bias refdist pytorch function |
| 23.013 | Path meta-eABF simulation of large scale conformational change in STING protein | methods | meta-eABF, path CV, large scale conformational change, STING protein, reciprocal barrier restraint | Istvan Kolossvary | PATHMSD CUSTOM DRR UNITS PRINT METAD FLUSH TIME UPPER_WALLS LOWER_WALLS BIASVALUE | setup generic drr colvar bias function |
| 23.007 | Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains | bio | metadynamics, peptoids, parallel-bias metadynamics | Jim Pfaendtner | WHOLEMOLECULES COORDINATION PRINT COM GYRATION TORSION RESTRAINT PBMETAD INCLUDE | vatom colvar bias 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 | PRINT PUT EXTRACV METAD TORSION READ | core colvar bias generic |
| 23.002 | Critical comparison of general-purpose collective variables for crystal nucleation | methods | metadynamics, umbrella sampling, commitor, entropy, PIV | Julien Lam | FUNCPATHMSD ENERGY CUSTOM VOLUME UNITS PRINT PIV Q4 METAD LOCAL_AVERAGE Q6 RESTRAINT UPPER_WALLS PAIRENTROPY | setup generic symfunc piv colvar bias gridtools function |
| 22.042 | Metadynamics of NSP10 and variants | bio | metadynamics, NSP10, crystal structure, variants | Shozeb Haider | METAD PRINT TORSION | colvar bias generic |
| 22.037 | Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site | chemistry | metadynamics, DNA, abasic | Mike Jones | DISTANCE PRINT MEAN METAD CENTER GROUP DISTANCES | vatom generic multicolvar core colvar bias function |
| 22.028 | N-glycan conformer distributions in atomistic simulation | bio | REST2, RECT, N-glycan, pucker | Isabell Grothaus | PUCKERING PRINT MOLINFO TORSION METAD HISTOGRAM CONVERT_TO_FES DUMPGRID READ | colvar bias generic gridtools |
| 22.004 | Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques | chemistry | reaction discovery, OPES, collective variables | Umberto Raucci | DISTANCE MATHEVAL CUSTOM UNITS PRINT LOAD COM OPES_METAD OPES_METAD_EXPLORE GROUP LOWER_WALLS UPPER_WALLS PYTORCH_MODEL COORDINATION | vatom opes setup generic core colvar bias pytorch function |
| 21.051 | Automatic learning of hydrogen-bond fixes in an AMBER RNA force field | methods | force field, RNA | Giovanni Bussi | WHOLEMOLECULES ERMSD PRINT MOLINFO METAD COMBINE BIASVALUE COORDINATION | colvar bias generic function |
| 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 | DISTANCE WHOLEMOLECULES PRINT MOLINFO BIASVALUE COM EMMI RESTART GROUP UPPER_WALLS | vatom setup generic core colvar bias isdb |
| 21.039 | Deep learning the slow modes for rare events sampling | methods | collective variables, machine learning, slow modes, deep-tica, opes | Luigi Bonati | PRINT MOLINFO ONES TORSION OPES_METAD FLUSH SUM SPHERICAL_HARMONIC LOAD MEAN ECV_MULTITHERMAL RMSD Q6 PYTORCH_MODEL INCLUDE DISTANCE WHOLEMOLECULES VOLUME UNITS DISTANCE_MATRIX COMBINE MATRIX_VECTOR_PRODUCT MORE_THAN ENDPLUMED ENERGY CUSTOM OPES_EXPANDED CONTACTMAP GROUP ENVIRONMENTSIMILARITY CONTACT_MATRIX | opes adjmat setup generic matrixtools symfunc envsim core colvar pytorch function |
| 21.038 | Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics | materials | metadynamics, SGOOP, nucleation, urea | Ziyue Zou | COORDINATIONNUMBER VOLUME PRINT ONES LOAD MEAN METAD COMBINE MATRIX_VECTOR_PRODUCT CENTER GROUP CONTACT_MATRIX ENERGY INCLUDE | vatom adjmat setup generic matrixtools symfunc core colvar bias function |
| 21.017 | All-atom simulations of the Vav1 AD construct | bio | metadynamics, parallel-bias, well-tempered | Simone Orioli | ALPHARMSD WHOLEMOLECULES CUSTOM PRINT MOLINFO LESS_THAN REWEIGHT_BIAS CONTACTMAP TORSION RESTART ALPHABETA CONSTANT SUM SECONDARY_STRUCTURE_RMSD METAD COMBINE GROUP PBMETAD | setup generic secondarystructure multicolvar core colvar bias function |
| 21.007 | Sampling enhancement by metadynamics driven by machine learning and de novo protein modelling | bio | metadynamics, machine learning, protein folding | Vojtech Spiwok | ALPHARMSD WHOLEMOLECULES MATHEVAL MOLINFO LESS_THAN SECONDARY_STRUCTURE_RMSD SUM POSITION COMBINE FIT_TO_TEMPLATE | secondarystructure colvar generic function |
| 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 | WHOLEMOLECULES PATHMSD PRINT METAD RESTART LOWER_WALLS UPPER_WALLS | colvar bias generic setup |
| 20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Faidon Brotzakis | WHOLEMOLECULES PRINT MOLINFO BIASVALUE HISTOGRAM EMMI CONVERT_TO_FES RMSD GROUP DISTANCES DUMPGRID READ | generic multicolvar core colvar bias gridtools isdb |
| 20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Michele Invernizzi | PRINT MOLINFO ONES ENVIRONMENTSIMILARITY TORSION SUM UPPER_WALLS ECV_LINEAR SPHERICAL_HARMONIC LOAD MEAN ECV_MULTITHERMAL POSITION RMSD Q6 WHOLEMOLECULES VOLUME UNITS DISTANCE_MATRIX ECV_MULTITHERMAL_MULTIBARIC ECV_UMBRELLAS_LINE COMBINE MATRIX_VECTOR_PRODUCT MORE_THAN ENDPLUMED ENERGY MATHEVAL CUSTOM OPES_EXPANDED GROUP CONTACT_MATRIX | opes adjmat setup generic matrixtools symfunc envsim core colvar bias function |
| 20.018 | Free energy barriers from biased molecular dynamics simulations | methods | kinetics, free energy barriers, chemical reactions, nucleation, metadynamics | Kristof Bal | PRINT REWEIGHT_BIAS SPRINT FLUSH CONVERT_TO_FES LOWER_WALLS UPPER_WALLS COORDINATION LOAD METAD HISTOGRAM REWEIGHT_METAD COORDINATIONNUMBER Q6 DISTANCE VOLUME UNITS DENSITY LOCAL_AVERAGE COMBINE CENTER DUMPGRID ENERGY PAIRENTROPY CONTACT_MATRIX | vatom adjmat setup generic sprint symfunc colvar bias gridtools volumes function |
| 20.013 | Improving accuracy of biased Alchemistic simulations | methods | flying Gaussian method, Alchemistic simulations, thermodynamic integration, reweighting | Vojtech Spiwok | METAD PRINT TORSION | colvar bias 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 | DISTANCE PRINT MOLINFO COM GYRATION METAD GROUP UPPER_WALLS ENERGY | vatom generic core colvar bias |
| 19.075 | PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python | other | Python, automatic differentiation | Toni Giorgino | DISTANCE CUSTOM PRINT TORSION ANGLE DUMPDERIVATIVES COMBINE CENTER GROUP RESTRAINT ENDPLUMED | vatom generic core colvar bias function |
| 19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Giovanni Bussi | DISTANCE WHOLEMOLECULES MATHEVAL COORDINATION PRINT MOLINFO COM MAXENT TORSION METAD FLUSH SORT INCLUDE | vatom generic colvar bias function |
| 19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Matteo Salvalaglio | DISTANCE MATHEVAL PRINT EXTERNAL REWEIGHT_BIAS METAD TORSION HISTOGRAM REWEIGHT_METAD READ CONVERT_TO_FES BIASVALUE DUMPGRID COMMITTOR | generic colvar bias gridtools function |
| 19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Gareth Tribello | ONES SUM FOURIER_TRANSFORM MULTICOLVARDENS FCCUBIC_FUNC ACCUMULATE POSITION CHARGE DISTANCES UNITS KDE FCCUBIC MATRIX_VECTOR_PRODUCT CENTER MORE_THAN DUMPGRID CUSTOM ARGS2VATOM MASS FIND_CONTOUR_SURFACE GROUP CONTACT_MATRIX | vatom contour adjmat setup generic matrixtools symfunc multicolvar core fourier gridtools colvar function |
| 19.035 | Dimerization of GPCRs from coarse-grained umbrella sampling | bio | Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization | Davide Provasi | DISTANCE PRINT COM TORSION GROUP RESTRAINT | vatom generic core colvar bias |
| 19.032 | Chemical reaction in solution using path collective variables based on coordination patterns | chemistry | chemical reactions, solutions, metadynamics, coordination patterns | Fabio Pietrucci | PRINT METAD RESTART FLUSH PATH UPPER_WALLS DISTANCES | setup generic multicolvar mapping bias |
| 19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Pratyush Tiwary | DISTANCE WHOLEMOLECULES CUSTOM PRINT EXTERNAL COM TORSION RESTART ALPHABETA CONSTANT SUM COMBINE COMMITTOR | vatom setup generic multicolvar colvar bias function |
| 19.023 | RECT | methods | metadynamics, replica exchange | Giovanni Bussi | WHOLEMOLECULES PRINT GYRATION METAD TORSION | colvar bias generic |
| 24.032 | DeepLNE++ | methods | PATHCV, OPES | Thorben Fröhlking | COORDINATION PRINT DISTANCE GROUP LOAD ENERGY OPES_METAD TORSION CUSTOM COMBINE | opes colvar setup generic core function |
| 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 UPPER_WALLS PRINT DISTANCE ENERGY OPES_METAD | bias colvar generic opes |
| 24.018 | A new route to the prebiotic synthesis of glycine via ab initio-based machine learning calculations | chemistry | prebiotic chemistry, glycine, Strecker synthesis, ab initio calculations, machine learning | Léon HUET | DISTANCE PRINT | colvar generic |
| 24.007 | SWISH-X | bio | swish-x, SWISH-X, swish, expanded SWISH | Alberto Borsatto | CONTACTMAP ECV_MULTITHERMAL OPES_EXPANDED UPPER_WALLS PRINT MOLINFO ENERGY WHOLEMOLECULES INCLUDE | bias colvar generic opes |
| 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 | UPPER_WALLS FIXEDATOM MEAN UNITS COORDINATIONNUMBER GROUP CONTACT_MATRIX DISTANCE PRINT CUSTOM SUM OPES_METAD ZDISTANCES MATRIX_VECTOR_PRODUCT FLUSH ONES | opes adjmat multicolvar bias vatom colvar symfunc setup core generic function matrixtools |
| 23.034 | Urea nucleation in water: do long-range forces matter? | materials | LMF theory, Metadynamics, Nucleation | Ziyue Zou | METAD ONES MEAN MORE_THAN GROUP COORDINATIONNUMBER PRINT LOAD CONTACT_MATRIX CUSTOM SUM CENTER MATRIX_VECTOR_PRODUCT INCLUDE | adjmat bias vatom symfunc setup generic core function matrixtools |
| 23.021 | Into the Dynamics of Rotaxanes at Atomistic Resolution | materials | metadynamics, rotaxanes, molecular shuttles, molecular machines | Luigi Leanza | METAD UPPER_WALLS FIXEDATOM MATHEVAL DISTANCE PRINT TORSION CENTER CUSTOM | bias vatom colvar generic function |
| 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 | REWEIGHT_METAD METAD MATHEVAL PRINT DISTANCE HISTOGRAM READ MOLINFO CONVERT_TO_FES RMSD DUMPGRID WHOLEMOLECULES | gridtools bias colvar generic function |
| 23.014 | Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 | bio | metadynamics, oligomerization, chemokine receptors, GPCR, membrane | Vittorio Limongelli | METAD UPPER_WALLS PRINT DISTANCE COM FLUSH TORSION WHOLEMOLECULES COMBINE | bias colvar vatom generic function |
| 23.005 | A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs | bio | metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A | Timothy Clark | REWEIGHT_METAD METAD MATHEVAL PRINT DISTANCE HISTOGRAM READ MOLINFO CONVERT_TO_FES RMSD DUMPGRID WHOLEMOLECULES | gridtools bias colvar generic function |
| 22.029 | Angiotensin-1-7_Metadynamics | bio | Metadynamics, Angiotensin-(1-7), peptide | L.-América Chi | COORDINATION METAD UPPER_WALLS GYRATION GROUP PRINT WHOLEMOLECULES FLUSH LOWER_WALLS | bias colvar generic core |
| 22.027 | Molecular Dynamics simulations of BANAL-236 RBD-hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, BANAL-236, receptor-binding domain | Max Bonomi | RMSD PRINT | colvar generic |
| 22.025 | Bubble nucleation rate predictions in a Lennard-Jones fluid | materials | free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation | Kristof Bal | VOLUME ANN UNITS GROUP RESTRAINT REWEIGHT_BIAS MATRIX_VECTOR_PRODUCT FLUSH UPPER_WALLS MEAN CONVERT_TO_FES PRINT COORDINATIONNUMBER LOAD COMMITTOR BIASVALUE CUSTOM HISTOGRAM LESS_THAN MOVINGRESTRAINT SUM DUMPGRID CONTACT_MATRIX ONES | gridtools annfunc adjmat bias colvar symfunc setup core generic function matrixtools |
| 22.020 | Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix–Junction–Helix RNA | bio | RNA force field, Helix-Junction-Helix RNA, SAXS, Well tempered metadynamics | Weiwei He | METAD PRINT GROUP DISTANCE COM TORSION WHOLEMOLECULES | bias colvar vatom generic core |
| 22.013 | Ligand dissociation from PreQ1 riboswitch | bio | ligand, RNA, metadynamics, pRAVE | Yihang Wang | METAD MEAN PRINT DISTANCE COORDINATIONNUMBER GROUP MOLINFO CONTACT_MATRIX RMSD CUSTOM SUM COMMITTOR COM MATRIX_VECTOR_PRODUCT WHOLEMOLECULES COMBINE ONES | adjmat bias colvar vatom symfunc generic core function matrixtools |
| 22.005 | Collective Variable for Metadynamics Derived from AlphaFold Output | bio | AlphaFold, protein folding, protein structure prediction, metadynamics, deep learning, free energy simulation, collective variable | Vojtech Spiwok | METAD LOAD WHOLEMOLECULES PRINT | bias setup generic |
| 22.003 | Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling | methods | opes, metadynamics, reweighting, alanine, muller | Michele Invernizzi | METAD ECV_MULTITHERMAL OPES_EXPANDED UPPER_WALLS PRINT UNITS PBMETAD ENERGY OPES_METAD_EXPLORE ENDPLUMED OPES_METAD POSITION CUSTOM BIASVALUE ECV_UMBRELLAS_FILE TORSION LOWER_WALLS | opes bias colvar setup generic function |
| 21.050 | N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity | methods | bio | Isabell Louise Grothaus | DISTANCE CENTER PRINT | colvar vatom generic |
| 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 RMSD PRINT | colvar generic |
| 21.023 | Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling | methods | enhanced sampling, collective variables, machine learning | Jakub Rydzewski | REWEIGHT_METAD METAD PRINT UNITS DISTANCE ENERGY CONSTANT BIASVALUE TORSION CUSTOM INCLUDE | bias colvar setup generic function |
| 21.022 | Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly | materials | parallel bias metadynamics, adsorption, peptide | Xin Qi | UPPER_WALLS GYRATION DISTANCE PRINT MOLINFO PBMETAD ENERGY COM LOWER_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 | METAD UPPER_WALLS PRINT DISTANCE FUNNEL_PS COM FUNNEL LOWER_WALLS | funnel bias colvar vatom generic |
| 21.011 | CmuMD simulations of NaCl(aq) at graphite | chemistry | CmuMD, DFS clustering | Aaron Finney | CLUSTER_DISTRIBUTION FIXEDATOM DENSITY GROUP COORDINATIONNUMBER PRINT CONTACT_MATRIX DFSCLUSTERING LOAD RESTRAINT MULTICOLVARDENS AROUND DUMPGRID CLUSTER_NATOMS MFILTER_MORE | gridtools adjmat multicolvar bias vatom symfunc setup core generic clusters volumes |
| 21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Adriana Pietropaolo | MATHEVAL PRINT PBMETAD RESTART CONSTANT BIASVALUE TORSION WHOLEMOLECULES | bias colvar setup generic function |
| 20.030 | Converging experimental and computational views of the knotting mechanism of the smallest knotted protein | bio | phi-values, transition state, knotted proteins | Cristina Paissoni | COORDINATION PRINT MOLINFO RESTRAINT STATS WHOLEMOLECULES COMBINE | bias colvar generic function |
| 20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Valerio Rizzi | COORDINATION ANGLE UPPER_WALLS FIXEDATOM MATHEVAL GROUP DISTANCE PRINT ENERGY PYTORCH_MODEL OPES_METAD ENDPLUMED FIT_TO_TEMPLATE CENTER WHOLEMOLECULES | opes bias colvar vatom core generic pytorch function |
| 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 | CONTACTMAP FUNCPATHGENERAL METAD UPPER_WALLS MATHEVAL PRINT GROUP DISTANCE LOAD MOLINFO PROJECTION_ON_AXIS CONSTANT BIASVALUE COM WHOLEMOLECULES INCLUDE LOWER_WALLS | bias colvar vatom setup generic core function |
| 19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Valerio Rizzi | METAD MEAN PRINT UNITS COORDINATIONNUMBER GROUP CONTACT_MATRIX COMBINE EXTERNAL RESTART CUSTOM SUM ENDPLUMED MATRIX_VECTOR_PRODUCT FLUSH ONES | adjmat bias symfunc setup generic core function matrixtools |
| 19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Kim Jelfs | ANGLE PRINT DISTANCE INPLANEDISTANCES SUM MOVINGRESTRAINT RESTART DISTANCES COM CUSTOM FLUSH | multicolvar bias colvar vatom setup generic function |
| 19.046 | Optimal Collective from short simulations for Benzamidine-Trypsin ligand binding | bio | VAC-MetaD, optimised collective variables, binding free energy, unbinding rates, benzamidine trypsin, Structure Activity Relation | Faidon Brotzakis | REWEIGHT_METAD METAD UPPER_WALLS PRINT GROUP DISTANCE ALPHABETA MOLINFO RMSD DISTANCES BRIDGE COM FUNNEL TORSION WHOLEMOLECULES COMBINE LOWER_WALLS | funnel adjmat multicolvar bias colvar vatom generic core function |
| 19.030 | Coarse-Grained MetaDynamics (CG-MetaD) | bio | Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy | Vittorio Limongelli | METAD UPPER_WALLS PRINT DISTANCE COM WHOLEMOLECULES LOWER_WALLS | bias colvar vatom generic |
| 19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Matteo Salvalaglio | METAD UPPER_WALLS PRINT DISTANCE COMMITTOR CENTER TORSION LOWER_WALLS | bias colvar vatom generic |
| 19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Matteo Salvalaglio | METAD LOWEST MEAN PRINT GROUP COORDINATIONNUMBER DISTANCE CONTACT_MATRIX GYRATION RESTART SUM ENDPLUMED DISTANCES MORE_THAN MATRIX_VECTOR_PRODUCT ONES | adjmat multicolvar bias colvar symfunc setup generic core function matrixtools |
| 19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Michele Invernizzi | METAD PRINT UNITS LOAD ENERGY VES_DELTA_F RESTART ENDPLUMED POSITION TORSION | bias colvar setup generic ves |
| 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 | TORSION PUCKERING MOVINGRESTRAINT RESTART DISTANCE PRINT METAD MOLINFO 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 | GROUP WHOLEMOLECULES RESTART UPPER_WALLS DISTANCE FUNCPATHGENERAL PRINT METAD MOLINFO COM | function bias core generic vatom setup colvar |
| 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 | LOWER_WALLS GROUP COMMITTOR RESTART UPPER_WALLS DISTANCE PRINT COORDINATION UNITS CUSTOM OPES_METAD | function bias core generic setup colvar 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 | GROUP FLUSH GYRATION TORSION PBMETAD WHOLEMOLECULES INCLUDE COMBINE ANTIBETARMSD ALPHARMSD ENDPLUMED DISTANCE PRINT COORDINATION MOLINFO PARABETARMSD DIHCOR | function bias core generic multicolvar colvar secondarystructure |
| 23.044 | Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition | materials | metadynamics, interlocked molecules | Luigi Leanza | GROUP COMMITTOR DUMPGRID ENDPLUMED HISTOGRAM PRINT METAD COORDINATION READ CONVERT_TO_FES | bias core generic colvar gridtools |
| 23.038 | Determinants of Neutral Antagonism and Inverse Agonism in the β2-adrenergic receptor | bio | protein coupled receptor, beta-adrenergic, receptor activation, antagonism, inverse agonism, metadynamics | Timothy Clark | WHOLEMOLECULES DISTANCE PRINT MOLINFO METAD MATHEVAL RMSD | 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 | FIT_TO_TEMPLATE GROUP WHOLEMOLECULES POSITION SHADOW SUM UPPER_WALLS CUSTOM DISTANCE PRINT WRAPAROUND METAD DISTANCES CENTER MOLINFO | function bias core generic vatom multicolvar colvar isdb |
| 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 | FLUSH PATHMSD PRINT METAD DRR BIASVALUE CUSTOM | function bias generic colvar drr |
| 22.031 | Rare Event Kinetics from Adaptive Bias Enhanced Sampling | methods | OPES Flooding, Kinetics, Rate, OPES, Machine Learning | Dhiman Ray | CONTACTMAP PYTORCH_MODEL UNITS RMSD GROUP COMBINE BIASVALUE CUSTOM OPES_METAD CONSTANT ENERGY ENDPLUMED PRINT MOLINFO COMMITTOR TORSION POSITION WHOLEMOLECULES INCLUDE DISTANCE | function bias core generic pytorch setup colvar 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 | MEAN GROUP ENERGY MORE_THAN VOLUME DUMPGRID SUM DISTANCE_MATRIX RESTART UPPER_WALLS AROUND HISTOGRAM ENVIRONMENTSIMILARITY ONES PRINT CUSTOM OPES_METAD MATRIX_VECTOR_PRODUCT | function bias core volumes generic matrixtools envsim setup colvar adjmat opes gridtools |
| 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 | CONSTANT TORSION FLUSH WHOLEMOLECULES COMBINE SUM LESS_THAN ALPHARMSD UPPER_WALLS DISTANCE SECONDARY_STRUCTURE_RMSD ANGLE PRINT COORDINATION METAD ALPHABETA CUSTOM MOLINFO | function bias generic multicolvar colvar secondarystructure |
| 22.000 | Amyloid precursor protein processing by human γ-secretase | bio | Bias Exchange Metadynamics, Helix unfolding, coupled binding | Xiaoli Lu | INCLUDE CONTACTMAP LESS_THAN SUM ALPHARMSD DISTANCE SECONDARY_STRUCTURE_RMSD PRINT COORDINATION METAD UNITS RANDOM_EXCHANGES CENTER MOLINFO ANTIBETARMSD | function bias generic vatom setup colvar secondarystructure |
| 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 | LOWER_WALLS TORSION UPPER_WALLS DISTANCE PRINT METAD UNITS CUSTOM COM | function bias generic vatom setup colvar |
| 21.046 | Ubiquitin Interacting Motifs, Duality Between Structured and Disordered Motifs | bio | wt metadynamics, ubiquitin, ataxin-3, short linear motifs, ubiquitin binding motif, moonlight functions, intrinsic disorder | Elena Papaleo | LOWER_WALLS GROUP CONSTANT GYRATION TORSION WHOLEMOLECULES COMBINE SUM ENDPLUMED UPPER_WALLS PRINT METAD ALPHABETA CUSTOM | function bias core generic multicolvar colvar |
| 21.018 | Localized Volume-based Metadynamics | bio | LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification | Riccardo Capelli | FIXEDATOM CONVERT_TO_FES RMSD GROUP FLUSH DUMPGRID REWEIGHT_METAD MATHEVAL ENDPLUMED PRINT COORDINATION COM WHOLEMOLECULES POSITION UPPER_WALLS HISTOGRAM DISTANCE METAD READ | function bias core generic vatom colvar gridtools |
| 21.006 | OPES, On-the-fly Probability Enhanced Sampling Method | methods | opes, alanine dipeptide, well-tempered, multithermal, multiumbrella | Michele Invernizzi | ENERGY TORSION ENDPLUMED OPES_EXPANDED PRINT ECV_UMBRELLAS_LINE ECV_MULTITHERMAL OPES_METAD | generic colvar opes |
| 20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Adriana Pietropaolo | PBMETAD WHOLEMOLECULES PRINT COORDINATION CENTER | generic vatom bias 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 | GROUP LOAD VOLUME INCLUDE UPPER_WALLS PRINT METAD CENTER | bias core generic vatom setup colvar |
| 19.076 | Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones | bio | molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics | Salvatore Assenza | GYRATION MOVINGRESTRAINT ENDPLUMED PRINT UNITS | generic setup bias 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 | MEAN LOWER_WALLS GROUP ENERGY MORE_THAN GYRATION CONTACT_MATRIX SUM LOWEST ENDPLUMED UPPER_WALLS DISTANCE COORDINATIONNUMBER ONES PRINT METAD DISTANCES MATRIX_VECTOR_PRODUCT | function bias core generic matrixtools multicolvar colvar adjmat symfunc |
| 19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Matteo Salvalaglio | GROUP INCLUDE ENDPLUMED DISTANCE PRINT CENTER | generic colvar core vatom |
| 19.059 | cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide | bio | bias-exchange metadynamics, cis-trans isomerization | Fabrizio Marinelli | TORSION INCLUDE PRINT METAD RANDOM_EXCHANGES | generic bias colvar |
| 19.055 | Flying Gaussian method | methods | flying Gaussians, alanine dipeptide, peptide bond, Met-enkephalin | Vojtech Spiwok | TORSION COMBINE DISTANCE PRINT METAD MATHEVAL | function generic bias colvar |
| 19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | GiovanniMaria Piccini | LOWER_WALLS ENERGY FLUSH COMBINE UPPER_WALLS DISTANCE PRINT METAD UNITS | function bias generic setup colvar |
| 19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | ENERGY FLUSH COMBINE UPPER_WALLS DISTANCE PRINT METAD UNITS | function bias generic setup colvar |
| 19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Davide Provasi | WHOLEMOLECULES CONTACTMAP ENDPLUMED DISTANCE FUNCPATHMSD PRINT METAD RMSD COM | function bias generic vatom colvar |
| 19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Jim Pfaendtner | EXTERNAL GROUP ENERGY METAD COORDINATION | colvar bias core |
| 19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Glen Hocky | TORSION COMBINE DISTANCE PRINT EDS RESTRAINT | function bias generic colvar eds |
| 19.013 | RNA FF FITTING | methods | force field, RNA | Giovanni Bussi | CONSTANT TORSION PUCKERING INCLUDE BIASVALUE MATHEVAL MOLINFO | generic function bias colvar |
| 24.034 | Umbrella sampling of ion in transporter SLC26A7 | bio | umbrella sampling, transporter, ions | Xiaoli Lu | POSITION UNITS PRINT RESTRAINT | generic bias setup colvar |
| 24.026 | Constant pH metadynamics of RNA oligomers | bio | metadynamics, pH, RNA | Giovanni Bussi | RESTART MOLINFO PRINT TORSION METAD PUCKERING | generic bias setup colvar |
| 24.024 | Host-Guest binding free energies à la carte, an automated OneOPES protocol | bio | OneOPES, ligand binding, binding free energy,SAMPL challenge, host-guest | Valerio Rizzi | UPPER_WALLS PRINT MATHEVAL LOWER_WALLS ENDPLUMED FIT_TO_TEMPLATE TORSION OPES_METAD_EXPLORE ECV_MULTITHERMAL ENERGY OPES_EXPANDED FIXEDATOM CENTER DISTANCE COORDINATION ANGLE WHOLEMOLECULES GROUP | colvar bias vatom core function generic opes |
| 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 | COMMITTOR UPPER_WALLS PRINT MATHEVAL FIT_TO_TEMPLATE CENTER GROUP OPES_METAD WHOLEMOLECULES ENDPLUMED TORSION METAD DISTANCE CONTACTMAP CUSTOM RMSD MOLINFO COMBINE FIXEDATOM COORDINATION ANGLE | bias colvar vatom core function generic opes |
| 24.016 | Cryo-EM guided simulations of ribozyme | bio | metainference, cryo-EM | Giovanni Bussi | EMMIVOX MOLINFO PRINT GROUP INCLUDE ERMSD WHOLEMOLECULES RESTRAINT BIASVALUE | isdb bias colvar core generic |
| 24.009 | Weighted Shape Gaussian Mixture Models | bio | metadynamics, clustering | Glen Hocky | PRINT TORSION METAD UNITS GROUP | bias colvar setup core generic |
| 24.008 | yCD Metadynamics | bio | volume-based MetaD, path CVs, infrequent MetaD, product release | James McCarty | COMMITTOR UPPER_WALLS PRINT MATHEVAL PATH FIT_TO_TEMPLATE READ GROUP HISTOGRAM FLUSH WRAPAROUND WHOLEMOLECULES DUMPGRID ENDPLUMED REWEIGHT_METAD COM METAD INCLUDE DISTANCE CONTACTMAP CONVERT_TO_FES RMSD MOLINFO GPATH COMBINE FIXEDATOM COORDINATION | gridtools bias colvar vatom core function mapping generic |
| 24.003 | Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations | chemistry | steered molecular dynamics, foldamers, peptoids, bio-inspired | Kaylyn Torkelson | PRINT ALPHABETA COM TORSION GYRATION INCLUDE MOVINGRESTRAINT DISTANCE COORDINATION WHOLEMOLECULES | bias colvar vatom multicolvar generic |
| 23.040 | Supramolecular capsules assembly dynamics | chemistry | Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics | Riccardo Capelli | POSITION PRINT LESS_THAN DISTANCES SUM COM BETWEEN FLUSH METAD UNITS CENTER DISTANCE CUSTOM WHOLEMOLECULES GROUP | colvar bias vatom setup core function multicolvar generic |
| 23.037 | Estimating binding free energy of solid binding peptides without extensive sampling | bio | metadynamics, solid binding peptides | Xin Qi | MOLINFO PBMETAD UPPER_WALLS PRINT LOWER_WALLS COM GYRATION DISTANCE | generic vatom colvar bias |
| 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 | COMMITTOR UPPER_WALLS PRINT MATHEVAL LOWER_WALLS FIT_TO_TEMPLATE CENTER GROUP POSITION FLUSH OPES_METAD UNITS WRAPAROUND WHOLEMOLECULES BIASVALUE ENDPLUMED COM OPES_METAD_EXPLORE TORSION ENERGY DISTANCE CUSTOM MOLINFO COORDINATION | bias colvar vatom setup core function generic opes |
| 23.015 | MPCs aggregation | bio | opes_explore, dimerization, MPCs, self-assembly | Vikas Tiwari | UPPER_WALLS PRINT LOWER_WALLS COM OPES_METAD_EXPLORE METAD CENTER DISTANCE COORDINATION CUSTOM WHOLEMOLECULES GROUP | colvar bias vatom core function generic opes |
| 23.001 | Quantum phase diagram of water | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn-Løland Bore | RESTART ECV_UMBRELLAS_LINE UPPER_WALLS PRINT MEAN LOWER_WALLS SUM ENVIRONMENTSIMILARITY INCLUDE OPES_EXPANDED MORE_THAN DISTANCE_MATRIX MATRIX_VECTOR_PRODUCT CUSTOM ONES GROUP | bias envsim setup matrixtools function core generic opes adjmat |
| 22.030 | Mixing physics across temperatures with generative artificial intelligence | methods | REMD, Generative AI, DDPM | Yihang Wang | TORSION PRINT WHOLEMOLECULES | generic colvar |
| 22.023 | Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy | bio | CryoEM, MEMMI,EMMI, Metadynamics, Metainference, IAPP, structural ensemble | Faidon Brotzakis | RESTART MOLINFO RMSD UPPER_WALLS PBMETAD PRINT TORSION COM BIASVALUE COORDINATION EMMI WHOLEMOLECULES GROUP | isdb bias colvar vatom setup core generic |
| 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 | ECV_UMBRELLAS_LINE UPPER_WALLS PRINT MEAN LOWER_WALLS SUM ENVIRONMENTSIMILARITY INCLUDE MORE_THAN OPES_EXPANDED DISTANCE_MATRIX MATRIX_VECTOR_PRODUCT CUSTOM ONES GROUP | bias envsim matrixtools function core generic opes adjmat |
| 22.002 | GAMBES_SAMPL5_RATES | other | GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding | Jayashrita Debnath | COMMITTOR UPPER_WALLS PRINT MATHEVAL ENDPLUMED PYTORCH_MODEL FIT_TO_TEMPLATE ENERGY FLUSH LOAD FIXEDATOM CENTER DISTANCE COORDINATION ANGLE WHOLEMOLECULES GROUP | colvar bias pytorch vatom setup core function generic |
| 21.045 | QM/MM metadynamics of thiol-disulfide exchange between methylthiolate and dimethyldisulfide in water with an imposed external electrostatic potential (ESP) | chemistry | metadynamics, QM/MM, electrostatic potential, thiol-disulfide exchange | Denis Maag | UPPER_WALLS PRINT MEAN LOWER_WALLS COMBINE CONTACT_MATRIX METAD DISTANCE COORDINATIONNUMBER COORDINATION MATRIX_VECTOR_PRODUCT ONES GROUP | colvar bias symfunc matrixtools function core generic adjmat |
| 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 | UPPER_WALLS PRINT LOWER_WALLS LOWEST DIHCOR RANDOM_EXCHANGES GROUP LESS_THAN PARABETARMSD SUM DIHEDRAL_CORRELATION ANTIBETARMSD WHOLEMOLECULES ALPHARMSD ENERGY METAD MOLINFO GYRATION SECONDARY_STRUCTURE_RMSD COORDINATION | secondarystructure bias colvar core function multicolvar generic |
| 21.026 | Probing allosteric regulations with coevolution-driven molecular simulations | bio | metadynamics, coevolution, allostery, adenylate cyclase | Francesco Colizzi | UPPER_WALLS PRINT COM METAD PATHMSD UNITS DISTANCE WHOLEMOLECULES | colvar bias vatom setup generic |
| 21.024 | Property map collective variable as a useful tool for force field correction | chemistry | molecular mechanics | Vojtech Spiwok | PROPERTYMAP PRINT TORSION METAD WHOLEMOLECULES BIASVALUE | generic bias colvar |
| 21.021 | ATLAS | methods | Machine Learning, Metadynamics | Federico Giberti | PRINT MEAN MATHEVAL COORDINATION TORSION GROUP GYRATION WHOLEMOLECULES DUMPATOMS METAD UNITS DISTANCE COORDINATIONNUMBER CONTACT_MATRIX MATRIX_VECTOR_PRODUCT ONES BIASVALUE | bias colvar symfunc setup core function matrixtools generic adjmat |
| 21.014 | how to determine statistically accurate conformational ensembles | bio | metadynamics, metainference, errors, cv, SAXS, ensemble determination | Cristina Paissoni | PBMETAD PRINT CENTER LESS_THAN SUM ANTIBETARMSD WHOLEMOLECULES BIASVALUE SAXS TORSION STATS METAD CONTACTMAP CUSTOM MOLINFO ALPHABETA COMBINE GYRATION SECONDARY_STRUCTURE_RMSD ENSEMBLE CONSTANT | isdb secondarystructure bias colvar vatom function multicolvar generic |
| 21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Tarsis Ferreira | MOLINFO UPPER_WALLS PRINT DUMPGRID LOWER_WALLS REWEIGHT_METAD HISTOGRAM ENERGY METAD INCLUDE DISTANCE COORDINATION RANDOM_EXCHANGES PUCKERING WHOLEMOLECULES GROUP | gridtools colvar bias core generic |
| 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 | RESTART MOLINFO PRINT ABMD TORSION CENTER ERMSD DISTANCE | colvar bias vatom setup generic |
| 20.026 | Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor | bio | Metadynamics, Umbrella sampling | Brandon Peters | POSITION PRINT DUMPGRID RMSD_VECTOR RESTRAINT COMBINE REWEIGHT_METAD HISTOGRAM METAD MULTI_RMSD CONCATENATE CONVERT_TO_FES CUSTOM WHOLEMOLECULES CONSTANT | gridtools bias colvar valtools function generic |
| 20.021 | Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins. | bio | phi-values, restrained MD, transition-state, protein folding, disordered proteins, protein evolution | Cristina Paissoni | MOLINFO PRINT STATS COORDINATION WHOLEMOLECULES RESTRAINT | generic function bias colvar |
| 20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Jim Pfaendtner | RESTART PRINT DISTANCES SUM CENTER DISTANCE COORDINATION CUSTOM WHOLEMOLECULES GROUP | colvar vatom setup core function multicolvar generic |
| 20.001 | Conformational stability and dynamics in solution and in crystals report similarly on unfolding and aggregation propensity of amyloidogenic proteins | bio | metainference, metadynamics, NMR, protein dynamics, b2m, protein crystals | Carlo Camilloni | PBMETAD UPPER_WALLS PRINT LOWER_WALLS CS2BACKBONE GROUP LESS_THAN SUM FLUSH ANTIBETARMSD WHOLEMOLECULES BIASVALUE ENDPLUMED TORSION CUSTOM MOLINFO ALPHABETA COMBINE SECONDARY_STRUCTURE_RMSD CONSTANT | isdb secondarystructure bias colvar core function multicolvar generic |
| 19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Giovanni Bussi | LOWER_WALLS ENDPLUMED DISTANCE COORDINATION WHOLEMOLECULES RESTRAINT | generic colvar bias |
| 19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Jakub Rydzewski | RESTART UPPER_WALLS PRINT LOWER_WALLS METAD PATHMSD UNITS | generic colvar setup bias |
| 19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Mattia Bernetti | UPPER_WALLS PRINT LOWER_WALLS METAD PATHMSD WHOLEMOLECULES | generic colvar bias |
| 19.056 | maze | methods | maze, ligand unbinding | Jakub Rydzewski | POSITION PRINT MAZE_OPTIMIZER_BIAS UNITS MAZE_SIMULATED_ANNEALING MAZE_LOSS | generic maze setup colvar |
| 19.041 | Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces | bio | metadynamics, collective variables, conformational changes, multiple walkers, Well-Tempered MetaD, peptide, binding, phosphorylation, post-transitional motif, sio2, adsorption | Jim Pfaendtner | UPPER_WALLS PRINT COM ENERGY METAD DISTANCE | generic vatom colvar bias |
| 19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Carlo Camilloni | RESTART PBMETAD UPPER_WALLS PRINT LOWER_WALLS CS2BACKBONE GROUP LESS_THAN SUM FLUSH ANTIBETARMSD WHOLEMOLECULES BIASVALUE ENDPLUMED TORSION CUSTOM MOLINFO ALPHABETA COMBINE SECONDARY_STRUCTURE_RMSD CONSTANT | isdb secondarystructure bias colvar setup core function multicolvar generic |
| 19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Elena Papaleo | MOLINFO UPPER_WALLS PRINT ALPHABETA SUM LOWER_WALLS COMBINE TORSION GYRATION METAD CUSTOM WHOLEMOLECULES CONSTANT GROUP | colvar bias core function multicolvar generic |
| 25.009 | Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water | chemistry | metadynamics, nitrate photolysis | Kam-Tung Chan | DISTANCE READ REWEIGHT_METAD DUMPGRID GROUP METAD COORDINATION FLUSH RESTART PRINT HISTOGRAM UPPER_WALLS CUSTOM | colvar function bias gridtools generic core setup |
| 25.008 | Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting | methods | metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting | Dhiman Ray | DISTANCE MOLINFO BIASVALUE WHOLEMOLECULES LOWER_WALLS TORSION GROUP UPPER_WALLS RMSD OPES_METAD PYTORCH_MODEL METAD ENERGY PRINT POSITION ENDPLUMED CUSTOM UNITS | colvar function bias generic pytorch core opes setup |
| 24.031 | DeepLNE | methods | PATHCV, OPES, OneOPES | Thorben Fröhlking | MOLINFO OPES_METAD_EXPLORE PYTORCH_MODEL OPES_EXPANDED RESTART COORDINATION ENERGY COMBINE PRINT ERMSD VOLUME ECV_MULTITHERMAL | colvar function generic pytorch opes setup |
| 24.030 | NMR guided simulation of dsRBD | bio | Metainference, NMR, protein dynamics | Debadutta Patra | DISTANCE MOLINFO WHOLEMOLECULES TORSION GROUP CONSTANT STATS METAINFERENCE ENSEMBLE SUM ALPHABETA RDC PRINT COMBINE FLUSH CUSTOM | colvar function isdb multicolvar generic core |
| 24.017 | Absolute Binding Free Energies with OneOPES | methods | protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy | Francesco Gervasio | LOWER_WALLS CONSTANT RMSD COORDINATION PRINT UPPER_WALLS ECV_MULTITHERMAL MOLINFO BIASVALUE WRAPAROUND ENERGY WHOLEMOLECULES OPES_EXPANDED METAD PROJECTION_ON_AXIS CONTACTMAP INCLUDE TORSION MATHEVAL GROUP OPES_METAD_EXPLORE COM RESTART CUSTOM | colvar function bias generic opes core vatom setup |
| 24.014 | Learning Collective Variables with Synthetic Data Augmentation through Physics-inspired Geodesic Interpolation | methods | data augmentation, geodesic interpolation, collective variables, protein folding | Juno Nam | MOLINFO WHOLEMOLECULES LOWER_WALLS DRR RMSD PYTORCH_MODEL METAD COORDINATION FLUSH PRINT UPPER_WALLS | colvar bias generic pytorch drr |
| 23.039 | Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation | chemistry | metadynamics, ligand dissociation | Eric Beyerle | DUMPMASSCHARGE DISTANCE MOLINFO RESTRAINT METAD PRINT COMBINE CENTER UPPER_WALLS FIXEDATOM | colvar function bias generic vatom |
| 23.028 | Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process | chemistry | Ammonia decomposition; Dynamics;OPES; Neural Network potential | Manyi Yang | LOWER_WALLS MATRIX_VECTOR_PRODUCT PRINT UPPER_WALLS LESS_THAN COMMITTOR OPES_METAD ENERGY COORDINATIONNUMBER MEAN DISTANCES ZDISTANCES FIXEDATOM UNITS DISTANCE MATHEVAL ONES GROUP COM SUM FLUSH CONTACT_MATRIX CUSTOM | colvar symfunc function multicolvar bias generic opes core adjmat vatom setup matrixtools |
| 23.023 | Rational design of novel biomimetic sequence-defined polymers for mineralization applications | methods | metadynamics, surface binding, biomimetic mineralization | Kaylyn Torkelson | DISTANCE GYRATION COM COORDINATION PBMETAD PRINT UPPER_WALLS | 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 | PROJECT_POINTS CONSTANT PRINT UPPER_WALLS PATHMSD MORE_THAN TRANSPOSE COLLECT_FRAMES WHOLEMOLECULES VSTACK SKETCHMAP_PROJECTION SKETCHMAP LANDMARK_SELECT_FPS METAD PDB2CONSTANT EUCLIDEAN_DISTANCE DISTANCE DISSIMILARITIES COM VORONOI SUM CUSTOM | colvar function valtools bias generic dimred landmarks vatom matrixtools refdist |
| 23.012 | JAK2 2D meta-eABF PMF with statistical analysis | bio | 2D meta-eABF, path CV, PMF | Istvan Kolossvary | BIASVALUE LOWER_WALLS DRR METAD FLUSH PRINT UPPER_WALLS CUSTOM PATHMSD | colvar function bias generic drr |
| 23.011 | OneOPES, a combined enhanced sampling method to rule them all | bio | OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding | Valerio Rizzi | DISTANCE MOLINFO TORSION OPES_METAD_EXPLORE OPES_EXPANDED METAD ENERGY PRINT ENDPLUMED ECV_MULTITHERMAL | colvar opes 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 | DISTANCE BIASVALUE WHOLEMOLECULES LOWER_WALLS MATHEVAL CONSTANT METAD PRINT UPPER_WALLS | colvar generic function 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 | LOWER_WALLS RMSD COORDINATION ANGLE PRINT CENTER UPPER_WALLS ENDPLUMED MOLINFO COMMITTOR OPES_METAD ENERGY WHOLEMOLECULES PYTORCH_MODEL FIXEDATOM FIT_TO_TEMPLATE DISTANCE CONTACTMAP INCLUDE MATHEVAL GROUP COMBINE CUSTOM | colvar function bias generic pytorch opes core vatom |
| 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 DUMPGRID MORE_THAN LOWER_WALLS ONES GROUP MATRIX_VECTOR_PRODUCT ECV_UMBRELLAS_LINE ENVIRONMENTSIMILARITY OPES_EXPANDED RESTART SUM PRINT HISTOGRAM UPPER_WALLS CUSTOM | envsim function bias matrixtools generic gridtools core opes setup adjmat |
| 22.033 | Reciprocal barrier restraint. Application to PROTAC passive permeability prediction | methods | PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR | Istvan Kolossvary | DISTANCE BIASVALUE DRR COM METAD FLUSH PRINT CUSTOM UNITS | colvar function bias generic drr vatom setup |
| 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 CONTACTMAP PRINT | colvar vatom generic |
| 21.033 | Multiple-path-metadynamics applied to DNA base-pairing transitions | bio | path-CV, metadynamics, multiple-walker, dna | Alberto Pérez-de-Alba-Ortíz | INCLUDE CONSTANT RESTRAINT METAD PRINT COMBINE UPPER_WALLS MOVINGRESTRAINT | generic function bias |
| 21.019 | Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations | materials | Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen | Matteo Salvalaglio | DISTANCE KDE MATHEVAL COM PRINT TORSIONS | colvar function multicolvar generic gridtools 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 | DISTANCE WHOLEMOLECULES GROUP COM PRINT | colvar core generic vatom |
| 20.032 | Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil | materials | clustering, conformational isomers | Matteo Salvalaglio | ENDPLUMED PRINT TORSION | colvar generic |
| 20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Cristina Paissoni | DISTANCE MOLINFO SAXS WHOLEMOLECULES BIASVALUE INCLUDE GROUP RESTRAINT ENSEMBLE PRINT STATS CENTER | colvar function isdb bias generic core vatom |
| 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 | COORDINATION PRINT ENDPLUMED PARABETARMSD MOLINFO ANTIBETARMSD WHOLEMOLECULES DIHCOR METAINFERENCE ALPHARMSD PBMETAD STATS INCLUDE TORSION GROUP GYRATION ENSEMBLE FLUSH COMBINE CS2BACKBONE | colvar secondarystructure function multicolvar isdb bias generic core |
| 20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Pratyush Tiwary | DISTANCE MOLINFO WHOLEMOLECULES TORSION RMSD RESTART METAD PRINT COMBINE UPPER_WALLS | colvar function bias generic setup |
| 20.005 | Muscarinic M2 receptor/ligand Frequency-Adaptive Metadynamics and QM/MM calculations | bio | Frequency-adaptive metadynamics, multiple-walkers metadynamics, well-tempered metadynamics, GPCR, receptor, Adiabatic Bias MD | Riccardo Capelli | READ LOWER_WALLS PRINT UPPER_WALLS ENDPLUMED ABMD MOLINFO REWEIGHT_METAD DUMPGRID HISTOGRAM WHOLEMOLECULES CONVERT_TO_FES FUNCPATHMSD METAD DISTANCE CONTACTMAP COM FLUSH COMBINE | colvar function bias gridtools generic vatom |
| 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 WHOLEMOLECULES GROUP RESTART METAD PRINT UPPER_WALLS PATHMSD | colvar bias generic core setup |
| 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 | READ LOWER_WALLS PRINT UPPER_WALLS LOAD DUMPGRID ENERGY HISTOGRAM OPT_DUMMY VES_LINEAR_EXPANSION CELL Q6 REWEIGHT_TEMP_PRESS TD_MULTITHERMAL_MULTIBARIC CONVERT_TO_FES VOLUME MATHEVAL OPT_AVERAGED_SGD BF_LEGENDRE RESTART TD_WELLTEMPERED REWEIGHT_BIAS COMBINE | colvar symfunc ves function bias gridtools generic setup |
| 19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Luigi Bonati | Q6 TORSION ENDPLUMED ENVIRONMENTSIMILARITY PRINT ENERGY POSITION LOAD UNITS | colvar symfunc envsim generic setup |
| 19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Gareth Tribello | CELL FCCUBIC MEAN MORE_THAN ONES GROUP MATRIX_VECTOR_PRODUCT METAD FCCUBIC_FUNC SUM CONTACT_MATRIX PRINT UPPER_WALLS ENDPLUMED CUSTOM UNITS | colvar symfunc function bias generic core adjmat setup matrixtools |
| 19.049 | Determining the sizes of solid/liquid clusters in MD trajectories of nucleation | methods | nucleation, metadynamics, clustering, Steinhardt order parameters | Gareth Tribello | DISTANCES Q6 MORE_THAN ONES OUTER_PRODUCT MATRIX_VECTOR_PRODUCT CLUSTER_PROPERTIES CLUSTER_NATOMS SMAC LOCAL_Q6 DFSCLUSTERING CLUSTER_DISTRIBUTION METAD CONTACT_MATRIX OUTPUT_CLUSTER PRINT COORDINATIONNUMBER CUSTOM | symfunc function multicolvar bias generic clusters adjmat matrixtools |
| 19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Paolo Raiteri | DISTANCE MATHEVAL RESTART METAD FLUSH PRINT UPPER_WALLS UNITS | colvar function bias generic setup |
| 19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Gabriele Cesare Sosso | Q6 COMMITTOR MFILTER_MORE CLUSTER_NATOMS CLUSTER_WITHSURFACE LOCAL_Q6 DFSCLUSTERING FLUSH CONTACT_MATRIX OUTPUT_CLUSTER ENDPLUMED | symfunc multicolvar generic clusters adjmat |