Browse the eggs in PLUMED-NEST
PLUMED-NEST provides all the data needed to reproduce the results of a PLUMED-enhanced molecular dynamics simulation or analysis contained in a published paper. Furthermore, PLUMED-NEST monitors the compatibility of the provided PLUMED input files with the current and development versions of the code and integrates links from these files to the PLUMED manual.
Here is the list of projects already deposited in PLUMED-NEST, while a complete bibliography can be found here.
| plumID | Name | Category | Keywords | Contributor | Actions | Modules |
|---|---|---|---|---|---|---|
| 25.005 | Mechanism of Nanocluster Formation from Machine-Learned Potential-based Simulations | chemistry | WT-metadynamics, metal nanoclusters, nucleation, neural network potential, deepMD | Vikas Tiwari, Tarak Karmakar | UNITS COMBINE UPPER_WALLS COM FLUSH GROUP DISTANCES LOWER_WALLS PRINT COORDINATION ANGLE METAD FIXEDATOM RESTRAINT DISTANCE COORDINATIONNUMBER | vatom core multicolvar colvar setup bias function symfunc generic |
| 25.017 | Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity | bio | EMMIVox, cryo-EM, allostery, decamer, filament, ensemble refinement, glutamine synthetase | Samuel Hoff | BIASVALUE WHOLEMOLECULES EMMIVOX PRINT MOLINFO GROUP | core generic bias isdb |
| 25.003 | Surrogate Model CV | methods | Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding | Sompriya Chatterjee | WHOLEMOLECULES COMBINE COMMITTOR PYTORCH_MODEL TORSION PRINT ENERGY OPES_METAD ENDPLUMED CUSTOM MOLINFO MATHEVAL DISTANCE GROUP | core opes pytorch colvar generic function |
| 24.026 | Constant pH metadynamics of RNA oligomers | bio | metadynamics, pH, RNA | Giovanni Bussi | PUCKERING RESTART TORSION PRINT METAD MOLINFO | setup generic colvar bias |
| 24.023 | Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21. A Machine-Learning-Aided Enhanced Sampling Study | bio | RNA, miRNA, OneOPES, ligand binding, conformational changes | Valerio Rizzi | RESTART COMBINE TORSION COORDINATION PRINT CUSTOM ENERGY OPES_EXPANDED ECV_MULTITHERMAL OPES_METAD_EXPLORE DISTANCE GROUP | setup core opes colvar generic 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 | BIASVALUE CENTER COMBINE GHBFIX DEBUG COORDINATION PRINT METAD UPPER_WALLS MOLINFO COM LOWER_WALLS DISTANCE GROUP | core colvar function generic bias vatom |
| 24.010 | Oxytocin metadynamics simulation | bio | metadynamics, oxytocin, peptide | Jan Beránek | FLUSH RESTART WHOLEMOLECULES TORSION PRINT METAD | setup generic colvar bias |
| 24.008 | yCD Metadynamics | bio | volume-based MetaD, path CVs, infrequent MetaD, product release | James McCarty | FLUSH COORDINATION INCLUDE READ HISTOGRAM PRINT ENDPLUMED MOLINFO COM FIT_TO_TEMPLATE DISTANCE REWEIGHT_METAD UPPER_WALLS CONTACTMAP MATHEVAL PATH RMSD GROUP WHOLEMOLECULES COMMITTOR DUMPGRID METAD FIXEDATOM WRAPAROUND CONVERT_TO_FES | core colvar function mapping generic vatom gridtools bias |
| 24.002 | Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes | chemistry | metadynamics, ligand design, solvent extraction | Xiaoyu Wang | RESTART TORSION PRINT METAD UNITS | setup generic colvar bias |
| 23.025 | Probing ion binding to G-quadruplexes and related events | chemistry | metadynamics, repulsive potential, nucleic acids, G-quadruplexes | Marcelo Poleto | FLUSH POSITION WHOLEMOLECULES RESTART PRINT FIT_TO_TEMPLATE DISTANCES UPPER_WALLS METAD MATHEVAL WRAPAROUND COM DUMPATOMS LOWER_WALLS UNITS DISTANCE GROUP | setup core colvar function generic vatom multicolvar bias |
| 23.015 | MPCs aggregation | bio | opes_explore, dimerization, MPCs, self-assembly | Vikas Tiwari | WHOLEMOLECULES CENTER COORDINATION PRINT CUSTOM METAD UPPER_WALLS COM OPES_METAD_EXPLORE LOWER_WALLS DISTANCE GROUP | core opes colvar function generic vatom bias |
| 23.014 | Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 | bio | metadynamics, oligomerization, chemokine receptors, GPCR, membrane | Vittorio Limongelli | FLUSH WHOLEMOLECULES COMBINE TORSION PRINT METAD UPPER_WALLS COM DISTANCE | colvar function generic vatom bias |
| 23.006 | Transcription factor unbinding | bio | metadynamics, DNA, conformational changes | Malin Lüking | ALPHARMSD ANGLE DUMPFORCES PRINT CONTACTMAP METAD MOLINFO COM DISTANCE | colvar generic bias vatom secondarystructure |
| 23.005 | A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs | bio | metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A | Timothy Clark | WHOLEMOLECULES DUMPGRID READ HISTOGRAM REWEIGHT_METAD PRINT METAD MOLINFO MATHEVAL CONVERT_TO_FES RMSD DISTANCE | colvar function generic gridtools 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 | generic colvar bias |
| 23.002 | Critical comparison of general-purpose collective variables for crystal nucleation | methods | metadynamics, umbrella sampling, commitor, entropy, PIV | Julien Lam | LOCAL_AVERAGE FUNCPATHMSD PAIRENTROPY PRINT CUSTOM ENERGY METAD UPPER_WALLS Q6 RESTRAINT Q4 VOLUME PIV UNITS | setup symfunc colvar generic bias gridtools piv function |
| 23.001 | Quantum phase diagram of water | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn-Løland Bore | RESTART INCLUDE PRINT ECV_UMBRELLAS_LINE ENVIRONMENTSIMILARITY UPPER_WALLS OPES_EXPANDED LOWER_WALLS | setup opes generic envsim bias |
| 22.030 | Mixing physics across temperatures with generative artificial intelligence | methods | REMD, Generative AI, DDPM | Yihang Wang | TORSION WHOLEMOLECULES PRINT | generic colvar |
| 22.015 | Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome | bio | photodynamics, bacteriophytochrome, variationally enhanced sampling | Jakub Rydzewski | OPT_AVERAGED_SGD VES_LINEAR_EXPANSION TD_UNIFORM TORSION PRINT BF_FOURIER | generic colvar ves |
| 22.003 | Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling | methods | opes, metadynamics, reweighting, alanine, muller | Michele Invernizzi | BIASVALUE POSITION LOWER_WALLS PBMETAD TORSION PRINT OPES_METAD ENERGY ENDPLUMED METAD OPES_EXPANDED CUSTOM ECV_UMBRELLAS_FILE ECV_MULTITHERMAL UPPER_WALLS OPES_METAD_EXPLORE UNITS | setup opes colvar function generic bias |
| 21.042 | Peptoid-mediated Au nanocrystal growth | materials | parallel-bias metadynamics, peptoid, Au | Xin Qi | PBMETAD PRINT UPPER_WALLS MOLINFO COM GYRATION DISTANCE | generic colvar vatom bias |
| 21.020 | Reweighted Jarzynski sampling | methods | free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions | Kristof Bal | FLUSH UNITS BIASVALUE OPT_AVERAGED_SGD COMBINE HISTOGRAM PRINT CUSTOM COORDINATIONNUMBER ANN LOAD DISTANCE VES_LINEAR_EXPANSION REWEIGHT_METAD OPES_METAD TD_WELLTEMPERED UPPER_WALLS RESTRAINT BF_CHEBYSHEV DUMPGRID MOVINGRESTRAINT REWEIGHT_BIAS METAD CONVERT_TO_FES CONSTANT | setup opes symfunc annfunc colvar ves generic bias gridtools function |
| 21.015 | Coarse-grained metadynamics and umbrella sampling simulations to investigate interactions of carbohydrate-binding modules with chitin | bio | metadynamics, umbrella sampling, coarse-grained, MARTINI, chitin, carbohydrate-binding module | Gaston Courtade | RESTART WHOLEMOLECULES POSITION CENTER COORDINATION PRINT REWEIGHT_BIAS METAD MATHEVAL RESTRAINT | setup colvar function generic vatom bias |
| 20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Faidon Brotzakis | BIASVALUE DUMPGRID WHOLEMOLECULES READ HISTOGRAM PRINT DISTANCES EMMI MOLINFO CONVERT_TO_FES RMSD GROUP | core colvar generic gridtools multicolvar bias isdb |
| 20.027 | Allosteric Regulation of SARS-CoV-2 Protease. Towards Informed Structure-Based Drug Discovery | bio | SARS-CoV2, MPro, Covid-19, Molecular Dynamics, Metadynamics, Computer-Aided Drug Discovery | Khaled Abdel-Maksoud | METAD TORSION PRINT DISTANCE | generic colvar bias |
| 20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Matteo Salvalaglio | PRINT CELL ENERGY UPPER_WALLS METAD MATHEVAL VOLUME LOWER_WALLS | generic colvar bias function |
| 20.016 | Predicting polymorphism in molecular crystals using orientational entropy | materials | metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy | Pablo Piaggi | INCLUDE CENTER PRINT METAD UPPER_WALLS VOLUME LOAD GROUP | setup core colvar generic vatom 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 | BIASVALUE WHOLEMOLECULES INCLUDE PRINT PROJECTION_ON_AXIS UPPER_WALLS METAD CONTACTMAP MATHEVAL MOLINFO CONSTANT COM LOAD FUNCPATHGENERAL LOWER_WALLS DISTANCE GROUP | setup core colvar function generic bias vatom |
| 20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Jim Pfaendtner | RESTART WHOLEMOLECULES CENTER COORDINATION PRINT DISTANCES DISTANCE GROUP | setup core colvar generic multicolvar vatom |
| 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 | COORDINATION PRINT CUSTOM DISTANCES METAD UNITS | setup colvar function generic multicolvar bias |
| 20.005 | Muscarinic M2 receptor/ligand Frequency-Adaptive Metadynamics and QM/MM calculations | bio | Frequency-adaptive metadynamics, multiple-walkers metadynamics, well-tempered metadynamics, GPCR, receptor, Adiabatic Bias MD | Riccardo Capelli | FLUSH ABMD COMBINE READ HISTOGRAM PRINT ENDPLUMED MOLINFO COM LOWER_WALLS DISTANCE REWEIGHT_METAD UPPER_WALLS CONTACTMAP WHOLEMOLECULES DUMPGRID FUNCPATHMSD METAD CONVERT_TO_FES | colvar function generic bias gridtools vatom |
| 20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Luigi Bonati | FLUSH PYTORCH_MODEL TORSION PRINT OPES_METAD ENDPLUMED UPPER_WALLS MATHEVAL COM LOAD LOWER_WALLS UNITS DISTANCE GROUP | setup core opes pytorch colvar function generic vatom 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 | CELL OPT_AVERAGED_SGD REWEIGHT_TEMP_PRESS COMBINE HISTOGRAM READ PRINT ENERGY Q6 OPT_DUMMY VOLUME LOAD LOWER_WALLS RESTART VES_LINEAR_EXPANSION TD_WELLTEMPERED UPPER_WALLS MATHEVAL DUMPGRID BF_LEGENDRE REWEIGHT_BIAS CONVERT_TO_FES TD_MULTITHERMAL_MULTIBARIC | setup symfunc colvar ves generic bias gridtools function |
| 19.073 | On the role of enthalpic and entropic contributions on the conformational free energy landscape of MIL-101(Cr) building units | materials | metadynamics, MOF, MIL101Cr, conformational | Matteo Salvalaglio | PRINT ENERGY DISTANCES COORDINATIONNUMBER UPPER_WALLS METAD ENDPLUMED LOWER_WALLS GYRATION | symfunc colvar generic multicolvar bias |
| 19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Giovanni Bussi | FLUSH WHOLEMOLECULES INCLUDE TORSION COORDINATION PRINT METAD SORT MOLINFO MATHEVAL COM MAXENT DISTANCE | colvar function generic bias 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 | PRINT ENERGY UPPER_WALLS METAD COM DISTANCE | generic colvar vatom bias |
| 19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Davide Provasi | WHOLEMOLECULES FUNCPATHMSD PRINT ENDPLUMED CONTACTMAP METAD COM RMSD DISTANCE | colvar function generic vatom bias |
| 19.004 | MI Ubiquitin | bio | metainference, NMR | Max Bonomi | GROUP WHOLEMOLECULES PRINT MOLINFO RDC CS2BACKBONE METAINFERENCE | core generic isdb |
| 19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Max Bonomi | BIASVALUE PRINT EMMI MOLINFO GROUP | core generic bias isdb |
| 25.013 | Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices | bio | umbrella sampling, temperature ramping | Alexander Berlaga | DISTANCE GYRATION PRINT PYTORCH_MODEL RESTRAINT | colvar pytorch bias generic |
| 25.006 | Characterizing the conformational ensemble of PROTAC degraders in solutions via atomistic simulations | methods | Enhanced sampling, Atomistic simulations, Conformational ensemble, PROTACs, Targeted Protein Degradation, Chamelonic molecules | Shikshya Bhusal, Omar Valsson | DISTANCE INCLUDE CENTER READ GYRATION PRINT PBMETAD ENERGY VOLUME RESTART TORSION | bias vatom colvar 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 | CUSTOM DISTANCE COMMITTOR OPES_METAD GROUP PRINT FIXEDATOM UNITS DISTANCES COORDINATIONNUMBER UPPER_WALLS ZDISTANCES FLUSH | bias vatom colvar core setup function opes generic symfunc multicolvar |
| 24.027 | Proline cis and trans subensembles of a disordered peptide | bio | intrinsically disordered proteins, proline cis trans isomerisation, metadynamics, collective variables | Alice Pettitt | WHOLEMOLECULES DISTANCE COMBINE INCLUDE DIHCOR GROUP GYRATION PRINT PBMETAD PARABETARMSD ALPHARMSD MOLINFO TORSION ANTIBETARMSD FLUSH COORDINATION ENDPLUMED | bias colvar core secondarystructure function generic multicolvar |
| 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 | DISTANCE ANGLE FIXEDATOM WHOLEMOLECULES UPPER_WALLS COORDINATION MATHEVAL CONTACTMAP CUSTOM METAD CENTER GROUP OPES_METAD RMSD ENDPLUMED COMMITTOR COMBINE PRINT TORSION FIT_TO_TEMPLATE MOLINFO | bias vatom colvar core function opes 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 | DISTANCE ENERGY PRINT UPPER_WALLS OPES_METAD COORDINATION | colvar opes bias generic |
| 24.004 | Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables | materials | metadynamics, nucleation, machine learning | Ziyue Zou | METAD LOAD INCLUDE GROUP PRINT RESTART | core setup bias 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 | DISTANCE OPES_METAD GROUP PRINT FIXEDATOM UNITS COORDINATIONNUMBER UPPER_WALLS ZDISTANCES FLUSH | bias vatom colvar core setup opes generic symfunc multicolvar |
| 23.032 | Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics | bio | metadynamics, tSNE, neural network, machine learning, trp-cage, folding | Vojtech Spiwok | WHOLEMOLECULES METAD COMBINE PRINT ALPHARMSD POSITION ANN FIT_TO_TEMPLATE MOLINFO | bias colvar secondarystructure function annfunc generic |
| 23.022 | A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar | methods | collective variables, machine learning, toy model | Enrico Trizio | CUSTOM PRINT UNITS BIASVALUE LOWER_WALLS POSITION UPPER_WALLS PYTORCH_MODEL OPES_METAD ENDPLUMED | pytorch bias colvar setup function opes generic |
| 22.041 | Skipping the Replica Exchange Ladder with Normalizing Flows | methods | OPES, alanine, normalizing flows, replica exchange | Michele Invernizzi | OPES_EXPANDED PRINT ENERGY ECV_MULTITHERMAL UNITS POSITION TORSION OPES_METAD ENDPLUMED | colvar setup opes generic |
| 22.038 | Enhanced Sampling Aided Design of Molecular Photoswitches | chemistry | reaction discovery, OPES explore, graph CV | Umberto Raucci | CUSTOM PRINT UNITS OPES_METAD_EXPLORE PYTORCH_MODEL COORDINATION | pytorch colvar setup function opes generic |
| 22.025 | Bubble nucleation rate predictions in a Lennard-Jones fluid | materials | free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation | Kristof Bal | CUSTOM HISTOGRAM COMMITTOR LOAD PRINT VOLUME REWEIGHT_BIAS UNITS CONVERT_TO_FES BIASVALUE DUMPGRID COORDINATIONNUMBER UPPER_WALLS ANN FLUSH MOVINGRESTRAINT RESTRAINT | bias colvar gridtools setup function annfunc generic symfunc |
| 21.052 | On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets | materials | Ibuprofen, unbinding, WTmetaD | Matteo Salvalaglio | DISTANCE COMMITTOR METAD CENTER PRINT COORDINATIONNUMBER TORSION ENDPLUMED | bias vatom colvar generic symfunc |
| 21.050 | N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity | methods | bio | Isabell Louise Grothaus | DISTANCE PRINT CENTER | colvar vatom generic |
| 21.044 | NaCl nucleation | chemistry | metadynamics, DFS clustering | Aaron Finney | HISTOGRAM METAD COMBINE CONTACT_MATRIX GROUP PRINT CLUSTER_DISTRIBUTION FIXEDATOM DFSCLUSTERING INSPHERE Q6 MFILTER_MORE DUMPGRID COORDINATIONNUMBER LOCAL_Q6 CLUSTER_NATOMS | bias adjmat vatom gridtools core function volumes generic symfunc multicolvar clusters |
| 21.031 | Photo-switchable sulfonulureas in KATP channel | bio | metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels | Katarzyna Walczewska-Szewc | WHOLEMOLECULES DISTANCE METAD PRINT UNITS UPPER_WALLS LOWER_WALLS COM | bias vatom colvar setup generic |
| 20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Valerio Rizzi | WHOLEMOLECULES DISTANCE FIT_TO_TEMPLATE CENTER ANGLE GROUP ENERGY PRINT MATHEVAL FIXEDATOM UPPER_WALLS PYTORCH_MODEL OPES_METAD COORDINATION ENDPLUMED | pytorch bias vatom colvar core function opes generic |
| 20.024 | Gaussian Mixture Based Enhanced Sampling (GAMBES) | methods | enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias | Jayashrita Debnath | DISTANCE LOAD COMBINE GROUP PRINT ENERGY UNITS DISTANCES UPPER_WALLS LOWER_WALLS TORSION | bias colvar core setup function generic multicolvar |
| 20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Michele Invernizzi | UNITS Q6 ECV_UMBRELLAS_LINE WHOLEMOLECULES ENERGY ECV_MULTITHERMAL ECV_LINEAR UPPER_WALLS POSITION MATHEVAL CUSTOM ENVIRONMENTSIMILARITY RMSD ENDPLUMED OPES_EXPANDED ECV_MULTITHERMAL_MULTIBARIC LOAD PRINT VOLUME TORSION MOLINFO | bias envsim colvar setup function opes generic symfunc |
| 20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Max Bonomi | WHOLEMOLECULES DIHCOR INCLUDE GYRATION PRINT ALPHABETA PBMETAD MOLINFO COORDINATION | colvar multicolvar bias generic |
| 20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Carlo Camilloni | METAINFERENCE WHOLEMOLECULES DISTANCE CENTER GYRATION PRINT ALPHABETA PBMETAD STATS ENSEMBLE TORSION SAXS FLUSH MOLINFO | bias vatom colvar isdb function generic multicolvar |
| 20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Pratyush Tiwary | WHOLEMOLECULES DISTANCE METAD COMBINE PRINT RESTART UPPER_WALLS TORSION MOLINFO RMSD | bias colvar setup function generic |
| 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 | WHOLEMOLECULES METAD PATHMSD GROUP PRINT RESTART UPPER_WALLS MOLINFO | bias colvar core setup generic |
| 19.075 | PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python | other | Python, automatic differentiation | Toni Giorgino | DISTANCE CUSTOM COMBINE CENTER ENDPLUMED ANGLE GROUP PRINT DUMPDERIVATIVES TORSION RESTRAINT | bias vatom colvar core function generic |
| 19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Sandro Bottaro | WHOLEMOLECULES DISTANCE METAD ERMSD PRINT TORSION RMSD MOLINFO | colvar bias generic |
| 19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Silvio Pipolo | METAD FUNCPATHMSD PRINT CELL UPPER_WALLS LOWER_WALLS PIV | bias colvar function generic piv |
| 19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Kresten Lindorff-Larsen | COMMITTOR METAD COMBINE PRINT ALPHABETA FLUSH MOLINFO | multicolvar function bias generic |
| 19.009 | RNA tetraloops folding | bio | metadynamics, RNA, folding | Giovanni Bussi | WHOLEMOLECULES METAD ERMSD PRINT RMSD MOLINFO ENDPLUMED | colvar bias generic |
| 19.003 | EMMI ClpP | bio | metainference, cryo-EM | Max Bonomi | GROUP PRINT BIASVALUE EMMI MOLINFO | bias isdb core generic |
| 19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Michele Invernizzi | METAD LOAD PRINT VES_DELTA_F ENERGY UNITS RESTART POSITION TORSION ENDPLUMED | bias colvar ves setup generic |
| 25.019 | The Arch from the Stones. Understanding Protein Folding Energy Landscapes via Bio-inspired Collective Variables | bio | protein folding, OPES, OneOPES, binding free energy | Valerio Rizzi | ECV_MULTITHERMAL GHOST DISTANCE CENTER PRINT OPES_EXPANDED GROUP RMSD OPES_METAD_EXPLORE MOLINFO CUSTOM COORDINATION ENERGY COMBINE | core generic opes vatom function colvar |
| 25.015 | Assessment of Force Fields for Describing Conformational Polymorphic Crystals of ROY | materials | Molecular crystal, Force Field, Collective Variable | Pradip Si and Omar Valsson | DISTANCES DUMPMULTICOLVAR TORSIONS PRINT SMAC | generic multicolvar symfunc |
| 25.011 | Chiral perovskite nucleation | chemistry | metadynamics, chiral perovskites, nucleation | Adriana Pietropaolo | UPPER_WALLS DISTANCE UNITS PRINT MATHEVAL PBMETAD MULTI_RMSD LOWER_WALLS RESTART | setup generic function bias colvar |
| 25.002 | M3_PCV-ABMD | chemistry | Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor | Gian Marco Elisi | UPPER_WALLS UNITS ABMD PRINT PATHMSD ENDPLUMED | setup bias generic colvar |
| 24.032 | DeepLNE++ | methods | PATHCV, OPES | Thorben Fröhlking | DISTANCE PRINT OPES_METAD GROUP LOAD CUSTOM TORSION COORDINATION ENERGY COMBINE | core setup generic opes function colvar |
| 24.005 | Learning Markovian Dynamics with Spectral Maps | methods | spectral map, collective variables, machine learning | Jakub Rydzewski | DISTANCE UNITS PRINT BIASVALUE CUSTOM | setup generic function bias colvar |
| 23.045 | Minute-timescale simulations of G Protein Coupled Receptor A2A activation mechanism reveal a receptor pseudo-active state | bio | Path CVs Metadynamics, GPCRs activation transition | Vittorio Limongelli | INCLUDE UPPER_WALLS DISTANCE CONTACTMAP ALPHARMSD PRINT METAD FUNCPATHMSD MOLINFO PATHMSD LOWER_WALLS | secondarystructure generic function bias colvar |
| 23.030 | Data Driven Classification of Ligand Unbinding Pathways | bio | OPES Explore, OPES Flooding, Benzene T4 Lysozyme, Ligand unbinding, Pathway classification, Kinetics, Residence time | Dhiman Ray | UNITS CENTER FLUSH OPES_METAD_EXPLORE MOLINFO TORSION WRAPAROUND WHOLEMOLECULES LOWER_WALLS POSITION UPPER_WALLS DISTANCE PRINT GROUP BIASVALUE CUSTOM COMMITTOR ENERGY FIT_TO_TEMPLATE OPES_METAD COM COORDINATION ENDPLUMED MATHEVAL | core setup generic vatom opes function bias colvar |
| 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 | UPPER_WALLS LOWER_WALLS FIT_TO_TEMPLATE UNITS DISTANCE CENTER PRINT OPES_METAD GROUP OPES_METAD_EXPLORE PYTORCH_MODEL CUSTOM TORSION COORDINATION WHOLEMOLECULES PATH FIXEDATOM | core setup generic pytorch vatom opes function bias mapping colvar |
| 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 | CONTACTMAP CENTER RMSD ENDPLUMED MOLINFO WHOLEMOLECULES UPPER_WALLS DISTANCE PRINT GROUP CUSTOM COMMITTOR COMBINE INCLUDE ANGLE ENERGY FIXEDATOM FIT_TO_TEMPLATE OPES_METAD PYTORCH_MODEL COORDINATION LOWER_WALLS MATHEVAL | core generic pytorch vatom function opes bias colvar |
| 23.008 | PBMetaD simulations of Histatin5 | bio | metadynamics, IDP, Rg, PPII | Francesco Pesce | PRINT GROUP GYRATION MOLINFO PBMETAD TORSION WHOLEMOLECULES | bias core generic colvar |
| 22.039 | Driving and characterizing nucleation of urea and glycine polymorphs in water | bio | metadynamics, nucleation, amino acids, polymorphism | Eric Beyerle | INCLUDE CENTER PAIRENTROPY PRINT METAD GROUP LOAD Q6 COORDINATIONNUMBER COMBINE Q4 MATHEVAL | core setup generic vatom function symfunc bias gridtools |
| 22.037 | Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site | chemistry | metadynamics, DNA, abasic | Mike Jones | METAD DISTANCES DISTANCE PRINT | generic bias multicolvar colvar |
| 22.024 | Conformational Entropy as a Potential Liability of Computationally Designed Antibodies | bio | metadynamics, conformational entropy, antibody, nanobody | Thomas Löhr | PRINT ALPHARMSD MOLINFO PBMETAD COM WHOLEMOLECULES ANTIBETARMSD TORSION ALPHABETA RESTART | secondarystructure setup generic multicolvar vatom bias colvar |
| 22.018 | Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations | bio | ligand binding, docking, EMMI, LAT1 | Max Bonomi | PRINT GROUP LOAD BIASVALUE MOLINFO EMMIVOX WHOLEMOLECULES | core setup isdb generic bias |
| 22.005 | Collective Variable for Metadynamics Derived from AlphaFold Output | bio | AlphaFold, protein folding, protein structure prediction, metadynamics, deep learning, free energy simulation, collective variable | Vojtech Spiwok | METAD LOAD PRINT WHOLEMOLECULES | setup bias generic |
| 21.046 | Ubiquitin Interacting Motifs, Duality Between Structured and Disordered Motifs | bio | wt metadynamics, ubiquitin, ataxin-3, short linear motifs, ubiquitin binding motif, moonlight functions, intrinsic disorder | Elena Papaleo | UPPER_WALLS LOWER_WALLS PRINT METAD GROUP GYRATION WHOLEMOLECULES ENDPLUMED ALPHABETA | core generic multicolvar bias colvar |
| 21.039 | Deep learning the slow modes for rare events sampling | methods | collective variables, machine learning, slow modes, deep-tica, opes | Luigi Bonati | ENVIRONMENTSIMILARITY UNITS CONTACTMAP OPES_EXPANDED RMSD FLUSH LOAD MOLINFO TORSION WHOLEMOLECULES DISTANCE PRINT GROUP COMBINE INCLUDE ENERGY OPES_METAD VOLUME PYTORCH_MODEL Q6 ECV_MULTITHERMAL ENDPLUMED | core setup generic envsim pytorch opes function symfunc colvar |
| 21.035 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, interface | Aaron Finney | RESTRAINT DISTANCE PRINT GROUP LOAD FIXEDATOM | core setup generic vatom bias colvar |
| 21.026 | Probing allosteric regulations with coevolution-driven molecular simulations | bio | metadynamics, coevolution, allostery, adenylate cyclase | Francesco Colizzi | UPPER_WALLS DISTANCE UNITS PRINT METAD COM WHOLEMOLECULES PATHMSD | setup generic vatom bias colvar |
| 21.018 | Localized Volume-based Metadynamics | bio | LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification | Riccardo Capelli | REWEIGHT_METAD RMSD FLUSH WHOLEMOLECULES POSITION UPPER_WALLS READ DISTANCE PRINT METAD GROUP DUMPGRID CONVERT_TO_FES HISTOGRAM FIXEDATOM COM COORDINATION ENDPLUMED MATHEVAL | core generic vatom function bias gridtools colvar |
| 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 | DISTANCE CENTER ERMSD PRINT ABMD MOLINFO TORSION RESTART | setup generic vatom bias colvar |
| 20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Adriana Pietropaolo | CENTER PRINT PBMETAD COORDINATION WHOLEMOLECULES | vatom bias generic colvar |
| 20.021 | Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins. | bio | phi-values, restrained MD, transition-state, protein folding, disordered proteins, protein evolution | Cristina Paissoni | RESTRAINT PRINT MOLINFO COORDINATION WHOLEMOLECULES STATS | function bias generic colvar |
| 20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Glen Hocky | RESTRAINT DISTANCE UNITS PRINT GROUP GYRATION BIASVALUE FISST ENERGY MATHEVAL | core setup generic fisst function bias colvar |
| 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 | FLUSH CS2BACKBONE MOLINFO DIHCOR TORSION WHOLEMOLECULES ALPHARMSD PRINT GROUP PARABETARMSD GYRATION STATS COMBINE INCLUDE ENSEMBLE METAINFERENCE PBMETAD ANTIBETARMSD COORDINATION ENDPLUMED | core secondarystructure isdb generic multicolvar function bias colvar |
| 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 | UPPER_WALLS ENVIRONMENTSIMILARITY TD_WELLTEMPERED VOLUME PRINT Q6 VES_LINEAR_EXPANSION OPT_DUMMY RESTART BF_LEGENDRE OPT_AVERAGED_SGD MATHEVAL | setup generic envsim function symfunc bias ves 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 | UPPER_WALLS LOWER_WALLS PRINT GROUP FLUSH CS2BACKBONE MOLINFO PBMETAD BIASVALUE ANTIBETARMSD WHOLEMOLECULES ENDPLUMED ALPHABETA | core secondarystructure isdb generic multicolvar bias |
| 19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Valerio Rizzi | UPPER_WALLS DISTANCES UNITS PRINT METAD GROUP FLUSH COORDINATIONNUMBER ENDPLUMED COMBINE RESTART | core setup generic multicolvar function symfunc bias |
| 19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Valerio Rizzi | UNITS PRINT METAD GROUP FLUSH COORDINATIONNUMBER ENDPLUMED COMBINE EXTERNAL RESTART | core setup generic function symfunc bias |
| 19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Kim E. Jelfs | UPPER_WALLS DISTANCE CENTER PRINT METAD GROUP COM LOWER_WALLS RESTART | core setup generic vatom bias colvar |
| 19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Cristina Paissoni | INCLUDE CENTER PRINT ENSEMBLE ANGLE GROUP MOLINFO PBMETAD SAXS BIASVALUE ALPHABETA WHOLEMOLECULES COORDINATION ENDPLUMED STATS COMBINE MATHEVAL | core isdb generic multicolvar vatom function bias colvar |
| 19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Gareth Tribello | UPPER_WALLS UNITS CELL PRINT METAD FCCUBIC ENDPLUMED | setup generic symfunc bias colvar |
| 19.048 | Understanding Ligand Binding Selectivity in a Prototypical GPCR Family | bio | metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | UPPER_WALLS DISTANCE PRINT METAD CONSTANT BIASVALUE COM WHOLEMOLECULES LOWER_WALLS MATHEVAL | generic vatom function bias colvar |
| 19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | UPPER_WALLS DISTANCES DISTANCE UNITS PRINT METAD FLUSH COMBINE RESTART | setup generic multicolvar function bias colvar |
| 19.023 | RECT | methods | metadynamics, replica exchange | Giovanni Bussi | PRINT METAD GYRATION TORSION WHOLEMOLECULES | bias generic colvar |
| 19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Matteo Salvalaglio | UPPER_WALLS LOWER_WALLS CELL PRINT VOLUME METAD TORSION ENERGY ENDPLUMED COMBINE MATHEVAL | function bias generic colvar |
| 19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Matteo Salvalaglio | DISTANCES PRINT METAD GYRATION COORDINATIONNUMBER ENDPLUMED RESTART | setup generic multicolvar symfunc bias colvar |
| 19.011 | Automatic Gradient Computation for Collective Variables | other | gradient, differentiation, curvature | Toni Giorgino | ENDPLUMED | generic |
| 25.007 | Shaping the glycan landscape. Hidden relationships between linkage and ring distortion induced by carbohydrate-active enzmyes | bio | REST-RECT, REST2, glycan, enzyme, CAZyme, steered | Isabell Grothaus | TORSION MOVINGRESTRAINT PRINT METAD MOLINFO DISTANCE PUCKERING RESTART RESTRAINT | generic setup colvar bias |
| 24.030 | NMR guided simulation of dsRBD | bio | Metainference, NMR, protein dynamics | Debadutta Patra | FLUSH STATS PRINT METAINFERENCE GROUP MOLINFO ALPHABETA DISTANCE ENSEMBLE RDC WHOLEMOLECULES | generic multicolvar isdb function core colvar |
| 24.011 | Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble | methods | committor, machine learning | Peilin Kang | TORSION MOLINFO ENDPLUMED UPPER_WALLS POSITION INCLUDE CELL DISTANCE COORDINATION LOWER_WALLS ENERGY MATHEVAL UNITS RMSD PRINT GROUP LOAD CUSTOM BIASVALUE WHOLEMOLECULES | generic bias function setup core colvar |
| 23.046 | Lasso Peptides - HLDA CV | bio | metadynamics, protein folding, HLDA, harmonic | Gabriel da Hora | COMBINE PRINT METAD DISTANCE UNITS WHOLEMOLECULES | generic bias function setup colvar |
| 23.039 | Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation | chemistry | metadynamics, ligand dissociation | Eric Beyerle | UPPER_WALLS COMBINE DUMPMASSCHARGE PRINT METAD MOLINFO DISTANCE FIXEDATOM RESTRAINT CENTER | generic bias function vatom colvar |
| 23.036 | Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? | bio | NaCl, nucleation, metadynamics | Ruiyu Wang | COMBINE COORDINATIONNUMBER Q6 ENERGY METAD Q4 PRINT MATHEVAL VOLUME | generic bias symfunc function colvar |
| 23.035 | An Extended Metadynamics Protocol for Binding/Unbinding of Peptide Ligands to Class A G-Protein Coupled Receptors | bio | G protein coupled receptor, peptide ligands, metadynamics, multiple-walker | Timothy Clark | LOWER_WALLS UPPER_WALLS CONSTANT PRINT METAD MATHEVAL DISTANCE BIASVALUE WHOLEMOLECULES CENTER | generic bias function vatom colvar |
| 23.034 | Urea nucleation in water: do long-range forces matter? | materials | LMF theory, Metadynamics, Nucleation | Ziyue Zou | COORDINATIONNUMBER PRINT METAD GROUP INCLUDE LOAD CENTER | generic bias symfunc setup vatom core |
| 23.026 | Machine Learning Nucleation Collective Variables with Graph Neural Networks | chemistry | Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks | Florian Dietrich | LOWER_WALLS COMBINE MOVINGRESTRAINT COORDINATIONNUMBER Q6 PRINT GROUP MFILTER_MORE METAD LOCAL_Q6 | generic bias multicolvar symfunc function core |
| 23.020 | FEP simulations of ATOX1 homodimer | chemistry | parallel bias metadynamics, FEP, free-energy of metal ion dissociation | Adriana Pietropaolo | ANGLE CONSTANT PRINT PBMETAD MATHEVAL DISTANCE BIASVALUE WHOLEMOLECULES | function generic colvar bias |
| 23.012 | JAK2 2D meta-eABF PMF with statistical analysis | bio | 2D meta-eABF, path CV, PMF | Istvan Kolossvary | LOWER_WALLS UPPER_WALLS FLUSH PATHMSD METAD PRINT DRR CUSTOM BIASVALUE | generic bias drr function colvar |
| 23.004 | Melting curves of ice polymorphs in the vicinity of the liquid-liquid critical point | chemistry | water, liquid-liquid transition, second critical point, ice, polymorphs, melting curves, environment similarity, opes, density-functional theory, scan, machine learning potential | Pablo Piaggi | LOWER_WALLS UPPER_WALLS ENVIRONMENTSIMILARITY PRINT OPES_EXPANDED DUMPGRID HISTOGRAM ECV_UMBRELLAS_LINE RESTART | generic envsim bias setup opes gridtools |
| 22.045 | Binding mode and mechanism of enzymatic polyethylene terephthalate degradation | bio | metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation | Francesco Colizzi | LOWER_WALLS UPPER_WALLS MOVINGRESTRAINT ANGLE PRINT METAD DISTANCE COM WHOLEMOLECULES | generic vatom colvar bias |
| 22.043 | Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES | bio | OPES, RNA, Tetraloop, Folding | Gül Zerze | ECV_MULTITHERMAL PRINT OPES_EXPANDED ENERGY CONTACTMAP ECV_UMBRELLAS_LINE WHOLEMOLECULES | opes generic colvar |
| 22.034 | Rationalising the difference in crystallisability of two Sulflowers using efficient in silico methods | materials | metadynamics, crystallizability, crystal structure prediction, sulflower, persulforated coronene | Matteo Salvalaglio | UPPER_WALLS LOWER_WALLS COMMITTOR PRINT METAD CELL MATHEVAL DRMSD CUSTOM | function generic colvar bias |
| 22.031 | Rare Event Kinetics from Adaptive Bias Enhanced Sampling | methods | OPES Flooding, Kinetics, Rate, OPES, Machine Learning | Dhiman Ray | TORSION COMMITTOR MOLINFO ENDPLUMED COMBINE POSITION INCLUDE DISTANCE CONTACTMAP OPES_METAD ENERGY PYTORCH_MODEL UNITS RMSD CONSTANT PRINT GROUP CUSTOM BIASVALUE WHOLEMOLECULES | generic bias function setup opes pytorch core colvar |
| 22.020 | Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix–Junction–Helix RNA | bio | RNA force field, Helix-Junction-Helix RNA, SAXS, Well tempered metadynamics | Weiwei He | TORSION PRINT METAD GROUP DISTANCE WHOLEMOLECULES COM | generic bias vatom core colvar |
| 21.051 | Automatic learning of hydrogen-bond fixes in an AMBER RNA force field | methods | force field, RNA | Giovanni Bussi | COMBINE PRINT METAD MOLINFO COORDINATION ERMSD BIASVALUE WHOLEMOLECULES | function colvar bias generic |
| 21.049 | Multiple-path-metadynamics and PathMaps | methods | path-CV, metadynamics, multiple-walker, multiple paths, pathmap | Alberto Pérez-de-Alba-Ortíz | TORSION UPPER_WALLS COMBINE LOWER_WALLS MOVINGRESTRAINT CONSTANT PRINT METAD ENSEMBLE LOAD UNITS CUSTOM RESTRAINT | generic bias function setup colvar |
| 21.045 | QM/MM metadynamics of thiol-disulfide exchange between methylthiolate and dimethyldisulfide in water with an imposed external electrostatic potential (ESP) | chemistry | metadynamics, QM/MM, electrostatic potential, thiol-disulfide exchange | Denis Maag | UPPER_WALLS LOWER_WALLS COMBINE COORDINATIONNUMBER PRINT METAD DISTANCE COORDINATION | generic bias symfunc function colvar |
| 21.037 | Molecular Dynamics simulations of RBD/hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain | Max Bonomi | DISTANCE PRINT RMSD | generic colvar |
| 21.036 | Modelling the structure and interactions of intrinsically disordered peptides with multiple-replica, metadynamics-based sampling methods and force-field combinations | bio | Bias Exchange Metadynamics, PTWTE-metaD | Matteo Salvalaglio | UPPER_WALLS LOWER_WALLS ANTIBETARMSD DIHCOR RANDOM_EXCHANGES PARABETARMSD PRINT METAD GROUP MOLINFO ENERGY GYRATION COORDINATION ALPHARMSD WHOLEMOLECULES | generic bias secondarystructure core multicolvar colvar |
| 21.033 | Multiple-path-metadynamics applied to DNA base-pairing transitions | bio | path-CV, metadynamics, multiple-walker, dna | Alberto Pérez-de-Alba-Ortíz | UPPER_WALLS COMBINE MOVINGRESTRAINT CONSTANT PRINT METAD INCLUDE RESTRAINT | function bias generic |
| 21.010 | Step by Step Strecker Amino Acid Synthesis from Ab Initio Prebiotic Chemistry | chemistry | Strecker reaction, free energy landscape, ab initio molecular dynamics, glycine, prebiotic synthesis | Théo Magrino | generic | |
| 20.028 | Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane | bio | metadynamics, KRas-4B, anionic membrane | Huixia Lu | FIT_TO_TEMPLATE PRINT METAD DISTANCE RESTART CENTER | generic bias setup vatom colvar |
| 20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Vojtech Spiwok | TORSION PRINT METAD | generic colvar bias |
| 19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | UPPER_WALLS PRINT ENERGY METAD MOLINFO GYRATION DISTANCE COM | generic vatom colvar bias |
| 19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Matteo Salvalaglio | TORSION CONVERT_TO_FES REWEIGHT_BIAS COMMITTOR PRINT METAD DUMPGRID MATHEVAL READ DISTANCE EXTERNAL REWEIGHT_METAD HISTOGRAM BIASVALUE | generic bias function gridtools colvar |
| 19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Jim Pfaendtner | PRINT ENERGY METAD GYRATION WHOLEMOLECULES | generic colvar 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 | TORSION STATS FLUSH PBMETAD PRINT METAINFERENCE JCOUPLING MOLINFO CS2BACKBONE GYRATION ENDPLUMED ENSEMBLE RDC BIASVALUE WHOLEMOLECULES | generic bias isdb function colvar |
| 19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Glen Hocky | TORSION COMBINE EDS PRINT DISTANCE RESTRAINT | generic bias eds function colvar |
| 19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Matteo Salvalaglio | TORSION UPPER_WALLS LOWER_WALLS COMMITTOR PRINT METAD DISTANCE CENTER | generic vatom colvar bias |
| 25.018 | Metainference simulation for dimerization of RNA binding protein | bio | Metainference, Metadynamics, SAXS, protein dimer | Debadutta Patra | PRINT SAXS UPPER_WALLS WHOLEMOLECULES MOLINFO DISTANCE PBMETAD METAINFERENCE ENSEMBLE FLUSH GYRATION STATS CENTER TORSION | colvar vatom isdb function generic bias |
| 25.014 | Atomic resolution ensembles of intrinsically disordered and multi-domain proteins with Alphafold | bio | bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement | Vincent Schnapka | GROUP BIASVALUE PRINT BAIES | bias core isdb 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 | CONSTANT UPPER_WALLS INCLUDE CUSTOM BIASVALUE TORSION OPES_METAD_EXPLORE GROUP COORDINATION CONTACTMAP RMSD PRINT ECV_MULTITHERMAL LOWER_WALLS PROJECTION_ON_AXIS MOLINFO COM METAD RESTART ENERGY WRAPAROUND WHOLEMOLECULES MATHEVAL OPES_EXPANDED | colvar vatom core function generic setup bias opes |
| 24.001 | A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations | bio | OPES, OPES-Flooding, QM/MM, Kinetics, Enzyme Catalysis | Dhiman Ray | PRINT LOWER_WALLS UPPER_WALLS OPES_METAD FLUSH COMBINE DISTANCE CUSTOM COMMITTOR UNITS TORSION | colvar function generic setup bias opes |
| 23.029 | An accurate and efficient SAXS/SANS implementation including solvation layer effects suitable for restrained Molecular Dynamics simulations | bio | SAXS, SANS, SAS, metainference, proteins, nucleic-acid | Federico Ballabio | WRAPAROUND PRINT GROUP SAXS MOLINFO UPPER_WALLS RMSD DISTANCE ENSEMBLE STATS CENTER BIASVALUE | colvar vatom core isdb function generic bias |
| 23.018 | Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention | materials | metadynamics, surface binding, peptide adsorption | Kaylyn Torkelson | PRINT UPPER_WALLS PBMETAD DISTANCE COM GYRATION | bias colvar generic vatom |
| 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 PRINT ECV_MULTITHERMAL ENDPLUMED MOLINFO DISTANCE OPES_EXPANDED METAD ENERGY TORSION | bias colvar opes generic |
| 22.026 | Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification | materials | Peptoid, silica | Jim Pfaendtner | PRINT UPPER_WALLS PBMETAD MOLINFO DISTANCE COM GYRATION | bias colvar generic vatom |
| 22.019 | Exploring aspartic protease inhibitor binding to design selective antimalarials | bio | ligand binding, loop opening, path CV, funnel metadynamics, drug development | Raitis Bobrovs | FUNNEL_PS PRINT LOWER_WALLS UPPER_WALLS PATHMSD WHOLEMOLECULES FUNNEL DISTANCE COM METAD | colvar funnel vatom generic bias |
| 22.006 | Peptide framework for screening the effects of amino acids on assembly | bio | metadynamics, peptides | Andrew White | DISTANCES GROUP PRINT COMBINE INCLUDE COM REWEIGHT_BIAS HISTOGRAM METAD CONVERT_TO_FES GYRATION DUMPGRID | colvar vatom function multicolvar bias generic gridtools core |
| 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 | TD_WELLTEMPERED VES_LINEAR_EXPANSION BF_CUBIC_B_SPLINES UPPER_WALLS INCLUDE BF_GAUSSIANS UNITS VES_OUTPUT_BASISFUNCTIONS COORDINATION DISTANCE BF_WAVELETS OPT_ADAM POSITION PRINT TD_UNIFORM FLUSH METAD ENERGY OPT_AVERAGED_SGD BF_CHEBYSHEV BF_LEGENDRE | colvar ves generic setup bias |
| 21.047 | Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations | materials | pair entropy, metadynamics, ves, solids, crystallization | Pablo Piaggi | TD_WELLTEMPERED VOLUME PAIRENTROPY PRINT VES_LINEAR_EXPANSION LOAD OPT_AVERAGED_SGD COMBINE METAD RESTART ENERGY BF_LEGENDRE | colvar function ves generic setup gridtools bias |
| 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 | EMMI PRINT GROUP UPPER_WALLS MOLINFO WHOLEMOLECULES DISTANCE COM RESTART BIASVALUE | colvar vatom core isdb generic setup bias |
| 21.028 | From Enhanced Sampling to Reaction Profiles | methods | collective variables, multi-state, machine learning, Deep-TDA | Enrico Trizio | DISTANCES UPPER_WALLS FIT_TO_TEMPLATE UNITS ANGLE TORSION GROUP ENDPLUMED COORDINATION DISTANCE PRINT LOWER_WALLS CENTER FIXEDATOM LOAD OPES_METAD WHOLEMOLECULES PYTORCH_MODEL MATHEVAL | colvar vatom core function multicolvar generic setup bias opes pytorch |
| 21.025 | Computational and biochemical analysis of type IV pilus dynamics and stability | bio | molecular dynamics, calcium binding, Type IV pilus | Yasaman Karami | LOWER_WALLS UPPER_WALLS PRINT DISTANCE | bias colvar generic |
| 21.016 | MD SAXS GTPase associated center | bio | metadynamics, RNA, folding, SAXS | Giovanni Bussi | PRINT GROUP LOWER_WALLS SAXS MOLINFO WHOLEMOLECULES UPPER_WALLS CUSTOM INCLUDE ERMSD METAD GYRATION | colvar core isdb function generic bias |
| 21.002 | Phase equilibrium of water with hexagonal and cubic ice using the SCAN functional | materials | ice, water, SCAN, OPES, VES, multithermal, crystallization, environment similarity, refcv, reweighting | Pablo Piaggi | VOLUME VES_LINEAR_EXPANSION PRINT OPT_AVERAGED_SGD ECV_MULTITHERMAL_MULTIBARIC TD_UNIFORM ENVIRONMENTSIMILARITY UPPER_WALLS RESTART MATHEVAL OPES_EXPANDED ECV_UMBRELLAS_LINE BF_LEGENDRE Q6 ENERGY | colvar symfunc envsim function ves generic setup bias opes |
| 19.049 | Determining the sizes of solid/liquid clusters in MD trajectories of nucleation | methods | nucleation, metadynamics, clustering, Steinhardt order parameters | Gareth Tribello | DISTANCES CLUSTER_NATOMS CONTACT_MATRIX PRINT ONES COORDINATIONNUMBER LOCAL_Q6 OUTER_PRODUCT MATRIX_VECTOR_PRODUCT SMAC CLUSTER_DISTRIBUTION CUSTOM OUTPUT_CLUSTER CLUSTER_PROPERTIES METAD Q6 MORE_THAN DFSCLUSTERING | clusters symfunc function multicolvar generic adjmat bias matrixtools |
| 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 GROUP LOWER_WALLS UPPER_WALLS COORDINATION FLUSH METAD RESTART UNITS POSITION | colvar core generic setup bias |
| 19.032 | Chemical reaction in solution using path collective variables based on coordination patterns | chemistry | chemical reactions, solutions, metadynamics, coordination patterns | Fabio Pietrucci | DISTANCES PRINT PATH UPPER_WALLS FLUSH METAD RESTART | mapping multicolvar generic setup bias |
| 25.016 | Advancing in silico drug design with Bayesian refinement of AlphaFold models | bio | bAIes, AlphaFold, Bayesian refinement, virtual screening, docking, small-molecule, enrichment | Samiran Sen | BIASVALUE BAIES PRINT GROUP | isdb bias generic core |
| 25.001 | RNA G-quadruplex folding with ST-metaD protocol | bio | RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | MOLINFO COMBINE WHOLEMOLECULES ERMSD METAD | function generic bias colvar |
| 25.000 | Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer | bio | metadynamics, pathCV | Sahithya Sridharan Iyer | MOLINFO UPPER_WALLS FUNCPATHGENERAL PRINT WHOLEMOLECULES RESTART DISTANCE METAD GROUP COM | function generic bias colvar vatom setup core |
| 24.033 | Transient interactions between the fuzzy coat and the cross-b core of brain-derived Ab42 filaments | bio | CryoEM, MEMMI, Metadynamics, Metainference, Ab42 Fibrils, structural ensemble | Maria Milanesi | ALPHARMSD PBMETAD MOLINFO UPPER_WALLS COORDINATION PRINT CENTER DUMPMASSCHARGE DUMPATOMS WHOLEMOLECULES DISTANCE PARABETARMSD BIASVALUE RMSD EMMI GROUP COM | core bias generic colvar vatom secondarystructure isdb |
| 24.031 | DeepLNE | methods | PATHCV, OPES, OneOPES | Thorben Fröhlking | ENERGY ECV_MULTITHERMAL MOLINFO OPES_EXPANDED COMBINE COORDINATION PRINT RESTART VOLUME OPES_METAD_EXPLORE ERMSD PYTORCH_MODEL | pytorch function generic colvar setup opes |
| 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 | ENERGY MATHEVAL COMMITTOR MOLINFO PRINT RESTRAINT RESTART DISTANCE TORSION COORDINATIONNUMBER BIASVALUE METAD FLUSH | function generic bias colvar symfunc setup |
| 24.007 | SWISH-X | bio | swish-x, SWISH-X, swish, expanded SWISH | Alberto Borsatto | CONTACTMAP ENERGY ECV_MULTITHERMAL MOLINFO UPPER_WALLS OPES_EXPANDED PRINT WHOLEMOLECULES INCLUDE | opes generic bias colvar |
| 24.006 | Water vapor condensation | chemistry | metadynamics, homogeneous condensation, chemical potential | Shenghui Zhong | UPPER_WALLS CLUSTER_PROPERTIES CLUSTER_NATOMS PRINT CONTACT_MATRIX DFSCLUSTERING COORDINATIONNUMBER METAD UNITS | adjmat generic bias clusters symfunc 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 | COORDINATION PRINT WHOLEMOLECULES GYRATION DISTANCE TORSION MOVINGRESTRAINT INCLUDE ALPHABETA COM | generic multicolvar bias colvar vatom |
| 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 | MOLINFO UPPER_WALLS WRAPAROUND POSITION PRINT SHADOW CENTER FIT_TO_TEMPLATE DISTANCES WHOLEMOLECULES METAD GROUP | generic bias colvar multicolvar vatom core isdb |
| 23.028 | Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process | chemistry | Ammonia decomposition; Dynamics;OPES; Neural Network potential | Manyi Yang | ZDISTANCES ENERGY GROUP OPES_METAD MATHEVAL UPPER_WALLS COMMITTOR PRINT DISTANCES FIXEDATOM DISTANCE LOWER_WALLS COORDINATIONNUMBER CUSTOM FLUSH UNITS COM | function bias multicolvar colvar generic symfunc vatom setup core opes |
| 23.021 | Into the Dynamics of Rotaxanes at Atomistic Resolution | materials | metadynamics, rotaxanes, molecular shuttles, molecular machines | Luigi Leanza | MATHEVAL UPPER_WALLS PRINT CENTER FIXEDATOM DISTANCE TORSION METAD CUSTOM | function bias generic colvar vatom |
| 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 | MATHEVAL UPPER_WALLS CONSTANT PRINT WHOLEMOLECULES DISTANCE LOWER_WALLS BIASVALUE METAD | function bias colvar generic |
| 22.040 | From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure | bio | SARS-CoV-2, Spike, Omicron | Miłosz Wieczór | UPPER_WALLS PRINT WHOLEMOLECULES LOWER_WALLS METAD PCAVARS | mapping bias generic |
| 22.036 | Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction | bio | Well-tempered MetaDynamics with Hamiltonian Replica Exchange | Miroslav Krepl | GHBFIX MOLINFO UPPER_WALLS COMBINE COORDINATION PRINT FLUSH LOAD BIASVALUE METAD CUSTOM GROUP | function generic bias colvar setup core |
| 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 MOLINFO UPPER_WALLS COORDINATION PRINT WHOLEMOLECULES RESTART TORSION EMMI BIASVALUE RMSD GROUP COM | bias generic colvar vatom setup core isdb |
| 22.017 | Water regulates the residence time of Benzamidine in Trypsin | bio | ligand binding, water, opes, benzamidine trypsin, unbinding rates, machine learning, Deep-LDA, Deep-TICA | Narjes Ansari | OPES_METAD MATHEVAL UPPER_WALLS COMMITTOR COORDINATION PRINT CENTER FIT_TO_TEMPLATE FIXEDATOM WHOLEMOLECULES DISTANCE LOWER_WALLS RMSD PYTORCH_MODEL CUSTOM GROUP | pytorch function bias generic colvar vatom core opes |
| 22.016 | Homogeneous ice nucleation in an ab initio machine learning model of water | chemistry | ice, water, nucleation, seeding, environment similarity, interfacial free energy, interfaces | Pablo Piaggi | ENERGY AROUND OPES_METAD UPPER_WALLS PRINT HISTOGRAM RESTART VOLUME ENVIRONMENTSIMILARITY CUSTOM DUMPGRID | function bias generic colvar gridtools volumes setup envsim opes |
| 21.048 | Enhancing ligand exploration within a channel pore and fenestrations using metadynamics | bio | well-tempered metadynamics, protein-ligand enhanced sampling, sodium channel, Nav, small molecule drug | Elaine Tao | UPPER_WALLS PRINT DISTANCE TORSION LOWER_WALLS METAD CUSTOM COM UNITS | function bias generic colvar vatom setup |
| 21.023 | Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling | methods | enhanced sampling, collective variables, machine learning | Jakub Rydzewski | ENERGY CONSTANT PRINT DISTANCE TORSION REWEIGHT_METAD BIASVALUE INCLUDE METAD CUSTOM UNITS | function generic bias colvar setup |
| 21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Adriana Pietropaolo | MATHEVAL PBMETAD CONSTANT PRINT WHOLEMOLECULES RESTART TORSION BIASVALUE | function bias generic colvar setup |
| 21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Tarsis Ferreira | ENERGY UPPER_WALLS MOLINFO RANDOM_EXCHANGES COORDINATION PRINT HISTOGRAM WHOLEMOLECULES DISTANCE LOWER_WALLS PUCKERING INCLUDE METAD REWEIGHT_METAD GROUP DUMPGRID | bias generic colvar gridtools core |
| 19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Giovanni Bussi | COORDINATION RESTRAINT WHOLEMOLECULES DISTANCE LOWER_WALLS ENDPLUMED | bias colvar generic |
| 19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Matteo Salvalaglio | PRINT CENTER DISTANCE INCLUDE ENDPLUMED GROUP | vatom generic colvar core |
| 19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Mattia Bernetti | UPPER_WALLS PRINT PATHMSD WHOLEMOLECULES LOWER_WALLS METAD | bias colvar generic |
| 19.040 | Optimal Metric for Path Collective Variables | bio | metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path | Francesco Luigi Gervasio | MATHEVAL PRINT TORSION ENDPLUMED METAD | function generic bias colvar |
| 19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Vittorio Limongelli | FUNNEL_PS UPPER_WALLS PRINT FUNNEL WHOLEMOLECULES DISTANCE LOWER_WALLS RMSD METAD COM | bias generic funnel colvar vatom |
| 19.035 | Dimerization of GPCRs from coarse-grained umbrella sampling | bio | Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization | Davide Provasi | RESTRAINT PRINT TORSION DISTANCE GROUP COM | bias generic colvar vatom core |
| 19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Mattia Bernetti | ALPHARMSD ENERGY MOLINFO PRINT WHOLEMOLECULES GYRATION ENDPLUMED METAD | generic bias colvar secondarystructure |
| 19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Carlo Camilloni | GROUP METAINFERENCE PBMETAD MOLINFO UPPER_WALLS PRINT CENTER RDC RESTRAINT STATS WHOLEMOLECULES DIHCOR ENSEMBLE DISTANCE TORSION ENDPLUMED ALPHABETA DHENERGY | function isdb bias generic multicolvar colvar vatom core |
| 19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Max Bonomi | MOLINFO PRINT WHOLEMOLECULES EMMI BIASVALUE GROUP | isdb generic bias core |
| 25.009 | Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water | chemistry | metadynamics, nitrate photolysis | Kam-Tung Chan | UPPER_WALLS READ CUSTOM RESTART METAD REWEIGHT_METAD DISTANCE HISTOGRAM COORDINATION GROUP DUMPGRID PRINT FLUSH | bias core generic function setup gridtools colvar |
| 25.008 | Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting | methods | metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting | Dhiman Ray | UPPER_WALLS MOLINFO PYTORCH_MODEL CUSTOM METAD OPES_METAD LOWER_WALLS DISTANCE TORSION ENERGY GROUP BIASVALUE WHOLEMOLECULES POSITION RMSD UNITS ENDPLUMED PRINT | bias core generic function setup pytorch opes colvar |
| 24.024 | Host-Guest binding free energies à la carte, an automated OneOPES protocol | bio | OneOPES, ligand binding, binding free energy,SAMPL challenge, host-guest | Valerio Rizzi | UPPER_WALLS MATHEVAL ECV_MULTITHERMAL LOWER_WALLS ANGLE DISTANCE TORSION GROUP COORDINATION ENERGY FIT_TO_TEMPLATE WHOLEMOLECULES FIXEDATOM OPES_EXPANDED OPES_METAD_EXPLORE ENDPLUMED PRINT CENTER | bias core generic function vatom opes colvar |
| 24.020 | Graph Neural Network-State Predictive Information Bottleneck (GNN-SPIB) approach for learning molecular thermodynamics and kinetics | bio | LJ7, alanine, well-tempered metadynamics, infrequent metadynamics, machine learning | Ziyue Zou, Dedi Wang, Pratyush Tiwary | METAD COMMITTOR GROUP LOAD TORSION PRINT | bias core generic setup colvar |
| 24.019 | Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning | bio | OPES, machine learning, protein folding, adaptive sampling | Mingyuan Zhang | MOLINFO CUSTOM OPES_METAD GYRATION DISTANCE COORDINATION WHOLEMOLECULES ALPHARMSD COMBINE TORSION PRINT | secondarystructure generic function opes colvar |
| 24.014 | Learning Collective Variables with Synthetic Data Augmentation through Physics-inspired Geodesic Interpolation | methods | data augmentation, geodesic interpolation, collective variables, protein folding | Juno Nam | UPPER_WALLS MOLINFO PYTORCH_MODEL METAD LOWER_WALLS DRR COORDINATION WHOLEMOLECULES RMSD PRINT FLUSH | bias generic drr pytorch colvar |
| 23.044 | Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition | materials | metadynamics, interlocked molecules | Luigi Leanza | READ CONVERT_TO_FES METAD COMMITTOR GROUP COORDINATION HISTOGRAM DUMPGRID ENDPLUMED PRINT | bias core generic gridtools colvar |
| 23.037 | Estimating binding free energy of solid binding peptides without extensive sampling | bio | metadynamics, solid binding peptides | Xin Qi | UPPER_WALLS MOLINFO LOWER_WALLS GYRATION DISTANCE COM PBMETAD PRINT | generic vatom bias colvar |
| 23.024 | Permutationally Invariant Networks for Enhanced Sampling (PINES) | methods | collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent | Nicholas Herringer | PBMETAD PRINT LOAD | generic setup bias |
| 23.023 | Rational design of novel biomimetic sequence-defined polymers for mineralization applications | methods | metadynamics, surface binding, biomimetic mineralization | Kaylyn Torkelson | UPPER_WALLS GYRATION DISTANCE COORDINATION COM PBMETAD PRINT | generic vatom bias colvar |
| 23.016 | Activation/deactivation free-energy profiles for the β2-adrenergic receptor: Ligand modes of action | bio | G protein coupled receptor, beta-adrenergic, receptor activation, partial agonism, metadynamics | Timothy Clark | MATHEVAL READ MOLINFO CONVERT_TO_FES METAD REWEIGHT_METAD DISTANCE HISTOGRAM DUMPGRID WHOLEMOLECULES RMSD PRINT | bias generic function gridtools colvar |
| 23.000 | Atomistic simulations of RNA tetraloop folding via PTWTE-WTM | bio | parallel tempering, well-tempered metadynamics, well-tempered ensemble, RNA, Tetraloop, Folding | Gül Zerze | UPPER_WALLS METAD LOWER_WALLS ENERGY WHOLEMOLECULES CONTACTMAP PRINT | generic bias colvar |
| 22.044 | Colloid Crystallisation Analyses | materials | Q4, Q6, Pair Entropy, DFS | Aaron Finney | MFILTER_MORE Q6 LOCAL_Q6 CONTACT_MATRIX CLUSTER_NATOMS LOCAL_AVERAGE GROUP Q4 COMBINE MFILTER_LESS DFSCLUSTERING LOCAL_Q4 PRINT COORDINATIONNUMBER | adjmat clusters core symfunc multicolvar generic function |
| 22.042 | Metadynamics of NSP10 and variants | bio | metadynamics, NSP10, crystal structure, variants | Shozeb Haider | METAD TORSION PRINT | generic bias colvar |
| 22.035 | Deciphering the alphabet of disorder — Glu and Asp act differently on local but not global properties | bio | intrinsically disordered proteins, parallel bias metadynamics, protein | Kresten Lindorff-Larsen | GYRATION WHOLEMOLECULES PBMETAD TORSION MOLINFO | generic bias colvar |
| 22.029 | Angiotensin-1-7_Metadynamics | bio | Metadynamics, Angiotensin-(1-7), peptide | L.-América Chi | UPPER_WALLS METAD GYRATION LOWER_WALLS GROUP COORDINATION WHOLEMOLECULES PRINT FLUSH | generic core bias colvar |
| 22.028 | N-glycan conformer distributions in atomistic simulation | bio | REST2, RECT, N-glycan, pucker | Isabell Grothaus | READ CONVERT_TO_FES PRINT METAD HISTOGRAM DUMPGRID PUCKERING TORSION MOLINFO | generic gridtools bias colvar |
| 22.027 | Molecular Dynamics simulations of BANAL-236 RBD-hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, BANAL-236, receptor-binding domain | Max Bonomi | RMSD PRINT | generic colvar |
| 22.013 | Ligand dissociation from PreQ1 riboswitch | bio | ligand, RNA, metadynamics, pRAVE | Yihang Wang | PRINT COMMITTOR METAD DISTANCE WHOLEMOLECULES COM RMSD COMBINE MOLINFO COORDINATIONNUMBER | bias symfunc generic function vatom colvar |
| 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 | UPPER_WALLS MATHEVAL MOLINFO CUSTOM METAD LOWER_WALLS DISTANCE WHOLEMOLECULES COM YANGLES ALPHABETA ZANGLES XANGLES COMBINE TORSION PRINT | bias multicolvar generic vatom function colvar |
| 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 | UPPER_WALLS METAD GYRATION LOWER_WALLS DISTANCE COORDINATION COM UNITS COMBINE COORDINATIONNUMBER FLUSH | bias symfunc generic function vatom setup colvar |
| 22.000 | Amyloid precursor protein processing by human γ-secretase | bio | Bias Exchange Metadynamics, Helix unfolding, coupled binding | Xiaoli Lu | RANDOM_EXCHANGES MOLINFO METAD INCLUDE DISTANCE COORDINATION ANTIBETARMSD UNITS CONTACTMAP ALPHARMSD PRINT CENTER | bias secondarystructure generic vatom setup 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 | METAD FIT_TO_TEMPLATE FIXEDATOM TORSION PRINT | generic vatom bias colvar |
| 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 METAD COORDINATION COMBINE ENDPLUMED PRINT | generic function bias colvar |
| 21.038 | Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics | materials | metadynamics, SGOOP, nucleation, urea | Ziyue Zou | VOLUME METAD INCLUDE GROUP ENERGY LOAD COMBINE COORDINATIONNUMBER PRINT CENTER | bias core symfunc generic function vatom setup colvar |
| 21.032 | Metal-coupled folding mechanism to metallothionein | bio | parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination | Manuel-Peris Diaz | GROUP COORDINATION WHOLEMOLECULES UNITS PBMETAD | bias core generic setup colvar |
| 21.022 | Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly | materials | parallel bias metadynamics, adsorption, peptide | Xin Qi | UPPER_WALLS MOLINFO GYRATION LOWER_WALLS DISTANCE ENERGY COM PBMETAD PRINT | generic vatom bias colvar |
| 21.017 | All-atom simulations of the Vav1 AD construct | bio | metadynamics, parallel-bias, well-tempered | Simone Orioli | MOLINFO RESTART PRINT METAD GROUP REWEIGHT_BIAS WHOLEMOLECULES ALPHABETA CONTACTMAP PBMETAD ALPHARMSD | bias core secondarystructure multicolvar generic setup colvar |
| 21.012 | NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition | bio | funnel metadynamics | Jim Pfaendtner | UPPER_WALLS FUNNEL_PS METAD LOWER_WALLS DISTANCE COM FUNNEL PRINT | funnel bias generic vatom colvar |
| 21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Kristof Bal | UPPER_WALLS CONVERT_TO_FES COMMITTOR MOVINGRESTRAINT METAD REWEIGHT_METAD HISTOGRAM DUMPGRID UNITS LOAD COORDINATIONNUMBER PRINT FLUSH | bias symfunc generic setup gridtools |
| 21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Kresten Lindorff-Larsen | METAINFERENCE SAXS EEFSOLV MOLINFO GYRATION ALPHARMSD BIASVALUE GROUP WHOLEMOLECULES CENTER PBMETAD PRINT FLUSH | bias core secondarystructure generic vatom isdb colvar |
| 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 | MOLINFO STATS COORDINATION WHOLEMOLECULES RESTRAINT COMBINE PRINT | generic function bias colvar |
| 20.006 | Class B GPCR activation mechanism | bio | metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | UPPER_WALLS MATHEVAL MOLINFO METAD LOWER_WALLS DISTANCE ENERGY WHOLEMOLECULES RMSD COMBINE PRINT CENTER | bias generic vatom function colvar |
| 19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Jakub Rydzewski | UPPER_WALLS RESTART METAD LOWER_WALLS PATHMSD UNITS PRINT | generic setup bias colvar |
| 19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | UPPER_WALLS MOLINFO METAD GYRATION DISTANCE ENERGY COM PRINT | generic vatom bias colvar |
| 19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Luigi Bonati | Q6 ENDPLUMED ENERGY POSITION ENVIRONMENTSIMILARITY UNITS LOAD TORSION PRINT | symfunc envsim generic setup colvar |
| 19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Gareth Tribello | MORE_THAN FOURIER_TRANSFORM MULTICOLVARDENS GROUP FIND_CONTOUR_SURFACE DUMPGRID UNITS FCCUBIC CENTER | contour core fourier symfunc function vatom setup gridtools |
| 19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Gareth Tribello | UPPER_WALLS AROUND METAD LOWER_WALLS CELL UNITS FCCUBIC ENDPLUMED PRINT | bias volumes symfunc generic setup colvar |
| 19.050 | Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes | chemistry | metadynamics, membranes, Willard Chandler surface | Gareth Tribello | UPPER_WALLS DISTANCE_FROM_CONTOUR READ CONVERT_TO_FES RESTART METAD HISTOGRAM REWEIGHT_BIAS DUMPGRID COMBINE PRINT | contour bias generic function setup gridtools |
| 19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | UPPER_WALLS METAD DISTANCE ENERGY UNITS COMBINE PRINT FLUSH | bias generic function setup colvar |
| 19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Paolo Raiteri | UPPER_WALLS MATHEVAL RESTART METAD DISTANCE UNITS PRINT FLUSH | bias generic function setup colvar |
| 19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Gabriele Cesare Sosso | MFILTER_MORE Q6 LOCAL_Q6 CONTACT_MATRIX CLUSTER_NATOMS CLUSTER_WITHSURFACE COMMITTOR OUTPUT_CLUSTER DFSCLUSTERING ENDPLUMED FLUSH | adjmat clusters symfunc multicolvar generic |
| 19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Adriana Pietropaolo | MATHEVAL METAD BIASVALUE WHOLEMOLECULES CONSTANT TORSION PRINT | generic function bias colvar |
| 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 | WHOLEMOLECULES GROUP CONVERT_TO_FES COORDINATION PRINT TORSION DISTANCE HISTOGRAM ANGLE DUMPGRID | gridtools core generic colvar |
| 24.035 | Data efficient machine learning potentials for modeling catalytic reactivity via active learning and enhanced sampling | chemistry | opes, catalysis, ammonia, machine learning potentials | Luigi Bonati | GROUP CUSTOM COORDINATION UNITS OPES_METAD UPPER_WALLS COMMITTOR PRINT LOWER_WALLS RESTART DISTANCE | bias setup function colvar opes core generic |
| 24.029 | Combination of OPES and OPES-Explore | methods | OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin | Dhiman Ray | FIT_TO_TEMPLATE GROUP CUSTOM METAD UPPER_WALLS PYTORCH_MODEL RMSD WHOLEMOLECULES FIXEDATOM BIASVALUE COORDINATION UNITS DISTANCE OPES_METAD_EXPLORE MATHEVAL ENDPLUMED INCLUDE PRINT FLUSH CONTACTMAP POSITION CENTER ENERGY MOLINFO OPES_METAD LOWER_WALLS COMBINE | bias vatom pytorch setup function colvar opes core generic |
| 24.018 | A new route to the prebiotic synthesis of glycine via ab initio-based machine learning calculations | chemistry | prebiotic chemistry, glycine, Strecker synthesis, ab initio calculations, machine learning | Léon HUET | PRINT DISTANCE | colvar generic |
| 24.016 | Cryo-EM guided simulations of ribozyme | bio | metainference, cryo-EM | Giovanni Bussi | EMMIVOX WHOLEMOLECULES GROUP ERMSD RESTRAINT BIASVALUE MOLINFO INCLUDE PRINT | bias colvar isdb core generic |
| 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 | EMMIVOX WHOLEMOLECULES GROUP MOLINFO BIASVALUE INCLUDE UPPER_WALLS PRINT DISTANCE WRAPAROUND | bias colvar isdb core generic |
| 23.038 | Determinants of Neutral Antagonism and Inverse Agonism in the β2-adrenergic receptor | bio | protein coupled receptor, beta-adrenergic, receptor activation, antagonism, inverse agonism, metadynamics | Timothy Clark | WHOLEMOLECULES MATHEVAL MOLINFO METAD PRINT DISTANCE RMSD | function bias generic colvar |
| 23.033 | DNA G-quadruplex and G-hairpin folding with ST-metaD protocol | bio | DNA, G4, GQ, quadruplex, hairpin, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | WHOLEMOLECULES ERMSD MOLINFO BIASVALUE METAD COORDINATION PRINT GHBFIX COMBINE | function colvar bias generic |
| 23.019 | Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors | bio | binding pathway, binding energy, sketch-map, drug development | Raitis Bobrovs | COM WHOLEMOLECULES VORONOI VSTACK SKETCHMAP_PROJECTION TRANSPOSE PATHMSD DISSIMILARITIES CUSTOM METAD UPPER_WALLS PRINT LANDMARK_SELECT_FPS DISTANCE SKETCHMAP COLLECT_FRAMES | dimred bias vatom colvar function landmarks matrixtools valtools generic |
| 22.033 | Reciprocal barrier restraint. Application to PROTAC passive permeability prediction | methods | PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR | Istvan Kolossvary | COM CUSTOM BIASVALUE METAD UNITS PRINT DISTANCE FLUSH DRR | bias vatom setup function colvar drr generic |
| 22.021 | Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn Løland Bore | ENVIRONMENTSIMILARITY OPES_EXPANDED INCLUDE ECV_UMBRELLAS_LINE UPPER_WALLS PRINT LOWER_WALLS | envsim bias opes generic |
| 22.009 | Glycosylation in calixarenes capsule | chemistry | Metadynamics, glycosylation, supramolecular catalysis | GiovanniMaria Piccini | FIT_TO_TEMPLATE WHOLEMOLECULES RMSD GROUP MATHEVAL DISTANCES METAD COORDINATION UNITS UPPER_WALLS PRINT BRIDGE LOWER_WALLS ANGLE FLUSH COMBINE DISTANCE | bias adjmat setup colvar function multicolvar core generic |
| 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 ALPHABETA MOLINFO METAD COORDINATION ALPHARMSD UPPER_WALLS TORSION ANGLE DISTANCE PRINT FLUSH | bias colvar secondarystructure multicolvar generic |
| 21.029 | Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs | bio | metadynamics, small peptide, machine learning | Pratyush Tiwary | ENERGY MOLINFO PRINT TORSION EXTERNAL FLUSH RESTART | colvar bias generic setup |
| 21.027 | EGFR activating mutations mechanism | bio | metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA | Francesco Gervasio | WHOLEMOLECULES MATHEVAL ENERGY MOLINFO METAD INCLUDE ALPHARMSD UPPER_WALLS PRINT LOWER_WALLS CONTACTMAP DISTANCE | bias function colvar secondarystructure generic |
| 21.019 | Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations | materials | Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen | Matteo Salvalaglio | COM MATHEVAL TORSIONS PRINT DISTANCE KDE | gridtools vatom function colvar multicolvar generic |
| 21.014 | how to determine statistically accurate conformational ensembles | bio | metadynamics, metainference, errors, cv, SAXS, ensemble determination | Cristina Paissoni | ENSEMBLE WHOLEMOLECULES GYRATION ALPHABETA MOLINFO BIASVALUE METAD SAXS STATS PBMETAD PRINT ANTIBETARMSD TORSION CONTACTMAP CENTER | bias vatom function colvar isdb secondarystructure multicolvar generic |
| 21.011 | CmuMD simulations of NaCl(aq) at graphite | chemistry | CmuMD, DFS clustering | Aaron Finney | CLUSTER_NATOMS DFSCLUSTERING DENSITY FIXEDATOM GROUP CONTACT_MATRIX DUMPGRID AROUND LOAD RESTRAINT MFILTER_MORE MULTICOLVARDENS PRINT COORDINATIONNUMBER CLUSTER_DISTRIBUTION | gridtools bias adjmat vatom volumes clusters setup symfunc multicolvar core generic |
| 21.006 | OPES, On-the-fly Probability Enhanced Sampling Method | methods | opes, alanine dipeptide, well-tempered, multithermal, multiumbrella | Michele Invernizzi | ECV_MULTITHERMAL ENERGY ENDPLUMED OPES_EXPANDED ECV_UMBRELLAS_LINE OPES_METAD PRINT TORSION | colvar opes generic |
| 21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Tarak Karmakar | GROUP MATHEVAL LOAD OPES_METAD UPPER_WALLS PYTORCH_MODEL PRINT LOWER_WALLS FLUSH | bias setup pytorch function opes core generic |
| 20.032 | Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil | materials | clustering, conformational isomers | Matteo Salvalaglio | PRINT ENDPLUMED TORSION | colvar generic |
| 20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Cristina Paissoni | ENSEMBLE WHOLEMOLECULES GROUP RESTRAINT MOLINFO BIASVALUE SAXS STATS INCLUDE PRINT DISTANCE CENTER | bias vatom function colvar isdb core generic |
| 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 | COM MATHEVAL CONVERT_TO_FES ENDPLUMED METAD REWEIGHT_METAD LOWER_WALLS UPPER_WALLS PRINT DISTANCE HISTOGRAM COMBINE DUMPGRID ABMD READ | gridtools bias vatom function colvar generic |
| 19.080 | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | methods | ves, variationally enhanced sampling, vibrational excitation, chemical reactions | Kristof Bal | VES_LINEAR_EXPANSION COMBINE TD_GRID OPT_AVERAGED_SGD CONVERT_TO_FES BF_CHEBYSHEV TD_WELLTEMPERED COORDINATION UNITS LOWER_WALLS UPPER_WALLS EXTERNAL ANGLE DISTANCE PRINT FLUSH HISTOGRAM DUMPGRID | ves gridtools bias setup function colvar generic |
| 19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_OPTIMIZER_BIAS POSITION MAZE_SIMULATED_ANNEALING UNITS PRINT MAZE_LOSS | generic colvar maze setup |
| 19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Wei Chen | COM RESTRAINT ANN COMBINE POSITION | annfunc bias vatom function colvar |
| 19.056 | maze | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_OPTIMIZER_BIAS POSITION MAZE_SIMULATED_ANNEALING UNITS PRINT MAZE_LOSS | generic colvar maze setup |
| 19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | GiovanniMaria Piccini | ENERGY METAD UNITS UPPER_WALLS PRINT LOWER_WALLS FLUSH COMBINE DISTANCE | bias setup function colvar generic |
| 19.046 | Optimal Collective from short simulations for Benzamidine-Trypsin ligand binding | bio | VAC-MetaD, optimised collective variables, binding free energy, unbinding rates, benzamidine trypsin, Structure Activity Relation | Faidon Brotzakis | COM FUNNEL RMSD WHOLEMOLECULES GROUP ALPHABETA DISTANCES MOLINFO METAD REWEIGHT_METAD UPPER_WALLS TORSION BRIDGE LOWER_WALLS PRINT COMBINE DISTANCE | bias vatom adjmat colvar function funnel multicolvar core generic |
| 19.030 | Coarse-Grained MetaDynamics (CG-MetaD) | bio | Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy | Vittorio Limongelli | COM WHOLEMOLECULES METAD UPPER_WALLS PRINT LOWER_WALLS DISTANCE | generic colvar bias vatom |
| 19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Elena Papaleo | WHOLEMOLECULES GYRATION GROUP ALPHABETA MOLINFO METAD UPPER_WALLS PRINT LOWER_WALLS | bias colvar multicolvar core generic |
| 19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Jim Pfaendtner | GROUP ENERGY METAD COORDINATION EXTERNAL | colvar bias core |
| 19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Haochuan Chen | DRR PRINT TORSION | colvar drr generic |
| 19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Carlo Camilloni | WHOLEMOLECULES CENTER GROUP RESTRAINT MOLINFO BIASVALUE SAXS STATS ENDPLUMED INCLUDE UPPER_WALLS PRINT DISTANCE RMSD | bias vatom function colvar isdb core generic |
| 19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Giovanni Bussi | ERMSD DISTANCES MOLINFO METAD INCLUDE UPPER_WALLS PRINT ANGLE LOWER_WALLS RANDOM_EXCHANGES FLUSH COMBINE DISTANCE | bias colvar function multicolvar generic |
| 25.012 | A Machine Learning-Driven, Probability-Based Approach to Enzyme Catalysis | bio | enzyme catalysis, transition state, structure-activity relationship, free energy surface, reaction mechanism, water, alpha-amylase, sugar, QM/MM MD, OPES, committor function, machine learning | Sudip Das | BIASVALUE LOAD FLUSH ENERGY COORDINATION CUSTOM CELL POSITION OPES_METAD INCLUDE COMBINE DISTANCE TORSION MATHEVAL UNITS PRINT | function colvar generic opes setup bias |
| 25.010 | Kinetic rates calculation with Ratchet&Pawl MD | methods | kinetics, ligand binding, ABMD, ratchet&pawl MD | Riccardo Capelli | FLUSH COMMITTOR WHOLEMOLECULES DISTANCE COM ABMD GROUP PRINT | colvar generic core vatom bias |
| 24.034 | Umbrella sampling of ion in transporter SLC26A7 | bio | umbrella sampling, transporter, ions | Xiaoli Lu | RESTRAINT POSITION UNITS PRINT | colvar generic bias setup |
| 24.028 | All-atom simulations of RNA-membrane interactions | bio | metadynamics, membrane, RNA | Giovanni Bussi | SORT PUCKERING WHOLEMOLECULES MOLINFO POSITION CENTER DISTANCE COMBINE LOWER_WALLS DISTANCES GHOST MATHEVAL UPPER_WALLS METAD GROUP PRINT GYRATION | function multicolvar colvar generic core vatom bias |
| 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 | PYTORCH_MODEL CUSTOM COORDINATION RESTART PATH WHOLEMOLECULES FIXEDATOM CENTER DISTANCE LOWER_WALLS TORSION UPPER_WALLS OPES_METAD FIT_TO_TEMPLATE GROUP PRINT | function colvar generic pytorch opes core mapping setup vatom bias |
| 24.009 | Weighted Shape Gaussian Mixture Models | bio | metadynamics, clustering | Glen Hocky | TORSION UNITS METAD GROUP PRINT | colvar generic core setup bias |
| 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 | FLUSH SELECT_COMPONENTS SUM MATHEVAL INCLUDE TRANSPOSE METAD PRINT | function generic valtools bias matrixtools |
| 23.040 | Supramolecular capsules assembly dynamics | chemistry | Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics | Riccardo Capelli | FLUSH CUSTOM WHOLEMOLECULES POSITION CENTER DISTANCE COM DISTANCES UNITS METAD GROUP PRINT | function multicolvar colvar generic core setup vatom bias |
| 23.027 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, DFS, Q3, Pair Entropy | Aaron Finney | AROUND LOAD DFSCLUSTERING CLUSTER_NATOMS RESTRAINT LOCAL_Q3 FIXEDATOM Q3 LOCAL_AVERAGE HISTOGRAM UNITS DUMPGRID COORDINATIONNUMBER CONTACT_MATRIX PRINT DENSITY GROUP CLUSTER_DISTRIBUTION | generic clusters symfunc gridtools core volumes setup vatom bias adjmat |
| 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 | BIASVALUE FLUSH CUSTOM DRR PATHMSD LOWER_WALLS UPPER_WALLS UNITS METAD PRINT TIME | function colvar generic setup bias drr |
| 23.007 | Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains | bio | metadynamics, peptoids, parallel-bias metadynamics | Jim Pfaendtner | COORDINATION RESTRAINT PBMETAD WHOLEMOLECULES INCLUDE COM TORSION PRINT GYRATION | colvar generic vatom bias |
| 22.032 | Reciprocal barrier restraint. Application to path-meta-eABF | methods | restraint, upper wall, lower wall, path colvar, meta-eABF, metadynamics, DRR, protein conformational transition, PROTAC | Istvan Kolossvary | BIASVALUE FLUSH CUSTOM DRR PATHMSD METAD PRINT | function colvar generic bias drr |
| 22.022 | Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir | bio | RMSD, protein-ligand interactions | Isabell Grothaus | PRINT RMSD | colvar generic |
| 22.012 | Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT | bio | contact maps, protein-protein interactions | Isabell-Louise Grothaus | DISTANCE CONTACTMAP PRINT CENTER | colvar generic vatom |
| 22.004 | Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques | chemistry | reaction discovery, OPES, collective variables | Umberto Raucci | PYTORCH_MODEL LOAD OPES_METAD_EXPLORE CUSTOM COORDINATION MATHEVAL LOWER_WALLS DISTANCE COM UPPER_WALLS OPES_METAD UNITS GROUP PRINT | function colvar generic pytorch core setup bias vatom opes |
| 22.002 | GAMBES_SAMPL5_RATES | other | GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding | Jayashrita Debnath | PYTORCH_MODEL LOAD FLUSH ENERGY COORDINATION ENDPLUMED COMMITTOR WHOLEMOLECULES FIXEDATOM CENTER DISTANCE MATHEVAL UPPER_WALLS ANGLE FIT_TO_TEMPLATE GROUP PRINT | function colvar generic pytorch core setup vatom 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 | ENDPLUMED RANDOM_EXCHANGES PBMETAD TORSION PRINT METAD INCLUDE | colvar generic bias |
| 21.030 | Thermodynamic Basis for Stabilization of Helical Peptoids by Chiral Sidechains | bio | parallel bias parallel tempered metadynamics in WTE, synthetic foldamers, self-assembly, peptoid secondary structure | Jim Pfaendtner | ENERGY COORDINATION PBMETAD ALPHABETA INCLUDE DISTANCE COM TORSION METAD PRINT GYRATION | multicolvar colvar generic vatom bias |
| 21.013 | Role of vibrational excitation in heterogeneous catalysis | chemistry | catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption | Kristof Bal | FLUSH REWEIGHT_BIAS REWEIGHT_METAD BF_CHEBYSHEV TD_GRID RESTRAINT DISTANCE DISTANCES PRINT UWALLS ANGLES LOWER_WALLS DUMPGRID OPT_AVERAGED_SGD LOAD CONVERT_TO_FES COORDINATION EXTERNAL UPPER_WALLS COMBINE HISTOGRAM COORDINATIONNUMBER UNITS VES_LINEAR_EXPANSION METAD | multicolvar function colvar generic gridtools symfunc ves setup 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 | RESTART WHOLEMOLECULES PATHMSD LOWER_WALLS UPPER_WALLS METAD PRINT | setup generic colvar bias |
| 21.000 | Uremic toxin time scale dynamics | bio | uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs) | Jim Pfaendtner | WHOLEMOLECULES DISTANCE COM GROUP PRINT | colvar generic vatom core |
| 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 MULTI_RMSD RESTRAINT REWEIGHT_METAD HISTOGRAM DUMPGRID METAD PRINT | colvar generic bias gridtools |
| 20.018 | Free energy barriers from biased molecular dynamics simulations | methods | kinetics, free energy barriers, chemical reactions, nucleation, metadynamics | Kristof Bal | VOLUME FLUSH REWEIGHT_BIAS REWEIGHT_METAD LOCAL_AVERAGE Q6 CENTER DISTANCE PRINT LOWER_WALLS SPRINT DUMPGRID DENSITY LOAD CONVERT_TO_FES ENERGY COORDINATION COMBINE UPPER_WALLS HISTOGRAM COORDINATIONNUMBER UNITS CONTACT_MATRIX PAIRENTROPY METAD | function colvar generic gridtools symfunc sprint volumes setup vatom bias adjmat |
| 20.015 | Rational design of ASCT2 inhibitors using an integrated experimental-computational approach | bio | ASCT2 transporter, small-molecules, cryo-EM, metainference | Max Bonomi | BIASVALUE LOAD DUMPATOMS EMMIVOX WHOLEMOLECULES MOLINFO GROUP PRINT | generic isdb core setup bias |
| 19.076 | Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones | bio | molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics | Salvatore Assenza | ENDPLUMED MOVINGRESTRAINT UNITS PRINT GYRATION | setup generic colvar bias |
| 19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Michele Invernizzi | EXTERNAL ENDPLUMED POSITION OPES_METAD TORSION UNITS METAD PRINT | colvar generic setup bias opes |
| 19.059 | cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide | bio | bias-exchange metadynamics, cis-trans isomerization | Fabrizio Marinelli | RANDOM_EXCHANGES INCLUDE TORSION METAD PRINT | colvar generic bias |
| 19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Kim Jelfs | FLUSH RESTART MOVINGRESTRAINT COM DISTANCES PRINT INPLANEDISTANCES | multicolvar generic setup vatom bias |
| 19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Carlo Camilloni | BIASVALUE FLUSH ANTIBETARMSD ENDPLUMED RESTART PBMETAD WHOLEMOLECULES MOLINFO ALPHABETA LOWER_WALLS UPPER_WALLS GROUP CS2BACKBONE PRINT | multicolvar generic isdb core secondarystructure setup bias |
| 19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Pratyush Tiwary | EXTERNAL RESTART COMMITTOR WHOLEMOLECULES ALPHABETA DISTANCE COM COMBINE TORSION PRINT | multicolvar function colvar generic setup vatom bias |
| 19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Riccardo Capelli | READ CONVERT_TO_FES FLUSH COORDINATION ENDPLUMED WHOLEMOLECULES POSITION MATHEVAL UPPER_WALLS COM REWEIGHT_METAD HISTOGRAM DUMPGRID FIT_TO_TEMPLATE METAD GROUP WRAPAROUND PRINT | function colvar generic gridtools core vatom bias |
| 19.013 | RNA FF FITTING | methods | force field, RNA | Giovanni Bussi | BIASVALUE CONSTANT PUCKERING MOLINFO MATHEVAL TORSION INCLUDE | colvar function generic bias |
| 19.005 | Cmyc small molecule interaction | bio | metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP | Gabriella Heller | METAINFERENCE COORDINATION PBMETAD WHOLEMOLECULES MOLINFO ALPHABETA INCLUDE CENTER DISTANCE GROUP CS2BACKBONE PRINT GYRATION | multicolvar colvar generic isdb core vatom bias |