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 |
|---|---|---|---|---|---|---|
| 25.029 | Energetic Constraints in the Enzymatic Depolymerization of Crystalline PET from enhanced molecular simulations | bio | HREX-Metadynamics, PETase, crystalline PET, amorphous PET, conformational ensembles, substrate binding, chain detachment | Ania Di Pede-Mattatelli and Francesco Colizzi | FIXEDATOM COM DUMPGRID REWEIGHT_BIAS DISTANCE LOWER_WALLS METAD UPPER_WALLS WHOLEMOLECULES MOLINFO HISTOGRAM PRINT CONVERT_TO_FES | vatom gridtools bias generic colvar |
| 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 FIXEDATOM COM COORDINATIONNUMBER RESTRAINT DISTANCE METAD ANGLE LOWER_WALLS UPPER_WALLS COMBINE DISTANCES UNITS PRINT COORDINATION GROUP | vatom symfunc bias generic function setup colvar multicolvar core |
| 24.002 | Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes | chemistry | metadynamics, ligand design, solvent extraction | Xiaoyu Wang | METAD RESTART TORSION UNITS PRINT | generic setup colvar bias |
| 23.033 | DNA G-quadruplex and G-hairpin folding with ST-metaD protocol | bio | DNA, G4, GQ, quadruplex, hairpin, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | METAD BIASVALUE ERMSD GHBFIX WHOLEMOLECULES COMBINE PRINT COORDINATION MOLINFO | generic colvar function bias |
| 23.012 | JAK2 2D meta-eABF PMF with statistical analysis | bio | 2D meta-eABF, path CV, PMF | Istvan Kolossvary | FLUSH CUSTOM DRR PATHMSD METAD LOWER_WALLS BIASVALUE UPPER_WALLS PRINT | bias generic function colvar drr |
| 22.042 | Metadynamics of NSP10 and variants | bio | metadynamics, NSP10, crystal structure, variants | Shozeb Haider | TORSION PRINT METAD | generic colvar bias |
| 22.038 | Enhanced Sampling Aided Design of Molecular Photoswitches | chemistry | reaction discovery, OPES explore, graph CV | Umberto Raucci | OPES_METAD_EXPLORE PRINT PYTORCH_MODEL UNITS CUSTOM COORDINATION | opes function generic setup colvar pytorch |
| 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 | COM GROUP EMMI RESTART BIASVALUE UPPER_WALLS TORSION WHOLEMOLECULES PRINT PBMETAD RMSD MOLINFO COORDINATION | vatom isdb bias generic setup colvar core |
| 19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Sandro Bottaro | DISTANCE METAD ERMSD TORSION WHOLEMOLECULES PRINT RMSD MOLINFO | generic colvar bias |
| 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 | COM DISTANCE METAD UPPER_WALLS PRINT ENERGY | generic vatom colvar bias |
| 19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Elena Papaleo | GROUP GYRATION LOWER_WALLS METAD ALPHABETA UPPER_WALLS WHOLEMOLECULES PRINT MOLINFO | bias generic colvar multicolvar core |
| 19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Pratyush Tiwary | COM COMMITTOR DISTANCE RESTART EXTERNAL COMBINE WHOLEMOLECULES ALPHABETA TORSION PRINT | vatom bias generic function setup colvar multicolvar |
| 19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Gabriele Cesare Sosso | FLUSH COMMITTOR Q6 DFSCLUSTERING OUTPUT_CLUSTER LOCAL_Q6 ENDPLUMED CLUSTER_WITHSURFACE MFILTER_MORE CLUSTER_NATOMS CONTACT_MATRIX | adjmat symfunc generic multicolvar clusters |
| 19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Max Bonomi | EMMI BIASVALUE MOLINFO PRINT GROUP | generic isdb core bias |
| 25.030 | Committor Regularization | methods | metadynamics, enhanced sampling, mlcvs, committor, machine learning | Florian Dietrich | PRINT UNITS METAD MOVINGRESTRAINT | bias generic setup |
| 25.028 | Designing transferable transition state guided collective variable via interpretable machine learning model for enhanced sampling. A case study on polymer collapse transition | bio | metadynamics, polymer collapse transition, transferable CV,interpretable ML-model | Saikat Dhibar and Biman Jana | GYRATION COMBINE COORDINATION PRINT UPPER_WALLS LOWER_WALLS DISTANCE METAD GROUP MATHEVAL WHOLEMOLECULES CENTER | bias colvar generic vatom function core |
| 25.022 | Imidazole Diffusion in SALEM-2 MOF | materials | OPES, Diffusion, Ring opening, MOFs, Machine Learning Potentials | Sudheesh Kumar Ethirajan | PROJECTION_ON_AXIS PRINT ENDPLUMED DISTANCE DISTANCES GROUP UNITS OPES_METAD WHOLEMOLECULES MOLINFO CENTER | opes setup colvar generic core vatom multicolvar |
| 25.017 | Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity | bio | EMMIVox, cryo-EM, allostery, decamer, filament, ensemble refinement, glutamine synthetase | Samuel Hoff | BIASVALUE PRINT EMMIVOX GROUP WHOLEMOLECULES MOLINFO | bias isdb generic core |
| 24.032 | DeepLNE++ | methods | PATHCV, OPES | Thorben Fröhlking | COMBINE COORDINATION CUSTOM PRINT DISTANCE ENERGY GROUP OPES_METAD TORSION LOAD | opes colvar setup generic function core |
| 24.029 | Combination of OPES and OPES-Explore | methods | OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin | Dhiman Ray | COMBINE UPPER_WALLS CUSTOM LOWER_WALLS FLUSH MOLINFO CENTER ENDPLUMED POSITION ENERGY GROUP BIASVALUE COORDINATION PRINT RMSD METAD FIXEDATOM UNITS MATHEVAL INCLUDE FIT_TO_TEMPLATE PYTORCH_MODEL DISTANCE OPES_METAD_EXPLORE OPES_METAD CONTACTMAP WHOLEMOLECULES | bias opes colvar setup generic vatom pytorch function core |
| 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 | COMBINE CUSTOM UPPER_WALLS COMMITTOR MOLINFO CENTER ENDPLUMED CONTACTMAP GROUP TORSION COORDINATION PRINT RMSD METAD FIXEDATOM FIT_TO_TEMPLATE ANGLE DISTANCE OPES_METAD MATHEVAL WHOLEMOLECULES | bias opes colvar generic vatom function core |
| 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 | generic colvar |
| 23.031 | Identifying small molecules binding sites in RNA conformational ensembles with SHAMAN | bio | RNA, metadynamics, probes, mixed-solvent MD, small molecules, binding sites | Max Bonomi | WRAPAROUND FIT_TO_TEMPLATE UPPER_WALLS PRINT POSITION METAD DISTANCES GROUP WHOLEMOLECULES SHADOW MOLINFO CENTER | bias colvar generic core vatom multicolvar isdb |
| 23.015 | MPCs aggregation | bio | opes_explore, dimerization, MPCs, self-assembly | Vikas Tiwari | COM COORDINATION CUSTOM UPPER_WALLS LOWER_WALLS PRINT DISTANCE METAD GROUP OPES_METAD_EXPLORE WHOLEMOLECULES CENTER | bias opes colvar generic vatom function core |
| 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 | COMBINE UPPER_WALLS CUSTOM LOWER_WALLS COMMITTOR MOLINFO CENTER ENDPLUMED ENERGY CONTACTMAP GROUP COORDINATION PRINT RMSD FIXEDATOM INCLUDE FIT_TO_TEMPLATE ANGLE PYTORCH_MODEL DISTANCE OPES_METAD MATHEVAL WHOLEMOLECULES | bias opes colvar generic vatom pytorch function core |
| 23.008 | PBMetaD simulations of Histatin5 | bio | metadynamics, IDP, Rg, PPII | Francesco Pesce | GYRATION PRINT PBMETAD GROUP TORSION WHOLEMOLECULES MOLINFO | bias generic colvar core |
| 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 | ENVIRONMENTSIMILARITY PRINT HISTOGRAM ECV_UMBRELLAS_LINE UPPER_WALLS LOWER_WALLS RESTART DUMPGRID OPES_EXPANDED | bias opes setup generic envsim gridtools |
| 22.032 | Reciprocal barrier restraint. Application to path-meta-eABF | methods | restraint, upper wall, lower wall, path colvar, meta-eABF, metadynamics, DRR, protein conformational transition, PROTAC | Istvan Kolossvary | BIASVALUE CUSTOM PRINT METAD FLUSH PATHMSD DRR | bias colvar generic drr function |
| 22.026 | Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification | materials | Peptoid, silica | Jim Pfaendtner | GYRATION COM UPPER_WALLS PRINT DISTANCE PBMETAD MOLINFO | bias vatom generic colvar |
| 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 | ANGLE COORDINATION UPPER_WALLS ALPHARMSD PRINT DISTANCE ALPHABETA METAD FLUSH TORSION WHOLEMOLECULES MOLINFO | bias colvar generic multicolvar secondarystructure |
| 21.052 | On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets | materials | Ibuprofen, unbinding, WTmetaD | Matteo Salvalaglio | PRINT ENDPLUMED COMMITTOR DISTANCE METAD COORDINATIONNUMBER TORSION CENTER | bias colvar generic vatom symfunc |
| 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 RMSD DISTANCE | generic colvar |
| 21.028 | From Enhanced Sampling to Reaction Profiles | methods | collective variables, multi-state, machine learning, Deep-TDA | Enrico Trizio | UPPER_WALLS LOWER_WALLS LOAD CENTER ENDPLUMED GROUP TORSION COORDINATION PRINT FIXEDATOM DISTANCES UNITS FIT_TO_TEMPLATE ANGLE PYTORCH_MODEL DISTANCE OPES_METAD MATHEVAL WHOLEMOLECULES | bias opes setup colvar generic vatom pytorch multicolvar function core |
| 20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Matteo Salvalaglio | UPPER_WALLS PRINT LOWER_WALLS METAD VOLUME ENERGY MATHEVAL CELL | bias generic colvar function |
| 20.018 | Free energy barriers from biased molecular dynamics simulations | methods | kinetics, free energy barriers, chemical reactions, nucleation, metadynamics | Kristof Bal | Q6 COMBINE PAIRENTROPY UPPER_WALLS CONTACT_MATRIX LOWER_WALLS FLUSH LOAD CENTER HISTOGRAM CONVERT_TO_FES ENERGY REWEIGHT_METAD DENSITY REWEIGHT_BIAS COORDINATION PRINT SPRINT METAD UNITS DUMPGRID DISTANCE VOLUME COORDINATIONNUMBER LOCAL_AVERAGE | bias setup colvar generic volumes sprint vatom function symfunc adjmat gridtools |
| 20.016 | Predicting polymorphism in molecular crystals using orientational entropy | materials | metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy | Pablo Piaggi | UPPER_WALLS PRINT VOLUME METAD GROUP INCLUDE LOAD CENTER | bias setup colvar generic vatom core |
| 20.015 | Rational design of ASCT2 inhibitors using an integrated experimental-computational approach | bio | ASCT2 transporter, small-molecules, cryo-EM, metainference | Max Bonomi | BIASVALUE PRINT LOAD EMMIVOX DUMPATOMS GROUP WHOLEMOLECULES MOLINFO | bias setup generic core isdb |
| 20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Carlo Camilloni | GYRATION METAINFERENCE STATS PRINT DISTANCE ALPHABETA PBMETAD FLUSH SAXS TORSION WHOLEMOLECULES ENSEMBLE MOLINFO CENTER | bias colvar generic vatom function multicolvar isdb |
| 19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Valerio Rizzi | COMBINE PRINT EXTERNAL ENDPLUMED METAD FLUSH COORDINATIONNUMBER GROUP UNITS RESTART | bias setup generic function core symfunc |
| 19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | GYRATION COM UPPER_WALLS PRINT DISTANCE METAD ENERGY MOLINFO | bias vatom generic colvar |
| 19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Jakub Rydzewski | UPPER_WALLS PRINT LOWER_WALLS METAD PATHMSD UNITS RESTART | bias setup generic colvar |
| 19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_LOSS PRINT MAZE_SIMULATED_ANNEALING POSITION UNITS MAZE_OPTIMIZER_BIAS | setup colvar generic maze |
| 19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Wei Chen | COMBINE COM ANN POSITION RESTRAINT | bias colvar annfunc vatom function |
| 19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Carlo Camilloni | BIASVALUE ANTIBETARMSD UPPER_WALLS CS2BACKBONE LOWER_WALLS PRINT ENDPLUMED FLUSH ALPHABETA PBMETAD GROUP RESTART WHOLEMOLECULES MOLINFO | bias setup generic core multicolvar secondarystructure isdb |
| 19.035 | Dimerization of GPCRs from coarse-grained umbrella sampling | bio | Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization | Davide Provasi | COM PRINT DISTANCE GROUP TORSION RESTRAINT | bias colvar generic vatom core |
| 19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Silvio Pipolo | UPPER_WALLS PIV LOWER_WALLS PRINT METAD CELL FUNCPATHMSD | bias colvar generic function piv |
| 25.027 | Enhanced-sampling MD simulations of a protein-peptide complex integrating SAXS and XL-MS experimental information | bio | steered MD, metadynamics, SAXS, XL-MS, ensemble reconstruction | Mattia Bernetti | SAXS UPPER_WALLS METAD CENTER DISTANCE WHOLEMOLECULES MOLINFO PRINT GYRATION MOVINGRESTRAINT INCLUDE GROUP | core vatom generic colvar bias isdb |
| 25.026 | Deciphering the Molecular Mechanisms of Startle Disease - the Role of the Asn46Lys Mutation in the Glycine Receptor | bio | metadynamics, glycine receptors, funnel metadynamics | Jacob Adam Clark | COM LOWER_WALLS UPPER_WALLS FUNNEL METAD FUNNEL_PS PRINT | generic vatom funnel bias |
| 25.013 | Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices | bio | umbrella sampling, temperature ramping | Alexander Berlaga | PYTORCH_MODEL DISTANCE PRINT GYRATION RESTRAINT | colvar pytorch generic bias |
| 24.035 | Data efficient machine learning potentials for modeling catalytic reactivity via active learning and enhanced sampling | chemistry | opes, catalysis, ammonia, machine learning potentials | Luigi Bonati | LOWER_WALLS UPPER_WALLS UNITS COORDINATION DISTANCE RESTART PRINT OPES_METAD COMMITTOR GROUP CUSTOM | function generic bias colvar opes setup core |
| 24.026 | Constant pH metadynamics of RNA oligomers | bio | metadynamics, pH, RNA | Giovanni Bussi | TORSION METAD MOLINFO RESTART PRINT PUCKERING | colvar setup generic bias |
| 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 | TORSION LOWER_WALLS OPES_METAD_EXPLORE ECV_MULTITHERMAL ENDPLUMED MATHEVAL UPPER_WALLS FIXEDATOM CENTER DISTANCE WHOLEMOLECULES COORDINATION ANGLE PRINT OPES_EXPANDED ENERGY FIT_TO_TEMPLATE GROUP | function vatom generic colvar opes bias core |
| 24.023 | Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21. A Machine-Learning-Aided Enhanced Sampling Study | bio | RNA, miRNA, OneOPES, ligand binding, conformational changes | Valerio Rizzi | TORSION OPES_METAD_EXPLORE ECV_MULTITHERMAL COMBINE COORDINATION DISTANCE RESTART PRINT OPES_EXPANDED ENERGY GROUP CUSTOM | function generic colvar opes setup 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 | TORSION METAD PRINT COMMITTOR LOAD GROUP | generic bias colvar setup core |
| 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 ALPHARMSD COMBINE DISTANCE WHOLEMOLECULES MOLINFO COORDINATION PRINT OPES_METAD GYRATION CUSTOM | function secondarystructure generic colvar opes |
| 23.035 | An Extended Metadynamics Protocol for Binding/Unbinding of Peptide Ligands to Class A G-Protein Coupled Receptors | bio | G protein coupled receptor, peptide ligands, metadynamics, multiple-walker | Timothy Clark | LOWER_WALLS MATHEVAL UPPER_WALLS CONSTANT CENTER METAD DISTANCE WHOLEMOLECULES BIASVALUE PRINT | function vatom generic colvar bias |
| 23.020 | FEP simulations of ATOX1 homodimer | chemistry | parallel bias metadynamics, FEP, free-energy of metal ion dissociation | Adriana Pietropaolo | MATHEVAL CONSTANT PBMETAD DISTANCE ANGLE WHOLEMOLECULES BIASVALUE PRINT | bias colvar function generic |
| 23.011 | OneOPES, a combined enhanced sampling method to rule them all | bio | OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding | Valerio Rizzi | TORSION OPES_METAD_EXPLORE ECV_MULTITHERMAL ENDPLUMED METAD DISTANCE MOLINFO PRINT OPES_EXPANDED ENERGY | colvar opes generic bias |
| 23.002 | Critical comparison of general-purpose collective variables for crystal nucleation | methods | metadynamics, umbrella sampling, commitor, entropy, PIV | Julien Lam | PIV LOCAL_AVERAGE UPPER_WALLS METAD Q6 FUNCPATHMSD UNITS PAIRENTROPY PRINT Q4 ENERGY VOLUME CUSTOM RESTRAINT | function gridtools symfunc generic bias colvar setup piv |
| 23.001 | Quantum phase diagram of water | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn-Løland Bore | LOWER_WALLS UPPER_WALLS ECV_UMBRELLAS_LINE RESTART PRINT OPES_EXPANDED INCLUDE ENVIRONMENTSIMILARITY | generic bias opes setup envsim |
| 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 METAD WHOLEMOLECULES PRINT ENERGY CONTACTMAP | colvar generic bias |
| 22.027 | Molecular Dynamics simulations of BANAL-236 RBD-hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, BANAL-236, receptor-binding domain | Max Bonomi | RMSD PRINT | colvar generic |
| 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 | COM TORSION METAD DISTANCE WHOLEMOLECULES PRINT GROUP | vatom generic colvar bias core |
| 22.002 | GAMBES_SAMPL5_RATES | other | GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding | Jayashrita Debnath | GROUP ENDPLUMED MATHEVAL UPPER_WALLS CENTER PYTORCH_MODEL FLUSH DISTANCE WHOLEMOLECULES COORDINATION ANGLE PRINT COMMITTOR ENERGY LOAD FIT_TO_TEMPLATE FIXEDATOM | pytorch function vatom generic colvar setup bias core |
| 22.000 | Amyloid precursor protein processing by human γ-secretase | bio | Bias Exchange Metadynamics, Helix unfolding, coupled binding | Xiaoli Lu | ALPHARMSD CENTER METAD CONTACTMAP UNITS COORDINATION MOLINFO DISTANCE PRINT ANTIBETARMSD INCLUDE RANDOM_EXCHANGES | secondarystructure vatom generic bias colvar setup |
| 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 ENDPLUMED METAD PBMETAD PRINT INCLUDE RANDOM_EXCHANGES | colvar generic bias |
| 21.016 | MD SAXS GTPase associated center | bio | metadynamics, RNA, folding, SAXS | Giovanni Bussi | LOWER_WALLS SAXS UPPER_WALLS ERMSD METAD WHOLEMOLECULES MOLINFO PRINT GYRATION INCLUDE GROUP CUSTOM | function core generic colvar bias isdb |
| 20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Faidon Brotzakis | DUMPGRID DISTANCES HISTOGRAM WHOLEMOLECULES MOLINFO RMSD PRINT BIASVALUE READ EMMI CONVERT_TO_FES GROUP | gridtools core generic multicolvar colvar bias isdb |
| 20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Jim Pfaendtner | DISTANCES CENTER DISTANCE COORDINATION WHOLEMOLECULES RESTART PRINT GROUP | vatom generic multicolvar colvar 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 | ENDPLUMED UNITS PRINT GYRATION MOVINGRESTRAINT | bias colvar generic setup |
| 19.056 | maze | methods | maze, ligand unbinding | Jakub Rydzewski | UNITS POSITION MAZE_SIMULATED_ANNEALING PRINT MAZE_OPTIMIZER_BIAS MAZE_LOSS | colvar generic maze setup |
| 19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | COMBINE UPPER_WALLS METAD FLUSH UNITS DISTANCE PRINT ENERGY | function generic bias colvar setup |
| 19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Davide Provasi | COM ENDPLUMED METAD FUNCPATHMSD DISTANCE WHOLEMOLECULES RMSD PRINT CONTACTMAP | function vatom generic colvar bias |
| 25.018 | Metainference simulation for dimerization of RNA binding protein | bio | Metainference, Metadynamics, SAXS, protein dimer | Debadutta Patra | GYRATION STATS FLUSH SAXS MOLINFO DISTANCE ENSEMBLE PRINT METAINFERENCE PBMETAD WHOLEMOLECULES TORSION CENTER UPPER_WALLS | bias function colvar vatom generic isdb |
| 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 | ENERGY GYRATION RESTART INCLUDE READ MOLINFO DISTANCE PRINT CENTER UPDATE_IF PBMETAD WHOLEMOLECULES VOLUME TORSION DUMPATOMS | bias setup colvar vatom generic |
| 25.002 | M3_PCV-ABMD | chemistry | Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor | Gian Marco Elisi | PATHMSD ABMD PRINT UNITS ENDPLUMED UPPER_WALLS | generic bias colvar setup |
| 24.031 | DeepLNE | methods | PATHCV, OPES, OneOPES | Thorben Fröhlking | PYTORCH_MODEL COMBINE COORDINATION ENERGY ECV_MULTITHERMAL RESTART ERMSD MOLINFO PRINT OPES_EXPANDED OPES_METAD_EXPLORE VOLUME | opes setup colvar generic function pytorch |
| 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 | BIASVALUE ENERGY FLUSH MATHEVAL RESTART MOLINFO DISTANCE PRINT COORDINATIONNUMBER TORSION RESTRAINT COMMITTOR METAD | bias setup colvar generic function symfunc |
| 24.011 | Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble | methods | committor, machine learning | Peilin Kang | POSITION COORDINATION GROUP UNITS UPPER_WALLS ENERGY PRINT CUSTOM BIASVALUE MATHEVAL INCLUDE MOLINFO DISTANCE CELL LOAD LOWER_WALLS TORSION RMSD WHOLEMOLECULES ENDPLUMED | bias setup colvar generic function core |
| 23.046 | Lasso Peptides - HLDA CV | bio | metadynamics, protein folding, HLDA, harmonic | Gabriel da Hora | COMBINE DISTANCE PRINT UNITS WHOLEMOLECULES METAD | bias setup colvar generic function |
| 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 | RMSD MATHEVAL MOLINFO DISTANCE PRINT WHOLEMOLECULES METAD | generic bias colvar 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 | POSITION COM COORDINATION GROUP OPES_METAD UNITS UPPER_WALLS ENERGY FIT_TO_TEMPLATE PRINT CUSTOM CENTER BIASVALUE FLUSH MATHEVAL WRAPAROUND MOLINFO DISTANCE LOWER_WALLS TORSION OPES_METAD_EXPLORE WHOLEMOLECULES ENDPLUMED COMMITTOR | bias opes setup colvar vatom generic function core |
| 23.025 | Probing ion binding to G-quadruplexes and related events | chemistry | metadynamics, repulsive potential, nucleic acids, G-quadruplexes | Marcelo Poleto | POSITION COM FLUSH MATHEVAL RESTART WRAPAROUND FIT_TO_TEMPLATE GROUP LOWER_WALLS DISTANCE PRINT UNITS WHOLEMOLECULES DISTANCES DUMPATOMS UPPER_WALLS METAD | bias setup colvar vatom multicolvar generic function core |
| 23.022 | A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar | methods | collective variables, machine learning, toy model | Enrico Trizio | POSITION BIASVALUE PYTORCH_MODEL OPES_METAD LOWER_WALLS PRINT ENDPLUMED UNITS CUSTOM UPPER_WALLS | bias opes setup colvar generic function pytorch |
| 23.018 | Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention | materials | metadynamics, surface binding, peptide adsorption | Kaylyn Torkelson | COM GYRATION DISTANCE PRINT PBMETAD UPPER_WALLS | generic bias colvar vatom |
| 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 | EXTRACV READ PRINT TORSION METAD | generic bias colvar |
| 22.036 | Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction | bio | Well-tempered MetaDynamics with Hamiltonian Replica Exchange | Miroslav Krepl | GHBFIX BIASVALUE COMBINE COORDINATION FLUSH GROUP MOLINFO PRINT LOAD CUSTOM UPPER_WALLS METAD | bias setup colvar generic function core |
| 22.033 | Reciprocal barrier restraint. Application to PROTAC passive permeability prediction | methods | PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR | Istvan Kolossvary | BIASVALUE COM FLUSH PRINT DISTANCE UNITS CUSTOM DRR METAD | bias setup drr colvar vatom generic function |
| 22.030 | Mixing physics across temperatures with generative artificial intelligence | methods | REMD, Generative AI, DDPM | Yihang Wang | WHOLEMOLECULES TORSION PRINT | generic colvar |
| 22.025 | Bubble nucleation rate predictions in a Lennard-Jones fluid | materials | free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation | Kristof Bal | REWEIGHT_BIAS BIASVALUE FLUSH ANN CONVERT_TO_FES DUMPGRID MOVINGRESTRAINT PRINT UPPER_WALLS LOAD COMMITTOR UNITS VOLUME COORDINATIONNUMBER CUSTOM RESTRAINT HISTOGRAM | bias setup colvar generic gridtools function symfunc annfunc |
| 22.022 | Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir | bio | RMSD, protein-ligand interactions | Isabell Grothaus | RMSD PRINT | generic colvar |
| 21.047 | Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations | materials | pair entropy, metadynamics, ves, solids, crystallization | Pablo Piaggi | BF_LEGENDRE COMBINE ENERGY RESTART TD_WELLTEMPERED PRINT LOAD PAIRENTROPY VOLUME OPT_AVERAGED_SGD METAD VES_LINEAR_EXPANSION | bias ves setup colvar generic gridtools 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 | FIT_TO_TEMPLATE PRINT TORSION FIXEDATOM METAD | generic bias colvar vatom |
| 21.027 | EGFR activating mutations mechanism | bio | metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA | Francesco Gervasio | ALPHARMSD ENERGY MATHEVAL INCLUDE MOLINFO DISTANCE LOWER_WALLS PRINT WHOLEMOLECULES CONTACTMAP UPPER_WALLS METAD | secondarystructure bias colvar generic function |
| 21.022 | Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly | materials | parallel bias metadynamics, adsorption, peptide | Xin Qi | ENERGY COM GYRATION LOWER_WALLS DISTANCE MOLINFO PRINT PBMETAD UPPER_WALLS | generic bias colvar vatom |
| 21.019 | Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations | materials | Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen | Matteo Salvalaglio | TORSIONS COM MATHEVAL DISTANCE PRINT KDE | colvar vatom multicolvar generic gridtools function |
| 21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Kresten Lindorff-Larsen | ALPHARMSD BIASVALUE GYRATION FLUSH GROUP SAXS EEFSOLV MOLINFO PRINT METAINFERENCE PBMETAD WHOLEMOLECULES CENTER | secondarystructure bias colvar vatom generic isdb core |
| 20.024 | Gaussian Mixture Based Enhanced Sampling (GAMBES) | methods | enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias | Jayashrita Debnath | COMBINE ENERGY GROUP LOWER_WALLS PRINT DISTANCE LOAD UNITS DISTANCES TORSION UPPER_WALLS | bias setup colvar multicolvar generic function core |
| 20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Luigi Bonati | PYTORCH_MODEL TORSION COM FLUSH MATHEVAL GROUP OPES_METAD LOWER_WALLS DISTANCE PRINT LOAD UNITS ENDPLUMED UPPER_WALLS | bias opes setup colvar vatom generic function core pytorch |
| 19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Matteo Salvalaglio | INCLUDE GROUP DISTANCE PRINT ENDPLUMED CENTER | generic core vatom colvar |
| 19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Mattia Bernetti | PATHMSD LOWER_WALLS PRINT WHOLEMOLECULES UPPER_WALLS METAD | generic bias colvar |
| 19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Jim Pfaendtner | ENERGY GYRATION PRINT WHOLEMOLECULES METAD | generic bias colvar |
| 19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Kim E. Jelfs | COM RESTART GROUP LOWER_WALLS DISTANCE PRINT CENTER UPPER_WALLS METAD | bias setup colvar vatom generic core |
| 19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Gareth Tribello | FCCUBIC PRINT CELL UNITS ENDPLUMED UPPER_WALLS METAD | bias setup colvar generic symfunc |
| 19.048 | Understanding Ligand Binding Selectivity in a Prototypical GPCR Family | bio | metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | BIASVALUE COM CONSTANT MATHEVAL LOWER_WALLS DISTANCE PRINT WHOLEMOLECULES UPPER_WALLS METAD | bias colvar vatom generic function |
| 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 | POSITION COORDINATION FLUSH RESTART GROUP LOWER_WALLS PRINT UNITS UPPER_WALLS METAD | bias setup colvar generic core |
| 19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Carlo Camilloni | DHENERGY STATS DIHCOR GROUP ENDPLUMED MOLINFO DISTANCE ENSEMBLE PRINT METAINFERENCE RESTRAINT ALPHABETA PBMETAD WHOLEMOLECULES TORSION CENTER UPPER_WALLS RDC | bias colvar multicolvar vatom generic function core isdb |
| 25.023 | Molecular simulations of Tau-protein oligomers | bio | metadynamics, proteins, aggregation | Giovanni Bussi | FLUSH RESTART RMSD CONVERT_TO_FES PRINT RESTRAINT HISTOGRAM CONTACTMAP DUMPGRID REWEIGHT_BIAS CUSTOM METAD | function colvar generic gridtools setup bias |
| 25.019 | The Arch from the Stones. Understanding Protein Folding Energy Landscapes via Bio-inspired Collective Variables | bio | protein folding, OPES, OneOPES, binding free energy | Valerio Rizzi | ECV_MULTITHERMAL RMSD GHOST GROUP PRINT COORDINATION MOLINFO DISTANCE ENERGY OPES_EXPANDED OPES_METAD_EXPLORE CENTER CUSTOM COMBINE | core colvar generic vatom opes function |
| 25.014 | Atomic resolution ensembles of intrinsically disordered proteins with Alphafold | bio | bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement | Vincent Schnapka | BAIES GROUP PRINT BIASVALUE | bias core generic isdb |
| 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 | FLUSH BIASVALUE INCLUDE PRINT CELL UNITS COORDINATION DISTANCE ENERGY LOAD MATHEVAL TORSION POSITION OPES_METAD CUSTOM COMBINE | colvar generic bias setup opes function |
| 25.011 | Chiral perovskite nucleation | chemistry | metadynamics, chiral perovskites, nucleation | Adriana Pietropaolo | RESTART PBMETAD MULTI_RMSD PRINT UPPER_WALLS UNITS DISTANCE MATHEVAL LOWER_WALLS | colvar generic bias setup 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 | PRINT UPPER_WALLS COORDINATION DISTANCE ENERGY OPES_METAD | colvar opes generic bias |
| 24.006 | Water vapor condensation | chemistry | metadynamics, homogeneous condensation, chemical potential | Shenghui Zhong | DFSCLUSTERING CLUSTER_NATOMS COORDINATIONNUMBER PRINT UPPER_WALLS UNITS CLUSTER_PROPERTIES METAD CONTACT_MATRIX | adjmat symfunc generic clusters setup bias |
| 23.045 | Minute-timescale simulations of G Protein Coupled Receptor A2A activation mechanism reveal a receptor pseudo-active state | bio | Path CVs Metadynamics, GPCRs activation transition | Vittorio Limongelli | INCLUDE ALPHARMSD PRINT UPPER_WALLS MOLINFO DISTANCE PATHMSD CONTACTMAP FUNCPATHMSD LOWER_WALLS METAD | colvar secondarystructure generic bias function |
| 23.040 | Supramolecular capsules assembly dynamics | chemistry | Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics | Riccardo Capelli | FLUSH DISTANCES WHOLEMOLECULES COM GROUP PRINT UNITS POSITION DISTANCE CENTER CUSTOM METAD | core colvar generic multicolvar bias setup vatom function |
| 23.039 | Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation | chemistry | metadynamics, ligand dissociation | Eric Beyerle | FIXEDATOM PRINT RESTRAINT UPPER_WALLS MOLINFO DISTANCE DUMPMASSCHARGE CENTER METAD COMBINE | colvar generic bias vatom 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 | COM GYRATION WHOLEMOLECULES PBMETAD INCLUDE PRINT RESTRAINT COORDINATION TORSION | bias vatom generic colvar |
| 22.043 | Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES | bio | OPES, RNA, Tetraloop, Folding | Gül Zerze | WHOLEMOLECULES ECV_MULTITHERMAL CONTACTMAP PRINT ENERGY OPES_EXPANDED ECV_UMBRELLAS_LINE | opes generic colvar |
| 22.035 | Deciphering the alphabet of disorder — Glu and Asp act differently on local but not global properties | bio | intrinsically disordered proteins, parallel bias metadynamics, protein | Kresten Lindorff-Larsen | WHOLEMOLECULES PBMETAD GYRATION MOLINFO TORSION | colvar generic bias |
| 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 | RESTART AROUND PRINT UPPER_WALLS ENERGY VOLUME HISTOGRAM DUMPGRID OPES_METAD CUSTOM ENVIRONMENTSIMILARITY | function colvar volumes generic gridtools envsim setup opes bias |
| 22.012 | Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT | bio | contact maps, protein-protein interactions | Isabell-Louise Grothaus | DISTANCE CENTER PRINT CONTACTMAP | vatom 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 | COM WHOLEMOLECULES XANGLES PRINT ALPHABETA UPPER_WALLS MOLINFO DISTANCE YANGLES ZANGLES MATHEVAL TORSION LOWER_WALLS CUSTOM METAD COMBINE | function colvar generic multicolvar vatom bias |
| 22.004 | Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques | chemistry | reaction discovery, OPES, collective variables | Umberto Raucci | COM PRINT GROUP UPPER_WALLS UNITS COORDINATION DISTANCE MATHEVAL LOAD PYTORCH_MODEL OPES_METAD_EXPLORE LOWER_WALLS OPES_METAD CUSTOM | core function pytorch colvar generic setup vatom opes bias |
| 21.046 | Ubiquitin Interacting Motifs, Duality Between Structured and Disordered Motifs | bio | wt metadynamics, ubiquitin, ataxin-3, short linear motifs, ubiquitin binding motif, moonlight functions, intrinsic disorder | Elena Papaleo | WHOLEMOLECULES GYRATION ALPHABETA GROUP PRINT UPPER_WALLS ENDPLUMED LOWER_WALLS METAD | core colvar generic multicolvar bias |
| 21.044 | NaCl nucleation | chemistry | metadynamics, DFS clustering | Aaron Finney | DFSCLUSTERING CLUSTER_NATOMS FIXEDATOM COORDINATIONNUMBER GROUP PRINT LOCAL_Q6 Q6 CONTACT_MATRIX INSPHERE HISTOGRAM CLUSTER_DISTRIBUTION MFILTER_MORE DUMPGRID METAD COMBINE | core function volumes adjmat symfunc generic gridtools multicolvar bias vatom clusters |
| 21.018 | Localized Volume-based Metadynamics | bio | LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification | Riccardo Capelli | WHOLEMOLECULES PRINT DISTANCE POSITION REWEIGHT_METAD RMSD READ ENDPLUMED COORDINATION MATHEVAL METAD FIXEDATOM GROUP UPPER_WALLS HISTOGRAM DUMPGRID COM FLUSH CONVERT_TO_FES | function core colvar generic gridtools vatom bias |
| 21.006 | OPES, On-the-fly Probability Enhanced Sampling Method | methods | opes, alanine dipeptide, well-tempered, multithermal, multiumbrella | Michele Invernizzi | ECV_MULTITHERMAL PRINT ENDPLUMED ENERGY TORSION OPES_EXPANDED ECV_UMBRELLAS_LINE OPES_METAD | generic opes colvar |
| 20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Valerio Rizzi | WHOLEMOLECULES ANGLE FIXEDATOM GROUP PRINT UPPER_WALLS COORDINATION DISTANCE MATHEVAL ENERGY ENDPLUMED PYTORCH_MODEL FIT_TO_TEMPLATE CENTER OPES_METAD | core function pytorch colvar generic vatom opes bias |
| 20.012 | Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies | bio | metadynamics, well-tempered ensemble, ligand binding, binding affinity calculations, novel COLVAR, funnel restraints, Hamiltonian replica-exchange, PathCV, COMetPath, SWISH | Francesco Gervasio | COM WHOLEMOLECULES BIASVALUE CONTACTMAP INCLUDE GROUP PRINT UPPER_WALLS DISTANCE CONSTANT LOAD MATHEVAL MOLINFO PROJECTION_ON_AXIS FUNCPATHGENERAL LOWER_WALLS METAD | core function colvar generic setup vatom bias |
| 20.006 | Class B GPCR activation mechanism | bio | metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | WHOLEMOLECULES RMSD PRINT UPPER_WALLS MOLINFO DISTANCE ENERGY MATHEVAL LOWER_WALLS CENTER METAD COMBINE | function colvar generic vatom bias |
| 20.002 | Exploring conformational dynamics of the extracellular Venus flytrap domain of the GABAB receptor, a path-metadynamics study | bio | Metadynamics, path CVs | Riccardo Ocello | RESTART WHOLEMOLECULES GROUP PRINT UPPER_WALLS MOLINFO PATHMSD METAD | core colvar generic setup bias |
| 19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Valerio Rizzi | FLUSH RESTART DISTANCES COORDINATIONNUMBER GROUP PRINT UPPER_WALLS UNITS ENDPLUMED METAD COMBINE | core function symfunc generic multicolvar setup bias |
| 19.080 | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | methods | ves, variationally enhanced sampling, vibrational excitation, chemical reactions | Kristof Bal | VES_LINEAR_EXPANSION FLUSH ANGLE CONVERT_TO_FES TD_WELLTEMPERED BF_CHEBYSHEV EXTERNAL LOWER_WALLS PRINT OPT_AVERAGED_SGD UPPER_WALLS UNITS DISTANCE COORDINATION TD_GRID HISTOGRAM DUMPGRID COMBINE | function colvar generic gridtools setup ves bias |
| 19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Giovanni Bussi | COM FLUSH WHOLEMOLECULES MAXENT SORT INCLUDE PRINT COORDINATION MOLINFO DISTANCE MATHEVAL TORSION METAD | colvar generic bias vatom function |
| 19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Matteo Salvalaglio | REWEIGHT_METAD BIASVALUE READ CONVERT_TO_FES EXTERNAL PRINT COMMITTOR DISTANCE MATHEVAL TORSION HISTOGRAM DUMPGRID REWEIGHT_BIAS METAD | colvar generic gridtools bias function |
| 19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Gareth Tribello | FCCUBIC FIND_CONTOUR_SURFACE MORE_THAN GROUP FOURIER_TRANSFORM MULTICOLVARDENS UNITS DUMPGRID CENTER | core symfunc gridtools fourier contour setup vatom function |
| 19.032 | Chemical reaction in solution using path collective variables based on coordination patterns | chemistry | chemical reactions, solutions, metadynamics, coordination patterns | Fabio Pietrucci | FLUSH RESTART DISTANCES PATH PRINT UPPER_WALLS METAD | generic multicolvar setup mapping bias |
| 19.030 | Coarse-Grained MetaDynamics (CG-MetaD) | bio | Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy | Vittorio Limongelli | COM WHOLEMOLECULES PRINT UPPER_WALLS DISTANCE LOWER_WALLS METAD | colvar vatom generic bias |
| 19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Matteo Salvalaglio | PRINT ENDPLUMED UPPER_WALLS MATHEVAL ENERGY VOLUME TORSION COMBINE LOWER_WALLS METAD CELL | function colvar generic bias |
| 19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Carlo Camilloni | WHOLEMOLECULES STATS BIASVALUE RMSD INCLUDE GROUP PRINT UPPER_WALLS RESTRAINT MOLINFO DISTANCE ENDPLUMED SAXS CENTER | core function colvar generic isdb vatom bias |
| 19.009 | RNA tetraloops folding | bio | metadynamics, RNA, folding | Giovanni Bussi | WHOLEMOLECULES RMSD PRINT ERMSD ENDPLUMED MOLINFO METAD | bias generic colvar |
| 19.003 | EMMI ClpP | bio | metainference, cryo-EM | Max Bonomi | BIASVALUE GROUP PRINT MOLINFO EMMI | isdb core generic bias |
| 19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Giovanni Bussi | FLUSH DISTANCES ANGLE INCLUDE PRINT ERMSD UPPER_WALLS MOLINFO DISTANCE RANDOM_EXCHANGES LOWER_WALLS METAD COMBINE | function colvar generic multicolvar bias |
| 24.030 | NMR guided simulation of dsRBD | bio | Metainference, NMR, protein dynamics | Debadutta Patra | STATS ENSEMBLE MOLINFO RDC DISTANCE WHOLEMOLECULES METAINFERENCE PRINT ALPHABETA FLUSH GROUP | multicolvar core function generic isdb colvar |
| 24.028 | All-atom simulations of RNA-membrane interactions | bio | metadynamics, membrane, RNA | Giovanni Bussi | LOWER_WALLS UPPER_WALLS SORT COMBINE MOLINFO DISTANCE METAD CENTER POSITION GHOST WHOLEMOLECULES DISTANCES GYRATION PRINT PUCKERING MATHEVAL GROUP | bias multicolvar core function generic vatom colvar |
| 24.025 | Correlating Enzymatic Reactivity for Different Substrates using Transferable Data-Driven Collective Variables | bio | enzymatic reactivity, k_cat, transfer learning, data-driven CVs, catalysis, ligand-binding modes, water, alpha-amylase, sugar, classical MD, OPES, machine learning, Deep TDA CV, path CV | Sudip Das | LOWER_WALLS OPES_METAD UPPER_WALLS FIT_TO_TEMPLATE FIXEDATOM DISTANCE CENTER WHOLEMOLECULES TORSION RESTART COORDINATION CUSTOM PRINT PATH PYTORCH_MODEL GROUP | bias core mapping function generic vatom pytorch setup opes colvar |
| 24.007 | SWISH-X | bio | swish-x, SWISH-X, swish, expanded SWISH | Alberto Borsatto | UPPER_WALLS INCLUDE MOLINFO CONTACTMAP WHOLEMOLECULES ECV_MULTITHERMAL OPES_EXPANDED ENERGY PRINT | bias opes colvar generic |
| 23.019 | Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors | bio | binding pathway, binding energy, sketch-map, drug development | Raitis Bobrovs | UPPER_WALLS DISSIMILARITIES VORONOI COM PATHMSD DISTANCE METAD WHOLEMOLECULES SKETCHMAP_PROJECTION CUSTOM TRANSPOSE VSTACK COLLECT_FRAMES SKETCHMAP PRINT LANDMARK_SELECT_FPS | bias landmarks function valtools generic vatom dimred colvar matrixtools |
| 22.044 | Colloid Crystallisation Analyses | materials | Q4, Q6, Pair Entropy, DFS | Aaron Finney | MFILTER_MORE DFSCLUSTERING LOCAL_AVERAGE COMBINE CLUSTER_NATOMS LOCAL_Q6 GROUP MFILTER_LESS COORDINATIONNUMBER LOCAL_Q4 Q4 PRINT Q6 CONTACT_MATRIX | multicolvar core function generic symfunc adjmat clusters |
| 22.040 | From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure | bio | SARS-CoV-2, Spike, Omicron | Miłosz Wieczór | UPPER_WALLS LOWER_WALLS METAD WHOLEMOLECULES PCAVARS PRINT | mapping bias generic |
| 22.039 | Driving and characterizing nucleation of urea and glycine polymorphs in water | bio | metadynamics, nucleation, amino acids, polymorphism | Eric Beyerle | LOAD INCLUDE COMBINE Q6 METAD CENTER PAIRENTROPY COORDINATIONNUMBER Q4 PRINT MATHEVAL GROUP | bias core function generic symfunc vatom setup gridtools |
| 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 | UPPER_WALLS LOWER_WALLS INCLUDE ECV_UMBRELLAS_LINE ENVIRONMENTSIMILARITY OPES_EXPANDED PRINT | bias envsim opes generic |
| 22.013 | Ligand dissociation from PreQ1 riboswitch | bio | ligand, RNA, metadynamics, pRAVE | Yihang Wang | COMMITTOR COM COMBINE MOLINFO DISTANCE METAD WHOLEMOLECULES COORDINATIONNUMBER PRINT RMSD | bias function generic symfunc vatom colvar |
| 22.009 | Glycosylation in calixarenes capsule | chemistry | Metadynamics, glycosylation, supramolecular catalysis | GiovanniMaria Piccini | UPPER_WALLS LOWER_WALLS ANGLE COMBINE UNITS FIT_TO_TEMPLATE DISTANCE METAD WHOLEMOLECULES GROUP BRIDGE DISTANCES PRINT MATHEVAL RMSD FLUSH COORDINATION | bias multicolvar core function generic setup adjmat colvar |
| 22.006 | Peptide framework for screening the effects of amino acids on assembly | bio | metadynamics, peptides | Andrew White | CONVERT_TO_FES INCLUDE COM COMBINE METAD PRINT DISTANCES GYRATION REWEIGHT_BIAS DUMPGRID HISTOGRAM GROUP | bias multicolvar core function generic vatom colvar gridtools |
| 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 | UNITS BF_GAUSSIANS DISTANCE BF_CHEBYSHEV POSITION BF_CUBIC_B_SPLINES FLUSH TD_UNIFORM PRINT ENERGY UPPER_WALLS METAD TD_WELLTEMPERED OPT_ADAM VES_OUTPUT_BASISFUNCTIONS COORDINATION INCLUDE OPT_AVERAGED_SGD VES_LINEAR_EXPANSION BF_LEGENDRE BF_WAVELETS | bias ves generic setup colvar |
| 21.039 | Deep learning the slow modes for rare events sampling | methods | collective variables, machine learning, slow modes, deep-tica, opes | Luigi Bonati | COMBINE MOLINFO UNITS CONTACTMAP DISTANCE ECV_MULTITHERMAL RMSD FLUSH OPES_METAD LOAD ENERGY PRINT OPES_EXPANDED Q6 PYTORCH_MODEL ENDPLUMED INCLUDE VOLUME WHOLEMOLECULES ENVIRONMENTSIMILARITY TORSION GROUP | core function envsim generic symfunc pytorch setup opes colvar |
| 21.036 | Modelling the structure and interactions of intrinsically disordered peptides with multiple-replica, metadynamics-based sampling methods and force-field combinations | bio | Bias Exchange Metadynamics, PTWTE-metaD | Matteo Salvalaglio | UPPER_WALLS LOWER_WALLS MOLINFO RANDOM_EXCHANGES ALPHARMSD METAD WHOLEMOLECULES DIHCOR ENERGY COORDINATION GYRATION PRINT PARABETARMSD ANTIBETARMSD GROUP | bias multicolvar core generic colvar secondarystructure |
| 21.020 | Reweighted Jarzynski sampling | methods | free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions | Kristof Bal | CONVERT_TO_FES COMBINE UNITS DISTANCE CONSTANT BF_CHEBYSHEV HISTOGRAM FLUSH OPES_METAD LOAD ANN PRINT UPPER_WALLS BIASVALUE METAD TD_WELLTEMPERED COORDINATIONNUMBER MOVINGRESTRAINT CUSTOM RESTRAINT REWEIGHT_METAD OPT_AVERAGED_SGD VES_LINEAR_EXPANSION REWEIGHT_BIAS DUMPGRID | bias ves annfunc function generic symfunc setup opes colvar gridtools |
| 21.013 | Role of vibrational excitation in heterogeneous catalysis | chemistry | catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption | Kristof Bal | CONVERT_TO_FES COMBINE UNITS DISTANCE BF_CHEBYSHEV DISTANCES HISTOGRAM FLUSH LOAD PRINT UPPER_WALLS LOWER_WALLS EXTERNAL UWALLS METAD COORDINATIONNUMBER RESTRAINT REWEIGHT_METAD COORDINATION ANGLES TD_GRID OPT_AVERAGED_SGD VES_LINEAR_EXPANSION REWEIGHT_BIAS DUMPGRID | bias ves multicolvar function generic symfunc setup colvar gridtools |
| 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 | UPPER_WALLS MATHEVAL ECV_UMBRELLAS_LINE VOLUME ENVIRONMENTSIMILARITY OPT_AVERAGED_SGD VES_LINEAR_EXPANSION OPES_EXPANDED BF_LEGENDRE RESTART PRINT ENERGY ECV_MULTITHERMAL_MULTIBARIC Q6 TD_UNIFORM | bias ves envsim function generic symfunc setup opes colvar |
| 19.075 | PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python | other | Python, automatic differentiation | Toni Giorgino | ENDPLUMED ANGLE COMBINE DISTANCE CENTER TORSION DUMPDERIVATIVES CUSTOM RESTRAINT PRINT GROUP | bias core function generic vatom 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 | INCLUDE METAD TORSION PRINT RANDOM_EXCHANGES | bias colvar generic |
| 19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Cristina Paissoni | STATS ANGLE ENSEMBLE BIASVALUE INCLUDE ENDPLUMED COMBINE MOLINFO CENTER WHOLEMOLECULES GROUP SAXS PBMETAD PRINT MATHEVAL ALPHABETA COORDINATION | bias multicolvar core function generic isdb vatom colvar |
| 19.004 | MI Ubiquitin | bio | metainference, NMR | Max Bonomi | MOLINFO RDC WHOLEMOLECULES CS2BACKBONE METAINFERENCE PRINT GROUP | isdb core generic |
| 26.006 | Metadynamics simulations of buried phosphorylation sites and proline isomerisation | bio | metadynamics | Julian Streit | PRINT TORSION METAD MOLINFO COORDINATION WHOLEMOLECULES | colvar generic bias |
| 25.025 | Enhanced Sampling of Ligand Binding Coupled to RNA Conformational Dynamics | bio | OPES, OPES Flooding , Metadynamics, RNA, Ligand binding, Free Energy, Kinetics, Funnel | Revanth Elangovan and Dhiman Ray | CENTER FUNNEL PRINT RMSD WRAPAROUND OPES_METAD TORSION CUSTOM LOWER_WALLS METAD MATHEVAL UPPER_WALLS GROUP COM COORDINATION COMMITTOR FUNNEL_PS WHOLEMOLECULES | vatom opes core generic bias colvar funnel function |
| 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 | CENTER PRINT OPES_METAD_EXPLORE FIXEDATOM ENERGY UPPER_WALLS GROUP DISTANCE COORDINATION FIT_TO_TEMPLATE MATHEVAL ANGLE WHOLEMOLECULES | vatom opes function core generic colvar 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 | PATHMSD DISTANCES PRINT OPES_METAD_EXPLORE RMSD ENERGY CUSTOM OPES_EXPANDED UPPER_WALLS ECV_MULTITHERMAL DISTANCE GROUP COORDINATION GHOST LOWER_WALLS CENTER | vatom opes core multicolvar generic bias colvar function |
| 25.008 | Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting | methods | metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting | Dhiman Ray | UNITS PRINT RMSD WHOLEMOLECULES ENERGY TORSION CUSTOM METAD MOLINFO BIASVALUE UPPER_WALLS DISTANCE GROUP PYTORCH_MODEL POSITION LOWER_WALLS ENDPLUMED OPES_METAD | opes pytorch core generic bias colvar setup function |
| 25.004 | Machine Learning-Driven Molecular Dynamics Unveil a Bulk Phase Transformation Driving Ammonia Synthesis on Barium Hydride | chemistry | OPES, OPES flooding, Catalysis, Ammonia Synthesis | Axel Tosello Gardini | DISTANCES UNITS PRINT FIXEDATOM CUSTOM FLUSH COORDINATIONNUMBER UPPER_WALLS GROUP ZDISTANCES DISTANCE COMMITTOR OPES_METAD | vatom symfunc opes core multicolvar generic bias colvar setup function |
| 24.034 | Umbrella sampling of ion in transporter SLC26A7 | bio | umbrella sampling, transporter, ions | Xiaoli Lu | POSITION UNITS RESTRAINT PRINT | colvar setup generic bias |
| 24.017 | Absolute Binding Free Energies with OneOPES | methods | protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy | Francesco Gervasio | RMSD CUSTOM BIASVALUE RESTART COM COORDINATION INCLUDE LOWER_WALLS PROJECTION_ON_AXIS OPES_METAD_EXPLORE CONSTANT ENERGY PRINT WRAPAROUND MOLINFO CONTACTMAP WHOLEMOLECULES OPES_EXPANDED TORSION METAD GROUP MATHEVAL ECV_MULTITHERMAL UPPER_WALLS | vatom opes core generic bias colvar setup function |
| 24.012 | Molecular simulations to investigate the impact of N6-methylation in RNA recognition | bio | metadynamics, alchemistry, RNA modification, RNA:protein interactions | Giovanni Bussi | COMBINE PRINT METAD BIASVALUE MOLINFO UPPER_WALLS GROUP DISTANCE COM COORDINATION GHBFIX LOWER_WALLS DEBUG CENTER | vatom core generic bias colvar function |
| 24.010 | Oxytocin metadynamics simulation | bio | metadynamics, oxytocin, peptide | Jan Beránek | PRINT TORSION FLUSH METAD RESTART WHOLEMOLECULES | colvar setup generic bias |
| 24.005 | Learning Markovian Dynamics with Spectral Maps | methods | spectral map, collective variables, machine learning | Jakub Rydzewski | UNITS PRINT CUSTOM BIASVALUE DISTANCE | generic bias colvar setup function |
| 23.036 | Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? | bio | NaCl, nucleation, metadynamics | Ruiyu Wang | COMBINE PRINT ENERGY METAD VOLUME Q4 MATHEVAL Q6 COORDINATIONNUMBER | symfunc generic bias colvar function |
| 23.028 | Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process | chemistry | Ammonia decomposition; Dynamics;OPES; Neural Network potential | Manyi Yang | COMMITTOR DISTANCES UNITS PRINT FIXEDATOM ENERGY FLUSH CUSTOM COORDINATIONNUMBER UPPER_WALLS GROUP DISTANCE COM ZDISTANCES MATHEVAL LOWER_WALLS OPES_METAD | vatom symfunc opes core multicolvar generic bias colvar setup function |
| 23.026 | Machine Learning Nucleation Collective Variables with Graph Neural Networks | chemistry | Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks | Florian Dietrich | LOCAL_Q6 COMBINE MOVINGRESTRAINT PRINT MFILTER_MORE LOWER_WALLS METAD GROUP Q6 COORDINATIONNUMBER | symfunc core multicolvar generic bias function |
| 22.045 | Binding mode and mechanism of enzymatic polyethylene terephthalate degradation | bio | metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation | Francesco Colizzi | MOVINGRESTRAINT PRINT METAD UPPER_WALLS DISTANCE COM ANGLE LOWER_WALLS WHOLEMOLECULES | vatom colvar generic bias |
| 22.029 | Angiotensin-1-7_Metadynamics | bio | Metadynamics, Angiotensin-(1-7), peptide | L.-América Chi | PRINT GYRATION FLUSH METAD UPPER_WALLS GROUP COORDINATION LOWER_WALLS WHOLEMOLECULES | colvar generic core bias |
| 22.024 | Conformational Entropy as a Potential Liability of Computationally Designed Antibodies | bio | metadynamics, conformational entropy, antibody, nanobody | Thomas Löhr | PBMETAD PRINT ALPHABETA TORSION ANTIBETARMSD RESTART MOLINFO COM ALPHARMSD WHOLEMOLECULES | vatom secondarystructure multicolvar generic colvar setup bias |
| 22.015 | Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome | bio | photodynamics, bacteriophytochrome, variationally enhanced sampling | Jakub Rydzewski | PRINT BF_FOURIER TORSION OPT_AVERAGED_SGD VES_LINEAR_EXPANSION TD_UNIFORM | colvar generic ves |
| 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 | LOAD METAD PRINT WHOLEMOLECULES | setup generic bias |
| 22.003 | Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling | methods | opes, metadynamics, reweighting, alanine, muller | Michele Invernizzi | PBMETAD UNITS OPES_METAD_EXPLORE PRINT OPES_EXPANDED ENERGY TORSION CUSTOM METAD LOWER_WALLS BIASVALUE UPPER_WALLS ECV_UMBRELLAS_FILE POSITION ECV_MULTITHERMAL ENDPLUMED OPES_METAD | opes function generic colvar setup bias |
| 21.048 | Enhancing ligand exploration within a channel pore and fenestrations using metadynamics | bio | well-tempered metadynamics, protein-ligand enhanced sampling, sodium channel, Nav, small molecule drug | Elaine Tao | UNITS PRINT TORSION CUSTOM METAD DISTANCE COM LOWER_WALLS UPPER_WALLS | vatom generic bias colvar setup function |
| 21.035 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, interface | Aaron Finney | PRINT RESTRAINT FIXEDATOM GROUP DISTANCE LOAD | vatom core generic colvar setup bias |
| 21.033 | Multiple-path-metadynamics applied to DNA base-pairing transitions | bio | path-CV, metadynamics, multiple-walker, dna | Alberto Pérez-de-Alba-Ortíz | MOVINGRESTRAINT PRINT RESTRAINT CONSTANT METAD UPPER_WALLS INCLUDE COMBINE | function generic bias |
| 21.031 | Photo-switchable sulfonulureas in KATP channel | bio | metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels | Katarzyna Walczewska-Szewc | UNITS PRINT METAD UPPER_WALLS DISTANCE COM LOWER_WALLS WHOLEMOLECULES | vatom generic colvar setup bias |
| 21.023 | Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling | methods | enhanced sampling, collective variables, machine learning | Jakub Rydzewski | UNITS PRINT CONSTANT CUSTOM TORSION METAD ENERGY BIASVALUE DISTANCE INCLUDE REWEIGHT_METAD | generic bias colvar setup function |
| 21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Tarak Karmakar | PRINT OPES_METAD FLUSH GROUP MATHEVAL LOAD LOWER_WALLS PYTORCH_MODEL UPPER_WALLS | opes pytorch core generic bias setup function |
| 21.004 | Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy | bio | machine learning, well-tempered metadynamics, path collective variable, potential of mean force, standard binding free energy calculations, host-guest, protein-ligand unbinding | Dorothea Gobbo | PATHMSD PRINT METAD RESTART UPPER_WALLS LOWER_WALLS WHOLEMOLECULES | colvar setup generic bias |
| 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 | COMBINE PRINT RESTRAINT MOLINFO COORDINATION STATS WHOLEMOLECULES | colvar generic function bias |
| 20.028 | Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane | bio | metadynamics, KRas-4B, anionic membrane | Huixia Lu | PRINT METAD RESTART DISTANCE FIT_TO_TEMPLATE CENTER | vatom generic colvar setup bias |
| 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 | TORSION METAD PRINT DISTANCE | colvar generic bias |
| 20.014 | amyloid beta small molecule interaction | bio | intrinsically disordered proteins, disordered proteins, IDPs, fuzzy binding, small molecule, drugs, entropy, binding, Alzheimer’s disease, amyloid beta | Gabriella Heller | ENSEMBLE FLUSH COORDINATION INCLUDE PARABETARMSD DIHCOR ANTIBETARMSD METAINFERENCE PRINT MOLINFO WHOLEMOLECULES PBMETAD GYRATION CS2BACKBONE TORSION GROUP ALPHARMSD STATS ENDPLUMED COMBINE | isdb secondarystructure core multicolvar generic bias colvar function |
| 20.008 | Simulating solvation and acidity in complex mixtures with first-principles accuracy. The case of CH3SO3H and H2O2 in phenol | chemistry | proton trasfer, metadynamics | Kevin Rossi | DISTANCES UNITS PRINT CUSTOM METAD COORDINATION | multicolvar generic bias colvar setup function |
| 20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Pratyush Tiwary | PRINT RMSD WHOLEMOLECULES TORSION METAD RESTART MOLINFO UPPER_WALLS DISTANCE COMBINE | generic bias colvar setup function |
| 20.001 | Conformational stability and dynamics in solution and in crystals report similarly on unfolding and aggregation propensity of amyloidogenic proteins | bio | metainference, metadynamics, NMR, protein dynamics, b2m, protein crystals | Carlo Camilloni | PBMETAD PRINT WHOLEMOLECULES ALPHABETA CS2BACKBONE ANTIBETARMSD FLUSH MOLINFO BIASVALUE GROUP LOWER_WALLS ENDPLUMED UPPER_WALLS | isdb secondarystructure core multicolvar generic bias |
| 19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Kim Jelfs | DISTANCES MOVINGRESTRAINT PRINT FLUSH RESTART INPLANEDISTANCES COM | vatom multicolvar generic setup bias |
| 19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Gareth Tribello | CELL UNITS PRINT FCCUBIC METAD LOWER_WALLS ENDPLUMED AROUND UPPER_WALLS | symfunc generic colvar setup volumes bias |
| 19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Paolo Raiteri | UNITS PRINT FLUSH METAD RESTART DISTANCE MATHEVAL UPPER_WALLS | generic bias colvar setup function |
| 19.025 | Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide | bio | metainference, NMR, protein dynamics, force-fields | Carlo Camilloni | PBMETAD RDC ENSEMBLE PRINT GYRATION TORSION JCOUPLING CS2BACKBONE FLUSH MOLINFO BIASVALUE METAINFERENCE STATS ENDPLUMED WHOLEMOLECULES | isdb generic bias colvar function |
| 26.002 | A Transferable and Robust Computational Framework for Class A GPCR Activation Free Energies | bio | OneOPES, GPCR, ADRB1, activation, euclidean path, microswitches, conformational changes, allostery | Valerio Rizzi | COORDINATION GROUP ECV_MULTITHERMAL PATHMSD LOWER_WALLS OPES_EXPANDED RMSD VOLUME PRINT UPPER_WALLS CENTER PATH CUSTOM DISTANCE OPES_METAD_EXPLORE ENERGY | opes core bias vatom colvar mapping function generic |
| 26.000 | OPES simulations of disordered proteins | bio | OPES, IDPs | Julian Streit | RESTART ECV_MULTITHERMAL OPES_EXPANDED PRINT ENERGY | setup colvar opes generic |
| 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 GROUP PRINT BAIES | core bias isdb generic |
| 25.003 | Surrogate Model CV | methods | Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding | Sompriya Chatterjee | WHOLEMOLECULES MOLINFO GROUP PRINT PYTORCH_MODEL MATHEVAL OPES_METAD CUSTOM DISTANCE ENDPLUMED ENERGY TORSION COMBINE COMMITTOR | pytorch opes core colvar function generic |
| 25.000 | Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer | bio | metadynamics, pathCV | Sahithya Sridharan Iyer | METAD FUNCPATHGENERAL RESTART MOLINFO GROUP PRINT UPPER_WALLS DISTANCE COM WHOLEMOLECULES | core bias vatom colvar function setup generic |
| 24.014 | Learning Collective Variables with Synthetic Data Augmentation through Physics-inspired Geodesic Interpolation | methods | data augmentation, geodesic interpolation, collective variables, protein folding | Juno Nam | COORDINATION METAD MOLINFO DRR LOWER_WALLS RMSD PRINT UPPER_WALLS PYTORCH_MODEL FLUSH WHOLEMOLECULES | pytorch drr bias colvar generic |
| 23.034 | Urea nucleation in water: do long-range forces matter? | materials | LMF theory, Metadynamics, Nucleation | Ziyue Zou | COORDINATIONNUMBER METAD INCLUDE LOAD GROUP PRINT CENTER | core bias vatom setup symfunc generic |
| 23.027 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, DFS, Q3, Pair Entropy | Aaron Finney | Q3 COORDINATIONNUMBER AROUND GROUP CONTACT_MATRIX DFSCLUSTERING RESTRAINT LOAD CLUSTER_NATOMS DENSITY PRINT UNITS CLUSTER_DISTRIBUTION HISTOGRAM LOCAL_Q3 FIXEDATOM LOCAL_AVERAGE DUMPGRID | clusters volumes adjmat core bias vatom setup symfunc gridtools generic |
| 23.024 | Permutationally Invariant Networks for Enhanced Sampling (PINES) | methods | collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent | Nicholas Herringer | LOAD PBMETAD PRINT | bias setup generic |
| 23.023 | Rational design of novel biomimetic sequence-defined polymers for mineralization applications | methods | metadynamics, surface binding, biomimetic mineralization | Kaylyn Torkelson | COORDINATION PRINT UPPER_WALLS DISTANCE COM PBMETAD GYRATION | bias vatom colvar generic |
| 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 | METAD REWEIGHT_METAD MOLINFO RMSD PRINT READ DUMPGRID MATHEVAL HISTOGRAM DISTANCE WHOLEMOLECULES CONVERT_TO_FES | bias colvar function gridtools generic |
| 23.013 | Path meta-eABF simulation of large scale conformational change in STING protein | methods | meta-eABF, path CV, large scale conformational change, STING protein, reciprocal barrier restraint | Istvan Kolossvary | METAD DRR BIASVALUE PATHMSD LOWER_WALLS PRINT UNITS UPPER_WALLS CUSTOM FLUSH TIME | drr bias colvar function setup 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 METAD BIASVALUE LOWER_WALLS PRINT UPPER_WALLS MATHEVAL DISTANCE WHOLEMOLECULES | bias function colvar 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 | METAD REWEIGHT_METAD MOLINFO RMSD PRINT READ DUMPGRID MATHEVAL HISTOGRAM DISTANCE WHOLEMOLECULES CONVERT_TO_FES | bias colvar function gridtools generic |
| 22.037 | Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site | chemistry | metadynamics, DNA, abasic | Mike Jones | DISTANCE METAD DISTANCES PRINT | bias multicolvar colvar generic |
| 22.034 | Rationalising the difference in crystallisability of two Sulflowers using efficient in silico methods | materials | metadynamics, crystallizability, crystal structure prediction, sulflower, persulforated coronene | Matteo Salvalaglio | CELL METAD DRMSD LOWER_WALLS PRINT UPPER_WALLS MATHEVAL CUSTOM COMMITTOR | bias function colvar generic |
| 22.031 | Rare Event Kinetics from Adaptive Bias Enhanced Sampling | methods | OPES Flooding, Kinetics, Rate, OPES, Machine Learning | Dhiman Ray | POSITION MOLINFO BIASVALUE CONTACTMAP ENDPLUMED TORSION COMBINE PYTORCH_MODEL OPES_METAD DISTANCE ENERGY COMMITTOR CONSTANT INCLUDE GROUP PRINT WHOLEMOLECULES RMSD UNITS CUSTOM | pytorch opes core bias setup colvar function 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 | COORDINATION GROUP LOWER_WALLS RMSD PRINT CENTER UPPER_WALLS FIT_TO_TEMPLATE MATHEVAL PYTORCH_MODEL OPES_METAD CUSTOM DISTANCE FIXEDATOM WHOLEMOLECULES COMMITTOR | pytorch opes core bias vatom colvar function generic |
| 22.008 | Ab initio metadynamics determination of temperature-dependent free-energy landscape in ultrasmall silver clusters | materials | Well tempered metadynamics, ab-initio, ase | Daniel Sucerquia | COORDINATIONNUMBER COORDINATION METAD LOWER_WALLS UNITS UPPER_WALLS FLUSH COM DISTANCE COMBINE GYRATION | bias vatom colvar function setup symfunc generic |
| 21.051 | Automatic learning of hydrogen-bond fixes in an AMBER RNA force field | methods | force field, RNA | Giovanni Bussi | COORDINATION METAD WHOLEMOLECULES MOLINFO BIASVALUE PRINT ERMSD COMBINE | bias function colvar generic |
| 21.040 | A structural ensemble of a tau-microtubule complex reveals regulatory tau phosphorylation and acetylation mechanisms | bio | EMMI, CryoEM, tau-microtubules, post-translational modifications, chemical mutagenesis, structural ensemble, Metainference | Faidon Brotzakis | RESTART MOLINFO BIASVALUE GROUP EMMI PRINT UPPER_WALLS DISTANCE COM WHOLEMOLECULES | core bias vatom isdb colvar setup generic |
| 21.032 | Metal-coupled folding mechanism to metallothionein | bio | parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination | Manuel-Peris Diaz | COORDINATION GROUP UNITS WHOLEMOLECULES PBMETAD | core bias colvar setup generic |
| 21.029 | Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs | bio | metadynamics, small peptide, machine learning | Pratyush Tiwary | EXTERNAL MOLINFO RESTART PRINT FLUSH ENERGY TORSION | bias setup colvar generic |
| 21.025 | Computational and biochemical analysis of type IV pilus dynamics and stability | bio | molecular dynamics, calcium binding, Type IV pilus | Yasaman Karami | DISTANCE LOWER_WALLS UPPER_WALLS PRINT | bias colvar generic |
| 21.017 | All-atom simulations of the Vav1 AD construct | bio | metadynamics, parallel-bias, well-tempered | Simone Orioli | REWEIGHT_BIAS METAD RESTART MOLINFO GROUP CONTACTMAP PRINT ALPHABETA WHOLEMOLECULES PBMETAD ALPHARMSD | core bias colvar secondarystructure multicolvar setup generic |
| 21.015 | Coarse-grained metadynamics and umbrella sampling simulations to investigate interactions of carbohydrate-binding modules with chitin | bio | metadynamics, umbrella sampling, coarse-grained, MARTINI, chitin, carbohydrate-binding module | Gaston Courtade | COORDINATION POSITION METAD REWEIGHT_BIAS RESTART RESTRAINT PRINT CENTER MATHEVAL WHOLEMOLECULES | bias vatom colvar function setup generic |
| 21.014 | how to determine statistically accurate conformational ensembles | bio | metadynamics, metainference, errors, cv, SAXS, ensemble determination | Cristina Paissoni | METAD ENSEMBLE MOLINFO ANTIBETARMSD SAXS BIASVALUE CONTACTMAP PRINT CENTER ALPHABETA STATS TORSION WHOLEMOLECULES PBMETAD GYRATION | bias vatom isdb colvar secondarystructure multicolvar function generic |
| 21.011 | CmuMD simulations of NaCl(aq) at graphite | chemistry | CmuMD, DFS clustering | Aaron Finney | COORDINATIONNUMBER MFILTER_MORE MULTICOLVARDENS CONTACT_MATRIX AROUND DFSCLUSTERING GROUP RESTRAINT LOAD CLUSTER_NATOMS DENSITY PRINT CLUSTER_DISTRIBUTION FIXEDATOM DUMPGRID | clusters volumes adjmat core bias vatom multicolvar setup symfunc gridtools generic |
| 21.010 | Step by Step Strecker Amino Acid Synthesis from Ab Initio Prebiotic Chemistry | chemistry | Strecker reaction, free energy landscape, ab initio molecular dynamics, glycine, prebiotic synthesis | Théo Magrino | generic | |
| 20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Vojtech Spiwok | METAD TORSION PRINT | bias colvar generic |
| 20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Max Bonomi | COORDINATION INCLUDE MOLINFO PRINT ALPHABETA DIHCOR WHOLEMOLECULES PBMETAD GYRATION | bias multicolvar colvar generic |
| 20.000 | Muscarinic M2 receptor-ligand funnel metadynamics | bio | multiple walker metadynamics, well-tempered metadynamics, funnel metadynamics, MC-HLDA, GPCR, receptor, Adiabatic Bias MD | Riccardo Capelli | ABMD METAD REWEIGHT_METAD LOWER_WALLS PRINT UPPER_WALLS READ MATHEVAL HISTOGRAM DUMPGRID COM DISTANCE ENDPLUMED COMBINE CONVERT_TO_FES | bias vatom colvar function gridtools generic |
| 19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Luigi Bonati | POSITION LOAD PRINT UNITS ENVIRONMENTSIMILARITY ENDPLUMED ENERGY TORSION Q6 | envsim colvar setup symfunc generic |
| 19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | METAD RESTART PRINT UNITS UPPER_WALLS DISTANCES FLUSH DISTANCE COMBINE | bias colvar multicolvar function setup generic |
| 19.023 | RECT | methods | metadynamics, replica exchange | Giovanni Bussi | METAD PRINT TORSION WHOLEMOLECULES GYRATION | bias colvar generic |
| 19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Haochuan Chen | TORSION DRR PRINT | drr colvar generic |
| 19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Glen Hocky | RESTRAINT PRINT EDS DISTANCE TORSION COMBINE | eds bias colvar function generic |
| 19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Adriana Pietropaolo | CONSTANT METAD BIASVALUE PRINT MATHEVAL TORSION WHOLEMOLECULES | bias function colvar generic |
| 19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Riccardo Capelli | POSITION COORDINATION METAD REWEIGHT_METAD WRAPAROUND GROUP ENDPLUMED PRINT UPPER_WALLS READ FIT_TO_TEMPLATE MATHEVAL HISTOGRAM DUMPGRID FLUSH COM WHOLEMOLECULES CONVERT_TO_FES | core bias vatom colvar function gridtools generic |
| 19.011 | Automatic Gradient Computation for Collective Variables | other | gradient, differentiation, curvature | Toni Giorgino | ENDPLUMED | generic |
| 19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Max Bonomi | MOLINFO GROUP BIASVALUE EMMI PRINT WHOLEMOLECULES | core bias isdb generic |
| 19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Michele Invernizzi | METAD POSITION RESTART LOAD PRINT UNITS ENDPLUMED ENERGY TORSION VES_DELTA_F | bias ves colvar setup generic |
| 26.005 | Cryptic pocket discovery in Alzheimer disease risk proteins BIN1, PICALM, and CD2AP via well-tempered metadynamics | methods | cryptic pockets, Alzheimer disease, BIN1, PICALM, CD2AP, well-tempered metadynamics, endocytosis, clathrin-mediated trafficking, virtual screening | Cagrı Ozkurt | WHOLEMOLECULES METAD DISTANCE ANGLE PRINT | bias colvar generic |
| 25.024 | Sampling glycan-glycan interactions for B22 calculations | bio | B22, glycan, carbohydrates, distance, REST2, metadynamics, RECT, replica exchange | Isabell Louise Grothaus | COM POSITION METAD DISTANCE PRINT COMBINE RESTRAINT | vatom generic function bias colvar |
| 25.010 | Kinetic rates calculation with Ratchet&Pawl MD | methods | kinetics, ligand binding, ABMD, ratchet&pawl MD | Riccardo Capelli | WHOLEMOLECULES ABMD COM FLUSH COMMITTOR DISTANCE PRINT GROUP | vatom core generic bias colvar |
| 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 TORSION MOVINGRESTRAINT METAD RESTART DISTANCE PRINT RESTRAINT MOLINFO | bias colvar setup generic |
| 25.001 | RNA G-quadruplex folding with ST-metaD protocol | bio | RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | WHOLEMOLECULES ERMSD METAD COMBINE MOLINFO | bias colvar function generic |
| 24.016 | Cryo-EM guided simulations of ribozyme | bio | metainference, cryo-EM | Giovanni Bussi | WHOLEMOLECULES EMMIVOX INCLUDE ERMSD BIASVALUE GROUP PRINT RESTRAINT MOLINFO | core generic isdb bias colvar |
| 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 | WHOLEMOLECULES WRAPAROUND UPPER_WALLS EMMIVOX INCLUDE BIASVALUE DISTANCE PRINT GROUP MOLINFO | core generic isdb bias colvar |
| 23.037 | Estimating binding free energy of solid binding peptides without extensive sampling | bio | metadynamics, solid binding peptides | Xin Qi | COM LOWER_WALLS PBMETAD DISTANCE GYRATION PRINT UPPER_WALLS MOLINFO | vatom bias colvar generic |
| 23.021 | Into the Dynamics of Rotaxanes at Atomistic Resolution | materials | metadynamics, rotaxanes, molecular shuttles, molecular machines | Luigi Leanza | FIXEDATOM CENTER MATHEVAL UPPER_WALLS TORSION METAD DISTANCE PRINT CUSTOM | vatom generic function bias colvar |
| 23.017 | How and When Does an Enzyme React? Unraveling α-Amylase Catalytic Activity with Enhanced Sampling Techniques | bio | enzymatic reaction discovery, reaction mechanism, catalysis, ligand-binding modes, water, alpha-amylase, sugar, QM/MM MD, OPES, OPES explore, graph CV, machine learning, Deep TDA CV, path CV | Sudip Das | WHOLEMOLECULES CENTER FIXEDATOM UPPER_WALLS PATH COORDINATION TORSION UNITS PYTORCH_MODEL LOWER_WALLS OPES_METAD GROUP FIT_TO_TEMPLATE DISTANCE OPES_METAD_EXPLORE PRINT CUSTOM | vatom mapping core setup generic pytorch function opes bias colvar |
| 23.006 | Transcription factor unbinding | bio | metadynamics, DNA, conformational changes | Malin Lüking | COM CONTACTMAP ALPHARMSD METAD DUMPFORCES DISTANCE ANGLE PRINT MOLINFO | secondarystructure vatom generic bias colvar |
| 22.028 | N-glycan conformer distributions in atomistic simulation | bio | REST2, RECT, N-glycan, pucker | Isabell Grothaus | PUCKERING CONVERT_TO_FES TORSION DUMPGRID HISTOGRAM METAD READ PRINT MOLINFO | bias colvar gridtools generic |
| 22.019 | Exploring aspartic protease inhibitor binding to design selective antimalarials | bio | ligand binding, loop opening, path CV, funnel metadynamics, drug development | Raitis Bobrovs | WHOLEMOLECULES PATHMSD COM LOWER_WALLS METAD DISTANCE FUNNEL PRINT UPPER_WALLS FUNNEL_PS | vatom generic funnel bias colvar |
| 22.018 | Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations | bio | ligand binding, docking, EMMI, LAT1 | Max Bonomi | WHOLEMOLECULES EMMIVOX PRINT BIASVALUE LOAD GROUP MOLINFO | core setup generic isdb bias |
| 21.049 | Multiple-path-metadynamics and PathMaps | methods | path-CV, metadynamics, multiple-walker, multiple paths, pathmap | Alberto Pérez-de-Alba-Ortíz | LOAD TORSION UNITS ENSEMBLE MOVINGRESTRAINT LOWER_WALLS METAD CONSTANT RESTRAINT CUSTOM PRINT COMBINE UPPER_WALLS | setup generic function bias colvar |
| 21.045 | QM/MM metadynamics of thiol-disulfide exchange between methylthiolate and dimethyldisulfide in water with an imposed external electrostatic potential (ESP) | chemistry | metadynamics, QM/MM, electrostatic potential, thiol-disulfide exchange | Denis Maag | COORDINATION COORDINATIONNUMBER LOWER_WALLS METAD DISTANCE PRINT COMBINE UPPER_WALLS | generic symfunc function bias colvar |
| 21.042 | Peptoid-mediated Au nanocrystal growth | materials | parallel-bias metadynamics, peptoid, Au | Xin Qi | PRINT COM PBMETAD DISTANCE GYRATION UPPER_WALLS MOLINFO | vatom bias colvar generic |
| 21.038 | Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics | materials | metadynamics, SGOOP, nucleation, urea | Ziyue Zou | CENTER PRINT INCLUDE COORDINATIONNUMBER ENERGY METAD VOLUME LOAD COMBINE GROUP | vatom core setup generic symfunc function bias colvar |
| 21.030 | Thermodynamic Basis for Stabilization of Helical Peptoids by Chiral Sidechains | bio | parallel bias parallel tempered metadynamics in WTE, synthetic foldamers, self-assembly, peptoid secondary structure | Jim Pfaendtner | PRINT COM COORDINATION TORSION INCLUDE ENERGY PBMETAD METAD ALPHABETA DISTANCE GYRATION | vatom generic multicolvar bias colvar |
| 21.026 | Probing allosteric regulations with coevolution-driven molecular simulations | bio | metadynamics, coevolution, allostery, adenylate cyclase | Francesco Colizzi | WHOLEMOLECULES PATHMSD COM UNITS METAD DISTANCE PRINT UPPER_WALLS | vatom setup generic bias colvar |
| 21.012 | NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition | bio | funnel metadynamics | Jim Pfaendtner | UPPER_WALLS COM METAD DISTANCE FUNNEL PRINT LOWER_WALLS FUNNEL_PS | vatom generic funnel bias colvar |
| 21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Kristof Bal | CONVERT_TO_FES LOAD COORDINATIONNUMBER UNITS FLUSH REWEIGHT_METAD MOVINGRESTRAINT HISTOGRAM DUMPGRID COMMITTOR METAD PRINT UPPER_WALLS | gridtools setup generic symfunc bias |
| 21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Adriana Pietropaolo | WHOLEMOLECULES MATHEVAL TORSION BIASVALUE PBMETAD RESTART CONSTANT PRINT | setup generic function bias colvar |
| 21.000 | Uremic toxin time scale dynamics | bio | uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs) | Jim Pfaendtner | WHOLEMOLECULES COM DISTANCE PRINT GROUP | vatom colvar core generic |
| 20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Cristina Paissoni | WHOLEMOLECULES CENTER SAXS STATS INCLUDE ENSEMBLE BIASVALUE GROUP DISTANCE PRINT RESTRAINT MOLINFO | vatom core generic isdb function bias colvar |
| 20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Michele Invernizzi | MATHEVAL TORSION RMSD LOAD MOLINFO WHOLEMOLECULES ENVIRONMENTSIMILARITY OPES_EXPANDED ECV_LINEAR UNITS ECV_UMBRELLAS_LINE CUSTOM ECV_MULTITHERMAL_MULTIBARIC VOLUME Q6 PRINT UPPER_WALLS ECV_MULTITHERMAL ENERGY POSITION ENDPLUMED | setup generic symfunc function opes envsim bias colvar |
| 20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Glen Hocky | MATHEVAL PRINT UNITS ENERGY FISST BIASVALUE DISTANCE RESTRAINT GYRATION GROUP | core fisst setup generic function bias colvar |
| 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 | ABMD FUNCPATHMSD DISTANCE MOLINFO WHOLEMOLECULES DUMPGRID LOWER_WALLS COM CONVERT_TO_FES REWEIGHT_METAD FLUSH HISTOGRAM PRINT COMBINE UPPER_WALLS CONTACTMAP METAD READ ENDPLUMED | vatom gridtools generic function bias colvar |
| 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 | MATHEVAL VES_LINEAR_EXPANSION BF_LEGENDRE LOAD DUMPGRID CELL OPT_DUMMY LOWER_WALLS CONVERT_TO_FES TD_MULTITHERMAL_MULTIBARIC REWEIGHT_TEMP_PRESS HISTOGRAM OPT_AVERAGED_SGD VOLUME Q6 RESTART TD_WELLTEMPERED PRINT COMBINE UPPER_WALLS ENERGY READ REWEIGHT_BIAS | gridtools setup generic symfunc function ves bias colvar |
| 19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Giovanni Bussi | WHOLEMOLECULES COORDINATION DISTANCE RESTRAINT ENDPLUMED LOWER_WALLS | bias colvar generic |
| 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 | DISTANCES COORDINATIONNUMBER ENERGY LOWER_WALLS METAD GYRATION ENDPLUMED PRINT UPPER_WALLS | generic symfunc multicolvar bias colvar |
| 19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Michele Invernizzi | EXTERNAL TORSION UNITS OPES_METAD POSITION METAD ENDPLUMED PRINT | setup generic opes bias colvar |
| 19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | COM ENERGY METAD DISTANCE GYRATION PRINT UPPER_WALLS MOLINFO | vatom bias colvar generic |
| 19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | GiovanniMaria Piccini | UPPER_WALLS UNITS FLUSH ENERGY METAD DISTANCE PRINT COMBINE LOWER_WALLS | setup generic function bias colvar |
| 19.049 | Determining the sizes of solid/liquid clusters in MD trajectories of nucleation | methods | nucleation, metadynamics, clustering, Steinhardt order parameters | Gareth Tribello | DISTANCES COORDINATIONNUMBER OUTPUT_CLUSTER MORE_THAN CLUSTER_PROPERTIES LOCAL_Q6 OUTER_PRODUCT Q6 CONTACT_MATRIX ONES CLUSTER_DISTRIBUTION DFSCLUSTERING CUSTOM METAD CLUSTER_NATOMS SMAC PRINT MATRIX_VECTOR_PRODUCT | clusters generic symfunc multicolvar matrixtools function bias adjmat |
| 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 | WHOLEMOLECULES UPPER_WALLS DISTANCES COM TORSION REWEIGHT_METAD BRIDGE GROUP METAD RMSD ALPHABETA DISTANCE FUNNEL PRINT COMBINE LOWER_WALLS MOLINFO | vatom core generic multicolvar function funnel bias colvar adjmat |
| 19.040 | Optimal Metric for Path Collective Variables | bio | metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path | Francesco Luigi Gervasio | MATHEVAL TORSION METAD ENDPLUMED PRINT | bias colvar function generic |
| 19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Jim Pfaendtner | EXTERNAL COORDINATION ENERGY METAD GROUP | core bias colvar |
| 19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Mattia Bernetti | WHOLEMOLECULES ALPHARMSD ENERGY METAD GYRATION ENDPLUMED PRINT MOLINFO | secondarystructure bias colvar generic |
| 19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Matteo Salvalaglio | CENTER TORSION LOWER_WALLS COMMITTOR METAD DISTANCE PRINT UPPER_WALLS | vatom bias colvar generic |
| 19.013 | RNA FF FITTING | methods | force field, RNA | Giovanni Bussi | MATHEVAL PUCKERING INCLUDE TORSION BIASVALUE CONSTANT MOLINFO | bias colvar function generic |
| 26.004 | Resolving the ambiguous binding site of quercetin at the calcineurin subunit junction using funnel metadynamics with deep learning collective variables | bio | metadynamics, funnel metadynamics, DeepTICA | Jason Loo | RMSD COORDINATION LOWER_WALLS WHOLEMOLECULES PYTORCH_MODEL DISTANCE FUNNEL_PS GROUP MATHEVAL METAD UPPER_WALLS WRAPAROUND PRINT ENERGY FUNNEL COM | colvar pytorch core vatom function bias generic funnel |
| 26.001 | Molecular simulations Alx riboswitch | bio | RNA, riboswitch | Giovanni Bussi | DISTANCE RESTRAINT ERMSD MATHEVAL MOLINFO MOVINGRESTRAINT PRINT | function bias colvar generic |
| 25.015 | Assessment of Force Fields for Describing Conformational Polymorphic Crystals of ROY | materials | Molecular crystal, Force Field, Collective Variable | Pradip Si and Omar Valsson | DISTANCES PRINT SMAC TORSIONS DUMPMULTICOLVAR | multicolvar symfunc generic |
| 25.009 | Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water | chemistry | metadynamics, nitrate photolysis | Kam-Tung Chan | COORDINATION RESTART HISTOGRAM CUSTOM DISTANCE READ GROUP METAD UPPER_WALLS FLUSH PRINT REWEIGHT_METAD DUMPGRID | colvar function bias setup generic gridtools core |
| 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 | COORDINATION WHOLEMOLECULES HISTOGRAM DISTANCE TORSION GROUP ANGLE PRINT DUMPGRID CONVERT_TO_FES | gridtools colvar generic core |
| 24.033 | Transient interactions between the fuzzy coat and the cross-b core of brain-derived Ab42 filaments | bio | CryoEM, MEMMI, Metadynamics, Metainference, Ab42 Fibrils, structural ensemble | Maria Milanesi | RMSD COORDINATION EMMI WHOLEMOLECULES CENTER DUMPMASSCHARGE DUMPATOMS DISTANCE PARABETARMSD GROUP ALPHARMSD MOLINFO PBMETAD UPPER_WALLS PRINT BIASVALUE COM | secondarystructure colvar vatom isdb bias generic core |
| 24.027 | Proline cis and trans subensembles of a disordered peptide | bio | intrinsically disordered proteins, proline cis trans isomerisation, metadynamics, collective variables | Alice Pettitt | COORDINATION WHOLEMOLECULES ANTIBETARMSD DIHCOR INCLUDE DISTANCE TORSION PARABETARMSD GROUP ALPHARMSD ENDPLUMED MOLINFO PBMETAD COMBINE GYRATION FLUSH PRINT | secondarystructure multicolvar colvar function bias generic core |
| 24.009 | Weighted Shape Gaussian Mixture Models | bio | metadynamics, clustering | Glen Hocky | UNITS TORSION GROUP METAD PRINT | colvar bias generic setup core |
| 24.008 | yCD Metadynamics | bio | volume-based MetaD, path CVs, infrequent MetaD, product release | James McCarty | MATHEVAL MOLINFO UPPER_WALLS CONVERT_TO_FES HISTOGRAM INCLUDE PATH CONTACTMAP PRINT DUMPGRID FIXEDATOM COM COMMITTOR GROUP FLUSH WRAPAROUND REWEIGHT_METAD RMSD FIT_TO_TEMPLATE COORDINATION WHOLEMOLECULES DISTANCE ENDPLUMED READ METAD | colvar vatom function bias generic mapping gridtools core |
| 24.004 | Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables | materials | metadynamics, nucleation, machine learning | Ziyue Zou | RESTART INCLUDE GROUP METAD PRINT LOAD | bias setup core generic |
| 24.003 | Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations | chemistry | steered molecular dynamics, foldamers, peptoids, bio-inspired | Kaylyn Torkelson | COORDINATION WHOLEMOLECULES INCLUDE DISTANCE TORSION GYRATION MOVINGRESTRAINT PRINT ALPHABETA COM | multicolvar colvar vatom bias generic |
| 24.001 | A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations | bio | OPES, OPES-Flooding, QM/MM, Kinetics, Enzyme Catalysis | Dhiman Ray | OPES_METAD LOWER_WALLS UNITS CUSTOM COMMITTOR DISTANCE TORSION COMBINE UPPER_WALLS FLUSH PRINT | colvar opes bias function generic setup |
| 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 | OPES_METAD UNITS ZDISTANCES DISTANCE GROUP COORDINATIONNUMBER UPPER_WALLS FLUSH PRINT FIXEDATOM | multicolvar colvar symfunc vatom opes bias generic setup core |
| 23.044 | Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition | materials | metadynamics, interlocked molecules | Luigi Leanza | COORDINATION HISTOGRAM COMMITTOR ENDPLUMED READ GROUP METAD PRINT DUMPGRID CONVERT_TO_FES | colvar bias generic gridtools core |
| 23.043 | Modeling the ferroelectric phase transition in barium titanate with DFT accuracy and converged sampling | materials | Barium Titanate, ferroelectric phase transition, Machine Learning, polarization order parameters | Lorenzo Gigli | SELECT_COMPONENTS SUM TRANSPOSE INCLUDE MATHEVAL METAD FLUSH PRINT | function bias generic valtools matrixtools |
| 23.032 | Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics | bio | metadynamics, tSNE, neural network, machine learning, trp-cage, folding | Vojtech Spiwok | FIT_TO_TEMPLATE WHOLEMOLECULES POSITION ANN ALPHARMSD MOLINFO COMBINE METAD PRINT | secondarystructure colvar function bias annfunc generic |
| 23.029 | An accurate and efficient SAXS/SANS implementation including solvation layer effects suitable for restrained Molecular Dynamics simulations | bio | SAXS, SANS, SAS, metainference, proteins, nucleic-acid | Federico Ballabio | RMSD CENTER SAXS DISTANCE GROUP ENSEMBLE MOLINFO UPPER_WALLS WRAPAROUND PRINT BIASVALUE STATS | colvar vatom isdb function bias generic core |
| 23.014 | Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 | bio | metadynamics, oligomerization, chemokine receptors, GPCR, membrane | Vittorio Limongelli | WHOLEMOLECULES DISTANCE TORSION COMBINE METAD UPPER_WALLS FLUSH PRINT COM | colvar vatom function bias generic |
| 22.041 | Skipping the Replica Exchange Ladder with Normalizing Flows | methods | OPES, alanine, normalizing flows, replica exchange | Michele Invernizzi | OPES_METAD UNITS POSITION ENDPLUMED TORSION OPES_EXPANDED ECV_MULTITHERMAL PRINT ENERGY | opes setup colvar generic |
| 21.050 | N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity | methods | bio | Isabell Louise Grothaus | PRINT CENTER DISTANCE | vatom colvar generic |
| 21.041 | Nucleating a Different Coordination in a Crystal under Pressure. A Study of the B1−B2 Transition in NaCl by Metadynamics | methods | metadynamics, structural phase transitions, pressure-induced phase transition, martensitic transitions | Matej Badin | COORDINATION CUSTOM ENDPLUMED VOLUME METAD COMBINE PRINT | function bias colvar generic |
| 21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Tarsis Ferreira | RANDOM_EXCHANGES LOWER_WALLS COORDINATION WHOLEMOLECULES HISTOGRAM INCLUDE DISTANCE ENERGY GROUP MOLINFO METAD UPPER_WALLS PRINT REWEIGHT_METAD DUMPGRID PUCKERING | colvar bias generic gridtools core |
| 20.034 | Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations | bio | RNA, SARS-CoV-2, partial tempering | Sandro Bottaro | RESTART CENTER DISTANCE TORSION ERMSD MOLINFO PRINT ABMD | colvar vatom bias generic setup |
| 20.032 | Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil | materials | clustering, conformational isomers | Matteo Salvalaglio | TORSION PRINT ENDPLUMED | colvar generic |
| 20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Adriana Pietropaolo | COORDINATION CENTER WHOLEMOLECULES PBMETAD PRINT | bias generic colvar vatom |
| 20.026 | Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor | bio | Metadynamics, Umbrella sampling | Brandon Peters | HISTOGRAM MULTI_RMSD RESTRAINT METAD PRINT REWEIGHT_METAD DUMPGRID CONVERT_TO_FES | bias gridtools colvar generic |
| 20.021 | Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins. | bio | phi-values, restrained MD, transition-state, protein folding, disordered proteins, protein evolution | Cristina Paissoni | COORDINATION WHOLEMOLECULES RESTRAINT MOLINFO PRINT STATS | function bias colvar 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 | ENVIRONMENTSIMILARITY RESTART TD_WELLTEMPERED MATHEVAL OPT_AVERAGED_SGD VES_LINEAR_EXPANSION VOLUME BF_LEGENDRE UPPER_WALLS Q6 OPT_DUMMY PRINT | colvar symfunc function bias ves envsim generic setup |
| 19.050 | Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes | chemistry | metadynamics, membranes, Willard Chandler surface | Gareth Tribello | RESTART HISTOGRAM READ DISTANCE_FROM_CONTOUR COMBINE METAD UPPER_WALLS REWEIGHT_BIAS PRINT DUMPGRID CONVERT_TO_FES | function bias setup contour generic gridtools |
| 19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Vittorio Limongelli | RMSD LOWER_WALLS WHOLEMOLECULES DISTANCE FUNNEL_PS METAD UPPER_WALLS PRINT FUNNEL COM | colvar vatom bias generic funnel |
| 19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Kresten Lindorff-Larsen | COMMITTOR MOLINFO COMBINE METAD FLUSH PRINT ALPHABETA | function bias multicolvar generic |
| 19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Matteo Salvalaglio | RESTART ENDPLUMED METAD COORDINATIONNUMBER DISTANCES GYRATION PRINT | multicolvar colvar symfunc bias generic setup |
| 19.005 | Cmyc small molecule interaction | bio | metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP | Gabriella Heller | COORDINATION CENTER WHOLEMOLECULES METAINFERENCE INCLUDE DISTANCE GROUP MOLINFO PBMETAD GYRATION PRINT ALPHABETA CS2BACKBONE | multicolvar colvar vatom isdb bias generic core |