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 |
|---|---|---|---|---|---|---|
| 25.011 | Chiral perovskite nucleation | chemistry | metadynamics, chiral perovskites, nucleation | Adriana Pietropaolo | MATHEVAL MULTI_RMSD PRINT PBMETAD RESTART UNITS DISTANCE LOWER_WALLS UPPER_WALLS | function generic bias colvar setup |
| 25.010 | Kinetic rates calculation with Ratchet&Pawl MD | methods | kinetics, ligand binding, ABMD, ratchet&pawl MD | Riccardo Capelli | COMMITTOR PRINT COM DISTANCE FLUSH GROUP ABMD WHOLEMOLECULES | bias generic colvar vatom core |
| 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 | PATH PYTORCH_MODEL PRINT RESTART DISTANCE FIT_TO_TEMPLATE TORSION GROUP LOWER_WALLS FIXEDATOM CENTER OPES_METAD UPPER_WALLS COORDINATION CUSTOM WHOLEMOLECULES | bias generic function colvar vatom mapping setup opes pytorch core |
| 24.024 | Host-Guest binding free energies à la carte, an automated OneOPES protocol | bio | OneOPES, ligand binding, binding free energy,SAMPL challenge, host-guest | Valerio Rizzi | MATHEVAL ENERGY PRINT OPES_EXPANDED DISTANCE TORSION FIT_TO_TEMPLATE GROUP LOWER_WALLS FIXEDATOM CENTER ENDPLUMED ECV_MULTITHERMAL UPPER_WALLS COORDINATION ANGLE OPES_METAD_EXPLORE WHOLEMOLECULES | function generic bias colvar vatom opes core |
| 24.020 | Graph Neural Network-State Predictive Information Bottleneck (GNN-SPIB) approach for learning molecular thermodynamics and kinetics | bio | LJ7, alanine, well-tempered metadynamics, infrequent metadynamics, machine learning | Ziyue Zou, Dedi Wang, Pratyush Tiwary | COMMITTOR PRINT METAD TORSION GROUP LOAD | bias generic colvar setup core |
| 24.017 | Absolute Binding Free Energies with OneOPES | methods | protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy | Francesco Gervasio | MATHEVAL ENERGY INCLUDE RMSD TORSION GROUP BIASVALUE OPES_METAD_EXPLORE WRAPAROUND PRINT OPES_EXPANDED RESTART CONSTANT COORDINATION COM PROJECTION_ON_AXIS MOLINFO METAD UPPER_WALLS CUSTOM LOWER_WALLS ECV_MULTITHERMAL CONTACTMAP WHOLEMOLECULES | function generic bias colvar vatom setup opes core |
| 24.009 | Weighted Shape Gaussian Mixture Models | bio | metadynamics, clustering | Glen Hocky | PRINT UNITS METAD TORSION GROUP | bias generic colvar setup core |
| 24.004 | Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables | materials | metadynamics, nucleation, machine learning | Ziyue Zou | PRINT INCLUDE RESTART METAD GROUP LOAD | setup generic bias core |
| 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 | MATHEVAL PRINT METAD DISTANCE BIASVALUE LOWER_WALLS CONSTANT CENTER UPPER_WALLS WHOLEMOLECULES | function generic bias colvar vatom |
| 23.020 | FEP simulations of ATOX1 homodimer | chemistry | parallel bias metadynamics, FEP, free-energy of metal ion dissociation | Adriana Pietropaolo | MATHEVAL PRINT PBMETAD DISTANCE BIASVALUE CONSTANT ANGLE WHOLEMOLECULES | function generic colvar bias |
| 22.039 | Driving and characterizing nucleation of urea and glycine polymorphs in water | bio | metadynamics, nucleation, amino acids, polymorphism | Eric Beyerle | COMBINE MATHEVAL PRINT INCLUDE PAIRENTROPY METAD COORDINATIONNUMBER GROUP Q4 CENTER Q6 LOAD | function generic bias symfunc vatom setup gridtools core |
| 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 | generic 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 | COMBINE MATHEVAL PRINT COM DISTANCE MOLINFO METAD ZANGLES TORSION XANGLES LOWER_WALLS UPPER_WALLS ALPHABETA YANGLES CUSTOM WHOLEMOLECULES | function generic bias colvar multicolvar vatom |
| 22.007 | Characterization of a natural variant of human NDP52 and its functional consequences on mitophagy | bio | metadynamics, well-tempered, protein-protein interactions, disordered proteins, mutations autophagy | Elena Papaleo | PRINT MOLINFO DISTANCE TORSION METAD FLUSH ALPHABETA UPPER_WALLS COORDINATION ALPHARMSD ANGLE WHOLEMOLECULES | bias generic multicolvar colvar secondarystructure |
| 21.042 | Peptoid-mediated Au nanocrystal growth | materials | parallel-bias metadynamics, peptoid, Au | Xin Qi | PRINT COM PBMETAD DISTANCE MOLINFO GYRATION UPPER_WALLS | bias generic colvar vatom |
| 21.031 | Photo-switchable sulfonulureas in KATP channel | bio | metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels | Katarzyna Walczewska-Szewc | PRINT COM UNITS METAD DISTANCE LOWER_WALLS UPPER_WALLS WHOLEMOLECULES | bias generic colvar vatom setup |
| 21.026 | Probing allosteric regulations with coevolution-driven molecular simulations | bio | metadynamics, coevolution, allostery, adenylate cyclase | Francesco Colizzi | PRINT COM PATHMSD UNITS DISTANCE METAD UPPER_WALLS WHOLEMOLECULES | bias generic colvar vatom setup |
| 21.025 | Computational and biochemical analysis of type IV pilus dynamics and stability | bio | molecular dynamics, calcium binding, Type IV pilus | Yasaman Karami | UPPER_WALLS DISTANCE LOWER_WALLS PRINT | bias generic colvar |
| 21.018 | Localized Volume-based Metadynamics | bio | LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification | Riccardo Capelli | MATHEVAL READ RMSD GROUP POSITION PRINT DISTANCE FLUSH CONVERT_TO_FES REWEIGHT_METAD COORDINATION COM METAD ENDPLUMED FIXEDATOM UPPER_WALLS HISTOGRAM DUMPGRID WHOLEMOLECULES | function generic bias colvar vatom gridtools core |
| 21.017 | All-atom simulations of the Vav1 AD construct | bio | metadynamics, parallel-bias, well-tempered | Simone Orioli | REWEIGHT_BIAS PRINT PBMETAD RESTART WHOLEMOLECULES MOLINFO METAD GROUP CONTACTMAP ALPHARMSD ALPHABETA | bias generic multicolvar colvar setup secondarystructure core |
| 21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Kristof Bal | COMMITTOR HISTOGRAM UPPER_WALLS PRINT MOVINGRESTRAINT UNITS METAD COORDINATIONNUMBER FLUSH CONVERT_TO_FES DUMPGRID REWEIGHT_METAD LOAD | bias generic symfunc setup gridtools |
| 21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Tarsis Ferreira | HISTOGRAM DUMPGRID ENERGY PRINT RANDOM_EXCHANGES INCLUDE PUCKERING METAD DISTANCE MOLINFO GROUP LOWER_WALLS COORDINATION UPPER_WALLS REWEIGHT_METAD WHOLEMOLECULES | bias generic colvar gridtools core |
| 20.028 | Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane | bio | metadynamics, KRas-4B, anionic membrane | Huixia Lu | PRINT RESTART METAD DISTANCE FIT_TO_TEMPLATE CENTER | bias generic colvar vatom setup |
| 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 | PRINT STATS RESTRAINT MOLINFO COORDINATION WHOLEMOLECULES | function generic colvar bias |
| 20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Max Bonomi | PRINT PBMETAD INCLUDE WHOLEMOLECULES DIHCOR MOLINFO GYRATION COORDINATION ALPHABETA | bias generic colvar multicolvar |
| 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 | MATHEVAL PRINT COM PROJECTION_ON_AXIS INCLUDE FUNCPATHGENERAL WHOLEMOLECULES DISTANCE METAD MOLINFO GROUP BIASVALUE LOWER_WALLS CONSTANT CONTACTMAP UPPER_WALLS LOAD | function generic bias colvar vatom setup core |
| 20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Carlo Camilloni | PRINT PBMETAD STATS WHOLEMOLECULES SAXS DISTANCE MOLINFO TORSION FLUSH GYRATION CENTER METAINFERENCE ENSEMBLE ALPHABETA | bias generic function colvar multicolvar vatom isdb |
| 20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Pratyush Tiwary | COMBINE PRINT RESTART DISTANCE RMSD TORSION METAD MOLINFO UPPER_WALLS WHOLEMOLECULES | function generic bias colvar setup |
| 19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Valerio Rizzi | COMBINE DISTANCES PRINT UNITS RESTART METAD COORDINATIONNUMBER FLUSH GROUP ENDPLUMED UPPER_WALLS | function multicolvar generic bias symfunc setup core |
| 19.076 | Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones | bio | molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics | Salvatore Assenza | PRINT MOVINGRESTRAINT UNITS GYRATION ENDPLUMED | bias generic colvar setup |
| 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 | ENERGY DISTANCES PRINT METAD COORDINATIONNUMBER GYRATION LOWER_WALLS ENDPLUMED UPPER_WALLS | bias multicolvar generic colvar symfunc |
| 19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Sandro Bottaro | ERMSD PRINT MOLINFO RMSD TORSION DISTANCE METAD WHOLEMOLECULES | bias generic colvar |
| 19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Luigi Bonati | ENERGY PRINT UNITS ENVIRONMENTSIMILARITY TORSION ENDPLUMED Q6 POSITION LOAD | generic colvar symfunc envsim setup |
| 19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | COMBINE ENERGY PRINT UNITS DISTANCE METAD FLUSH UPPER_WALLS | function generic bias colvar setup |
| 19.032 | Chemical reaction in solution using path collective variables based on coordination patterns | chemistry | chemical reactions, solutions, metadynamics, coordination patterns | Fabio Pietrucci | PATH DISTANCES PRINT RESTART METAD FLUSH UPPER_WALLS | bias multicolvar generic mapping setup |
| 19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Matteo Salvalaglio | COMMITTOR PRINT METAD DISTANCE TORSION LOWER_WALLS CENTER UPPER_WALLS | bias generic colvar vatom |
| 25.022 | Imidazole Diffusion in SALEM-2 MOF | materials | OPES, Diffusion, Ring opening, MOFs, Machine Learning Potentials | Sudheesh Kumar Ethirajan | PRINT DISTANCES WHOLEMOLECULES ENDPLUMED CENTER DISTANCE MOLINFO GROUP OPES_METAD UNITS PROJECTION_ON_AXIS | generic colvar opes setup multicolvar core vatom |
| 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 PRINT BAIES GROUP | generic isdb bias core |
| 25.013 | Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices | bio | umbrella sampling, temperature ramping | Alexander Berlaga | PRINT DISTANCE RESTRAINT PYTORCH_MODEL GYRATION | generic bias colvar pytorch |
| 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 | INCLUDE POSITION PRINT MATHEVAL COMBINE CELL DISTANCE FLUSH BIASVALUE CUSTOM TORSION OPES_METAD UNITS ENERGY LOAD COORDINATION | generic bias colvar opes setup function |
| 25.008 | Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting | methods | metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting | Dhiman Ray | PYTORCH_MODEL PRINT WHOLEMOLECULES UPPER_WALLS ENDPLUMED DISTANCE MOLINFO GROUP BIASVALUE CUSTOM TORSION UNITS OPES_METAD LOWER_WALLS ENERGY METAD POSITION RMSD | generic bias colvar setup opes function core pytorch |
| 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 | UPPER_WALLS PRINT DISTANCES COMMITTOR COORDINATIONNUMBER GROUP FLUSH DISTANCE CUSTOM OPES_METAD UNITS FIXEDATOM ZDISTANCES | generic bias colvar symfunc opes setup multicolvar function core vatom |
| 25.002 | M3_PCV-ABMD | chemistry | Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor | Gian Marco Elisi | UPPER_WALLS PRINT ENDPLUMED UNITS ABMD PATHMSD | setup generic bias colvar |
| 24.034 | Umbrella sampling of ion in transporter SLC26A7 | bio | umbrella sampling, transporter, ions | Xiaoli Lu | UNITS POSITION PRINT RESTRAINT | generic setup colvar bias |
| 24.026 | Constant pH metadynamics of RNA oligomers | bio | metadynamics, pH, RNA | Giovanni Bussi | PRINT PUCKERING RESTART MOLINFO TORSION METAD | generic setup colvar bias |
| 24.014 | Learning Collective Variables with Synthetic Data Augmentation through Physics-inspired Geodesic Interpolation | methods | data augmentation, geodesic interpolation, collective variables, protein folding | Juno Nam | UPPER_WALLS PRINT PYTORCH_MODEL WHOLEMOLECULES MOLINFO FLUSH DRR LOWER_WALLS METAD RMSD COORDINATION | generic bias colvar drr pytorch |
| 24.012 | Molecular simulations to investigate the impact of N6-methylation in RNA recognition | bio | metadynamics, alchemistry, RNA modification, RNA:protein interactions | Giovanni Bussi | UPPER_WALLS PRINT COMBINE CENTER DEBUG DISTANCE MOLINFO GROUP COM BIASVALUE GHBFIX LOWER_WALLS METAD COORDINATION | generic bias colvar function core vatom |
| 24.001 | A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations | bio | OPES, OPES-Flooding, QM/MM, Kinetics, Enzyme Catalysis | Dhiman Ray | UPPER_WALLS PRINT COMBINE DISTANCE COMMITTOR FLUSH CUSTOM TORSION OPES_METAD UNITS LOWER_WALLS | generic bias colvar opes setup function |
| 23.044 | Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition | materials | metadynamics, interlocked molecules | Luigi Leanza | CONVERT_TO_FES PRINT HISTOGRAM READ ENDPLUMED COMMITTOR GROUP DUMPGRID METAD COORDINATION | generic bias colvar gridtools core |
| 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 | PRINT WHOLEMOLECULES DISTANCE MOLINFO METAD MATHEVAL RMSD | generic bias colvar function |
| 23.032 | Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics | bio | metadynamics, tSNE, neural network, machine learning, trp-cage, folding | Vojtech Spiwok | PRINT WHOLEMOLECULES ANN COMBINE ALPHARMSD MOLINFO FIT_TO_TEMPLATE METAD POSITION | generic bias colvar annfunc secondarystructure function |
| 23.017 | How and When Does an Enzyme React? Unraveling α-Amylase Catalytic Activity with Enhanced Sampling Techniques | bio | enzymatic reaction discovery, reaction mechanism, catalysis, ligand-binding modes, water, alpha-amylase, sugar, QM/MM MD, OPES, OPES explore, graph CV, machine learning, Deep TDA CV, path CV | Sudip Das | OPES_METAD_EXPLORE PRINT UPPER_WALLS WHOLEMOLECULES FIXEDATOM CENTER PATH DISTANCE GROUP FIT_TO_TEMPLATE CUSTOM TORSION LOWER_WALLS UNITS OPES_METAD PYTORCH_MODEL COORDINATION | generic mapping bias colvar pytorch opes setup function core vatom |
| 23.008 | PBMetaD simulations of Histatin5 | bio | metadynamics, IDP, Rg, PPII | Francesco Pesce | PRINT WHOLEMOLECULES MOLINFO GROUP TORSION PBMETAD GYRATION | generic core colvar bias |
| 22.025 | Bubble nucleation rate predictions in a Lennard-Jones fluid | materials | free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation | Kristof Bal | CONVERT_TO_FES UPPER_WALLS HISTOGRAM PRINT REWEIGHT_BIAS VOLUME ANN RESTRAINT COMMITTOR COORDINATIONNUMBER FLUSH BIASVALUE CUSTOM DUMPGRID UNITS MOVINGRESTRAINT LOAD | generic bias colvar annfunc symfunc setup gridtools function |
| 22.012 | Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT | bio | contact maps, protein-protein interactions | Isabell-Louise Grothaus | PRINT CENTER CONTACTMAP DISTANCE | generic colvar vatom |
| 22.009 | Glycosylation in calixarenes capsule | chemistry | Metadynamics, glycosylation, supramolecular catalysis | GiovanniMaria Piccini | UPPER_WALLS PRINT WHOLEMOLECULES DISTANCES COMBINE DISTANCE GROUP FLUSH FIT_TO_TEMPLATE ANGLE BRIDGE LOWER_WALLS UNITS METAD MATHEVAL RMSD COORDINATION | generic bias colvar setup multicolvar function core adjmat |
| 21.050 | N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity | methods | bio | Isabell Louise Grothaus | PRINT CENTER DISTANCE | generic colvar vatom |
| 21.045 | QM/MM metadynamics of thiol-disulfide exchange between methylthiolate and dimethyldisulfide in water with an imposed external electrostatic potential (ESP) | chemistry | metadynamics, QM/MM, electrostatic potential, thiol-disulfide exchange | Denis Maag | UPPER_WALLS PRINT COMBINE DISTANCE COORDINATIONNUMBER LOWER_WALLS METAD COORDINATION | generic bias colvar symfunc function |
| 20.034 | Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations | bio | RNA, SARS-CoV-2, partial tempering | Sandro Bottaro | PRINT ERMSD CENTER RESTART DISTANCE MOLINFO TORSION ABMD | generic bias colvar setup vatom |
| 20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Valerio Rizzi | UPPER_WALLS PRINT WHOLEMOLECULES FIXEDATOM ENDPLUMED CENTER DISTANCE GROUP FIT_TO_TEMPLATE ANGLE OPES_METAD ENERGY PYTORCH_MODEL MATHEVAL COORDINATION | generic bias colvar pytorch opes function core vatom |
| 20.024 | Gaussian Mixture Based Enhanced Sampling (GAMBES) | methods | enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias | Jayashrita Debnath | UPPER_WALLS PRINT DISTANCES COMBINE DISTANCE GROUP TORSION LOWER_WALLS UNITS ENERGY LOAD | generic bias colvar setup multicolvar function core |
| 20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Vojtech Spiwok | METAD PRINT TORSION | generic 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 PRINT WHOLEMOLECULES COMBINE CENTER DISTANCE MOLINFO LOWER_WALLS ENERGY METAD MATHEVAL RMSD | generic bias colvar function vatom |
| 19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_LOSS PRINT MAZE_OPTIMIZER_BIAS MAZE_SIMULATED_ANNEALING UNITS POSITION | setup generic maze colvar |
| 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 | UPPER_WALLS PRINT RESTART GROUP FLUSH LOWER_WALLS UNITS METAD POSITION COORDINATION | generic bias colvar setup core |
| 19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Paolo Raiteri | UPPER_WALLS PRINT RESTART DISTANCE FLUSH UNITS METAD MATHEVAL | generic bias colvar setup function |
| 19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Pratyush Tiwary | PRINT WHOLEMOLECULES COMBINE RESTART DISTANCE COM COMMITTOR TORSION ALPHABETA EXTERNAL | generic bias colvar setup multicolvar function vatom |
| 19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Mattia Bernetti | PRINT WHOLEMOLECULES ENDPLUMED ALPHARMSD MOLINFO ENERGY METAD GYRATION | secondarystructure generic bias colvar |
| 19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Matteo Salvalaglio | PRINT DISTANCES ENDPLUMED RESTART COORDINATIONNUMBER METAD GYRATION | generic bias colvar symfunc setup multicolvar |
| 19.003 | EMMI ClpP | bio | metainference, cryo-EM | Max Bonomi | PRINT MOLINFO GROUP EMMI BIASVALUE | generic isdb core bias |
| 25.020 | Revealing Water-Mediated Activation Mechanisms in the Beta 1-Adrenergic Receptor via OneOPES-Enhanced Free Energy Landscapes | bio | OneOPES, GPCR, ADRB1, activation, microswitches, conformational changes, allostery | Valerio Rizzi | ENERGY DISTANCES PATHMSD PRINT OPES_METAD_EXPLORE DISTANCE CUSTOM ECV_MULTITHERMAL OPES_EXPANDED GHOST RMSD LOWER_WALLS UPPER_WALLS CENTER COORDINATION GROUP | generic colvar function core multicolvar vatom bias opes |
| 25.019 | The Arch from the Stones. Understanding Protein Folding Energy Landscapes via Bio-inspired Collective Variables | bio | protein folding, OPES, OneOPES, binding free energy | Valerio Rizzi | ENERGY PRINT GHOST DISTANCE CUSTOM OPES_METAD_EXPLORE ECV_MULTITHERMAL OPES_EXPANDED RMSD COMBINE CENTER MOLINFO COORDINATION GROUP | generic colvar function core vatom opes |
| 25.018 | Metainference simulation for dimerization of RNA binding protein | bio | Metainference, Metadynamics, SAXS, protein dimer | Debadutta Patra | PRINT DISTANCE TORSION METAINFERENCE ENSEMBLE GYRATION CENTER MOLINFO WHOLEMOLECULES UPPER_WALLS PBMETAD SAXS FLUSH STATS | isdb generic colvar function vatom bias |
| 24.032 | DeepLNE++ | methods | PATHCV, OPES | Thorben Fröhlking | ENERGY PRINT DISTANCE CUSTOM TORSION COMBINE LOAD OPES_METAD COORDINATION GROUP | generic colvar function core 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 PRINT DISTANCE BIASVALUE MATHEVAL METAD RESTRAINT TORSION COMMITTOR COORDINATIONNUMBER MOLINFO RESTART FLUSH | generic colvar function bias setup symfunc |
| 24.011 | Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble | methods | committor, machine learning | Peilin Kang | PRINT MATHEVAL INCLUDE ENDPLUMED GROUP DISTANCE UNITS MOLINFO CELL COORDINATION CUSTOM RMSD POSITION UPPER_WALLS ENERGY BIASVALUE TORSION LOWER_WALLS LOAD WHOLEMOLECULES | generic colvar core function bias setup |
| 24.007 | SWISH-X | bio | swish-x, SWISH-X, swish, expanded SWISH | Alberto Borsatto | ENERGY ECV_MULTITHERMAL CONTACTMAP PRINT OPES_EXPANDED UPPER_WALLS INCLUDE MOLINFO WHOLEMOLECULES | opes colvar 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 | FIXEDATOM PRINT DISTANCE UNITS COORDINATIONNUMBER UPPER_WALLS OPES_METAD FLUSH GROUP ZDISTANCES | generic colvar core multicolvar vatom bias setup opes symfunc |
| 23.046 | Lasso Peptides - HLDA CV | bio | metadynamics, protein folding, HLDA, harmonic | Gabriel da Hora | PRINT DISTANCE METAD UNITS COMBINE WHOLEMOLECULES | generic colvar function bias setup |
| 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 | PRINT DISTANCE BIASVALUE EMMIVOX INCLUDE UPPER_WALLS MOLINFO WHOLEMOLECULES GROUP WRAPAROUND | isdb generic colvar core bias |
| 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 | DISTANCES PRINT SHADOW METAD POSITION UPPER_WALLS CENTER MOLINFO WHOLEMOLECULES FIT_TO_TEMPLATE GROUP WRAPAROUND | isdb generic colvar core multicolvar vatom bias |
| 23.023 | Rational design of novel biomimetic sequence-defined polymers for mineralization applications | methods | metadynamics, surface binding, biomimetic mineralization | Kaylyn Torkelson | PRINT DISTANCE COM GYRATION UPPER_WALLS PBMETAD COORDINATION | colvar bias vatom generic |
| 23.005 | A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs | bio | metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A | Timothy Clark | HISTOGRAM PRINT DISTANCE MATHEVAL METAD REWEIGHT_METAD RMSD MOLINFO WHOLEMOLECULES READ CONVERT_TO_FES DUMPGRID | generic colvar function gridtools bias |
| 22.038 | Enhanced Sampling Aided Design of Molecular Photoswitches | chemistry | reaction discovery, OPES explore, graph CV | Umberto Raucci | PYTORCH_MODEL PRINT OPES_METAD_EXPLORE CUSTOM UNITS COORDINATION | generic colvar function setup opes pytorch |
| 22.032 | Reciprocal barrier restraint. Application to path-meta-eABF | methods | restraint, upper wall, lower wall, path colvar, meta-eABF, metadynamics, DRR, protein conformational transition, PROTAC | Istvan Kolossvary | PRINT METAD BIASVALUE CUSTOM FLUSH DRR PATHMSD | drr generic colvar function bias |
| 22.029 | Angiotensin-1-7_Metadynamics | bio | Metadynamics, Angiotensin-(1-7), peptide | L.-América Chi | PRINT METAD GROUP UPPER_WALLS LOWER_WALLS GYRATION WHOLEMOLECULES COORDINATION FLUSH | colvar core bias generic |
| 22.026 | Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification | materials | Peptoid, silica | Jim Pfaendtner | PRINT DISTANCE COM GYRATION UPPER_WALLS MOLINFO PBMETAD | colvar bias vatom generic |
| 22.015 | Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome | bio | photodynamics, bacteriophytochrome, variationally enhanced sampling | Jakub Rydzewski | BF_FOURIER PRINT TORSION TD_UNIFORM VES_LINEAR_EXPANSION OPT_AVERAGED_SGD | ves colvar generic |
| 22.000 | Amyloid precursor protein processing by human γ-secretase | bio | Bias Exchange Metadynamics, Helix unfolding, coupled binding | Xiaoli Lu | PRINT DISTANCE CONTACTMAP METAD UNITS ALPHARMSD RANDOM_EXCHANGES INCLUDE ANTIBETARMSD MOLINFO CENTER COORDINATION | generic colvar vatom bias setup secondarystructure |
| 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 | PRINT METAD ALPHABETA LOWER_WALLS UPPER_WALLS GYRATION WHOLEMOLECULES ENDPLUMED GROUP | generic colvar core multicolvar bias |
| 21.044 | NaCl nucleation | chemistry | metadynamics, DFS clustering | Aaron Finney | FIXEDATOM HISTOGRAM PRINT METAD MFILTER_MORE DFSCLUSTERING INSPHERE COORDINATIONNUMBER CLUSTER_NATOMS COMBINE LOCAL_Q6 Q6 CONTACT_MATRIX DUMPGRID GROUP CLUSTER_DISTRIBUTION | generic clusters function core multicolvar vatom gridtools volumes bias adjmat symfunc |
| 21.033 | Multiple-path-metadynamics applied to DNA base-pairing transitions | bio | path-CV, metadynamics, multiple-walker, dna | Alberto Pérez-de-Alba-Ortíz | CONSTANT PRINT METAD RESTRAINT MOVINGRESTRAINT COMBINE INCLUDE UPPER_WALLS | function bias generic |
| 21.030 | Thermodynamic Basis for Stabilization of Helical Peptoids by Chiral Sidechains | bio | parallel bias parallel tempered metadynamics in WTE, synthetic foldamers, self-assembly, peptoid secondary structure | Jim Pfaendtner | ENERGY PRINT DISTANCE COM METAD ALPHABETA TORSION GYRATION INCLUDE PBMETAD COORDINATION | generic colvar multicolvar vatom bias |
| 21.014 | how to determine statistically accurate conformational ensembles | bio | metadynamics, metainference, errors, cv, SAXS, ensemble determination | Cristina Paissoni | PRINT CONTACTMAP METAD BIASVALUE ALPHABETA TORSION ENSEMBLE GYRATION CENTER MOLINFO WHOLEMOLECULES ANTIBETARMSD PBMETAD SAXS STATS | isdb generic colvar function multicolvar vatom bias secondarystructure |
| 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 | ENERGY BF_LEGENDRE PRINT ECV_MULTITHERMAL_MULTIBARIC ECV_UMBRELLAS_LINE MATHEVAL OPES_EXPANDED TD_UNIFORM UPPER_WALLS VOLUME Q6 ENVIRONMENTSIMILARITY RESTART VES_LINEAR_EXPANSION OPT_AVERAGED_SGD | generic colvar function ves envsim bias setup opes symfunc |
| 20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Cristina Paissoni | PRINT DISTANCE BIASVALUE RESTRAINT ENSEMBLE INCLUDE CENTER MOLINFO WHOLEMOLECULES SAXS GROUP STATS | isdb generic colvar function core vatom bias |
| 20.018 | Free energy barriers from biased molecular dynamics simulations | methods | kinetics, free energy barriers, chemical reactions, nucleation, metadynamics | Kristof Bal | PAIRENTROPY PRINT COORDINATIONNUMBER SPRINT VOLUME CONVERT_TO_FES DUMPGRID HISTOGRAM DISTANCE UNITS CENTER COORDINATION METAD LOCAL_AVERAGE COMBINE UPPER_WALLS Q6 CONTACT_MATRIX ENERGY REWEIGHT_BIAS REWEIGHT_METAD LOWER_WALLS LOAD FLUSH DENSITY | sprint generic colvar function gridtools vatom volumes bias setup adjmat symfunc |
| 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 | PRINT ENDPLUMED CONVERT_TO_FES DUMPGRID HISTOGRAM DISTANCE ABMD MOLINFO METAD COMBINE UPPER_WALLS READ FUNCPATHMSD CONTACTMAP COM REWEIGHT_METAD LOWER_WALLS WHOLEMOLECULES FLUSH | generic colvar function gridtools vatom bias |
| 20.001 | Conformational stability and dynamics in solution and in crystals report similarly on unfolding and aggregation propensity of amyloidogenic proteins | bio | metainference, metadynamics, NMR, protein dynamics, b2m, protein crystals | Carlo Camilloni | PRINT BIASVALUE ALPHABETA LOWER_WALLS ANTIBETARMSD MOLINFO WHOLEMOLECULES UPPER_WALLS PBMETAD ENDPLUMED FLUSH CS2BACKBONE GROUP | isdb generic core multicolvar bias secondarystructure |
| 19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Matteo Salvalaglio | HISTOGRAM REWEIGHT_BIAS PRINT DISTANCE BIASVALUE MATHEVAL METAD EXTERNAL REWEIGHT_METAD TORSION COMMITTOR READ CONVERT_TO_FES DUMPGRID | generic colvar function gridtools bias |
| 19.040 | Optimal Metric for Path Collective Variables | bio | metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path | Francesco Luigi Gervasio | PRINT MATHEVAL METAD TORSION ENDPLUMED | colvar function bias generic |
| 19.030 | Coarse-Grained MetaDynamics (CG-MetaD) | bio | Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy | Vittorio Limongelli | PRINT DISTANCE METAD COM UPPER_WALLS LOWER_WALLS WHOLEMOLECULES | colvar bias vatom generic |
| 19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Jim Pfaendtner | ENERGY METAD EXTERNAL COORDINATION GROUP | colvar bias core |
| 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 | FLUSH GROUP COMBINE FIXEDATOM ANGLE LOWER_WALLS COM METAD COORDINATIONNUMBER RESTRAINT DISTANCES PRINT UPPER_WALLS UNITS COORDINATION DISTANCE | vatom symfunc multicolvar colvar function setup generic bias core |
| 24.003 | Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations | chemistry | steered molecular dynamics, foldamers, peptoids, bio-inspired | Kaylyn Torkelson | INCLUDE MOVINGRESTRAINT GYRATION COM DISTANCE COORDINATION ALPHABETA PRINT TORSION WHOLEMOLECULES | bias vatom generic colvar multicolvar |
| 23.040 | Supramolecular capsules assembly dynamics | chemistry | Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics | Riccardo Capelli | UNITS CENTER DISTANCE COM FLUSH CUSTOM PRINT POSITION GROUP METAD DISTANCES WHOLEMOLECULES | bias vatom generic colvar setup function core multicolvar |
| 23.034 | Urea nucleation in water: do long-range forces matter? | materials | LMF theory, Metadynamics, Nucleation | Ziyue Zou | INCLUDE CENTER PRINT GROUP METAD COORDINATIONNUMBER LOAD | bias vatom generic setup symfunc core |
| 23.033 | DNA G-quadruplex and G-hairpin folding with ST-metaD protocol | bio | DNA, G4, GQ, quadruplex, hairpin, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | MOLINFO BIASVALUE COORDINATION ERMSD PRINT METAD GHBFIX WHOLEMOLECULES COMBINE | generic colvar bias function |
| 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 | DISTANCE OPES_METAD PRINT UNITS CENTER LOWER_WALLS MOLINFO COORDINATION UPPER_WALLS WRAPAROUND COM ENDPLUMED CUSTOM BIASVALUE POSITION FIT_TO_TEMPLATE COMMITTOR ENERGY MATHEVAL OPES_METAD_EXPLORE FLUSH GROUP TORSION WHOLEMOLECULES | bias vatom generic opes colvar setup function core |
| 23.021 | Into the Dynamics of Rotaxanes at Atomistic Resolution | materials | metadynamics, rotaxanes, molecular shuttles, molecular machines | Luigi Leanza | MATHEVAL CENTER DISTANCE CUSTOM UPPER_WALLS PRINT FIXEDATOM METAD TORSION | bias vatom generic colvar function |
| 23.019 | Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors | bio | binding pathway, binding energy, sketch-map, drug development | Raitis Bobrovs | COM DISTANCE VSTACK TRANSPOSE DISSIMILARITIES CUSTOM SKETCHMAP_PROJECTION PATHMSD UPPER_WALLS COLLECT_FRAMES PRINT VORONOI METAD SKETCHMAP LANDMARK_SELECT_FPS WHOLEMOLECULES | valtools bias vatom generic landmarks colvar function matrixtools dimred |
| 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 | DISTANCE OPES_METAD PRINT INCLUDE CENTER ANGLE LOWER_WALLS RMSD MOLINFO COORDINATION UPPER_WALLS ENDPLUMED CUSTOM PYTORCH_MODEL FIXEDATOM FIT_TO_TEMPLATE COMBINE COMMITTOR ENERGY MATHEVAL CONTACTMAP GROUP WHOLEMOLECULES | bias vatom generic opes pytorch colvar function core |
| 22.037 | Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site | chemistry | metadynamics, DNA, abasic | Mike Jones | DISTANCES PRINT DISTANCE METAD | generic colvar bias multicolvar |
| 22.036 | Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction | bio | Well-tempered MetaDynamics with Hamiltonian Replica Exchange | Miroslav Krepl | FLUSH CUSTOM MOLINFO BIASVALUE COORDINATION UPPER_WALLS PRINT GROUP METAD GHBFIX LOAD COMBINE | bias generic colvar function setup core |
| 22.033 | Reciprocal barrier restraint. Application to PROTAC passive permeability prediction | methods | PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR | Istvan Kolossvary | UNITS COM DISTANCE FLUSH CUSTOM BIASVALUE DRR PRINT METAD | bias vatom drr generic colvar setup function |
| 22.031 | Rare Event Kinetics from Adaptive Bias Enhanced Sampling | methods | OPES Flooding, Kinetics, Rate, OPES, Machine Learning | Dhiman Ray | DISTANCE OPES_METAD PRINT INCLUDE UNITS RMSD MOLINFO CONSTANT ENDPLUMED CUSTOM BIASVALUE POSITION PYTORCH_MODEL COMBINE COMMITTOR ENERGY CONTACTMAP GROUP TORSION WHOLEMOLECULES | bias generic opes pytorch function colvar setup core |
| 22.027 | Molecular Dynamics simulations of BANAL-236 RBD-hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, BANAL-236, receptor-binding domain | Max Bonomi | RMSD PRINT | generic colvar |
| 22.003 | Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling | methods | opes, metadynamics, reweighting, alanine, muller | Michele Invernizzi | ENERGY ECV_UMBRELLAS_FILE UNITS OPES_METAD_EXPLORE OPES_EXPANDED LOWER_WALLS ENDPLUMED OPES_METAD CUSTOM BIASVALUE UPPER_WALLS PRINT ECV_MULTITHERMAL POSITION METAD TORSION PBMETAD | bias generic opes colvar setup function |
| 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 | UNITS COM DISTANCE LOWER_WALLS CUSTOM UPPER_WALLS PRINT METAD TORSION | bias vatom generic colvar setup function |
| 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 | VOLUME ENDPLUMED CUSTOM COORDINATION PRINT METAD COMBINE | generic colvar bias function |
| 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 | ANTIBETARMSD PARABETARMSD ENERGY GYRATION LOWER_WALLS MOLINFO COORDINATION UPPER_WALLS PRINT ALPHARMSD GROUP METAD WHOLEMOLECULES DIHCOR RANDOM_EXCHANGES | bias generic colvar core secondarystructure multicolvar |
| 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 INCLUDE UNITS DISTANCE CUSTOM CONSTANT REWEIGHT_METAD BIASVALUE PRINT METAD TORSION | bias generic colvar setup function |
| 21.020 | Reweighted Jarzynski sampling | methods | free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions | Kristof Bal | RESTRAINT DUMPGRID DISTANCE OPES_METAD PRINT TD_WELLTEMPERED REWEIGHT_BIAS UNITS ANN CONSTANT REWEIGHT_METAD UPPER_WALLS BF_CHEBYSHEV OPT_AVERAGED_SGD VES_LINEAR_EXPANSION CUSTOM BIASVALUE COORDINATIONNUMBER COMBINE CONVERT_TO_FES MOVINGRESTRAINT FLUSH METAD LOAD HISTOGRAM | bias gridtools annfunc generic opes ves colvar setup function symfunc |
| 21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Tarak Karmakar | MATHEVAL LOWER_WALLS OPES_METAD FLUSH UPPER_WALLS PRINT PYTORCH_MODEL GROUP LOAD | bias generic pytorch opes function setup core |
| 21.004 | Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy | bio | machine learning, well-tempered metadynamics, path collective variable, potential of mean force, standard binding free energy calculations, host-guest, protein-ligand unbinding | Dorothea Gobbo | LOWER_WALLS RESTART PATHMSD UPPER_WALLS PRINT METAD WHOLEMOLECULES | generic bias colvar setup |
| 21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Kresten Lindorff-Larsen | SAXS GYRATION CENTER METAINFERENCE FLUSH MOLINFO BIASVALUE ALPHARMSD PRINT EEFSOLV GROUP PBMETAD WHOLEMOLECULES | isdb bias vatom generic colvar core secondarystructure |
| 20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Michele Invernizzi | VOLUME OPES_EXPANDED ECV_LINEAR PRINT ECV_UMBRELLAS_LINE UNITS RMSD MOLINFO UPPER_WALLS ENDPLUMED ENVIRONMENTSIMILARITY CUSTOM POSITION ECV_MULTITHERMAL_MULTIBARIC ENERGY MATHEVAL Q6 ECV_MULTITHERMAL TORSION LOAD WHOLEMOLECULES | bias envsim generic opes colvar setup function symfunc |
| 20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Matteo Salvalaglio | ENERGY MATHEVAL VOLUME LOWER_WALLS UPPER_WALLS PRINT CELL METAD | generic bias colvar function |
| 20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Jim Pfaendtner | CENTER DISTANCE RESTART COORDINATION PRINT GROUP DISTANCES WHOLEMOLECULES | vatom generic colvar setup core multicolvar |
| 20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Luigi Bonati | MATHEVAL UNITS DISTANCE COM LOWER_WALLS OPES_METAD ENDPLUMED FLUSH UPPER_WALLS PRINT PYTORCH_MODEL GROUP TORSION LOAD | bias vatom generic opes pytorch colvar function setup core |
| 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 | DUMPGRID VOLUME RESTART PRINT TD_WELLTEMPERED REWEIGHT_BIAS REWEIGHT_TEMP_PRESS LOWER_WALLS UPPER_WALLS OPT_AVERAGED_SGD TD_MULTITHERMAL_MULTIBARIC READ VES_LINEAR_EXPANSION BF_LEGENDRE OPT_DUMMY COMBINE ENERGY CONVERT_TO_FES MATHEVAL Q6 CELL LOAD HISTOGRAM | bias gridtools generic ves colvar setup function symfunc |
| 19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | ENERGY GYRATION COM DISTANCE MOLINFO UPPER_WALLS PRINT METAD | vatom generic colvar bias |
| 19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Michele Invernizzi | UNITS OPES_METAD ENDPLUMED EXTERNAL PRINT POSITION METAD TORSION | bias generic opes colvar setup |
| 19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Wei Chen | RESTRAINT COM ANN POSITION COMBINE | bias annfunc vatom colvar function |
| 19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Jim Pfaendtner | ENERGY GYRATION PRINT METAD WHOLEMOLECULES | generic colvar bias |
| 19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Kim E. Jelfs | COM CENTER LOWER_WALLS DISTANCE RESTART UPPER_WALLS PRINT GROUP METAD | bias vatom generic colvar setup core |
| 19.049 | Determining the sizes of solid/liquid clusters in MD trajectories of nucleation | methods | nucleation, metadynamics, clustering, Steinhardt order parameters | Gareth Tribello | DISTANCES OUTPUT_CLUSTER LOCAL_Q6 MORE_THAN CLUSTER_PROPERTIES OUTER_PRODUCT MATRIX_VECTOR_PRODUCT CUSTOM Q6 DFSCLUSTERING CONTACT_MATRIX PRINT ONES CLUSTER_NATOMS METAD COORDINATIONNUMBER SMAC CLUSTER_DISTRIBUTION | bias multicolvar adjmat generic function matrixtools symfunc clusters |
| 19.041 | Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces | bio | metadynamics, collective variables, conformational changes, multiple walkers, Well-Tempered MetaD, peptide, binding, phosphorylation, post-transitional motif, sio2, adsorption | Jim Pfaendtner | ENERGY COM DISTANCE UPPER_WALLS PRINT METAD | generic vatom bias colvar |
| 19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Carlo Camilloni | ANTIBETARMSD LOWER_WALLS FLUSH ENDPLUMED MOLINFO RESTART CS2BACKBONE BIASVALUE ALPHABETA UPPER_WALLS PRINT GROUP PBMETAD WHOLEMOLECULES | isdb bias generic setup core secondarystructure multicolvar |
| 19.025 | Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide | bio | metainference, NMR, protein dynamics, force-fields | Carlo Camilloni | ENSEMBLE JCOUPLING GYRATION METAINFERENCE FLUSH ENDPLUMED MOLINFO CS2BACKBONE STATS BIASVALUE RDC PRINT PBMETAD TORSION WHOLEMOLECULES | isdb bias generic colvar function |
| 19.023 | RECT | methods | metadynamics, replica exchange | Giovanni Bussi | GYRATION PRINT METAD TORSION WHOLEMOLECULES | generic colvar bias |
| 19.013 | RNA FF FITTING | methods | force field, RNA | Giovanni Bussi | INCLUDE MATHEVAL MOLINFO CONSTANT BIASVALUE PUCKERING TORSION | colvar generic function bias |
| 19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Max Bonomi | MOLINFO BIASVALUE PRINT GROUP EMMI | isdb generic core bias |
| 25.023 | Molecular simulations of Tau-protein oligomers | bio | metadynamics, proteins, aggregation | Giovanni Bussi | PRINT RESTRAINT RESTART CONTACTMAP RMSD METAD FLUSH CUSTOM | bias setup generic function colvar |
| 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 | PRINT MOLINFO BIASVALUE GROUP EMMIVOX WHOLEMOLECULES | bias generic core isdb |
| 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 | PRINT DISTANCES SMAC DUMPMULTICOLVAR TORSIONS | generic symfunc multicolvar |
| 25.014 | Atomic resolution ensembles of intrinsically disordered proteins with Alphafold | bio | bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement | Vincent Schnapka | PRINT BIASVALUE BAIES GROUP | bias generic core isdb |
| 25.003 | Surrogate Model CV | methods | Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding | Sompriya Chatterjee | PRINT MOLINFO DISTANCE GROUP ENERGY MATHEVAL COMMITTOR WHOLEMOLECULES TORSION PYTORCH_MODEL OPES_METAD COMBINE ENDPLUMED CUSTOM | core generic opes function colvar pytorch |
| 24.006 | Water vapor condensation | chemistry | metadynamics, homogeneous condensation, chemical potential | Shenghui Zhong | PRINT CONTACT_MATRIX UNITS DFSCLUSTERING CLUSTER_PROPERTIES CLUSTER_NATOMS UPPER_WALLS COORDINATIONNUMBER METAD | bias setup clusters generic symfunc adjmat |
| 24.005 | Learning Markovian Dynamics with Spectral Maps | methods | spectral map, collective variables, machine learning | Jakub Rydzewski | PRINT BIASVALUE DISTANCE UNITS CUSTOM | bias setup generic function colvar |
| 24.002 | Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes | chemistry | metadynamics, ligand design, solvent extraction | Xiaoyu Wang | PRINT RESTART UNITS TORSION METAD | colvar bias generic setup |
| 23.039 | Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation | chemistry | metadynamics, ligand dissociation | Eric Beyerle | PRINT MOLINFO RESTRAINT DISTANCE FIXEDATOM UPPER_WALLS DUMPMASSCHARGE COMBINE METAD CENTER | bias generic vatom function colvar |
| 23.024 | Permutationally Invariant Networks for Enhanced Sampling (PINES) | methods | collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent | Nicholas Herringer | PRINT LOAD PBMETAD | bias generic setup |
| 23.018 | Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention | materials | metadynamics, surface binding, peptide adsorption | Kaylyn Torkelson | PRINT DISTANCE COM PBMETAD GYRATION UPPER_WALLS | colvar bias generic vatom |
| 23.016 | Activation/deactivation free-energy profiles for the β2-adrenergic receptor: Ligand modes of action | bio | G protein coupled receptor, beta-adrenergic, receptor activation, partial agonism, metadynamics | Timothy Clark | PRINT MOLINFO HISTOGRAM DISTANCE READ MATHEVAL DUMPGRID WHOLEMOLECULES CONVERT_TO_FES REWEIGHT_METAD RMSD METAD | bias generic gridtools function colvar |
| 23.015 | MPCs aggregation | bio | opes_explore, dimerization, MPCs, self-assembly | Vikas Tiwari | COORDINATION PRINT OPES_METAD_EXPLORE DISTANCE GROUP LOWER_WALLS COM CENTER WHOLEMOLECULES UPPER_WALLS METAD CUSTOM | bias core generic vatom opes function colvar |
| 23.013 | Path meta-eABF simulation of large scale conformational change in STING protein | methods | meta-eABF, path CV, large scale conformational change, STING protein, reciprocal barrier restraint | Istvan Kolossvary | PRINT BIASVALUE DRR TIME PATHMSD LOWER_WALLS UNITS UPPER_WALLS METAD FLUSH CUSTOM | bias setup generic function drr colvar |
| 23.011 | OneOPES, a combined enhanced sampling method to rule them all | bio | OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding | Valerio Rizzi | PRINT MOLINFO OPES_METAD_EXPLORE DISTANCE OPES_EXPANDED TORSION ECV_MULTITHERMAL ENERGY ENDPLUMED METAD | colvar bias generic opes |
| 23.001 | Quantum phase diagram of water | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn-Løland Bore | PRINT RESTART ECV_UMBRELLAS_LINE LOWER_WALLS OPES_EXPANDED ENVIRONMENTSIMILARITY UPPER_WALLS INCLUDE | bias setup generic envsim opes |
| 22.042 | Metadynamics of NSP10 and variants | bio | metadynamics, NSP10, crystal structure, variants | Shozeb Haider | PRINT METAD TORSION | bias generic colvar |
| 22.040 | From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure | bio | SARS-CoV-2, Spike, Omicron | Miłosz Wieczór | PRINT LOWER_WALLS WHOLEMOLECULES PCAVARS UPPER_WALLS METAD | bias generic mapping |
| 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 | MOLINFO WHOLEMOLECULES PBMETAD GYRATION TORSION | bias generic colvar |
| 22.020 | Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix–Junction–Helix RNA | bio | RNA force field, Helix-Junction-Helix RNA, SAXS, Well tempered metadynamics | Weiwei He | PRINT DISTANCE GROUP COM WHOLEMOLECULES TORSION METAD | bias core generic vatom colvar |
| 22.006 | Peptide framework for screening the effects of amino acids on assembly | bio | metadynamics, peptides | Andrew White | PRINT DISTANCES HISTOGRAM GROUP COM DUMPGRID REWEIGHT_BIAS GYRATION CONVERT_TO_FES INCLUDE COMBINE METAD | bias core generic vatom gridtools multicolvar function colvar |
| 21.049 | Multiple-path-metadynamics and PathMaps | methods | path-CV, metadynamics, multiple-walker, multiple paths, pathmap | Alberto Pérez-de-Alba-Ortíz | PRINT RESTRAINT COMBINE LOWER_WALLS LOAD ENSEMBLE UNITS UPPER_WALLS TORSION MOVINGRESTRAINT CONSTANT METAD CUSTOM | bias setup generic function colvar |
| 21.038 | Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics | materials | metadynamics, SGOOP, nucleation, urea | Ziyue Zou | PRINT GROUP LOAD COORDINATIONNUMBER INCLUDE ENERGY VOLUME COMBINE METAD CENTER | bias core setup generic symfunc vatom function colvar |
| 21.019 | Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations | materials | Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen | Matteo Salvalaglio | PRINT DISTANCE COM MATHEVAL KDE TORSIONS | generic vatom gridtools function multicolvar colvar |
| 20.027 | Allosteric Regulation of SARS-CoV-2 Protease. Towards Informed Structure-Based Drug Discovery | bio | SARS-CoV2, MPro, Covid-19, Molecular Dynamics, Metadynamics, Computer-Aided Drug Discovery | Khaled Abdel-Maksoud | PRINT DISTANCE METAD TORSION | colvar bias generic |
| 20.016 | Predicting polymorphism in molecular crystals using orientational entropy | materials | metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy | Pablo Piaggi | PRINT GROUP LOAD CENTER UPPER_WALLS INCLUDE VOLUME METAD | bias core setup generic vatom 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 | WHOLEMOLECULES ANTIBETARMSD FLUSH PRINT MOLINFO DIHCOR COORDINATION GROUP ENSEMBLE CS2BACKBONE PARABETARMSD PBMETAD INCLUDE COMBINE ENDPLUMED STATS GYRATION ALPHARMSD TORSION METAINFERENCE | isdb bias core generic secondarystructure multicolvar function colvar |
| 19.075 | PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python | other | Python, automatic differentiation | Toni Giorgino | PRINT RESTRAINT DUMPDERIVATIVES DISTANCE GROUP CUSTOM ANGLE TORSION COMBINE ENDPLUMED CENTER | bias core generic vatom function colvar |
| 19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Giovanni Bussi | COORDINATION MOLINFO MAXENT SORT PRINT DISTANCE COM MATHEVAL WHOLEMOLECULES TORSION INCLUDE METAD FLUSH | bias generic vatom function colvar |
| 19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Mattia Bernetti | PRINT LOWER_WALLS WHOLEMOLECULES UPPER_WALLS PATHMSD METAD | bias generic colvar |
| 19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Gareth Tribello | MORE_THAN FCCUBIC GROUP MULTICOLVARDENS DUMPGRID UNITS FIND_CONTOUR_SURFACE FOURIER_TRANSFORM CENTER | core setup symfunc vatom gridtools contour function fourier |
| 19.035 | Dimerization of GPCRs from coarse-grained umbrella sampling | bio | Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization | Davide Provasi | PRINT RESTRAINT DISTANCE GROUP COM TORSION | bias core generic vatom colvar |
| 19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Glen Hocky | PRINT RESTRAINT DISTANCE EDS TORSION COMBINE | bias generic eds function colvar |
| 19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Carlo Camilloni | STATS MOLINFO DHENERGY RDC PRINT DISTANCE GROUP RESTRAINT METAINFERENCE ENSEMBLE DIHCOR WHOLEMOLECULES PBMETAD UPPER_WALLS TORSION ALPHABETA ENDPLUMED CENTER | isdb bias core generic vatom function multicolvar colvar |
| 24.030 | NMR guided simulation of dsRBD | bio | Metainference, NMR, protein dynamics | Debadutta Patra | METAINFERENCE GROUP PRINT MOLINFO DISTANCE STATS FLUSH WHOLEMOLECULES ALPHABETA ENSEMBLE RDC | generic isdb core function colvar multicolvar |
| 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 | TORSION DISTANCE MOLINFO PRINT CUSTOM COMBINE WHOLEMOLECULES GYRATION ALPHARMSD COORDINATION OPES_METAD | generic function colvar opes secondarystructure |
| 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 | PRINT DISTANCE MOLINFO FUNCPATHMSD LOWER_WALLS PATHMSD CONTACTMAP INCLUDE ALPHARMSD METAD UPPER_WALLS | generic function bias colvar secondarystructure |
| 23.022 | A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar | methods | collective variables, machine learning, toy model | Enrico Trizio | PRINT UNITS CUSTOM BIASVALUE LOWER_WALLS PYTORCH_MODEL POSITION ENDPLUMED UPPER_WALLS OPES_METAD | pytorch generic function bias setup colvar opes |
| 23.006 | Transcription factor unbinding | bio | metadynamics, DNA, conformational changes | Malin Lüking | PRINT DISTANCE MOLINFO ANGLE COM CONTACTMAP ALPHARMSD METAD DUMPFORCES | generic vatom bias colvar secondarystructure |
| 23.003 | Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations | methods | metadynamics, alchemical variable, alchemical free energy calculations | Wei-Tse Hsu | PRINT TORSION READ METAD EXTRACV | bias generic colvar |
| 22.045 | Binding mode and mechanism of enzymatic polyethylene terephthalate degradation | bio | metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation | Francesco Colizzi | PRINT DISTANCE ANGLE COM LOWER_WALLS WHOLEMOLECULES MOVINGRESTRAINT METAD UPPER_WALLS | bias generic colvar vatom |
| 22.043 | Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES | bio | OPES, RNA, Tetraloop, Folding | Gül Zerze | PRINT WHOLEMOLECULES CONTACTMAP ECV_MULTITHERMAL ECV_UMBRELLAS_LINE ENERGY OPES_EXPANDED | generic colvar opes |
| 22.034 | Rationalising the difference in crystallisability of two Sulflowers using efficient in silico methods | materials | metadynamics, crystallizability, crystal structure prediction, sulflower, persulforated coronene | Matteo Salvalaglio | PRINT MATHEVAL CUSTOM COMMITTOR LOWER_WALLS DRMSD METAD UPPER_WALLS CELL | function generic colvar bias |
| 22.021 | Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn Løland Bore | PRINT ENVIRONMENTSIMILARITY LOWER_WALLS INCLUDE ECV_UMBRELLAS_LINE UPPER_WALLS OPES_EXPANDED | bias generic envsim opes |
| 22.004 | Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques | chemistry | reaction discovery, OPES, collective variables | Umberto Raucci | GROUP OPES_METAD_EXPLORE DISTANCE PRINT COORDINATION CUSTOM COM UNITS MATHEVAL PYTORCH_MODEL LOWER_WALLS LOAD UPPER_WALLS OPES_METAD | pytorch generic vatom core function bias setup colvar opes |
| 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 | PRINT UNITS POSITION BF_WAVELETS FLUSH OPT_AVERAGED_SGD METAD COORDINATION ENERGY TD_UNIFORM VES_OUTPUT_BASISFUNCTIONS INCLUDE UPPER_WALLS OPT_ADAM BF_LEGENDRE DISTANCE BF_CHEBYSHEV BF_GAUSSIANS TD_WELLTEMPERED BF_CUBIC_B_SPLINES VES_LINEAR_EXPANSION | generic ves bias setup colvar |
| 21.037 | Molecular Dynamics simulations of RBD/hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain | Max Bonomi | PRINT DISTANCE RMSD | generic colvar |
| 21.029 | Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs | bio | metadynamics, small peptide, machine learning | Pratyush Tiwary | EXTERNAL TORSION PRINT MOLINFO FLUSH RESTART ENERGY | setup bias generic colvar |
| 21.012 | NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition | bio | funnel metadynamics | Jim Pfaendtner | PRINT DISTANCE FUNNEL_PS COM LOWER_WALLS FUNNEL METAD UPPER_WALLS | generic vatom funnel bias colvar |
| 20.032 | Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil | materials | clustering, conformational isomers | Matteo Salvalaglio | TORSION ENDPLUMED PRINT | generic colvar |
| 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 | HISTOGRAM PRINT DISTANCE MATHEVAL METAD DUMPGRID COM REWEIGHT_METAD READ LOWER_WALLS ENDPLUMED ABMD UPPER_WALLS CONVERT_TO_FES COMBINE | generic vatom function bias colvar gridtools |
| 19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Matteo Salvalaglio | GROUP PRINT DISTANCE CENTER INCLUDE ENDPLUMED | generic colvar vatom core |
| 19.050 | Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes | chemistry | metadynamics, membranes, Willard Chandler surface | Gareth Tribello | HISTOGRAM PRINT DUMPGRID READ RESTART UPPER_WALLS METAD REWEIGHT_BIAS DISTANCE_FROM_CONTOUR CONVERT_TO_FES COMBINE | generic contour bias function setup gridtools |
| 19.048 | Understanding Ligand Binding Selectivity in a Prototypical GPCR Family | bio | metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | PRINT DISTANCE MATHEVAL COM LOWER_WALLS BIASVALUE WHOLEMOLECULES CONSTANT METAD UPPER_WALLS | generic vatom function bias colvar |
| 19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Silvio Pipolo | PIV PRINT FUNCPATHMSD LOWER_WALLS METAD UPPER_WALLS CELL | generic piv function bias colvar |
| 19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Matteo Salvalaglio | TORSION MATHEVAL PRINT COMBINE LOWER_WALLS ENDPLUMED METAD UPPER_WALLS CELL ENERGY VOLUME | function generic colvar bias |
| 25.024 | Sampling glycan-glycan interactions for B22 calculations | bio | B22, glycan, carbohydrates, distance, REST2, metadynamics, RECT, replica exchange | Isabell Louise Grothaus | COM POSITION PRINT COMBINE METAD RESTRAINT DISTANCE | vatom colvar function 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 | INCLUDE READ PBMETAD TORSION PRINT RESTART CENTER ENERGY GYRATION MOLINFO UPDATE_IF DUMPATOMS VOLUME DISTANCE WHOLEMOLECULES | vatom setup colvar bias generic |
| 24.035 | Data efficient machine learning potentials for modeling catalytic reactivity via active learning and enhanced sampling | chemistry | opes, catalysis, ammonia, machine learning potentials | Luigi Bonati | CUSTOM LOWER_WALLS COORDINATION PRINT RESTART UPPER_WALLS GROUP COMMITTOR OPES_METAD DISTANCE UNITS | setup opes colvar function bias core generic |
| 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 | COM PBMETAD ALPHARMSD EMMI BIASVALUE COORDINATION DUMPMASSCHARGE RMSD PARABETARMSD UPPER_WALLS GROUP PRINT CENTER MOLINFO DUMPATOMS DISTANCE WHOLEMOLECULES | isdb vatom colvar bias core generic secondarystructure |
| 24.031 | DeepLNE | methods | PATHCV, OPES, OneOPES | Thorben Fröhlking | PYTORCH_MODEL OPES_EXPANDED COORDINATION OPES_METAD_EXPLORE PRINT RESTART COMBINE ENERGY MOLINFO ECV_MULTITHERMAL VOLUME ERMSD | opes setup colvar function pytorch 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 | INCLUDE BIASVALUE PRINT EMMIVOX GROUP MOLINFO RESTRAINT ERMSD WHOLEMOLECULES | isdb colvar bias core generic |
| 24.010 | Oxytocin metadynamics simulation | bio | metadynamics, oxytocin, peptide | Jan Beránek | TORSION PRINT RESTART METAD FLUSH WHOLEMOLECULES | bias setup colvar generic |
| 23.037 | Estimating binding free energy of solid binding peptides without extensive sampling | bio | metadynamics, solid binding peptides | Xin Qi | COM PBMETAD LOWER_WALLS PRINT UPPER_WALLS GYRATION MOLINFO DISTANCE | bias generic colvar vatom |
| 23.028 | Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process | chemistry | Ammonia decomposition; Dynamics;OPES; Neural Network potential | Manyi Yang | FIXEDATOM CUSTOM MATHEVAL COORDINATIONNUMBER COM DISTANCE DISTANCES LOWER_WALLS PRINT UPPER_WALLS GROUP ENERGY COMMITTOR OPES_METAD ZDISTANCES FLUSH UNITS | vatom opes setup colvar function bias core symfunc generic multicolvar |
| 23.027 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, DFS, Q3, Pair Entropy | Aaron Finney | LOCAL_Q3 LOAD FIXEDATOM HISTOGRAM CLUSTER_NATOMS CLUSTER_DISTRIBUTION LOCAL_AVERAGE COORDINATIONNUMBER AROUND Q3 DENSITY DUMPGRID PRINT GROUP DFSCLUSTERING CONTACT_MATRIX RESTRAINT UNITS | gridtools vatom setup bias core clusters symfunc volumes generic adjmat |
| 23.025 | Probing ion binding to G-quadruplexes and related events | chemistry | metadynamics, repulsive potential, nucleic acids, G-quadruplexes | Marcelo Poleto | MATHEVAL WRAPAROUND DISTANCES COM DISTANCE FIT_TO_TEMPLATE WHOLEMOLECULES LOWER_WALLS POSITION PRINT RESTART UPPER_WALLS GROUP METAD DUMPATOMS FLUSH UNITS | vatom setup colvar function bias core generic multicolvar |
| 23.012 | JAK2 2D meta-eABF PMF with statistical analysis | bio | 2D meta-eABF, path CV, PMF | Istvan Kolossvary | CUSTOM BIASVALUE LOWER_WALLS PRINT UPPER_WALLS DRR PATHMSD METAD FLUSH | drr colvar function bias generic |
| 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 | CONSTANT MATHEVAL BIASVALUE LOWER_WALLS PRINT UPPER_WALLS METAD DISTANCE WHOLEMOLECULES | bias colvar function generic |
| 22.044 | Colloid Crystallisation Analyses | materials | Q4, Q6, Pair Entropy, DFS | Aaron Finney | MFILTER_LESS CLUSTER_NATOMS LOCAL_AVERAGE Q6 LOCAL_Q4 PRINT COMBINE GROUP LOCAL_Q6 DFSCLUSTERING CONTACT_MATRIX MFILTER_MORE Q4 COORDINATIONNUMBER | function core clusters symfunc generic multicolvar adjmat |
| 22.030 | Mixing physics across temperatures with generative artificial intelligence | methods | REMD, Generative AI, DDPM | Yihang Wang | TORSION PRINT WHOLEMOLECULES | colvar generic |
| 22.024 | Conformational Entropy as a Potential Liability of Computationally Designed Antibodies | bio | metadynamics, conformational entropy, antibody, nanobody | Thomas Löhr | COM PBMETAD ALPHARMSD TORSION PRINT RESTART MOLINFO ALPHABETA ANTIBETARMSD WHOLEMOLECULES | vatom setup colvar bias generic multicolvar secondarystructure |
| 22.019 | Exploring aspartic protease inhibitor binding to design selective antimalarials | bio | ligand binding, loop opening, path CV, funnel metadynamics, drug development | Raitis Bobrovs | COM LOWER_WALLS PRINT FUNNEL_PS UPPER_WALLS PATHMSD FUNNEL METAD DISTANCE WHOLEMOLECULES | vatom funnel colvar bias generic |
| 22.017 | Water regulates the residence time of Benzamidine in Trypsin | bio | ligand binding, water, opes, benzamidine trypsin, unbinding rates, machine learning, Deep-LDA, Deep-TICA | Narjes Ansari | FIXEDATOM PYTORCH_MODEL MATHEVAL CUSTOM FIT_TO_TEMPLATE COORDINATION LOWER_WALLS RMSD PRINT UPPER_WALLS GROUP CENTER COMMITTOR OPES_METAD DISTANCE WHOLEMOLECULES | vatom opes colvar function bias core pytorch generic |
| 21.052 | On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets | materials | Ibuprofen, unbinding, WTmetaD | Matteo Salvalaglio | TORSION PRINT CENTER COMMITTOR ENDPLUMED METAD DISTANCE COORDINATIONNUMBER | vatom colvar bias symfunc generic |
| 21.039 | Deep learning the slow modes for rare events sampling | methods | collective variables, machine learning, slow modes, deep-tica, opes | Luigi Bonati | ENVIRONMENTSIMILARITY RMSD ENDPLUMED MOLINFO DISTANCE Q6 CONTACTMAP OPES_METAD VOLUME ECV_MULTITHERMAL INCLUDE LOAD PYTORCH_MODEL OPES_EXPANDED PRINT WHOLEMOLECULES UNITS TORSION COMBINE GROUP ENERGY FLUSH | envsim opes setup colvar function core symfunc pytorch generic |
| 21.035 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, interface | Aaron Finney | LOAD FIXEDATOM PRINT GROUP RESTRAINT DISTANCE | vatom setup colvar bias core generic |
| 21.028 | From Enhanced Sampling to Reaction Profiles | methods | collective variables, multi-state, machine learning, Deep-TDA | Enrico Trizio | CENTER ENDPLUMED DISTANCE FIXEDATOM MATHEVAL LOWER_WALLS ANGLE OPES_METAD LOAD PYTORCH_MODEL DISTANCES FIT_TO_TEMPLATE COORDINATION PRINT UNITS WHOLEMOLECULES TORSION UPPER_WALLS GROUP | vatom opes setup colvar function bias core pytorch generic multicolvar |
| 21.022 | Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly | materials | parallel bias metadynamics, adsorption, peptide | Xin Qi | COM PBMETAD LOWER_WALLS PRINT UPPER_WALLS ENERGY GYRATION MOLINFO DISTANCE | bias generic colvar vatom |
| 21.016 | MD SAXS GTPase associated center | bio | metadynamics, RNA, folding, SAXS | Giovanni Bussi | INCLUDE CUSTOM SAXS LOWER_WALLS PRINT UPPER_WALLS GROUP GYRATION MOLINFO METAD ERMSD WHOLEMOLECULES | isdb colvar function bias core generic |
| 21.015 | Coarse-grained metadynamics and umbrella sampling simulations to investigate interactions of carbohydrate-binding modules with chitin | bio | metadynamics, umbrella sampling, coarse-grained, MARTINI, chitin, carbohydrate-binding module | Gaston Courtade | MATHEVAL COORDINATION POSITION PRINT RESTART CENTER REWEIGHT_BIAS METAD RESTRAINT WHOLEMOLECULES | vatom setup colvar function bias generic |
| 21.011 | CmuMD simulations of NaCl(aq) at graphite | chemistry | CmuMD, DFS clustering | Aaron Finney | LOAD FIXEDATOM CLUSTER_NATOMS CLUSTER_DISTRIBUTION AROUND DENSITY DUMPGRID PRINT GROUP DFSCLUSTERING MULTICOLVARDENS MFILTER_MORE CONTACT_MATRIX RESTRAINT COORDINATIONNUMBER | gridtools vatom setup bias core clusters volumes symfunc generic multicolvar adjmat |
| 21.010 | Step by Step Strecker Amino Acid Synthesis from Ab Initio Prebiotic Chemistry | chemistry | Strecker reaction, free energy landscape, ab initio molecular dynamics, glycine, prebiotic synthesis | Théo Magrino | generic | |
| 21.006 | OPES, On-the-fly Probability Enhanced Sampling Method | methods | opes, alanine dipeptide, well-tempered, multithermal, multiumbrella | Michele Invernizzi | OPES_EXPANDED TORSION PRINT ECV_UMBRELLAS_LINE ENERGY ENDPLUMED OPES_METAD ECV_MULTITHERMAL | opes colvar generic |
| 21.000 | Uremic toxin time scale dynamics | bio | uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs) | Jim Pfaendtner | COM PRINT GROUP DISTANCE WHOLEMOLECULES | generic core colvar vatom |
| 20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Adriana Pietropaolo | PBMETAD COORDINATION PRINT CENTER WHOLEMOLECULES | bias colvar vatom generic |
| 20.015 | Rational design of ASCT2 inhibitors using an integrated experimental-computational approach | bio | ASCT2 transporter, small-molecules, cryo-EM, metainference | Max Bonomi | LOAD BIASVALUE PRINT EMMIVOX GROUP MOLINFO DUMPATOMS WHOLEMOLECULES | isdb setup bias core generic |
| 20.010 | Phase equilibrium of liquid water and hexagonal ice from enhanced sampling molecular dynamics simulations | materials | water, ice, TIP4P, crystallization, EnvironmentSimilarity, RefCV, kernel, VES, variationally enhanced sampling | Pablo Piaggi | BF_LEGENDRE OPT_AVERAGED_SGD MATHEVAL ENVIRONMENTSIMILARITY Q6 OPT_DUMMY RESTART UPPER_WALLS PRINT TD_WELLTEMPERED VOLUME VES_LINEAR_EXPANSION | envsim setup ves function colvar bias symfunc generic |
| 19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Jakub Rydzewski | LOWER_WALLS PRINT RESTART UPPER_WALLS PATHMSD METAD UNITS | bias setup colvar generic |
| 19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | COM PRINT UPPER_WALLS ENERGY GYRATION MOLINFO METAD DISTANCE | bias generic colvar vatom |
| 19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Kim Jelfs | COM INPLANEDISTANCES DISTANCES PRINT RESTART MOVINGRESTRAINT FLUSH | vatom setup bias generic multicolvar |
| 19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Cristina Paissoni | INCLUDE ENSEMBLE MATHEVAL PBMETAD SAXS BIASVALUE COORDINATION ANGLE PRINT COMBINE CENTER GROUP ENDPLUMED MOLINFO STATS ALPHABETA WHOLEMOLECULES | isdb vatom colvar function bias core generic multicolvar |
| 19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | GiovanniMaria Piccini | DISTANCE LOWER_WALLS PRINT COMBINE UPPER_WALLS ENERGY METAD FLUSH UNITS | setup colvar function bias generic |
| 19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Adriana Pietropaolo | CONSTANT MATHEVAL BIASVALUE TORSION PRINT METAD WHOLEMOLECULES | bias colvar function generic |
| 19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Max Bonomi | EMMI BIASVALUE PRINT GROUP MOLINFO WHOLEMOLECULES | bias core isdb generic |
| 19.005 | Cmyc small molecule interaction | bio | metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP | Gabriella Heller | INCLUDE CS2BACKBONE PBMETAD COORDINATION PRINT GROUP METAINFERENCE CENTER GYRATION MOLINFO ALPHABETA DISTANCE WHOLEMOLECULES | isdb vatom colvar bias core generic multicolvar |
| 25.021 | All You Need Is Water. Converging Ligand Binding Simulations with Hydration Collective Variables | bio | OPES Explore, ligand binding, binding free energy, water, hydration CVs, SAMPL challenge, host-guest | Valerio Rizzi | MATHEVAL DISTANCE CENTER FIXEDATOM UPPER_WALLS ENERGY GROUP WHOLEMOLECULES FIT_TO_TEMPLATE COORDINATION ANGLE OPES_METAD_EXPLORE PRINT | vatom generic bias opes colvar core function |
| 25.001 | RNA G-quadruplex folding with ST-metaD protocol | bio | RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | ERMSD COMBINE WHOLEMOLECULES MOLINFO METAD | bias generic colvar function |
| 25.000 | Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer | bio | metadynamics, pathCV | Sahithya Sridharan Iyer | DISTANCE FUNCPATHGENERAL RESTART UPPER_WALLS GROUP WHOLEMOLECULES PRINT COM MOLINFO METAD | setup vatom generic bias colvar core function |
| 24.036 | Leveraging cryptic ligand envelopes through enhanced molecular simulations | bio | HREX, conformational heterogeneity, drug discovery, ligand binding, plitidepsin, aplidin, ligand-target complexes, cryptic ligand envelope | Francesco Colizzi | CONVERT_TO_FES DISTANCE TORSION HISTOGRAM PRINT WHOLEMOLECULES GROUP COORDINATION ANGLE DUMPGRID | gridtools core generic colvar |
| 24.029 | Combination of OPES and OPES-Explore | methods | OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin | Dhiman Ray | CENTER PYTORCH_MODEL RMSD BIASVALUE WHOLEMOLECULES COMBINE DISTANCE UNITS LOWER_WALLS FIXEDATOM CONTACTMAP OPES_METAD_EXPLORE FIT_TO_TEMPLATE INCLUDE MATHEVAL CUSTOM POSITION GROUP ENDPLUMED FLUSH MOLINFO METAD OPES_METAD UPPER_WALLS ENERGY PRINT COORDINATION | setup vatom generic bias opes colvar pytorch core function |
| 24.028 | All-atom simulations of RNA-membrane interactions | bio | metadynamics, membrane, RNA | Giovanni Bussi | GYRATION MATHEVAL PUCKERING POSITION DISTANCE CENTER LOWER_WALLS GHOST UPPER_WALLS GROUP COMBINE PRINT SORT WHOLEMOLECULES DISTANCES MOLINFO METAD | vatom generic bias multicolvar colvar core function |
| 24.027 | Proline cis and trans subensembles of a disordered peptide | bio | intrinsically disordered proteins, proline cis trans isomerisation, metadynamics, collective variables | Alice Pettitt | GYRATION DISTANCE TORSION ALPHARMSD GROUP WHOLEMOLECULES COMBINE COORDINATION INCLUDE FLUSH ANTIBETARMSD PBMETAD PRINT MOLINFO ENDPLUMED DIHCOR PARABETARMSD | generic bias multicolvar colvar secondarystructure core function |
| 24.021 | Ab initio machine learning simulation of calcium carbonate from aqueous solutions to the solid state | chemistry | ion pairing, caco3, opes, proton transfer, crystallization | Pablo Piaggi | DISTANCE OPES_METAD UPPER_WALLS ENERGY PRINT COORDINATION | opes generic colvar bias |
| 24.008 | yCD Metadynamics | bio | volume-based MetaD, path CVs, infrequent MetaD, product release | James McCarty | CONVERT_TO_FES RMSD WHOLEMOLECULES PATH DISTANCE FIXEDATOM CONTACTMAP FIT_TO_TEMPLATE INCLUDE REWEIGHT_METAD MATHEVAL GROUP ENDPLUMED FLUSH MOLINFO DUMPGRID READ METAD WRAPAROUND HISTOGRAM UPPER_WALLS PRINT COORDINATION COMMITTOR COM | vatom generic bias colvar mapping gridtools core function |
| 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 | MATHEVAL SUM PRINT INCLUDE FLUSH SELECT_COMPONENTS TRANSPOSE METAD | valtools generic bias matrixtools function |
| 23.029 | An accurate and efficient SAXS/SANS implementation including solvation layer effects suitable for restrained Molecular Dynamics simulations | bio | SAXS, SANS, SAS, metainference, proteins, nucleic-acid | Federico Ballabio | SAXS WRAPAROUND DISTANCE CENTER ENSEMBLE RMSD UPPER_WALLS BIASVALUE PRINT STATS GROUP MOLINFO | vatom isdb generic bias colvar core function |
| 23.007 | Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains | bio | metadynamics, peptoids, parallel-bias metadynamics | Jim Pfaendtner | GYRATION TORSION RESTRAINT PRINT WHOLEMOLECULES COORDINATION INCLUDE PBMETAD COM | vatom bias generic colvar |
| 23.004 | Melting curves of ice polymorphs in the vicinity of the liquid-liquid critical point | chemistry | water, liquid-liquid transition, second critical point, ice, polymorphs, melting curves, environment similarity, opes, density-functional theory, scan, machine learning potential | Pablo Piaggi | ECV_UMBRELLAS_LINE LOWER_WALLS HISTOGRAM RESTART UPPER_WALLS OPES_EXPANDED PRINT ENVIRONMENTSIMILARITY DUMPGRID | setup generic opes bias envsim gridtools |
| 23.002 | Critical comparison of general-purpose collective variables for crystal nucleation | methods | metadynamics, umbrella sampling, commitor, entropy, PIV | Julien Lam | LOCAL_AVERAGE UNITS CUSTOM PIV Q4 UPPER_WALLS RESTRAINT ENERGY PRINT PAIRENTROPY FUNCPATHMSD Q6 VOLUME METAD | setup generic symfunc bias colvar gridtools piv function |
| 23.000 | Atomistic simulations of RNA tetraloop folding via PTWTE-WTM | bio | parallel tempering, well-tempered metadynamics, well-tempered ensemble, RNA, Tetraloop, Folding | Gül Zerze | LOWER_WALLS UPPER_WALLS CONTACTMAP ENERGY PRINT WHOLEMOLECULES METAD | bias generic colvar |
| 22.041 | Skipping the Replica Exchange Ladder with Normalizing Flows | methods | OPES, alanine, normalizing flows, replica exchange | Michele Invernizzi | ECV_MULTITHERMAL POSITION TORSION UNITS OPES_METAD OPES_EXPANDED ENERGY PRINT ENDPLUMED | setup opes generic colvar |
| 22.018 | Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations | bio | ligand binding, docking, EMMI, LAT1 | Max Bonomi | LOAD BIASVALUE GROUP WHOLEMOLECULES EMMIVOX PRINT MOLINFO | setup isdb generic bias core |
| 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 | GYRATION UNITS DISTANCE LOWER_WALLS UPPER_WALLS COMBINE COORDINATION FLUSH COORDINATIONNUMBER COM METAD | setup vatom generic bias symfunc colvar function |
| 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 | TORSION FIXEDATOM PRINT FIT_TO_TEMPLATE METAD | vatom bias generic colvar |
| 21.034 | Efficient sampling of high-dimensional free energy landscapes using adaptive reinforced dynamics | bio | reinforced dynamics, bias-exchange metadynamics, parallel-bias metadynamics | Dongdong Wang | TORSION PRINT ENDPLUMED INCLUDE PBMETAD RANDOM_EXCHANGES METAD | bias generic colvar |
| 21.032 | Metal-coupled folding mechanism to metallothionein | bio | parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination | Manuel-Peris Diaz | UNITS GROUP WHOLEMOLECULES COORDINATION PBMETAD | setup generic bias colvar core |
| 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 | RESTRAINT PRINT COMBINE WHOLEMOLECULES COORDINATION STATS MOLINFO | bias colvar generic function |
| 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 HISTOGRAM RESTRAINT PRINT MULTI_RMSD DUMPGRID REWEIGHT_METAD METAD | gridtools bias generic colvar |
| 20.008 | Simulating solvation and acidity in complex mixtures with first-principles accuracy. The case of CH3SO3H and H2O2 in phenol | chemistry | proton trasfer, metadynamics | Kevin Rossi | UNITS CUSTOM PRINT COORDINATION DISTANCES METAD | setup generic bias multicolvar colvar function |
| 19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Valerio Rizzi | UNITS RESTART PRINT GROUP ENDPLUMED COMBINE EXTERNAL COORDINATIONNUMBER FLUSH METAD | setup generic bias symfunc core function |
| 19.080 | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | methods | ves, variationally enhanced sampling, vibrational excitation, chemical reactions | Kristof Bal | CONVERT_TO_FES VES_LINEAR_EXPANSION UNITS BF_CHEBYSHEV DISTANCE OPT_AVERAGED_SGD HISTOGRAM UPPER_WALLS LOWER_WALLS EXTERNAL PRINT COMBINE COORDINATION ANGLE FLUSH TD_GRID DUMPGRID TD_WELLTEMPERED | setup generic bias colvar ves gridtools function |
| 19.056 | maze | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_OPTIMIZER_BIAS UNITS POSITION PRINT MAZE_LOSS MAZE_SIMULATED_ANNEALING | setup maze generic colvar |
| 19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Gareth Tribello | UNITS UPPER_WALLS PRINT FCCUBIC CELL ENDPLUMED METAD | setup generic bias symfunc colvar |
| 19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Gareth Tribello | AROUND UNITS LOWER_WALLS UPPER_WALLS PRINT FCCUBIC CELL ENDPLUMED METAD | setup generic volumes bias symfunc colvar |
| 19.046 | Optimal Collective from short simulations for Benzamidine-Trypsin ligand binding | bio | VAC-MetaD, optimised collective variables, binding free energy, unbinding rates, benzamidine trypsin, Structure Activity Relation | Faidon Brotzakis | DISTANCE TORSION LOWER_WALLS RMSD FUNNEL UPPER_WALLS COM GROUP WHOLEMOLECULES COMBINE PRINT BRIDGE DISTANCES MOLINFO REWEIGHT_METAD METAD ALPHABETA | vatom adjmat generic bias multicolvar colvar function core funnel |
| 19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Vittorio Limongelli | DISTANCE LOWER_WALLS RMSD FUNNEL UPPER_WALLS PRINT WHOLEMOLECULES COM FUNNEL_PS METAD | vatom generic bias colvar funnel |
| 19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Gabriele Cesare Sosso | CLUSTER_WITHSURFACE OUTPUT_CLUSTER MFILTER_MORE CLUSTER_NATOMS ENDPLUMED COMMITTOR LOCAL_Q6 CONTACT_MATRIX FLUSH Q6 DFSCLUSTERING | generic symfunc clusters multicolvar adjmat |
| 19.004 | MI Ubiquitin | bio | metainference, NMR | Max Bonomi | CS2BACKBONE PRINT WHOLEMOLECULES GROUP RDC MOLINFO METAINFERENCE | core isdb generic |
| 19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Giovanni Bussi | ERMSD DISTANCE LOWER_WALLS UPPER_WALLS PRINT COMBINE INCLUDE FLUSH ANGLE DISTANCES MOLINFO RANDOM_EXCHANGES METAD | generic bias multicolvar colvar function |
| 25.009 | Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water | chemistry | metadynamics, nitrate photolysis | Kam-Tung Chan | GROUP UPPER_WALLS FLUSH COORDINATION RESTART CUSTOM METAD REWEIGHT_METAD HISTOGRAM READ PRINT DUMPGRID DISTANCE | core function colvar bias gridtools setup 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 | PUCKERING RESTART TORSION MOLINFO PRINT METAD RESTRAINT MOVINGRESTRAINT DISTANCE | bias setup generic colvar |
| 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 | ENERGY GROUP DISTANCE OPES_EXPANDED ECV_MULTITHERMAL COORDINATION RESTART CUSTOM TORSION OPES_METAD_EXPLORE PRINT COMBINE | function core colvar setup opes generic |
| 24.022 | Integrating Path Sampling with Enhanced Sampling for Rare-event Kinetics | methods | OPES Flooding, Weighted Ensemble, Metadynamics, Kinetics, Infrequent Metadynamics, Integrated Sampling | Dhiman Ray | COMMITTOR RMSD CUSTOM METAD GROUP COORDINATION FIXEDATOM MOLINFO OPES_METAD CONTACTMAP PRINT FIT_TO_TEMPLATE COMBINE ENDPLUMED ANGLE DISTANCE UPPER_WALLS WHOLEMOLECULES TORSION MATHEVAL CENTER | core function colvar bias vatom opes generic |
| 23.036 | Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? | bio | NaCl, nucleation, metadynamics | Ruiyu Wang | ENERGY Q4 MATHEVAL COORDINATIONNUMBER PRINT METAD COMBINE VOLUME Q6 | function symfunc colvar bias generic |
| 23.026 | Machine Learning Nucleation Collective Variables with Graph Neural Networks | chemistry | Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks | Florian Dietrich | GROUP MFILTER_MORE LOWER_WALLS LOCAL_Q6 COORDINATIONNUMBER PRINT METAD MOVINGRESTRAINT COMBINE Q6 | core function symfunc bias multicolvar generic |
| 23.014 | Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 | bio | metadynamics, oligomerization, chemokine receptors, GPCR, membrane | Vittorio Limongelli | UPPER_WALLS FLUSH WHOLEMOLECULES DISTANCE TORSION PRINT METAD COM COMBINE | function colvar bias vatom generic |
| 22.028 | N-glycan conformer distributions in atomistic simulation | bio | REST2, RECT, N-glycan, pucker | Isabell Grothaus | CONVERT_TO_FES PUCKERING MOLINFO TORSION HISTOGRAM PRINT METAD DUMPGRID READ | bias gridtools generic colvar |
| 22.023 | Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy | bio | CryoEM, MEMMI,EMMI, Metadynamics, Metainference, IAPP, structural ensemble | Faidon Brotzakis | GROUP UPPER_WALLS PBMETAD WHOLEMOLECULES RMSD COORDINATION RESTART MOLINFO TORSION EMMI PRINT COM BIASVALUE | core colvar bias setup vatom isdb generic |
| 22.016 | Homogeneous ice nucleation in an ab initio machine learning model of water | chemistry | ice, water, nucleation, seeding, environment similarity, interfacial free energy, interfaces | Pablo Piaggi | ENERGY UPPER_WALLS RESTART CUSTOM DUMPGRID OPES_METAD HISTOGRAM AROUND VOLUME ENVIRONMENTSIMILARITY PRINT | volumes function envsim colvar bias gridtools setup opes generic |
| 22.013 | Ligand dissociation from PreQ1 riboswitch | bio | ligand, RNA, metadynamics, pRAVE | Yihang Wang | COMMITTOR WHOLEMOLECULES RMSD MOLINFO METAD COMBINE PRINT COORDINATIONNUMBER COM DISTANCE | function symfunc colvar bias vatom generic |
| 22.005 | Collective Variable for Metadynamics Derived from AlphaFold Output | bio | AlphaFold, protein folding, protein structure prediction, metadynamics, deep learning, free energy simulation, collective variable | Vojtech Spiwok | WHOLEMOLECULES LOAD PRINT METAD | bias generic setup |
| 22.002 | GAMBES_SAMPL5_RATES | other | GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding | Jayashrita Debnath | ENERGY GROUP UPPER_WALLS FLUSH WHOLEMOLECULES ENDPLUMED COMMITTOR COORDINATION FIXEDATOM MATHEVAL CENTER PRINT FIT_TO_TEMPLATE PYTORCH_MODEL ANGLE DISTANCE LOAD | core function pytorch colvar bias setup vatom generic |
| 21.051 | Automatic learning of hydrogen-bond fixes in an AMBER RNA force field | methods | force field, RNA | Giovanni Bussi | WHOLEMOLECULES ERMSD COORDINATION MOLINFO PRINT METAD COMBINE BIASVALUE | bias function generic colvar |
| 21.047 | Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations | materials | pair entropy, metadynamics, ves, solids, crystallization | Pablo Piaggi | ENERGY BF_LEGENDRE PAIRENTROPY RESTART TD_WELLTEMPERED OPT_AVERAGED_SGD PRINT METAD VES_LINEAR_EXPANSION COMBINE VOLUME LOAD | function colvar bias gridtools ves setup generic |
| 21.040 | A structural ensemble of a tau-microtubule complex reveals regulatory tau phosphorylation and acetylation mechanisms | bio | EMMI, CryoEM, tau-microtubules, post-translational modifications, chemical mutagenesis, structural ensemble, Metainference | Faidon Brotzakis | GROUP UPPER_WALLS WHOLEMOLECULES RESTART MOLINFO EMMI PRINT COM DISTANCE BIASVALUE | core colvar bias setup vatom isdb generic |
| 21.027 | EGFR activating mutations mechanism | bio | metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA | Francesco Gervasio | ENERGY UPPER_WALLS WHOLEMOLECULES MOLINFO MATHEVAL INCLUDE CONTACTMAP LOWER_WALLS ALPHARMSD PRINT METAD DISTANCE | function secondarystructure colvar bias generic |
| 21.013 | Role of vibrational excitation in heterogeneous catalysis | chemistry | catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption | Kristof Bal | CONVERT_TO_FES BF_CHEBYSHEV DISTANCES REWEIGHT_METAD COORDINATIONNUMBER METAD RESTRAINT COORDINATION ANGLES HISTOGRAM PRINT COMBINE REWEIGHT_BIAS UWALLS UNITS DUMPGRID VES_LINEAR_EXPANSION DISTANCE LOAD UPPER_WALLS FLUSH EXTERNAL LOWER_WALLS OPT_AVERAGED_SGD TD_GRID | function symfunc colvar bias gridtools multicolvar ves setup generic |
| 21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Adriana Pietropaolo | CONSTANT PBMETAD WHOLEMOLECULES RESTART TORSION MATHEVAL PRINT BIASVALUE | function colvar bias setup generic |
| 20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Faidon Brotzakis | CONVERT_TO_FES GROUP WHOLEMOLECULES RMSD MOLINFO DISTANCES EMMI HISTOGRAM READ PRINT DUMPGRID BIASVALUE | core colvar bias gridtools multicolvar isdb generic |
| 20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Glen Hocky | ENERGY GROUP GYRATION MATHEVAL UNITS PRINT FISST RESTRAINT DISTANCE BIASVALUE | function core colvar bias fisst setup 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 | GROUP UPPER_WALLS WHOLEMOLECULES PATHMSD RESTART MOLINFO PRINT METAD | core colvar bias setup generic |
| 19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Giovanni Bussi | ENDPLUMED WHOLEMOLECULES COORDINATION LOWER_WALLS RESTRAINT DISTANCE | bias generic colvar |
| 19.059 | cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide | bio | bias-exchange metadynamics, cis-trans isomerization | Fabrizio Marinelli | TORSION INCLUDE PRINT METAD RANDOM_EXCHANGES | bias generic colvar |
| 19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | UPPER_WALLS FLUSH DISTANCE RESTART DISTANCES UNITS PRINT METAD COMBINE | function colvar bias multicolvar setup generic |
| 19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Davide Provasi | ENDPLUMED WHOLEMOLECULES RMSD FUNCPATHMSD CONTACTMAP PRINT METAD COM DISTANCE | function colvar bias vatom generic |
| 19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Elena Papaleo | GROUP UPPER_WALLS WHOLEMOLECULES GYRATION MOLINFO LOWER_WALLS PRINT METAD ALPHABETA | core colvar bias multicolvar generic |
| 19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Haochuan Chen | DRR TORSION PRINT | drr generic colvar |
| 19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Kresten Lindorff-Larsen | FLUSH COMMITTOR MOLINFO PRINT METAD ALPHABETA COMBINE | bias multicolvar generic function |
| 19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Riccardo Capelli | CONVERT_TO_FES GROUP UPPER_WALLS FLUSH WHOLEMOLECULES ENDPLUMED COORDINATION DUMPGRID MATHEVAL REWEIGHT_METAD HISTOGRAM POSITION PRINT METAD READ WRAPAROUND COM FIT_TO_TEMPLATE | core function colvar bias gridtools vatom generic |
| 19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Carlo Camilloni | ENDPLUMED GROUP UPPER_WALLS WHOLEMOLECULES RMSD MOLINFO INCLUDE CENTER PRINT SAXS RESTRAINT STATS DISTANCE BIASVALUE | core function colvar bias vatom isdb generic |
| 19.011 | Automatic Gradient Computation for Collective Variables | other | gradient, differentiation, curvature | Toni Giorgino | ENDPLUMED | generic |
| 19.009 | RNA tetraloops folding | bio | metadynamics, RNA, folding | Giovanni Bussi | ENDPLUMED WHOLEMOLECULES ERMSD RMSD MOLINFO PRINT METAD | bias generic colvar |
| 19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Michele Invernizzi | ENDPLUMED ENERGY RESTART TORSION VES_DELTA_F UNITS POSITION PRINT METAD LOAD | colvar bias ves setup generic |