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 |
|---|---|---|---|---|---|---|
| 25.006 | 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 | PBMETAD PRINT ENERGY CENTER GYRATION INCLUDE TORSION DISTANCE VOLUME RESTART READ | colvar setup bias generic vatom |
| 25.001 | RNA G-quadruplex folding with ST-metaD protocol | bio | RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | ERMSD MOLINFO COMBINE METAD WHOLEMOLECULES | colvar function generic bias |
| 25.000 | Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer | bio | metadynamics, pathCV | Sahithya Sridharan Iyer | PRINT GROUP FUNCPATHGENERAL MOLINFO METAD WHOLEMOLECULES COM UPPER_WALLS RESTART DISTANCE | colvar core setup bias function generic vatom |
| 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 | PRINT HISTOGRAM GROUP ANGLE CONVERT_TO_FES TORSION COORDINATION WHOLEMOLECULES DUMPGRID DISTANCE | gridtools colvar core generic |
| 24.031 | DeepLNE | methods | PATHCV, OPES, OneOPES | Thorben Fröhlking | PRINT ERMSD MOLINFO COMBINE ENERGY ECV_MULTITHERMAL OPES_METAD_EXPLORE COORDINATION PYTORCH_MODEL VOLUME RESTART OPES_EXPANDED | colvar pytorch setup function opes generic |
| 24.026 | Constant pH metadynamics of RNA oligomers | bio | metadynamics, pH, RNA | Giovanni Bussi | PRINT PUCKERING MOLINFO METAD TORSION RESTART | colvar bias setup generic |
| 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 | PRINT GROUP COMMITTOR METAD LOAD TORSION | colvar core setup bias generic |
| 24.017 | Absolute Binding Free Energies with OneOPES | methods | protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy | Francesco Gervasio | ENERGY ECV_MULTITHERMAL INCLUDE PRINT CONSTANT GROUP WRAPAROUND OPES_METAD_EXPLORE COORDINATION WHOLEMOLECULES CUSTOM PROJECTION_ON_AXIS RESTART METAD LOWER_WALLS RMSD COM OPES_EXPANDED MOLINFO MATHEVAL TORSION CONTACTMAP UPPER_WALLS BIASVALUE | colvar core setup bias function opes generic vatom |
| 24.004 | Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables | materials | metadynamics, nucleation, machine learning | Ziyue Zou | PRINT GROUP METAD INCLUDE LOAD RESTART | core setup generic bias |
| 24.002 | Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes | chemistry | metadynamics, ligand design, solvent extraction | Xiaoyu Wang | PRINT METAD TORSION RESTART UNITS | colvar bias setup generic |
| 24.000 | Ammonia Decomposition on Non-stoichiometric Lithium Imide | chemistry | ammonia decomposition, non-stoichiometric lithium imide, machine learning interatomic potentials, enhanced sampling, heterogeneous catalysis | Francesco Mambretti | PRINT GROUP OPES_METAD FLUSH FIXEDATOM COORDINATIONNUMBER UPPER_WALLS ZDISTANCES DISTANCE UNITS | colvar core multicolvar symfunc setup bias opes generic vatom |
| 23.022 | A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar | methods | collective variables, machine learning, toy model | Enrico Trizio | PRINT POSITION OPES_METAD ENDPLUMED LOWER_WALLS PYTORCH_MODEL CUSTOM UPPER_WALLS BIASVALUE UNITS | colvar pytorch function setup bias opes generic |
| 23.008 | PBMetaD simulations of Histatin5 | bio | metadynamics, IDP, Rg, PPII | Francesco Pesce | PBMETAD PRINT GROUP MOLINFO GYRATION TORSION WHOLEMOLECULES | colvar core bias generic |
| 23.000 | Atomistic simulations of RNA tetraloop folding via PTWTE-WTM | bio | parallel tempering, well-tempered metadynamics, well-tempered ensemble, RNA, Tetraloop, Folding | Gül Zerze | PRINT ENERGY METAD LOWER_WALLS WHOLEMOLECULES CONTACTMAP UPPER_WALLS | colvar bias generic |
| 22.035 | Deciphering the alphabet of disorder — Glu and Asp act differently on local but not global properties | bio | intrinsically disordered proteins, parallel bias metadynamics, protein | Kresten Lindorff-Larsen | PBMETAD MOLINFO GYRATION TORSION WHOLEMOLECULES | colvar bias generic |
| 22.023 | Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy | bio | CryoEM, MEMMI,EMMI, Metadynamics, Metainference, IAPP, structural ensemble | Faidon Brotzakis | PBMETAD PRINT GROUP MOLINFO EMMI TORSION COORDINATION RMSD WHOLEMOLECULES UPPER_WALLS COM RESTART BIASVALUE | colvar core isdb setup bias generic vatom |
| 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 | PRINT ECV_UMBRELLAS_LINE ENVIRONMENTSIMILARITY LOWER_WALLS INCLUDE UPPER_WALLS OPES_EXPANDED | envsim bias opes generic |
| 22.011 | Accelerating all-atom simulations and gaining mechanistic understanding of biophysical systems through State Predictive Information Bottleneck | methods | metadynamics, membrane permeation, protein folding | Shams Mehdi | PRINT XANGLES YANGLES COMBINE MOLINFO MATHEVAL METAD LOWER_WALLS TORSION WHOLEMOLECULES CUSTOM UPPER_WALLS COM ALPHABETA ZANGLES DISTANCE | colvar multicolvar bias function generic vatom |
| 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 | BF_GAUSSIANS ENERGY INCLUDE BF_LEGENDRE OPT_AVERAGED_SGD PRINT VES_LINEAR_EXPANSION BF_CUBIC_B_SPLINES COORDINATION FLUSH BF_CHEBYSHEV METAD TD_WELLTEMPERED POSITION OPT_ADAM BF_WAVELETS UPPER_WALLS TD_UNIFORM DISTANCE UNITS VES_OUTPUT_BASISFUNCTIONS | colvar ves setup bias generic |
| 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 | PRINT METAD LOWER_WALLS TORSION CUSTOM COM UPPER_WALLS DISTANCE UNITS | colvar function setup bias generic vatom |
| 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 | PRINT COMBINE METAD LOWER_WALLS COORDINATION COORDINATIONNUMBER UPPER_WALLS DISTANCE | colvar symfunc bias function generic |
| 21.040 | A structural ensemble of a tau-microtubule complex reveals regulatory tau phosphorylation and acetylation mechanisms | bio | EMMI, CryoEM, tau-microtubules, post-translational modifications, chemical mutagenesis, structural ensemble, Metainference | Faidon Brotzakis | PRINT GROUP BIASVALUE MOLINFO EMMI WHOLEMOLECULES COM UPPER_WALLS RESTART DISTANCE | colvar core isdb setup bias generic vatom |
| 21.035 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, interface | Aaron Finney | PRINT GROUP FIXEDATOM LOAD RESTRAINT DISTANCE | colvar core setup bias generic vatom |
| 21.032 | Metal-coupled folding mechanism to metallothionein | bio | parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination | Manuel-Peris Diaz | PBMETAD GROUP COORDINATION WHOLEMOLECULES UNITS | colvar core setup bias generic |
| 21.026 | Probing allosteric regulations with coevolution-driven molecular simulations | bio | metadynamics, coevolution, allostery, adenylate cyclase | Francesco Colizzi | PRINT METAD PATHMSD WHOLEMOLECULES COM UPPER_WALLS DISTANCE UNITS | colvar setup bias generic vatom |
| 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 READ PRINT GROUP COORDINATION WHOLEMOLECULES DUMPGRID FLUSH METAD RMSD COM REWEIGHT_METAD ENDPLUMED POSITION HISTOGRAM MATHEVAL UPPER_WALLS DISTANCE | gridtools colvar function core bias generic vatom |
| 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 | PRINT ECV_MULTITHERMAL_MULTIBARIC Q6 ECV_UMBRELLAS_LINE ENERGY ENVIRONMENTSIMILARITY MATHEVAL VES_LINEAR_EXPANSION VOLUME BF_LEGENDRE UPPER_WALLS RESTART TD_UNIFORM OPES_EXPANDED OPT_AVERAGED_SGD | colvar envsim ves symfunc setup bias function opes 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 | PRINT METAD COORDINATION CUSTOM DISTANCES UNITS | colvar function multicolvar setup bias generic |
| 20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Pratyush Tiwary | PRINT COMBINE MOLINFO METAD TORSION WHOLEMOLECULES RMSD UPPER_WALLS RESTART DISTANCE | colvar setup bias function generic |
| 19.056 | maze | methods | maze, ligand unbinding | Jakub Rydzewski | PRINT POSITION MAZE_OPTIMIZER_BIAS MAZE_LOSS MAZE_SIMULATED_ANNEALING UNITS | maze colvar setup generic |
| 19.047 | Close Structure | methods | metadynamics, RMSD, path collective variables, property map | Vojtech Spiwok | PROPERTYMAP WHOLEMOLECULES METAD PRINT | colvar bias generic |
| 19.035 | Dimerization of GPCRs from coarse-grained umbrella sampling | bio | Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization | Davide Provasi | PRINT GROUP TORSION RESTRAINT COM DISTANCE | colvar core bias generic vatom |
| 19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Adriana Pietropaolo | PRINT CONSTANT MATHEVAL METAD TORSION WHOLEMOLECULES BIASVALUE | colvar function generic bias |
| 25.009 | Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water | chemistry | metadynamics, nitrate photolysis | Kam-Tung Chan | FLUSH HISTOGRAM CUSTOM UPPER_WALLS GROUP RESTART READ DISTANCE PRINT REWEIGHT_METAD COORDINATION METAD DUMPGRID | colvar gridtools bias function core setup generic |
| 24.029 | Combination of OPES and OPES-Explore | methods | OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin | Dhiman Ray | RMSD OPES_METAD_EXPLORE CUSTOM GROUP FIT_TO_TEMPLATE METAD ENERGY FIXEDATOM BIASVALUE WHOLEMOLECULES PYTORCH_MODEL DISTANCE CENTER MATHEVAL UNITS POSITION ENDPLUMED COMBINE OPES_METAD PRINT CONTACTMAP MOLINFO INCLUDE COORDINATION LOWER_WALLS FLUSH UPPER_WALLS | vatom colvar pytorch opes function bias core setup generic |
| 24.027 | Proline cis and trans subensembles of a disordered peptide | bio | intrinsically disordered proteins, proline cis trans isomerisation, metadynamics, collective variables | Alice Pettitt | DIHCOR FLUSH ALPHARMSD ENDPLUMED WHOLEMOLECULES COMBINE GROUP PARABETARMSD PBMETAD GYRATION DISTANCE PRINT INCLUDE MOLINFO TORSION COORDINATION ANTIBETARMSD | colvar secondarystructure function multicolvar core bias generic |
| 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 | UPPER_WALLS OPES_METAD DISTANCE PRINT COORDINATION ENERGY | generic colvar bias opes |
| 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 | ALPHARMSD CUSTOM WHOLEMOLECULES COMBINE OPES_METAD DISTANCE GYRATION COORDINATION PRINT MOLINFO TORSION | colvar opes secondarystructure function generic |
| 23.044 | Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition | materials | metadynamics, interlocked molecules | Luigi Leanza | COMMITTOR HISTOGRAM ENDPLUMED GROUP READ PRINT CONVERT_TO_FES COORDINATION METAD DUMPGRID | colvar gridtools bias core generic |
| 23.032 | Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics | bio | metadynamics, tSNE, neural network, machine learning, trp-cage, folding | Vojtech Spiwok | ALPHARMSD ANN WHOLEMOLECULES COMBINE PRINT FIT_TO_TEMPLATE MOLINFO METAD POSITION | colvar secondarystructure bias function annfunc generic |
| 23.029 | An accurate and efficient SAXS/SANS implementation including solvation layer effects suitable for restrained Molecular Dynamics simulations | bio | SAXS, SANS, SAS, metainference, proteins, nucleic-acid | Federico Ballabio | BIASVALUE RMSD ENSEMBLE WRAPAROUND SAXS UPPER_WALLS GROUP STATS DISTANCE PRINT CENTER MOLINFO | vatom colvar function bias core isdb generic |
| 23.023 | Rational design of novel biomimetic sequence-defined polymers for mineralization applications | methods | metadynamics, surface binding, biomimetic mineralization | Kaylyn Torkelson | UPPER_WALLS PBMETAD DISTANCE GYRATION PRINT COM COORDINATION | vatom generic colvar 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 | SKETCHMAP TRANSPOSE DISSIMILARITIES UPPER_WALLS CUSTOM PATHMSD WHOLEMOLECULES DISTANCE PRINT VSTACK COM VORONOI COLLECT_FRAMES METAD LANDMARK_SELECT_FPS SKETCHMAP_PROJECTION | vatom colvar landmarks dimred function bias valtools matrixtools generic |
| 23.018 | Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention | materials | metadynamics, surface binding, peptide adsorption | Kaylyn Torkelson | UPPER_WALLS PBMETAD DISTANCE GYRATION PRINT COM | vatom generic colvar 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 | RMSD CUSTOM GROUP FIT_TO_TEMPLATE ENERGY FIXEDATOM WHOLEMOLECULES PYTORCH_MODEL DISTANCE CENTER MATHEVAL ENDPLUMED COMMITTOR COMBINE OPES_METAD PRINT CONTACTMAP MOLINFO INCLUDE LOWER_WALLS COORDINATION ANGLE UPPER_WALLS | vatom colvar pytorch opes function bias core generic |
| 23.004 | Melting curves of ice polymorphs in the vicinity of the liquid-liquid critical point | chemistry | water, liquid-liquid transition, second critical point, ice, polymorphs, melting curves, environment similarity, opes, density-functional theory, scan, machine learning potential | Pablo Piaggi | HISTOGRAM OPES_EXPANDED UPPER_WALLS ENVIRONMENTSIMILARITY ECV_UMBRELLAS_LINE RESTART PRINT LOWER_WALLS DUMPGRID | gridtools opes envsim bias setup generic |
| 22.031 | Rare Event Kinetics from Adaptive Bias Enhanced Sampling | methods | OPES Flooding, Kinetics, Rate, OPES, Machine Learning | Dhiman Ray | RMSD CUSTOM GROUP ENERGY BIASVALUE WHOLEMOLECULES PYTORCH_MODEL DISTANCE UNITS POSITION COMMITTOR ENDPLUMED COMBINE OPES_METAD PRINT CONSTANT CONTACTMAP MOLINFO INCLUDE TORSION | colvar pytorch opes bias function core setup generic |
| 22.019 | Exploring aspartic protease inhibitor binding to design selective antimalarials | bio | ligand binding, loop opening, path CV, funnel metadynamics, drug development | Raitis Bobrovs | UPPER_WALLS PATHMSD WHOLEMOLECULES FUNNEL_PS DISTANCE PRINT COM FUNNEL LOWER_WALLS METAD | vatom colvar bias funnel generic |
| 22.018 | Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations | bio | ligand binding, docking, EMMI, LAT1 | Max Bonomi | EMMIVOX BIASVALUE LOAD WHOLEMOLECULES GROUP PRINT MOLINFO | bias setup core isdb generic |
| 22.016 | Homogeneous ice nucleation in an ab initio machine learning model of water | chemistry | ice, water, nucleation, seeding, environment similarity, interfacial free energy, interfaces | Pablo Piaggi | HISTOGRAM CUSTOM UPPER_WALLS ENVIRONMENTSIMILARITY OPES_METAD RESTART AROUND PRINT VOLUME ENERGY DUMPGRID | colvar gridtools opes envsim bias function setup volumes generic |
| 22.009 | Glycosylation in calixarenes capsule | chemistry | Metadynamics, glycosylation, supramolecular catalysis | GiovanniMaria Piccini | BRIDGE FLUSH RMSD LOWER_WALLS UPPER_WALLS WHOLEMOLECULES COMBINE GROUP DISTANCES DISTANCE PRINT FIT_TO_TEMPLATE MATHEVAL COORDINATION METAD UNITS ANGLE | colvar function bias adjmat core multicolvar setup generic |
| 21.052 | On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets | materials | Ibuprofen, unbinding, WTmetaD | Matteo Salvalaglio | COMMITTOR ENDPLUMED COORDINATIONNUMBER DISTANCE CENTER PRINT TORSION METAD | vatom colvar bias symfunc generic |
| 21.044 | NaCl nucleation | chemistry | metadynamics, DFS clustering | Aaron Finney | FIXEDATOM CONTACT_MATRIX MFILTER_MORE Q6 HISTOGRAM CLUSTER_DISTRIBUTION CLUSTER_NATOMS COMBINE COORDINATIONNUMBER GROUP PRINT LOCAL_Q6 DFSCLUSTERING INSPHERE METAD DUMPGRID | vatom gridtools clusters multicolvar adjmat function core bias symfunc volumes generic |
| 21.042 | Peptoid-mediated Au nanocrystal growth | materials | parallel-bias metadynamics, peptoid, Au | Xin Qi | UPPER_WALLS PBMETAD DISTANCE GYRATION PRINT COM MOLINFO | vatom generic colvar bias |
| 21.039 | Deep learning the slow modes for rare events sampling | methods | collective variables, machine learning, slow modes, deep-tica, opes | Luigi Bonati | RMSD GROUP ENERGY Q6 LOAD ENVIRONMENTSIMILARITY WHOLEMOLECULES PYTORCH_MODEL DISTANCE UNITS ENDPLUMED COMBINE OPES_METAD PRINT INCLUDE MOLINFO CONTACTMAP FLUSH OPES_EXPANDED VOLUME TORSION ECV_MULTITHERMAL | colvar pytorch opes envsim function setup core symfunc generic |
| 21.033 | Multiple-path-metadynamics applied to DNA base-pairing transitions | bio | path-CV, metadynamics, multiple-walker, dna | Alberto Pérez-de-Alba-Ortíz | MOVINGRESTRAINT UPPER_WALLS RESTRAINT COMBINE PRINT CONSTANT INCLUDE METAD | function generic bias |
| 21.006 | OPES, On-the-fly Probability Enhanced Sampling Method | methods | opes, alanine dipeptide, well-tempered, multithermal, multiumbrella | Michele Invernizzi | ENDPLUMED OPES_EXPANDED ECV_UMBRELLAS_LINE OPES_METAD PRINT TORSION ECV_MULTITHERMAL ENERGY | generic colvar opes |
| 21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Tarak Karmakar | FLUSH LOAD UPPER_WALLS OPES_METAD PYTORCH_MODEL GROUP PRINT MATHEVAL LOWER_WALLS | pytorch opes bias setup core function generic |
| 20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Valerio Rizzi | FIXEDATOM ENDPLUMED UPPER_WALLS WHOLEMOLECULES PYTORCH_MODEL OPES_METAD GROUP DISTANCE CENTER PRINT FIT_TO_TEMPLATE MATHEVAL COORDINATION ENERGY ANGLE | vatom colvar pytorch opes bias function core generic |
| 20.024 | Gaussian Mixture Based Enhanced Sampling (GAMBES) | methods | enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias | Jayashrita Debnath | LOAD UPPER_WALLS ENERGY COMBINE GROUP DISTANCES DISTANCE PRINT TORSION UNITS LOWER_WALLS | colvar function bias core setup multicolvar generic |
| 20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Michele Invernizzi | RMSD CUSTOM ENERGY ECV_MULTITHERMAL_MULTIBARIC Q6 LOAD ENVIRONMENTSIMILARITY WHOLEMOLECULES MATHEVAL UNITS POSITION ENDPLUMED PRINT ECV_LINEAR MOLINFO OPES_EXPANDED UPPER_WALLS ECV_UMBRELLAS_LINE VOLUME TORSION ECV_MULTITHERMAL | colvar opes envsim function setup bias symfunc generic |
| 20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Matteo Salvalaglio | UPPER_WALLS CELL PRINT MATHEVAL VOLUME LOWER_WALLS METAD ENERGY | function generic colvar bias |
| 19.081 | Calculation of phase diagrams in the multithermal-multibaric ensemble | methods | VES, variationally enhanced sampling, multithermal-multibaric, energy, Wang Landau, RefCV, kernel, bcc, fcc, sodium, aluminum | Pablo Piaggi | HISTOGRAM TD_MULTITHERMAL_MULTIBARIC CELL RESTART OPT_DUMMY READ BF_LEGENDRE ENERGY Q6 LOAD MATHEVAL TD_WELLTEMPERED VES_LINEAR_EXPANSION REWEIGHT_TEMP_PRESS OPT_AVERAGED_SGD COMBINE PRINT CONVERT_TO_FES LOWER_WALLS UPPER_WALLS VOLUME REWEIGHT_BIAS DUMPGRID | colvar gridtools function setup bias symfunc generic ves |
| 19.073 | On the role of enthalpic and entropic contributions on the conformational free energy landscape of MIL-101(Cr) building units | materials | metadynamics, MOF, MIL101Cr, conformational | Matteo Salvalaglio | ENDPLUMED UPPER_WALLS COORDINATIONNUMBER DISTANCES GYRATION PRINT LOWER_WALLS METAD ENERGY | colvar bias multicolvar symfunc generic |
| 19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Wei Chen | ANN RESTRAINT COMBINE COM POSITION | vatom colvar function bias annfunc |
| 19.032 | Chemical reaction in solution using path collective variables based on coordination patterns | chemistry | chemical reactions, solutions, metadynamics, coordination patterns | Fabio Pietrucci | FLUSH UPPER_WALLS RESTART DISTANCES PRINT PATH METAD | mapping bias multicolvar setup generic |
| 19.011 | Automatic Gradient Computation for Collective Variables | other | gradient, differentiation, curvature | Toni Giorgino | ENDPLUMED | generic |
| 19.008 | anncolvar | methods | neural network, dimensionality reduction | Vojtech Spiwok | ALPHARMSD WHOLEMOLECULES COMBINE PRINT FIT_TO_TEMPLATE MATHEVAL MOLINFO METAD POSITION | colvar secondarystructure bias function generic |
| 25.010 | Kinetic rates calculation with Ratchet&Pawl MD | methods | kinetics, ligand binding, ABMD, ratchet&pawl MD | Riccardo Capelli | PRINT ABMD COM WHOLEMOLECULES FLUSH DISTANCE COMMITTOR GROUP | bias generic colvar vatom 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 | CUSTOM ECV_MULTITHERMAL PRINT OPES_EXPANDED COMBINE OPES_METAD_EXPLORE DISTANCE RESTART TORSION COORDINATION ENERGY GROUP | opes setup generic core colvar function |
| 23.036 | Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? | bio | NaCl, nucleation, metadynamics | Ruiyu Wang | Q6 COORDINATIONNUMBER VOLUME PRINT Q4 COMBINE MATHEVAL METAD ENERGY | bias symfunc generic colvar function |
| 23.026 | Machine Learning Nucleation Collective Variables with Graph Neural Networks | chemistry | Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks | Florian Dietrich | Q6 COORDINATIONNUMBER MFILTER_MORE PRINT LOCAL_Q6 COMBINE METAD LOWER_WALLS MOVINGRESTRAINT GROUP | bias symfunc generic multicolvar core function |
| 23.025 | Probing ion binding to G-quadruplexes and related events | chemistry | metadynamics, repulsive potential, nucleic acids, G-quadruplexes | Marcelo Poleto | PRINT UNITS UPPER_WALLS DISTANCES RESTART COM WHOLEMOLECULES MATHEVAL FLUSH POSITION FIT_TO_TEMPLATE METAD DISTANCE LOWER_WALLS DUMPATOMS WRAPAROUND GROUP | bias setup generic multicolvar core colvar vatom function |
| 22.039 | Driving and characterizing nucleation of urea and glycine polymorphs in water | bio | metadynamics, nucleation, amino acids, polymorphism | Eric Beyerle | Q6 COORDINATIONNUMBER PRINT Q4 COMBINE LOAD CENTER PAIRENTROPY MATHEVAL METAD INCLUDE GROUP | bias symfunc gridtools setup generic core vatom function |
| 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 | CUSTOM PYTORCH_MODEL PRINT RMSD OPES_METAD UPPER_WALLS MATHEVAL WHOLEMOLECULES CENTER FIT_TO_TEMPLATE FIXEDATOM DISTANCE LOWER_WALLS COMMITTOR COORDINATION GROUP | bias opes generic pytorch core colvar vatom function |
| 22.013 | Ligand dissociation from PreQ1 riboswitch | bio | ligand, RNA, metadynamics, pRAVE | Yihang Wang | COORDINATIONNUMBER MOLINFO PRINT RMSD COMBINE WHOLEMOLECULES METAD DISTANCE COMMITTOR COM | bias symfunc generic colvar vatom function |
| 22.012 | Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT | bio | contact maps, protein-protein interactions | Isabell-Louise Grothaus | CENTER CONTACTMAP DISTANCE PRINT | colvar vatom generic |
| 22.006 | Peptide framework for screening the effects of amino acids on assembly | bio | metadynamics, peptides | Andrew White | PRINT GROUP DISTANCES REWEIGHT_BIAS COMBINE METAD CONVERT_TO_FES HISTOGRAM DUMPGRID INCLUDE GYRATION COM | bias gridtools generic multicolvar core colvar vatom function |
| 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 | WHOLEMOLECULES METAD PRINT LOAD | setup generic bias |
| 21.034 | Efficient sampling of high-dimensional free energy landscapes using adaptive reinforced dynamics | bio | reinforced dynamics, bias-exchange metadynamics, parallel-bias metadynamics | Dongdong Wang | PRINT RANDOM_EXCHANGES ENDPLUMED METAD PBMETAD TORSION INCLUDE | colvar generic bias |
| 21.025 | Computational and biochemical analysis of type IV pilus dynamics and stability | bio | molecular dynamics, calcium binding, Type IV pilus | Yasaman Karami | UPPER_WALLS PRINT DISTANCE LOWER_WALLS | colvar generic bias |
| 21.015 | Coarse-grained metadynamics and umbrella sampling simulations to investigate interactions of carbohydrate-binding modules with chitin | bio | metadynamics, umbrella sampling, coarse-grained, MARTINI, chitin, carbohydrate-binding module | Gaston Courtade | PRINT RESTRAINT MATHEVAL WHOLEMOLECULES CENTER POSITION METAD RESTART COORDINATION REWEIGHT_BIAS | bias setup generic colvar vatom function |
| 21.014 | how to determine statistically accurate conformational ensembles | bio | metadynamics, metainference, errors, cv, SAXS, ensemble determination | Cristina Paissoni | SAXS MOLINFO PRINT ALPHABETA WHOLEMOLECULES CENTER CONTACTMAP METAD PBMETAD ENSEMBLE BIASVALUE TORSION ANTIBETARMSD STATS GYRATION | bias secondarystructure isdb generic multicolvar colvar vatom function |
| 21.011 | CmuMD simulations of NaCl(aq) at graphite | chemistry | CmuMD, DFS clustering | Aaron Finney | COORDINATIONNUMBER CONTACT_MATRIX CLUSTER_NATOMS CLUSTER_DISTRIBUTION PRINT MFILTER_MORE RESTRAINT MULTICOLVARDENS LOAD AROUND DFSCLUSTERING FIXEDATOM DUMPGRID DENSITY GROUP | volumes clusters adjmat symfunc bias gridtools setup generic multicolvar vatom core |
| 21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Adriana Pietropaolo | CONSTANT PRINT MATHEVAL WHOLEMOLECULES PBMETAD RESTART BIASVALUE TORSION | bias setup generic colvar function |
| 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 | MOLINFO PRINT ABMD ERMSD CENTER DISTANCE RESTART TORSION | bias setup generic colvar vatom |
| 20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Adriana Pietropaolo | PRINT WHOLEMOLECULES CENTER PBMETAD COORDINATION | colvar vatom generic bias |
| 20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Max Bonomi | MOLINFO PRINT ALPHABETA WHOLEMOLECULES INCLUDE DIHCOR PBMETAD COORDINATION GYRATION | colvar bias generic multicolvar |
| 20.016 | Predicting polymorphism in molecular crystals using orientational entropy | materials | metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy | Pablo Piaggi | VOLUME PRINT UPPER_WALLS LOAD CENTER METAD INCLUDE GROUP | bias setup generic colvar vatom core |
| 20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Carlo Camilloni | SAXS MOLINFO PRINT ALPHABETA WHOLEMOLECULES CENTER FLUSH PBMETAD METAINFERENCE DISTANCE ENSEMBLE TORSION STATS GYRATION | bias isdb generic multicolvar colvar vatom function |
| 20.006 | Class B GPCR activation mechanism | bio | metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | MOLINFO PRINT RMSD UPPER_WALLS COMBINE WHOLEMOLECULES CENTER MATHEVAL METAD DISTANCE ENERGY LOWER_WALLS | bias generic colvar vatom function |
| 19.080 | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | methods | ves, variationally enhanced sampling, vibrational excitation, chemical reactions | Kristof Bal | DUMPGRID PRINT UNITS UPPER_WALLS BF_CHEBYSHEV TD_WELLTEMPERED VES_LINEAR_EXPANSION FLUSH COMBINE ANGLE CONVERT_TO_FES EXTERNAL HISTOGRAM DISTANCE TD_GRID OPT_AVERAGED_SGD COORDINATION LOWER_WALLS | bias gridtools setup generic function colvar ves |
| 19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Kim Jelfs | INPLANEDISTANCES PRINT DISTANCES FLUSH RESTART MOVINGRESTRAINT COM | bias setup generic multicolvar vatom |
| 19.049 | Determining the sizes of solid/liquid clusters in MD trajectories of nucleation | methods | nucleation, metadynamics, clustering, Steinhardt order parameters | Gareth Tribello | Q6 COORDINATIONNUMBER CONTACT_MATRIX CUSTOM MATRIX_VECTOR_PRODUCT CLUSTER_DISTRIBUTION PRINT CLUSTER_NATOMS OUTER_PRODUCT DISTANCES LOCAL_Q6 ONES DFSCLUSTERING METAD MORE_THAN OUTPUT_CLUSTER SMAC CLUSTER_PROPERTIES | clusters adjmat symfunc bias generic multicolvar matrixtools function |
| 19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Silvio Pipolo | PRINT PIV UPPER_WALLS METAD FUNCPATHMSD CELL LOWER_WALLS | piv bias generic colvar function |
| 19.027 | Multithermal-multibaric simulations using VES | methods | ves, Wang Landau, multicanonical, liquid sodium, density anomaly | Pablo Piaggi | READ AVERAGE PRINT UNITS COMBINE VES_LINEAR_EXPANSION REWEIGHT_TEMP_PRESS CONVERT_TO_FES TD_MULTICANONICAL HISTOGRAM OPT_DUMMY RESTART OPT_AVERAGED_SGD DUMPGRID BF_LEGENDRE ENERGY REWEIGHT_BIAS | bias gridtools setup generic colvar function ves |
| 19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Jim Pfaendtner | METAD EXTERNAL COORDINATION ENERGY GROUP | colvar core bias |
| 19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Carlo Camilloni | SAXS MOLINFO PRINT STATS RMSD UPPER_WALLS RESTRAINT ENDPLUMED WHOLEMOLECULES CENTER DISTANCE BIASVALUE INCLUDE GROUP | bias isdb generic core colvar vatom function |
| 19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Carlo Camilloni | MOLINFO PRINT UPPER_WALLS RESTRAINT DHENERGY RDC ENDPLUMED ALPHABETA WHOLEMOLECULES CENTER DIHCOR PBMETAD METAINFERENCE DISTANCE ENSEMBLE TORSION STATS GROUP | bias generic isdb multicolvar core colvar vatom function |
| 19.009 | RNA tetraloops folding | bio | metadynamics, RNA, folding | Giovanni Bussi | MOLINFO PRINT RMSD ENDPLUMED ERMSD WHOLEMOLECULES METAD | colvar generic bias |
| 19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Giovanni Bussi | MOLINFO PRINT RANDOM_EXCHANGES UPPER_WALLS DISTANCES FLUSH COMBINE ERMSD ANGLE METAD DISTANCE INCLUDE LOWER_WALLS | bias generic multicolvar colvar function |
| 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 | LOWER_WALLS PRINT COORDINATION FIXEDATOM METAD COM DISTANCE UPPER_WALLS ANGLE COORDINATIONNUMBER DISTANCES GROUP FLUSH COMBINE RESTRAINT UNITS | setup core symfunc multicolvar colvar bias generic vatom function |
| 25.003 | Surrogate Model CV | methods | Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding | Sompriya Chatterjee | PYTORCH_MODEL PRINT WHOLEMOLECULES COMBINE DISTANCE CUSTOM ENDPLUMED OPES_METAD MOLINFO TORSION MATHEVAL GROUP ENERGY COMMITTOR | function colvar generic opes pytorch core |
| 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 PRINT DISTANCE CUSTOM OPES_METAD UPPER_WALLS UNITS RESTART COORDINATION GROUP COMMITTOR | colvar generic setup bias opes function 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 | PRINT FLUSH RESTRAINT DISTANCE BIASVALUE MOLINFO TORSION MATHEVAL RESTART COORDINATIONNUMBER ENERGY COMMITTOR METAD | colvar generic setup symfunc bias function |
| 24.012 | Molecular simulations to investigate the impact of N6-methylation in RNA recognition | bio | metadynamics, alchemistry, RNA modification, RNA:protein interactions | Giovanni Bussi | CENTER LOWER_WALLS PRINT COMBINE DISTANCE BIASVALUE MOLINFO UPPER_WALLS GHBFIX COORDINATION DEBUG GROUP COM METAD | colvar vatom generic bias function core |
| 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 | ALPHARMSD LOWER_WALLS PRINT DISTANCE FUNCPATHMSD INCLUDE MOLINFO UPPER_WALLS CONTACTMAP PATHMSD METAD | secondarystructure colvar generic bias function |
| 23.031 | Identifying small molecules binding sites in RNA conformational ensembles with SHAMAN | bio | RNA, metadynamics, probes, mixed-solvent MD, small molecules, binding sites | Max Bonomi | WHOLEMOLECULES PRINT CENTER FIT_TO_TEMPLATE MOLINFO UPPER_WALLS DISTANCES GROUP POSITION WRAPAROUND SHADOW METAD | colvar vatom generic multicolvar bias isdb core |
| 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 | OPES_METAD MOLINFO COORDINATION GROUP COM PRINT BIASVALUE UNITS WRAPAROUND ENERGY FLUSH CENTER OPES_METAD_EXPLORE DISTANCE ENDPLUMED FIT_TO_TEMPLATE COMMITTOR WHOLEMOLECULES LOWER_WALLS CUSTOM TORSION MATHEVAL UPPER_WALLS POSITION | colvar vatom generic setup opes bias function core |
| 23.027 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, DFS, Q3, Pair Entropy | Aaron Finney | PRINT RESTRAINT DUMPGRID LOCAL_Q3 FIXEDATOM CLUSTER_DISTRIBUTION Q3 LOAD UNITS HISTOGRAM AROUND DFSCLUSTERING GROUP COORDINATIONNUMBER CLUSTER_NATOMS DENSITY CONTACT_MATRIX LOCAL_AVERAGE | adjmat gridtools vatom generic setup symfunc bias core clusters volumes |
| 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 | WHOLEMOLECULES PRINT REWEIGHT_METAD CONVERT_TO_FES DISTANCE DUMPGRID MOLINFO MATHEVAL RMSD HISTOGRAM READ METAD | colvar gridtools generic bias function |
| 23.012 | JAK2 2D meta-eABF PMF with statistical analysis | bio | 2D meta-eABF, path CV, PMF | Istvan Kolossvary | LOWER_WALLS PRINT FLUSH CUSTOM BIASVALUE UPPER_WALLS DRR PATHMSD METAD | colvar drr generic bias function |
| 22.044 | Colloid Crystallisation Analyses | materials | Q4, Q6, Pair Entropy, DFS | Aaron Finney | PRINT MFILTER_LESS COMBINE LOCAL_Q4 Q4 Q6 LOCAL_Q6 GROUP DFSCLUSTERING CLUSTER_NATOMS COORDINATIONNUMBER CONTACT_MATRIX LOCAL_AVERAGE MFILTER_MORE | adjmat generic multicolvar symfunc function core clusters |
| 22.043 | Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES | bio | OPES, RNA, Tetraloop, Folding | Gül Zerze | WHOLEMOLECULES PRINT OPES_EXPANDED ECV_UMBRELLAS_LINE ECV_MULTITHERMAL CONTACTMAP ENERGY | opes colvar generic |
| 22.041 | Skipping the Replica Exchange Ladder with Normalizing Flows | methods | OPES, alanine, normalizing flows, replica exchange | Michele Invernizzi | PRINT OPES_EXPANDED ENDPLUMED OPES_METAD TORSION UNITS POSITION ECV_MULTITHERMAL ENERGY | opes setup colvar generic |
| 22.002 | GAMBES_SAMPL5_RATES | other | GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding | Jayashrita Debnath | WHOLEMOLECULES CENTER PYTORCH_MODEL PRINT FLUSH DISTANCE FIXEDATOM ENDPLUMED FIT_TO_TEMPLATE ANGLE UPPER_WALLS MATHEVAL LOAD COORDINATION GROUP ENERGY COMMITTOR | colvar function vatom generic setup bias pytorch core |
| 21.046 | Ubiquitin Interacting Motifs, Duality Between Structured and Disordered Motifs | bio | wt metadynamics, ubiquitin, ataxin-3, short linear motifs, ubiquitin binding motif, moonlight functions, intrinsic disorder | Elena Papaleo | WHOLEMOLECULES LOWER_WALLS PRINT ENDPLUMED ALPHABETA UPPER_WALLS GROUP GYRATION METAD | colvar generic multicolvar bias core |
| 21.037 | Molecular Dynamics simulations of RBD/hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain | Max Bonomi | RMSD PRINT DISTANCE | colvar generic |
| 21.029 | Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs | bio | metadynamics, small peptide, machine learning | Pratyush Tiwary | FLUSH PRINT MOLINFO TORSION RESTART ENERGY EXTERNAL | colvar setup bias generic |
| 21.017 | All-atom simulations of the Vav1 AD construct | bio | metadynamics, parallel-bias, well-tempered | Simone Orioli | WHOLEMOLECULES ALPHARMSD PRINT PBMETAD MOLINFO ALPHABETA RESTART REWEIGHT_BIAS GROUP CONTACTMAP METAD | secondarystructure colvar generic multicolvar setup bias core |
| 21.013 | Role of vibrational excitation in heterogeneous catalysis | chemistry | catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption | Kristof Bal | DUMPGRID OPT_AVERAGED_SGD DISTANCES VES_LINEAR_EXPANSION COORDINATION UWALLS PRINT TD_GRID BF_CHEBYSHEV UNITS COORDINATIONNUMBER EXTERNAL FLUSH DISTANCE ANGLES LOAD HISTOGRAM REWEIGHT_BIAS REWEIGHT_METAD CONVERT_TO_FES LOWER_WALLS COMBINE RESTRAINT UPPER_WALLS METAD | colvar gridtools generic multicolvar setup symfunc bias ves 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 | WHOLEMOLECULES PRINT COMBINE RESTRAINT MOLINFO COORDINATION STATS | function colvar bias generic |
| 20.010 | Phase equilibrium of liquid water and hexagonal ice from enhanced sampling molecular dynamics simulations | materials | water, ice, TIP4P, crystallization, EnvironmentSimilarity, RefCV, kernel, VES, variationally enhanced sampling | Pablo Piaggi | PRINT Q6 TD_WELLTEMPERED MATHEVAL OPT_DUMMY UPPER_WALLS RESTART VES_LINEAR_EXPANSION OPT_AVERAGED_SGD ENVIRONMENTSIMILARITY VOLUME BF_LEGENDRE | colvar generic setup envsim symfunc bias ves function |
| 19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Valerio Rizzi | PRINT FLUSH COMBINE ENDPLUMED UNITS RESTART GROUP COORDINATIONNUMBER EXTERNAL METAD | generic setup symfunc bias function core |
| 19.076 | Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones | bio | molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics | Salvatore Assenza | PRINT ENDPLUMED MOVINGRESTRAINT UNITS GYRATION | bias setup colvar generic |
| 19.059 | cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide | bio | bias-exchange metadynamics, cis-trans isomerization | Fabrizio Marinelli | PRINT INCLUDE TORSION RANDOM_EXCHANGES METAD | colvar bias generic |
| 19.055 | Flying Gaussian method | methods | flying Gaussians, alanine dipeptide, peptide bond, Met-enkephalin | Vojtech Spiwok | PRINT COMBINE DISTANCE TORSION MATHEVAL METAD | function bias colvar generic |
| 19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Gareth Tribello | PRINT CELL ENDPLUMED UPPER_WALLS UNITS FCCUBIC METAD | colvar generic setup symfunc bias |
| 19.048 | Understanding Ligand Binding Selectivity in a Prototypical GPCR Family | bio | metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | WHOLEMOLECULES LOWER_WALLS PRINT DISTANCE CONSTANT BIASVALUE UPPER_WALLS MATHEVAL COM METAD | colvar vatom generic bias function |
| 19.044 | Multithermal-multibaric simulations using VES | methods | ves, Wang Landau, multicanonical, water, density anomaly | Pablo Piaggi | PRINT CONVERT_TO_FES COMBINE AVERAGE DUMPGRID TD_MULTITHERMAL_MULTIBARIC BF_LEGENDRE REWEIGHT_TEMP_PRESS OPT_DUMMY OPT_AVERAGED_SGD RESTART HISTOGRAM REWEIGHT_BIAS VES_LINEAR_EXPANSION READ ENERGY VOLUME | colvar gridtools generic setup bias ves function |
| 19.040 | Optimal Metric for Path Collective Variables | bio | metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path | Francesco Luigi Gervasio | PRINT ENDPLUMED TORSION MATHEVAL METAD | colvar function bias generic |
| 19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Davide Provasi | WHOLEMOLECULES PRINT DISTANCE FUNCPATHMSD ENDPLUMED RMSD COM CONTACTMAP METAD | colvar vatom generic bias function |
| 19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Glen Hocky | PRINT RESTRAINT COMBINE DISTANCE TORSION EDS | colvar generic eds bias function |
| 19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Mattia Bernetti | WHOLEMOLECULES ALPHARMSD PRINT GYRATION ENDPLUMED MOLINFO ENERGY METAD | secondarystructure colvar bias generic |
| 19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Matteo Salvalaglio | PRINT ENDPLUMED DISTANCES RESTART COORDINATIONNUMBER GYRATION METAD | colvar generic multicolvar setup symfunc bias |
| 19.013 | RNA FF FITTING | methods | force field, RNA | Giovanni Bussi | CONSTANT INCLUDE BIASVALUE MOLINFO TORSION MATHEVAL PUCKERING | bias function colvar generic |
| 19.006 | Flying Gaussian proof | methods | flying Gaussians, alanine dipeptide | Vojtech Spiwok | PRINT TORSION METAD | colvar bias generic |
| 19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Michele Invernizzi | PRINT ENERGY ENDPLUMED TORSION LOAD UNITS RESTART POSITION VES_DELTA_F METAD | colvar generic setup bias ves |
| 25.008 | Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting | methods | metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting | Dhiman Ray | ENDPLUMED CUSTOM METAD BIASVALUE UPPER_WALLS OPES_METAD UNITS MOLINFO PYTORCH_MODEL RMSD LOWER_WALLS POSITION TORSION WHOLEMOLECULES GROUP DISTANCE ENERGY PRINT | generic opes setup function core bias colvar pytorch |
| 25.002 | M3_PCV-ABMD | chemistry | Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor | Gian Marco Elisi | ENDPLUMED UPPER_WALLS UNITS PATHMSD PRINT ABMD | generic bias colvar setup |
| 24.024 | Host-Guest binding free energies à la carte, an automated OneOPES protocol | bio | OneOPES, ligand binding, binding free energy,SAMPL challenge, host-guest | Valerio Rizzi | COORDINATION OPES_METAD_EXPLORE UPPER_WALLS ENDPLUMED FIT_TO_TEMPLATE LOWER_WALLS MATHEVAL ANGLE WHOLEMOLECULES GROUP TORSION ECV_MULTITHERMAL FIXEDATOM DISTANCE CENTER ENERGY OPES_EXPANDED PRINT | generic opes function core bias colvar vatom |
| 23.040 | Supramolecular capsules assembly dynamics | chemistry | Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics | Riccardo Capelli | CUSTOM METAD UNITS COM FLUSH DISTANCES WHOLEMOLECULES GROUP DISTANCE CENTER POSITION PRINT | generic setup function multicolvar core bias colvar vatom |
| 23.038 | Determinants of Neutral Antagonism and Inverse Agonism in the β2-adrenergic receptor | bio | protein coupled receptor, beta-adrenergic, receptor activation, antagonism, inverse agonism, metadynamics | Timothy Clark | METAD MOLINFO RMSD MATHEVAL WHOLEMOLECULES DISTANCE PRINT | generic bias colvar function |
| 23.017 | How and When Does an Enzyme React? Unraveling α-Amylase Catalytic Activity with Enhanced Sampling Techniques | bio | enzymatic reaction discovery, reaction mechanism, catalysis, ligand-binding modes, water, alpha-amylase, sugar, QM/MM MD, OPES, OPES explore, graph CV, machine learning, Deep TDA CV, path CV | Sudip Das | COORDINATION OPES_METAD_EXPLORE CUSTOM UPPER_WALLS UNITS FIT_TO_TEMPLATE OPES_METAD PYTORCH_MODEL LOWER_WALLS GROUP WHOLEMOLECULES TORSION PATH FIXEDATOM DISTANCE CENTER PRINT | mapping generic opes setup function core bias colvar pytorch vatom |
| 23.014 | Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 | bio | metadynamics, oligomerization, chemokine receptors, GPCR, membrane | Vittorio Limongelli | UPPER_WALLS METAD COMBINE COM FLUSH TORSION WHOLEMOLECULES DISTANCE PRINT | generic function bias colvar vatom |
| 22.045 | Binding mode and mechanism of enzymatic polyethylene terephthalate degradation | bio | metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation | Francesco Colizzi | UPPER_WALLS METAD MOVINGRESTRAINT COM LOWER_WALLS ANGLE WHOLEMOLECULES DISTANCE PRINT | generic bias colvar vatom |
| 22.020 | Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix–Junction–Helix RNA | bio | RNA force field, Helix-Junction-Helix RNA, SAXS, Well tempered metadynamics | Weiwei He | METAD COM WHOLEMOLECULES TORSION GROUP DISTANCE PRINT | generic core bias colvar vatom |
| 22.015 | Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome | bio | photodynamics, bacteriophytochrome, variationally enhanced sampling | Jakub Rydzewski | BF_FOURIER OPT_AVERAGED_SGD TD_UNIFORM TORSION VES_LINEAR_EXPANSION PRINT | generic colvar ves |
| 22.000 | Amyloid precursor protein processing by human γ-secretase | bio | Bias Exchange Metadynamics, Helix unfolding, coupled binding | Xiaoli Lu | COORDINATION INCLUDE RANDOM_EXCHANGES METAD UNITS CONTACTMAP MOLINFO ANTIBETARMSD ALPHARMSD DISTANCE CENTER PRINT | generic setup secondarystructure colvar bias vatom |
| 21.051 | Automatic learning of hydrogen-bond fixes in an AMBER RNA force field | methods | force field, RNA | Giovanni Bussi | COORDINATION ERMSD BIASVALUE METAD MOLINFO COMBINE WHOLEMOLECULES PRINT | bias colvar generic function |
| 21.050 | N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity | methods | bio | Isabell Louise Grothaus | CENTER PRINT DISTANCE | generic colvar vatom |
| 21.038 | Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics | materials | metadynamics, SGOOP, nucleation, urea | Ziyue Zou | INCLUDE METAD VOLUME COMBINE COORDINATIONNUMBER GROUP LOAD CENTER ENERGY PRINT | generic function setup core symfunc bias colvar vatom |
| 21.031 | Photo-switchable sulfonulureas in KATP channel | bio | metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels | Katarzyna Walczewska-Szewc | UPPER_WALLS METAD UNITS COM LOWER_WALLS WHOLEMOLECULES DISTANCE PRINT | generic setup bias colvar vatom |
| 21.024 | Property map collective variable as a useful tool for force field correction | chemistry | molecular mechanics | Vojtech Spiwok | METAD BIASVALUE WHOLEMOLECULES TORSION PROPERTYMAP PRINT | generic bias colvar |
| 21.019 | Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations | materials | Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen | Matteo Salvalaglio | KDE COM MATHEVAL TORSIONS DISTANCE PRINT | generic function multicolvar gridtools colvar vatom |
| 21.010 | Step by Step Strecker Amino Acid Synthesis from Ab Initio Prebiotic Chemistry | chemistry | Strecker reaction, free energy landscape, ab initio molecular dynamics, glycine, prebiotic synthesis | Théo Magrino | generic | |
| 21.000 | Uremic toxin time scale dynamics | bio | uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs) | Jim Pfaendtner | COM WHOLEMOLECULES GROUP DISTANCE PRINT | generic core colvar vatom |
| 20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Faidon Brotzakis | CONVERT_TO_FES BIASVALUE DUMPGRID MOLINFO RMSD DISTANCES GROUP WHOLEMOLECULES READ HISTOGRAM PRINT EMMI | generic isdb multicolvar core bias colvar gridtools |
| 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 | CONTACTMAP MOLINFO READ FUNCPATHMSD UPPER_WALLS REWEIGHT_METAD FLUSH WHOLEMOLECULES PRINT CONVERT_TO_FES DUMPGRID COM DISTANCE ENDPLUMED METAD COMBINE LOWER_WALLS HISTOGRAM ABMD | generic function vatom colvar bias gridtools |
| 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 | UPPER_WALLS METAD MOLINFO WHOLEMOLECULES PATHMSD GROUP PRINT RESTART | generic setup core bias colvar |
| 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 | ALPHABETA ENDPLUMED UPPER_WALLS BIASVALUE MOLINFO LOWER_WALLS FLUSH WHOLEMOLECULES GROUP ANTIBETARMSD CS2BACKBONE PRINT PBMETAD | generic isdb secondarystructure multicolvar core bias |
| 19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | UPPER_WALLS METAD MOLINFO COM GYRATION DISTANCE ENERGY PRINT | generic bias colvar vatom |
| 19.075 | PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python | other | Python, automatic differentiation | Toni Giorgino | ENDPLUMED CUSTOM COMBINE ANGLE GROUP TORSION RESTRAINT DUMPDERIVATIVES DISTANCE CENTER PRINT | generic function core colvar bias vatom |
| 19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Giovanni Bussi | COORDINATION ENDPLUMED LOWER_WALLS WHOLEMOLECULES RESTRAINT DISTANCE | generic colvar bias |
| 19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Giovanni Bussi | COORDINATION INCLUDE METAD MOLINFO COM MATHEVAL FLUSH WHOLEMOLECULES TORSION DISTANCE MAXENT SORT PRINT | generic function colvar bias vatom |
| 19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Sandro Bottaro | ERMSD METAD MOLINFO RMSD WHOLEMOLECULES TORSION DISTANCE PRINT | bias colvar generic |
| 19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_SIMULATED_ANNEALING UNITS MAZE_LOSS MAZE_OPTIMIZER_BIAS POSITION PRINT | generic setup colvar maze |
| 19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | GiovanniMaria Piccini | UPPER_WALLS METAD UNITS COMBINE LOWER_WALLS FLUSH DISTANCE ENERGY PRINT | generic function setup bias colvar |
| 19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Carlo Camilloni | ALPHABETA ENDPLUMED UPPER_WALLS BIASVALUE MOLINFO LOWER_WALLS FLUSH WHOLEMOLECULES GROUP ANTIBETARMSD CS2BACKBONE PRINT RESTART PBMETAD | generic isdb setup secondarystructure multicolvar core bias |
| 19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Pratyush Tiwary | ALPHABETA COMBINE COM EXTERNAL WHOLEMOLECULES TORSION DISTANCE COMMITTOR PRINT RESTART | generic function setup multicolvar bias colvar vatom |
| 19.023 | RECT | methods | metadynamics, replica exchange | Giovanni Bussi | METAD GYRATION WHOLEMOLECULES TORSION PRINT | generic bias colvar |
| 19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Matteo Salvalaglio | UPPER_WALLS METAD LOWER_WALLS TORSION DISTANCE CENTER PRINT COMMITTOR | generic bias colvar vatom |
| 19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Max Bonomi | BIASVALUE MOLINFO WHOLEMOLECULES GROUP PRINT EMMI | generic bias core isdb |
| 19.005 | Cmyc small molecule interaction | bio | metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP | Gabriella Heller | ALPHABETA INCLUDE COORDINATION MOLINFO METAINFERENCE GYRATION WHOLEMOLECULES GROUP CS2BACKBONE DISTANCE CENTER PRINT PBMETAD | generic isdb multicolvar core colvar bias vatom |
| 25.011 | Chiral perovskite nucleation | chemistry | metadynamics, chiral perovskites, nucleation | Adriana Pietropaolo | PRINT UPPER_WALLS UNITS MATHEVAL PBMETAD RESTART MULTI_RMSD DISTANCE LOWER_WALLS | bias generic function setup colvar |
| 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 | WHOLEMOLECULES PATH UPPER_WALLS PRINT RESTART TORSION CUSTOM CENTER PYTORCH_MODEL OPES_METAD COORDINATION DISTANCE LOWER_WALLS GROUP FIXEDATOM FIT_TO_TEMPLATE | core bias opes generic mapping setup function colvar pytorch vatom |
| 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 | WHOLEMOLECULES ANGLE MOLINFO CONTACTMAP PRINT COMMITTOR TORSION ENDPLUMED FIXEDATOM FIT_TO_TEMPLATE MATHEVAL OPES_METAD CUSTOM RMSD GROUP COMBINE UPPER_WALLS CENTER METAD COORDINATION DISTANCE | core bias opes generic function colvar vatom |
| 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 |
| 24.008 | yCD Metadynamics | bio | volume-based MetaD, path CVs, infrequent MetaD, product release | James McCarty | WHOLEMOLECULES MOLINFO CONTACTMAP WRAPAROUND REWEIGHT_METAD PRINT PATH COMMITTOR HISTOGRAM ENDPLUMED FIXEDATOM FIT_TO_TEMPLATE INCLUDE MATHEVAL COM FLUSH RMSD DUMPGRID GROUP READ CONVERT_TO_FES UPPER_WALLS METAD COORDINATION DISTANCE | core bias generic mapping function colvar gridtools vatom |
| 23.024 | Permutationally Invariant Networks for Enhanced Sampling (PINES) | methods | collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent | Nicholas Herringer | PBMETAD LOAD PRINT | generic bias setup |
| 23.006 | Transcription factor unbinding | bio | metadynamics, DNA, conformational changes | Malin Lüking | PRINT ANGLE MOLINFO ALPHARMSD CONTACTMAP COM METAD DUMPFORCES DISTANCE | bias generic secondarystructure colvar vatom |
| 22.037 | Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site | chemistry | metadynamics, DNA, abasic | Mike Jones | PRINT DISTANCE DISTANCES METAD | colvar bias generic multicolvar |
| 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 | PRINT COMMITTOR UPPER_WALLS MATHEVAL DRMSD CUSTOM METAD CELL LOWER_WALLS | colvar bias generic function |
| 22.032 | Reciprocal barrier restraint. Application to path-meta-eABF | methods | restraint, upper wall, lower wall, path colvar, meta-eABF, metadynamics, DRR, protein conformational transition, PROTAC | Istvan Kolossvary | PRINT PATHMSD DRR CUSTOM METAD FLUSH BIASVALUE | bias generic drr function colvar |
| 22.030 | Mixing physics across temperatures with generative artificial intelligence | methods | REMD, Generative AI, DDPM | Yihang Wang | PRINT WHOLEMOLECULES TORSION | colvar generic |
| 22.022 | Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir | bio | RMSD, protein-ligand interactions | Isabell Grothaus | RMSD PRINT | colvar generic |
| 22.008 | Ab initio metadynamics determination of temperature-dependent free-energy landscape in ultrasmall silver clusters | materials | Well tempered metadynamics, ab-initio, ase | Daniel Sucerquia | COMBINE UPPER_WALLS UNITS COM GYRATION METAD FLUSH COORDINATIONNUMBER COORDINATION DISTANCE LOWER_WALLS | symfunc bias generic function setup colvar vatom |
| 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 | WHOLEMOLECULES PRINT UPPER_WALLS ANGLE MOLINFO ALPHARMSD TORSION ALPHABETA METAD FLUSH COORDINATION DISTANCE | bias generic secondarystructure multicolvar colvar |
| 21.043 | Predicting the Conformational Variability of Oncogenic GTP-bound G12D Mutated KRas-4B Proteins at Cell Membranes | chemistry | well-tempered metadynamics, KRas-4B, anionic membrane, conformational variability | Huixia Lu | PRINT TORSION METAD FIXEDATOM FIT_TO_TEMPLATE | colvar bias generic vatom |
| 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 | PRINT INCLUDE PBMETAD TORSION ALPHABETA COM GYRATION METAD ENERGY COORDINATION DISTANCE | bias generic multicolvar colvar vatom |
| 21.027 | EGFR activating mutations mechanism | bio | metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA | Francesco Gervasio | WHOLEMOLECULES PRINT UPPER_WALLS INCLUDE MOLINFO MATHEVAL CONTACTMAP ALPHARMSD METAD ENERGY DISTANCE LOWER_WALLS | bias generic secondarystructure function colvar |
| 21.022 | Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly | materials | parallel bias metadynamics, adsorption, peptide | Xin Qi | PRINT UPPER_WALLS MOLINFO PBMETAD COM GYRATION ENERGY DISTANCE LOWER_WALLS | colvar bias generic vatom |
| 21.020 | Reweighted Jarzynski sampling | methods | free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions | Kristof Bal | REWEIGHT_BIAS REWEIGHT_METAD CONSTANT PRINT HISTOGRAM MOVINGRESTRAINT BF_CHEBYSHEV UNITS ANN TD_WELLTEMPERED CUSTOM OPES_METAD FLUSH RESTRAINT VES_LINEAR_EXPANSION DUMPGRID CONVERT_TO_FES COMBINE UPPER_WALLS OPT_AVERAGED_SGD METAD COORDINATIONNUMBER LOAD DISTANCE BIASVALUE | symfunc bias opes ves generic function setup annfunc colvar gridtools |
| 21.016 | MD SAXS GTPase associated center | bio | metadynamics, RNA, folding, SAXS | Giovanni Bussi | WHOLEMOLECULES PRINT UPPER_WALLS INCLUDE MOLINFO CUSTOM GYRATION METAD ERMSD SAXS LOWER_WALLS GROUP | core isdb bias generic function colvar |
| 20.028 | Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane | bio | metadynamics, KRas-4B, anionic membrane | Huixia Lu | PRINT RESTART CENTER METAD DISTANCE FIT_TO_TEMPLATE | bias generic setup colvar vatom |
| 20.026 | Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor | bio | Metadynamics, Umbrella sampling | Brandon Peters | CONVERT_TO_FES PRINT MULTI_RMSD RESTRAINT METAD HISTOGRAM DUMPGRID REWEIGHT_METAD | colvar bias gridtools generic |
| 20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Glen Hocky | PRINT UNITS MATHEVAL FISST GYRATION RESTRAINT ENERGY DISTANCE GROUP BIASVALUE | core bias generic function setup colvar fisst |
| 20.015 | Rational design of ASCT2 inhibitors using an integrated experimental-computational approach | bio | ASCT2 transporter, small-molecules, cryo-EM, metainference | Max Bonomi | WHOLEMOLECULES PRINT MOLINFO EMMIVOX DUMPATOMS LOAD GROUP BIASVALUE | core isdb bias generic setup |
| 20.014 | amyloid beta small molecule interaction | bio | intrinsically disordered proteins, disordered proteins, IDPs, fuzzy binding, small molecule, drugs, entropy, binding, Alzheimer’s disease, amyloid beta | Gabriella Heller | PARABETARMSD WHOLEMOLECULES MOLINFO PRINT ANTIBETARMSD ALPHARMSD TORSION ENDPLUMED DIHCOR INCLUDE CS2BACKBONE PBMETAD FLUSH METAINFERENCE GROUP COMBINE STATS GYRATION ENSEMBLE COORDINATION | core isdb bias generic secondarystructure multicolvar function colvar |
| 20.013 | Improving accuracy of biased Alchemistic simulations | methods | flying Gaussian method, Alchemistic simulations, thermodynamic integration, reweighting | Vojtech Spiwok | METAD PRINT TORSION | generic colvar bias |
| 20.012 | Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies | bio | metadynamics, well-tempered ensemble, ligand binding, binding affinity calculations, novel COLVAR, funnel restraints, Hamiltonian replica-exchange, PathCV, COMetPath, SWISH | Francesco Gervasio | CONSTANT FUNCPATHGENERAL WHOLEMOLECULES PRINT UPPER_WALLS INCLUDE MATHEVAL MOLINFO CONTACTMAP COM METAD PROJECTION_ON_AXIS LOAD DISTANCE LOWER_WALLS GROUP BIASVALUE | core bias generic function setup colvar vatom |
| 20.000 | Muscarinic M2 receptor-ligand funnel metadynamics | bio | multiple walker metadynamics, well-tempered metadynamics, funnel metadynamics, MC-HLDA, GPCR, receptor, Adiabatic Bias MD | Riccardo Capelli | CONVERT_TO_FES COMBINE ABMD PRINT UPPER_WALLS MATHEVAL REWEIGHT_METAD COM METAD HISTOGRAM ENDPLUMED DUMPGRID DISTANCE LOWER_WALLS READ | bias generic function colvar gridtools vatom |
| 19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Matteo Salvalaglio | CONVERT_TO_FES PRINT COMMITTOR MATHEVAL READ REWEIGHT_METAD TORSION REWEIGHT_BIAS METAD HISTOGRAM DUMPGRID DISTANCE EXTERNAL BIASVALUE | bias generic function colvar gridtools |
| 19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Matteo Salvalaglio | PRINT INCLUDE CENTER ENDPLUMED DISTANCE GROUP | colvar generic core vatom |
| 19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Michele Invernizzi | PRINT UNITS POSITION TORSION OPES_METAD METAD ENDPLUMED EXTERNAL | bias opes generic setup colvar |
| 19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Gareth Tribello | MULTICOLVARDENS UNITS FOURIER_TRANSFORM CENTER FIND_CONTOUR_SURFACE FCCUBIC DUMPGRID GROUP MORE_THAN | contour core symfunc fourier function setup gridtools vatom |
| 19.050 | Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes | chemistry | metadynamics, membranes, Willard Chandler surface | Gareth Tribello | CONVERT_TO_FES DISTANCE_FROM_CONTOUR COMBINE PRINT UPPER_WALLS RESTART REWEIGHT_BIAS METAD HISTOGRAM DUMPGRID READ | contour bias generic function setup gridtools |
| 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 | PRINT UPPER_WALLS UNITS POSITION RESTART METAD FLUSH COORDINATION LOWER_WALLS GROUP | core bias generic setup colvar |
| 19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | COMBINE PRINT UPPER_WALLS UNITS METAD FLUSH ENERGY DISTANCE | bias generic function setup colvar |
| 19.030 | Coarse-Grained MetaDynamics (CG-MetaD) | bio | Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy | Vittorio Limongelli | WHOLEMOLECULES PRINT UPPER_WALLS COM METAD DISTANCE LOWER_WALLS | colvar bias generic vatom |
| 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 RESTRAINT PRINT DISTANCE MOLINFO MOVINGRESTRAINT RESTART METAD PUCKERING | colvar bias setup generic |
| 25.004 | Machine Learning-Driven Molecular Dynamics Unveil a Bulk Phase Transformation Driving Ammonia Synthesis on Barium Hydride | chemistry | OPES, OPES flooding, Catalysis, Ammonia Synthesis | Axel Tosello Gardini | COMMITTOR UNITS FLUSH PRINT GROUP FIXEDATOM DISTANCES DISTANCE UPPER_WALLS CUSTOM ZDISTANCES OPES_METAD COORDINATIONNUMBER | function vatom opes multicolvar symfunc core colvar generic bias setup |
| 24.032 | DeepLNE++ | methods | PATHCV, OPES | Thorben Fröhlking | LOAD TORSION COORDINATION ENERGY PRINT COMBINE GROUP DISTANCE CUSTOM OPES_METAD | function opes core colvar generic setup |
| 24.011 | Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble | methods | committor, machine learning | Peilin Kang | MATHEVAL INCLUDE COORDINATION DISTANCE WHOLEMOLECULES MOLINFO ENDPLUMED RMSD ENERGY LOWER_WALLS GROUP CELL CUSTOM TORSION POSITION UNITS PRINT LOAD UPPER_WALLS BIASVALUE | function core colvar generic bias setup |
| 23.046 | Lasso Peptides - HLDA CV | bio | metadynamics, protein folding, HLDA, harmonic | Gabriel da Hora | UNITS PRINT COMBINE DISTANCE WHOLEMOLECULES METAD | function colvar generic bias setup |
| 23.039 | Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation | chemistry | metadynamics, ligand dissociation | Eric Beyerle | DUMPMASSCHARGE RESTRAINT PRINT COMBINE FIXEDATOM CENTER DISTANCE MOLINFO UPPER_WALLS METAD | function vatom colvar generic bias |
| 23.037 | Estimating binding free energy of solid binding peptides without extensive sampling | bio | metadynamics, solid binding peptides | Xin Qi | PBMETAD LOWER_WALLS PRINT DISTANCE UPPER_WALLS MOLINFO GYRATION COM | vatom colvar bias generic |
| 23.028 | Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process | chemistry | Ammonia decomposition; Dynamics;OPES; Neural Network potential | Manyi Yang | MATHEVAL COMMITTOR UNITS ENERGY COM PRINT FLUSH GROUP LOWER_WALLS FIXEDATOM DISTANCES DISTANCE UPPER_WALLS CUSTOM ZDISTANCES OPES_METAD COORDINATIONNUMBER | function vatom opes multicolvar symfunc core colvar generic bias setup |
| 23.015 | MPCs aggregation | bio | opes_explore, dimerization, MPCs, self-assembly | Vikas Tiwari | COORDINATION LOWER_WALLS PRINT GROUP CENTER WHOLEMOLECULES DISTANCE UPPER_WALLS CUSTOM METAD OPES_METAD_EXPLORE COM | function vatom opes core colvar generic bias |
| 23.007 | Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains | bio | metadynamics, peptoids, parallel-bias metadynamics | Jim Pfaendtner | PBMETAD INCLUDE TORSION COORDINATION RESTRAINT PRINT WHOLEMOLECULES GYRATION COM | vatom colvar bias generic |
| 23.005 | A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs | bio | metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A | Timothy Clark | MATHEVAL READ RMSD PRINT DISTANCE WHOLEMOLECULES MOLINFO REWEIGHT_METAD CONVERT_TO_FES DUMPGRID HISTOGRAM METAD | function gridtools colvar generic bias |
| 23.003 | Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations | methods | metadynamics, alchemical variable, alchemical free energy calculations | Wei-Tse Hsu | READ TORSION PRINT METAD EXTRACV | colvar bias generic |
| 23.001 | Quantum phase diagram of water | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn-Løland Bore | INCLUDE LOWER_WALLS PRINT ENVIRONMENTSIMILARITY UPPER_WALLS ECV_UMBRELLAS_LINE RESTART OPES_EXPANDED | opes envsim generic bias setup |
| 22.042 | Metadynamics of NSP10 and variants | bio | metadynamics, NSP10, crystal structure, variants | Shozeb Haider | PRINT METAD TORSION | colvar bias generic |
| 22.033 | Reciprocal barrier restraint. Application to PROTAC passive permeability prediction | methods | PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR | Istvan Kolossvary | UNITS FLUSH PRINT DISTANCE CUSTOM DRR BIASVALUE METAD COM | function vatom drr colvar generic bias setup |
| 22.026 | Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification | materials | Peptoid, silica | Jim Pfaendtner | PBMETAD PRINT DISTANCE UPPER_WALLS MOLINFO GYRATION COM | vatom colvar bias generic |
| 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 | DIHCOR COORDINATION RANDOM_EXCHANGES LOWER_WALLS ENERGY PRINT GROUP ANTIBETARMSD WHOLEMOLECULES MOLINFO UPPER_WALLS ALPHARMSD GYRATION METAD PARABETARMSD | multicolvar secondarystructure core colvar generic bias |
| 21.023 | Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling | methods | enhanced sampling, collective variables, machine learning | Jakub Rydzewski | INCLUDE TORSION UNITS ENERGY PRINT DISTANCE REWEIGHT_METAD CUSTOM CONSTANT BIASVALUE METAD | function colvar generic bias setup |
| 21.021 | ATLAS | methods | Machine Learning, Metadynamics | Federico Giberti | DUMPATOMS MATHEVAL TORSION COORDINATION UNITS PRINT GROUP DISTANCE WHOLEMOLECULES GYRATION BIASVALUE METAD COORDINATIONNUMBER | function symfunc core colvar generic bias setup |
| 21.012 | NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition | bio | funnel metadynamics | Jim Pfaendtner | FUNNEL LOWER_WALLS PRINT DISTANCE UPPER_WALLS FUNNEL_PS METAD COM | vatom funnel colvar generic bias |
| 21.004 | Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy | bio | machine learning, well-tempered metadynamics, path collective variable, potential of mean force, standard binding free energy calculations, host-guest, protein-ligand unbinding | Dorothea Gobbo | LOWER_WALLS PRINT PATHMSD WHOLEMOLECULES UPPER_WALLS RESTART METAD | colvar bias setup generic |
| 21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Tarsis Ferreira | INCLUDE COORDINATION RANDOM_EXCHANGES LOWER_WALLS ENERGY PRINT GROUP DISTANCE UPPER_WALLS MOLINFO WHOLEMOLECULES REWEIGHT_METAD DUMPGRID HISTOGRAM METAD PUCKERING | gridtools core colvar generic bias |
| 20.032 | Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil | materials | clustering, conformational isomers | Matteo Salvalaglio | PRINT TORSION ENDPLUMED | colvar generic |
| 20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Cristina Paissoni | INCLUDE RESTRAINT PRINT SAXS GROUP CENTER WHOLEMOLECULES MOLINFO DISTANCE ENSEMBLE BIASVALUE STATS | function vatom isdb core colvar generic bias |
| 20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Vojtech Spiwok | PRINT METAD TORSION | colvar bias generic |
| 20.021 | Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins. | bio | phi-values, restrained MD, transition-state, protein folding, disordered proteins, protein evolution | Cristina Paissoni | RESTRAINT COORDINATION PRINT WHOLEMOLECULES MOLINFO STATS | function 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 | ENERGY PRINT GROUP DISTANCE UPPER_WALLS MOLINFO GYRATION METAD COM | vatom core colvar generic bias |
| 19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | ENERGY PRINT DISTANCE UPPER_WALLS MOLINFO GYRATION METAD COM | vatom colvar bias generic |
| 19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Mattia Bernetti | LOWER_WALLS PRINT PATHMSD WHOLEMOLECULES UPPER_WALLS METAD | colvar bias generic |
| 19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Jim Pfaendtner | ENERGY PRINT WHOLEMOLECULES GYRATION METAD | colvar bias generic |
| 19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Kim E. Jelfs | LOWER_WALLS PRINT GROUP DISTANCE CENTER UPPER_WALLS RESTART METAD COM | vatom core colvar generic bias setup |
| 19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Luigi Bonati | LOAD POSITION TORSION UNITS ENERGY PRINT ENVIRONMENTSIMILARITY ENDPLUMED Q6 | symfunc envsim colvar generic setup |
| 19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Gareth Tribello | UNITS LOWER_WALLS PRINT AROUND CELL FCCUBIC UPPER_WALLS ENDPLUMED METAD | symfunc colvar volumes generic bias setup |
| 19.046 | Optimal Collective from short simulations for Benzamidine-Trypsin ligand binding | bio | VAC-MetaD, optimised collective variables, binding free energy, unbinding rates, benzamidine trypsin, Structure Activity Relation | Faidon Brotzakis | FUNNEL TORSION RMSD LOWER_WALLS PRINT GROUP COMBINE DISTANCES DISTANCE WHOLEMOLECULES MOLINFO UPPER_WALLS BRIDGE ALPHABETA REWEIGHT_METAD METAD COM | adjmat function vatom multicolvar funnel core colvar generic bias |
| 19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | UNITS FLUSH PRINT COMBINE DISTANCES DISTANCE UPPER_WALLS RESTART METAD | function multicolvar colvar generic bias setup |
| 19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Paolo Raiteri | MATHEVAL UNITS FLUSH PRINT DISTANCE UPPER_WALLS RESTART METAD | function colvar generic bias setup |
| 19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Elena Papaleo | LOWER_WALLS PRINT GROUP WHOLEMOLECULES MOLINFO UPPER_WALLS ALPHABETA GYRATION METAD | multicolvar core colvar generic bias |
| 19.025 | Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide | bio | metainference, NMR, protein dynamics, force-fields | Carlo Camilloni | PBMETAD TORSION JCOUPLING FLUSH PRINT RDC METAINFERENCE ENSEMBLE WHOLEMOLECULES MOLINFO ENDPLUMED GYRATION BIASVALUE STATS CS2BACKBONE | function isdb colvar generic bias |
| 19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Haochuan Chen | DRR PRINT TORSION | drr colvar generic |
| 19.003 | EMMI ClpP | bio | metainference, cryo-EM | Max Bonomi | PRINT EMMI GROUP MOLINFO BIASVALUE | core isdb bias generic |
| 24.034 | Umbrella sampling of ion in transporter SLC26A7 | bio | umbrella sampling, transporter, ions | Xiaoli Lu | RESTRAINT PRINT POSITION UNITS | generic colvar bias 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 | EMMI ALPHARMSD PBMETAD COM PRINT CENTER DUMPMASSCHARGE GROUP DUMPATOMS WHOLEMOLECULES COORDINATION MOLINFO PARABETARMSD UPPER_WALLS BIASVALUE RMSD DISTANCE | isdb colvar core bias generic secondarystructure vatom |
| 24.030 | NMR guided simulation of dsRBD | bio | Metainference, NMR, protein dynamics | Debadutta Patra | STATS FLUSH PRINT METAINFERENCE GROUP WHOLEMOLECULES ENSEMBLE MOLINFO ALPHABETA RDC DISTANCE | isdb function colvar core multicolvar generic |
| 24.016 | Cryo-EM guided simulations of ribozyme | bio | metainference, cryo-EM | Giovanni Bussi | ERMSD RESTRAINT PRINT EMMIVOX GROUP WHOLEMOLECULES INCLUDE MOLINFO BIASVALUE | isdb colvar core bias generic |
| 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 | LOWER_WALLS RMSD FLUSH PRINT UPPER_WALLS WHOLEMOLECULES COORDINATION PYTORCH_MODEL METAD MOLINFO DRR | colvar drr pytorch bias generic |
| 24.010 | Oxytocin metadynamics simulation | bio | metadynamics, oxytocin, peptide | Jan Beránek | FLUSH PRINT WHOLEMOLECULES TORSION RESTART METAD | generic colvar setup bias |
| 24.009 | Weighted Shape Gaussian Mixture Models | bio | metadynamics, clustering | Glen Hocky | PRINT UNITS GROUP TORSION METAD | colvar core bias generic setup |
| 24.006 | Water vapor condensation | chemistry | metadynamics, homogeneous condensation, chemical potential | Shenghui Zhong | DFSCLUSTERING PRINT UPPER_WALLS UNITS CLUSTER_NATOMS CLUSTER_PROPERTIES METAD COORDINATIONNUMBER CONTACT_MATRIX | clusters adjmat bias symfunc generic setup |
| 24.005 | Learning Markovian Dynamics with Spectral Maps | methods | spectral map, collective variables, machine learning | Jakub Rydzewski | PRINT UNITS CUSTOM BIASVALUE DISTANCE | function colvar bias generic setup |
| 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 COM ALPHABETA WHOLEMOLECULES COORDINATION TORSION GYRATION MOVINGRESTRAINT INCLUDE DISTANCE | colvar multicolvar bias generic vatom |
| 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 | WRAPAROUND PRINT EMMIVOX GROUP WHOLEMOLECULES INCLUDE MOLINFO UPPER_WALLS BIASVALUE DISTANCE | isdb colvar core bias generic |
| 23.035 | An Extended Metadynamics Protocol for Binding/Unbinding of Peptide Ligands to Class A G-Protein Coupled Receptors | bio | G protein coupled receptor, peptide ligands, metadynamics, multiple-walker | Timothy Clark | LOWER_WALLS MATHEVAL PRINT CENTER METAD WHOLEMOLECULES CONSTANT UPPER_WALLS BIASVALUE DISTANCE | function colvar bias generic vatom |
| 23.021 | Into the Dynamics of Rotaxanes at Atomistic Resolution | materials | metadynamics, rotaxanes, molecular shuttles, molecular machines | Luigi Leanza | MATHEVAL FIXEDATOM PRINT CENTER UPPER_WALLS METAD TORSION CUSTOM DISTANCE | function colvar bias generic vatom |
| 23.020 | FEP simulations of ATOX1 homodimer | chemistry | parallel bias metadynamics, FEP, free-energy of metal ion dissociation | Adriana Pietropaolo | MATHEVAL PRINT ANGLE WHOLEMOLECULES CONSTANT PBMETAD BIASVALUE DISTANCE | function generic bias colvar |
| 23.013 | Path meta-eABF simulation of large scale conformational change in STING protein | methods | meta-eABF, path CV, large scale conformational change, STING protein, reciprocal barrier restraint | Istvan Kolossvary | LOWER_WALLS FLUSH PRINT TIME UNITS UPPER_WALLS METAD CUSTOM BIASVALUE PATHMSD DRR | function colvar drr bias generic setup |
| 23.011 | OneOPES, a combined enhanced sampling method to rule them all | bio | OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding | Valerio Rizzi | OPES_METAD_EXPLORE ENERGY ECV_MULTITHERMAL PRINT ENDPLUMED TORSION OPES_EXPANDED MOLINFO METAD DISTANCE | generic colvar opes bias |
| 23.002 | Critical comparison of general-purpose collective variables for crystal nucleation | methods | metadynamics, umbrella sampling, commitor, entropy, PIV | Julien Lam | ENERGY VOLUME RESTRAINT PRINT UPPER_WALLS UNITS METAD Q4 Q6 LOCAL_AVERAGE PAIRENTROPY CUSTOM PIV FUNCPATHMSD | function colvar piv gridtools bias symfunc generic setup |
| 22.040 | From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure | bio | SARS-CoV-2, Spike, Omicron | Miłosz Wieczór | LOWER_WALLS PCAVARS PRINT UPPER_WALLS WHOLEMOLECULES METAD | generic mapping bias |
| 22.038 | Enhanced Sampling Aided Design of Molecular Photoswitches | chemistry | reaction discovery, OPES explore, graph CV | Umberto Raucci | OPES_METAD_EXPLORE PRINT UNITS COORDINATION PYTORCH_MODEL CUSTOM | function colvar pytorch opes generic setup |
| 22.036 | Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction | bio | Well-tempered MetaDynamics with Hamiltonian Replica Exchange | Miroslav Krepl | CUSTOM GHBFIX FLUSH COMBINE PRINT UPPER_WALLS GROUP METAD COORDINATION MOLINFO LOAD BIASVALUE | function colvar core bias generic setup |
| 22.028 | N-glycan conformer distributions in atomistic simulation | bio | REST2, RECT, N-glycan, pucker | Isabell Grothaus | PUCKERING PRINT READ HISTOGRAM CONVERT_TO_FES TORSION MOLINFO METAD DUMPGRID | generic colvar gridtools bias |
| 22.027 | Molecular Dynamics simulations of BANAL-236 RBD-hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, BANAL-236, receptor-binding domain | Max Bonomi | PRINT RMSD | generic colvar |
| 22.025 | Bubble nucleation rate predictions in a Lennard-Jones fluid | materials | free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation | Kristof Bal | CUSTOM VOLUME REWEIGHT_BIAS FLUSH PRINT RESTRAINT COMMITTOR UPPER_WALLS UNITS HISTOGRAM CONVERT_TO_FES BIASVALUE ANN MOVINGRESTRAINT LOAD COORDINATIONNUMBER DUMPGRID | function colvar gridtools bias symfunc generic setup annfunc |
| 22.024 | Conformational Entropy as a Potential Liability of Computationally Designed Antibodies | bio | metadynamics, conformational entropy, antibody, nanobody | Thomas Löhr | ANTIBETARMSD ALPHARMSD PBMETAD PRINT COM WHOLEMOLECULES TORSION RESTART ALPHABETA MOLINFO | colvar setup multicolvar bias generic secondarystructure vatom |
| 21.049 | Multiple-path-metadynamics and PathMaps | methods | path-CV, metadynamics, multiple-walker, multiple paths, pathmap | Alberto Pérez-de-Alba-Ortíz | LOWER_WALLS CUSTOM COMBINE RESTRAINT PRINT UPPER_WALLS UNITS METAD CONSTANT TORSION ENSEMBLE MOVINGRESTRAINT LOAD | function colvar bias generic setup |
| 21.041 | Nucleating a Different Coordination in a Crystal under Pressure. A Study of the B1−B2 Transition in NaCl by Metadynamics | methods | metadynamics, structural phase transitions, pressure-induced phase transition, martensitic transitions | Matej Badin | CUSTOM VOLUME COMBINE PRINT ENDPLUMED COORDINATION METAD | function colvar generic bias |
| 21.028 | From Enhanced Sampling to Reaction Profiles | methods | collective variables, multi-state, machine learning, Deep-TDA | Enrico Trizio | PRINT DISTANCES UPPER_WALLS MATHEVAL COORDINATION LOAD DISTANCE FIXEDATOM CENTER FIT_TO_TEMPLATE ENDPLUMED OPES_METAD TORSION LOWER_WALLS UNITS GROUP ANGLE WHOLEMOLECULES PYTORCH_MODEL | function colvar core multicolvar pytorch opes bias generic setup vatom |
| 21.007 | Sampling enhancement by metadynamics driven by machine learning and de novo protein modelling | bio | metadynamics, machine learning, protein folding | Vojtech Spiwok | ALPHARMSD MATHEVAL COMBINE FIT_TO_TEMPLATE WHOLEMOLECULES POSITION MOLINFO | function secondarystructure generic 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 | PRINT METAD TORSION DISTANCE | generic colvar bias |
| 20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Jim Pfaendtner | PRINT CENTER GROUP DISTANCES WHOLEMOLECULES COORDINATION RESTART DISTANCE | colvar core multicolvar generic setup vatom |
| 20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Luigi Bonati | LOWER_WALLS MATHEVAL FLUSH PRINT COM UPPER_WALLS UNITS GROUP ENDPLUMED OPES_METAD TORSION PYTORCH_MODEL LOAD DISTANCE | function colvar core pytorch opes bias generic setup vatom |
| 20.003 | Enhanced sampling of transition states | methods | Variationally Enhanced Sampling, Target distribution, Transition state, Enhanced Sampling, Nucleation, chemical reaction | Jayashrita Debnath | OPT_AVERAGED_SGD ENERGY VES_LINEAR_EXPANSION PRINT BF_LEGENDRE UNITS POSITION LOAD | ves generic colvar setup |
| 19.078 | Iterative unbiasing of quasi-equilibrium sampling | methods | metadynamics, reweighting | Federico Giberti | COORDINATIONNUMBER MATHEVAL REWEIGHT_BIAS PRINT UNITS COLLECT_FRAMES METAD BIASVALUE DUMPATOMS DISTANCE | function colvar landmarks bias symfunc generic setup |
| 19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Jakub Rydzewski | LOWER_WALLS PRINT UPPER_WALLS UNITS RESTART METAD PATHMSD | generic setup bias colvar |
| 19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Cristina Paissoni | MATHEVAL STATS COMBINE PBMETAD CENTER PRINT GROUP ANGLE BIASVALUE ENDPLUMED WHOLEMOLECULES COORDINATION ENSEMBLE INCLUDE MOLINFO ALPHABETA SAXS | isdb function colvar core multicolvar bias generic vatom |
| 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 | ENERGY PRINT COM UPPER_WALLS METAD DISTANCE | generic colvar vatom bias |
| 19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Vittorio Limongelli | FUNNEL LOWER_WALLS FUNNEL_PS PRINT COM UPPER_WALLS WHOLEMOLECULES METAD RMSD DISTANCE | funnel colvar bias generic vatom |
| 19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Gabriele Cesare Sosso | OUTPUT_CLUSTER COMMITTOR DFSCLUSTERING MFILTER_MORE FLUSH Q6 LOCAL_Q6 CLUSTER_WITHSURFACE ENDPLUMED CLUSTER_NATOMS CONTACT_MATRIX | clusters multicolvar adjmat symfunc generic |
| 19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Riccardo Capelli | MATHEVAL WRAPAROUND FLUSH REWEIGHT_METAD PRINT COM READ FIT_TO_TEMPLATE GROUP METAD HISTOGRAM CONVERT_TO_FES WHOLEMOLECULES POSITION COORDINATION ENDPLUMED UPPER_WALLS DUMPGRID | function colvar core gridtools bias generic vatom |
| 19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Matteo Salvalaglio | LOWER_WALLS MATHEVAL ENERGY VOLUME COMBINE CELL PRINT UPPER_WALLS ENDPLUMED TORSION METAD | function colvar generic bias |
| 24.028 | All-atom simulations of RNA-membrane interactions | bio | metadynamics, membrane, RNA | Giovanni Bussi | LOWER_WALLS UPPER_WALLS CENTER WHOLEMOLECULES PRINT MATHEVAL MOLINFO SORT PUCKERING GROUP DISTANCE GHOST METAD GYRATION POSITION COMBINE DISTANCES | generic colvar bias multicolvar function vatom core |
| 24.007 | SWISH-X | bio | swish-x, SWISH-X, swish, expanded SWISH | Alberto Borsatto | ECV_MULTITHERMAL UPPER_WALLS WHOLEMOLECULES PRINT MOLINFO OPES_EXPANDED CONTACTMAP INCLUDE ENERGY | generic colvar opes bias |
| 24.001 | A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations | bio | OPES, OPES-Flooding, QM/MM, Kinetics, Enzyme Catalysis | Dhiman Ray | LOWER_WALLS UPPER_WALLS UNITS COMMITTOR PRINT TORSION DISTANCE OPES_METAD CUSTOM FLUSH COMBINE | generic colvar bias opes function setup |
| 23.043 | Modeling the ferroelectric phase transition in barium titanate with DFT accuracy and converged sampling | materials | Barium Titanate, ferroelectric phase transition, Machine Learning, polarization order parameters | Lorenzo Gigli | PRINT SELECT_COMPONENTS MATHEVAL METAD TRANSPOSE FLUSH INCLUDE SUM | generic bias valtools function matrixtools |
| 23.034 | Urea nucleation in water: do long-range forces matter? | materials | LMF theory, Metadynamics, Nucleation | Ziyue Zou | CENTER LOAD PRINT GROUP COORDINATIONNUMBER METAD INCLUDE | generic bias vatom symfunc setup core |
| 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 | ERMSD COORDINATION BIASVALUE WHOLEMOLECULES PRINT GHBFIX MOLINFO METAD COMBINE | function colvar generic bias |
| 23.010 | An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G‑Protein-Coupled Receptor Ligands | bio | GPCR, binding free energy, free energy surface | Timothy Clark | LOWER_WALLS UPPER_WALLS WHOLEMOLECULES BIASVALUE PRINT MATHEVAL DISTANCE METAD CONSTANT | function generic colvar bias |
| 22.029 | Angiotensin-1-7_Metadynamics | bio | Metadynamics, Angiotensin-(1-7), peptide | L.-América Chi | LOWER_WALLS UPPER_WALLS COORDINATION WHOLEMOLECULES PRINT GROUP METAD GYRATION FLUSH | colvar generic core bias |
| 22.004 | Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques | chemistry | reaction discovery, OPES, collective variables | Umberto Raucci | LOWER_WALLS UPPER_WALLS COORDINATION UNITS PYTORCH_MODEL OPES_METAD_EXPLORE PRINT COM LOAD MATHEVAL GROUP DISTANCE OPES_METAD CUSTOM | colvar generic pytorch bias opes function vatom setup core |
| 22.003 | Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling | methods | opes, metadynamics, reweighting, alanine, muller | Michele Invernizzi | LOWER_WALLS ECV_MULTITHERMAL UPPER_WALLS UNITS BIASVALUE PRINT OPES_METAD_EXPLORE METAD PBMETAD ENERGY TORSION ECV_UMBRELLAS_FILE OPES_METAD CUSTOM POSITION OPES_EXPANDED ENDPLUMED | generic colvar bias opes function setup |
| 21.047 | Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations | materials | pair entropy, metadynamics, ves, solids, crystallization | Pablo Piaggi | LOAD TD_WELLTEMPERED OPT_AVERAGED_SGD RESTART PRINT PAIRENTROPY BF_LEGENDRE ENERGY VES_LINEAR_EXPANSION METAD COMBINE VOLUME | generic colvar bias ves function gridtools setup |
| 21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Kristof Bal | REWEIGHT_METAD UPPER_WALLS UNITS COMMITTOR LOAD PRINT HISTOGRAM MOVINGRESTRAINT COORDINATIONNUMBER CONVERT_TO_FES METAD DUMPGRID FLUSH | generic bias gridtools symfunc setup |
| 21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Kresten Lindorff-Larsen | CENTER BIASVALUE WHOLEMOLECULES PRINT MOLINFO PBMETAD GROUP SAXS EEFSOLV METAINFERENCE ALPHARMSD GYRATION FLUSH | secondarystructure generic colvar bias vatom isdb core |
| 20.018 | Free energy barriers from biased molecular dynamics simulations | methods | kinetics, free energy barriers, chemical reactions, nucleation, metadynamics | Kristof Bal | CENTER PAIRENTROPY DENSITY COORDINATIONNUMBER VOLUME Q6 COORDINATION PRINT LOCAL_AVERAGE CONVERT_TO_FES DUMPGRID ENERGY HISTOGRAM LOAD SPRINT CONTACT_MATRIX METAD FLUSH LOWER_WALLS REWEIGHT_METAD UPPER_WALLS UNITS REWEIGHT_BIAS DISTANCE COMBINE | sprint volumes colvar generic bias function vatom gridtools symfunc adjmat setup |
| 19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Valerio Rizzi | UPPER_WALLS UNITS RESTART PRINT GROUP COORDINATIONNUMBER METAD ENDPLUMED FLUSH COMBINE DISTANCES | generic bias multicolvar function symfunc setup core |
| 19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Kresten Lindorff-Larsen | COMMITTOR PRINT MOLINFO METAD ALPHABETA FLUSH COMBINE | function multicolvar generic bias |
| 19.004 | MI Ubiquitin | bio | metainference, NMR | Max Bonomi | WHOLEMOLECULES RDC PRINT MOLINFO GROUP METAINFERENCE CS2BACKBONE | generic isdb core |
| 19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Max Bonomi | BIASVALUE PRINT MOLINFO GROUP EMMI | generic isdb core bias |