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 |
|---|---|---|---|---|---|---|
| 26.011 | Lets Stalk About Membranes. Committor-Based Enhanced Sampling of Stalk Formation. | bio | committor, machine learning, enhanced sampling, OPES, membrane fusion, stalk formation, nanoparticles | Giorgia Rossi | COORDINATION GROUP PRINT CENTER LOAD LOWER_WALLS OPES_METAD_EXPLORE CUSTOM BIASVALUE | generic colvar vatom core bias setup opes function |
| 26.008 | Ensemble Dynamics | methods | State Exploration, Protein Folding, Drug Binding, Phase Transition | Florian M. Dietrich | TORSION GROUP PRINT DISTANCE UNITS CELL LOAD OPES_METAD_EXPLORE CUSTOM BIASVALUE POSITION | generic colvar core bias setup opes function |
| 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 | WRAPAROUND COORDINATION GROUP PRINT DISTANCE FUNNEL_PS MATHEVAL ENERGY COM LOWER_WALLS METAD FUNNEL PYTORCH_MODEL UPPER_WALLS WHOLEMOLECULES RMSD | generic colvar funnel vatom pytorch core bias function |
| 25.023 | Molecular simulations of Tau-protein oligomers | bio | metadynamics, proteins, aggregation | Giovanni Bussi | PRINT DUMPGRID CONVERT_TO_FES HISTOGRAM CUSTOM METAD REWEIGHT_BIAS CONTACTMAP FLUSH RESTART RESTRAINT RMSD | gridtools generic colvar bias setup function |
| 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 | COORDINATION GROUP DISTANCE PRINT MOLINFO ECV_MULTITHERMAL CENTER COMBINE ENERGY OPES_EXPANDED CUSTOM OPES_METAD_EXPLORE GHOST RMSD | generic colvar vatom core opes function |
| 25.013 | Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices | bio | umbrella sampling, temperature ramping | Alexander Berlaga | DISTANCE PRINT GYRATION PYTORCH_MODEL RESTRAINT | pytorch generic bias colvar |
| 24.035 | Data efficient machine learning potentials for modeling catalytic reactivity via active learning and enhanced sampling | chemistry | opes, catalysis, ammonia, machine learning potentials | Luigi Bonati | GROUP PRINT DISTANCE OPES_METAD UNITS RESTART LOWER_WALLS COMMITTOR COORDINATION UPPER_WALLS CUSTOM | generic colvar core bias setup opes function |
| 24.030 | NMR guided simulation of dsRBD | bio | Metainference, NMR, protein dynamics | Debadutta Patra | GROUP PRINT METAINFERENCE MOLINFO DISTANCE ENSEMBLE STATS ALPHABETA FLUSH RDC WHOLEMOLECULES | generic colvar isdb core multicolvar function |
| 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 | COORDINATION TORSION GROUP PRINT DISTANCE ECV_MULTITHERMAL COMBINE ENERGY OPES_EXPANDED CUSTOM OPES_METAD_EXPLORE RESTART | generic colvar core setup opes 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 | MOLINFO PRINT DISTANCE MATHEVAL METAD WHOLEMOLECULES RMSD | generic function bias colvar |
| 23.030 | Data Driven Classification of Ligand Unbinding Pathways | bio | OPES Explore, OPES Flooding, Benzene T4 Lysozyme, Ligand unbinding, Pathway classification, Kinetics, Residence time | Dhiman Ray | UPPER_WALLS FIT_TO_TEMPLATE CENTER OPES_METAD COORDINATION OPES_METAD_EXPLORE ENDPLUMED GROUP PRINT UNITS COMMITTOR LOWER_WALLS BIASVALUE TORSION MOLINFO DISTANCE WRAPAROUND MATHEVAL ENERGY COM FLUSH CUSTOM POSITION WHOLEMOLECULES | generic colvar vatom core bias setup opes 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 | GROUP PRINT COMBINE LOWER_WALLS METAD MOVINGRESTRAINT LOCAL_Q6 COORDINATIONNUMBER Q6 MFILTER_MORE | symfunc generic core bias multicolvar function |
| 23.022 | A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar | methods | collective variables, machine learning, toy model | Enrico Trizio | PRINT OPES_METAD UNITS LOWER_WALLS PYTORCH_MODEL UPPER_WALLS CUSTOM BIASVALUE POSITION ENDPLUMED | generic colvar pytorch bias setup opes function |
| 23.016 | Activation/deactivation free-energy profiles for the β2-adrenergic receptor: Ligand modes of action | bio | G protein coupled receptor, beta-adrenergic, receptor activation, partial agonism, metadynamics | Timothy Clark | MOLINFO PRINT DISTANCE DUMPGRID CONVERT_TO_FES MATHEVAL HISTOGRAM METAD REWEIGHT_METAD WHOLEMOLECULES RMSD READ | gridtools generic colvar bias function |
| 23.012 | JAK2 2D meta-eABF PMF with statistical analysis | bio | 2D meta-eABF, path CV, PMF | Istvan Kolossvary | PRINT UPPER_WALLS DRR LOWER_WALLS METAD PATHMSD FLUSH CUSTOM BIASVALUE | generic colvar drr bias function |
| 23.001 | Quantum phase diagram of water | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn-Løland Bore | INCLUDE PRINT ENVIRONMENTSIMILARITY OPES_EXPANDED LOWER_WALLS UPPER_WALLS RESTART ECV_UMBRELLAS_LINE | generic envsim bias setup opes |
| 23.000 | Atomistic simulations of RNA tetraloop folding via PTWTE-WTM | bio | parallel tempering, well-tempered metadynamics, well-tempered ensemble, RNA, Tetraloop, Folding | Gül Zerze | PRINT ENERGY LOWER_WALLS METAD CONTACTMAP UPPER_WALLS WHOLEMOLECULES | generic bias colvar |
| 22.041 | Skipping the Replica Exchange Ladder with Normalizing Flows | methods | OPES, alanine, normalizing flows, replica exchange | Michele Invernizzi | TORSION PRINT ECV_MULTITHERMAL OPES_METAD UNITS ENERGY OPES_EXPANDED POSITION ENDPLUMED | generic opes colvar setup |
| 22.020 | Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix–Junction–Helix RNA | bio | RNA force field, Helix-Junction-Helix RNA, SAXS, Well tempered metadynamics | Weiwei He | TORSION GROUP PRINT DISTANCE COM METAD WHOLEMOLECULES | generic colvar vatom core bias |
| 22.019 | Exploring aspartic protease inhibitor binding to design selective antimalarials | bio | ligand binding, loop opening, path CV, funnel metadynamics, drug development | Raitis Bobrovs | DISTANCE PRINT FUNNEL_PS COM LOWER_WALLS METAD FUNNEL PATHMSD UPPER_WALLS WHOLEMOLECULES | generic colvar funnel vatom bias |
| 22.013 | Ligand dissociation from PreQ1 riboswitch | bio | ligand, RNA, metadynamics, pRAVE | Yihang Wang | MOLINFO PRINT DISTANCE COMBINE COM COMMITTOR METAD COORDINATIONNUMBER WHOLEMOLECULES RMSD | generic symfunc colvar vatom bias function |
| 22.009 | Glycosylation in calixarenes capsule | chemistry | Metadynamics, glycosylation, supramolecular catalysis | GiovanniMaria Piccini | ANGLE GROUP PRINT DISTANCE FIT_TO_TEMPLATE BRIDGE UPPER_WALLS UNITS MATHEVAL COMBINE LOWER_WALLS METAD DISTANCES COORDINATION FLUSH WHOLEMOLECULES RMSD | generic colvar core bias multicolvar setup adjmat function |
| 22.005 | Collective Variable for Metadynamics Derived from AlphaFold Output | bio | AlphaFold, protein folding, protein structure prediction, metadynamics, deep learning, free energy simulation, collective variable | Vojtech Spiwok | METAD WHOLEMOLECULES LOAD PRINT | generic bias setup |
| 22.004 | Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques | chemistry | reaction discovery, OPES, collective variables | Umberto Raucci | DISTANCE PRINT GROUP OPES_METAD UNITS PYTORCH_MODEL MATHEVAL LOAD COM LOWER_WALLS OPES_METAD_EXPLORE COORDINATION UPPER_WALLS CUSTOM | generic colvar vatom pytorch core bias setup opes function |
| 21.042 | Peptoid-mediated Au nanocrystal growth | materials | parallel-bias metadynamics, peptoid, Au | Xin Qi | MOLINFO PRINT DISTANCE GYRATION PBMETAD COM UPPER_WALLS | generic vatom bias colvar |
| 21.031 | Photo-switchable sulfonulureas in KATP channel | bio | metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels | Katarzyna Walczewska-Szewc | DISTANCE PRINT UNITS COM LOWER_WALLS METAD UPPER_WALLS WHOLEMOLECULES | generic colvar vatom bias setup |
| 21.023 | Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling | methods | enhanced sampling, collective variables, machine learning | Jakub Rydzewski | CONSTANT INCLUDE DISTANCE PRINT TORSION UNITS ENERGY METAD REWEIGHT_METAD CUSTOM BIASVALUE | generic colvar bias setup function |
| 20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Cristina Paissoni | INCLUDE GROUP PRINT DISTANCE MOLINFO CENTER SAXS ENSEMBLE STATS BIASVALUE RESTRAINT WHOLEMOLECULES | generic colvar vatom isdb core bias function |
| 20.006 | Class B GPCR activation mechanism | bio | metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | MOLINFO PRINT DISTANCE CENTER MATHEVAL ENERGY COMBINE LOWER_WALLS METAD UPPER_WALLS WHOLEMOLECULES RMSD | generic colvar vatom bias 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 | GROUP PRINT MOLINFO UPPER_WALLS ANTIBETARMSD PBMETAD CS2BACKBONE LOWER_WALLS ALPHABETA FLUSH BIASVALUE WHOLEMOLECULES ENDPLUMED | generic isdb core bias multicolvar secondarystructure |
| 19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Giovanni Bussi | DISTANCE LOWER_WALLS COORDINATION RESTRAINT WHOLEMOLECULES ENDPLUMED | generic bias colvar |
| 19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Sandro Bottaro | ERMSD TORSION MOLINFO PRINT DISTANCE METAD WHOLEMOLECULES RMSD | generic bias colvar |
| 19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Jakub Rydzewski | PRINT UNITS LOWER_WALLS METAD PATHMSD UPPER_WALLS RESTART | generic bias colvar setup |
| 19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Gabriele Cesare Sosso | CLUSTER_WITHSURFACE CONTACT_MATRIX COMMITTOR LOCAL_Q6 DFSCLUSTERING FLUSH Q6 CLUSTER_NATOMS OUTPUT_CLUSTER ENDPLUMED MFILTER_MORE | symfunc generic multicolvar clusters adjmat |
| 19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Jim Pfaendtner | EXTERNAL GROUP ENERGY METAD COORDINATION | core bias colvar |
| 19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Kresten Lindorff-Larsen | MOLINFO PRINT COMBINE COMMITTOR METAD ALPHABETA FLUSH | generic function bias multicolvar |
| 19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Adriana Pietropaolo | CONSTANT TORSION PRINT MATHEVAL METAD BIASVALUE WHOLEMOLECULES | generic function bias colvar |
| 26.006 | Metadynamics simulations of buried phosphorylation sites and proline isomerisation | bio | metadynamics | Julian Streit | METAD PRINT WHOLEMOLECULES TORSION COORDINATION MOLINFO | generic colvar bias |
| 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 | METAD PRINT DISTANCE WHOLEMOLECULES ANGLE | generic colvar bias |
| 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 | METAD UPPER_WALLS PRINT COM FUNNEL FUNNEL_PS LOWER_WALLS | generic vatom bias funnel |
| 25.018 | Metainference simulation for dimerization of RNA binding protein | bio | Metainference, Metadynamics, SAXS, protein dimer | Debadutta Patra | UPPER_WALLS PRINT STATS DISTANCE CENTER WHOLEMOLECULES SAXS TORSION GYRATION PBMETAD MOLINFO ENSEMBLE METAINFERENCE FLUSH | function generic vatom isdb colvar bias |
| 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 | UNITS COMMITTOR CUSTOM PRINT UPPER_WALLS ZDISTANCES COORDINATIONNUMBER DISTANCE OPES_METAD GROUP FIXEDATOM DISTANCES FLUSH | function generic core vatom setup opes multicolvar colvar bias symfunc |
| 24.006 | Water vapor condensation | chemistry | metadynamics, homogeneous condensation, chemical potential | Shenghui Zhong | UNITS METAD UPPER_WALLS PRINT COORDINATIONNUMBER CONTACT_MATRIX DFSCLUSTERING CLUSTER_NATOMS CLUSTER_PROPERTIES | generic adjmat setup clusters bias symfunc |
| 24.003 | Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations | chemistry | steered molecular dynamics, foldamers, peptoids, bio-inspired | Kaylyn Torkelson | PRINT COM DISTANCE WHOLEMOLECULES MOVINGRESTRAINT GYRATION TORSION COORDINATION INCLUDE ALPHABETA | generic vatom multicolvar colvar bias |
| 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 | UNITS UPPER_WALLS PRINT COORDINATIONNUMBER DISTANCE ZDISTANCES OPES_METAD GROUP FIXEDATOM FLUSH | generic core vatom setup opes multicolvar colvar bias symfunc |
| 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 | METAD PRINT MATHEVAL TRANSPOSE SUM SELECT_COMPONENTS INCLUDE FLUSH | function generic matrixtools valtools bias |
| 23.040 | Supramolecular capsules assembly dynamics | chemistry | Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics | Riccardo Capelli | CUSTOM UNITS METAD PRINT COM DISTANCE WHOLEMOLECULES CENTER POSITION GROUP DISTANCES FLUSH | function generic core vatom setup multicolvar colvar bias |
| 23.039 | Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation | chemistry | metadynamics, ligand dissociation | Eric Beyerle | METAD UPPER_WALLS PRINT DISTANCE CENTER DUMPMASSCHARGE MOLINFO RESTRAINT COMBINE FIXEDATOM | function generic vatom 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 PRINT WHOLEMOLECULES ERMSD COORDINATION MOLINFO GHBFIX COMBINE BIASVALUE | generic colvar function bias |
| 23.028 | Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process | chemistry | Ammonia decomposition; Dynamics;OPES; Neural Network potential | Manyi Yang | UNITS CUSTOM UPPER_WALLS PRINT COM COORDINATIONNUMBER DISTANCE ZDISTANCES COMMITTOR MATHEVAL OPES_METAD ENERGY GROUP FIXEDATOM LOWER_WALLS DISTANCES FLUSH | function generic core vatom setup opes multicolvar colvar bias symfunc |
| 23.027 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, DFS, Q3, Pair Entropy | Aaron Finney | UNITS AROUND PRINT LOAD COORDINATIONNUMBER CONTACT_MATRIX LOCAL_AVERAGE Q3 DUMPGRID DFSCLUSTERING DENSITY CLUSTER_NATOMS HISTOGRAM GROUP CLUSTER_DISTRIBUTION RESTRAINT LOCAL_Q3 FIXEDATOM | generic core gridtools vatom adjmat setup clusters volumes bias symfunc |
| 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 | UNITS CUSTOM UPPER_WALLS PRINT METAD TIME DRR LOWER_WALLS PATHMSD BIASVALUE FLUSH | function drr generic setup colvar bias |
| 22.037 | Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site | chemistry | metadynamics, DNA, abasic | Mike Jones | METAD PRINT DISTANCES DISTANCE | generic multicolvar colvar bias |
| 22.028 | N-glycan conformer distributions in atomistic simulation | bio | REST2, RECT, N-glycan, pucker | Isabell Grothaus | METAD PRINT READ DUMPGRID TORSION HISTOGRAM MOLINFO PUCKERING CONVERT_TO_FES | generic gridtools colvar bias |
| 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 | UPPER_WALLS PRINT COM WHOLEMOLECULES RMSD TORSION COORDINATION GROUP MOLINFO PBMETAD BIASVALUE EMMI RESTART | generic core vatom setup isdb colvar bias |
| 22.008 | Ab initio metadynamics determination of temperature-dependent free-energy landscape in ultrasmall silver clusters | materials | Well tempered metadynamics, ab-initio, ase | Daniel Sucerquia | UNITS METAD UPPER_WALLS COM COORDINATIONNUMBER DISTANCE GYRATION COORDINATION LOWER_WALLS COMBINE FLUSH | function generic vatom setup colvar bias symfunc |
| 21.033 | Multiple-path-metadynamics applied to DNA base-pairing transitions | bio | path-CV, metadynamics, multiple-walker, dna | Alberto Pérez-de-Alba-Ortíz | METAD UPPER_WALLS PRINT MOVINGRESTRAINT INCLUDE RESTRAINT CONSTANT COMBINE | generic function bias |
| 21.030 | Thermodynamic Basis for Stabilization of Helical Peptoids by Chiral Sidechains | bio | parallel bias parallel tempered metadynamics in WTE, synthetic foldamers, self-assembly, peptoid secondary structure | Jim Pfaendtner | METAD PRINT COM DISTANCE TORSION GYRATION ENERGY COORDINATION PBMETAD ALPHABETA INCLUDE | generic vatom multicolvar colvar bias |
| 21.026 | Probing allosteric regulations with coevolution-driven molecular simulations | bio | metadynamics, coevolution, allostery, adenylate cyclase | Francesco Colizzi | UNITS METAD UPPER_WALLS PRINT COM DISTANCE WHOLEMOLECULES PATHMSD | generic vatom setup colvar bias |
| 20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Adriana Pietropaolo | PRINT WHOLEMOLECULES CENTER COORDINATION PBMETAD | bias vatom colvar generic |
| 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 | STATS PRINT WHOLEMOLECULES COORDINATION MOLINFO RESTRAINT COMBINE | bias function colvar generic |
| 20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Glen Hocky | UNITS PRINT FISST DISTANCE MATHEVAL GYRATION ENERGY GROUP RESTRAINT BIASVALUE | function fisst generic core setup colvar bias |
| 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 | METAD UPPER_WALLS PRINT COORDINATIONNUMBER ENDPLUMED GYRATION ENERGY LOWER_WALLS DISTANCES | generic multicolvar colvar bias symfunc |
| 19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Michele Invernizzi | METAD UNITS PRINT OPES_METAD ENDPLUMED TORSION POSITION EXTERNAL | generic setup colvar bias opes |
| 19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Wei Chen | COM POSITION ANN RESTRAINT COMBINE | annfunc function vatom colvar bias |
| 19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Jim Pfaendtner | METAD PRINT WHOLEMOLECULES GYRATION ENERGY | generic colvar bias |
| 19.049 | Determining the sizes of solid/liquid clusters in MD trajectories of nucleation | methods | nucleation, metadynamics, clustering, Steinhardt order parameters | Gareth Tribello | CUSTOM LOCAL_Q6 METAD PRINT CONTACT_MATRIX DFSCLUSTERING COORDINATIONNUMBER CLUSTER_NATOMS OUTER_PRODUCT Q6 CLUSTER_PROPERTIES DISTANCES MORE_THAN OUTPUT_CLUSTER CLUSTER_DISTRIBUTION SMAC MATRIX_VECTOR_PRODUCT ONES | function generic matrixtools adjmat clusters multicolvar bias symfunc |
| 19.045 | Adsorption free energy of Ca/CO3 ions on calcite steps in contact with water | materials | metadynamics, well-tempered, multiple walkers, LAMMPS | Marco De La Pierre | UNITS METAD UPPER_WALLS PRINT POSITION GROUP COORDINATION LOWER_WALLS RESTART FLUSH | generic core setup colvar bias |
| 19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | UNITS METAD UPPER_WALLS PRINT DISTANCE DISTANCES COMBINE RESTART FLUSH | function generic setup multicolvar colvar bias |
| 19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Mattia Bernetti | METAD PRINT WHOLEMOLECULES ENDPLUMED ALPHARMSD GYRATION ENERGY MOLINFO | generic colvar bias secondarystructure |
| 19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Riccardo Capelli | METAD UPPER_WALLS PRINT COM READ WRAPAROUND WHOLEMOLECULES MATHEVAL DUMPGRID ENDPLUMED POSITION GROUP COORDINATION HISTOGRAM CONVERT_TO_FES REWEIGHT_METAD FIT_TO_TEMPLATE FLUSH | function generic core gridtools vatom colvar bias |
| 26.015 | Ensemble Dynamics | methods | State Exploration, Protein Folding, Drug Binding, Phase Transition | Florian M. Dietrich | OPES_METAD_EXPLORE DISTANCE PRINT GROUP LOAD BIASVALUE CELL UNITS TORSION POSITION CUSTOM | colvar core function opes bias setup generic |
| 26.014 | Dissociation free energy (DFE) calculationsfor GPR15L–polySia | bio | metadynamics, protein-carbohydrate interaction | Davide Luciano and Gaston Courtade | METAD UPPER_WALLS DISTANCE PRINT GROUP COM | colvar core bias vatom generic |
| 26.007 | Metadynamics Simulations Reveal the Protonation-Dependent Conformational Landscape of GSK-3β Dual Inhibitors | chemistry | metadynamics, ligand unbinding, path CVs, funnel metadynamics | Gian Marco Elisi | METAD UPPER_WALLS DISTANCE FUNNEL_PS PRINT FUNNEL MOLINFO COMBINE RMSD PATHMSD ANGLE LOWER_WALLS ENDPLUMED UNITS MATHEVAL COM WHOLEMOLECULES | colvar function bias vatom funnel setup generic |
| 25.017 | Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity | bio | EMMIVox, cryo-EM, allostery, decamer, filament, ensemble refinement, glutamine synthetase | Samuel Hoff | PRINT MOLINFO EMMIVOX BIASVALUE GROUP WHOLEMOLECULES | bias generic core isdb |
| 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 | BAIES GROUP BIASVALUE PRINT | bias isdb generic core |
| 25.002 | M3_PCV-ABMD | chemistry | Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor | Gian Marco Elisi | UPPER_WALLS PRINT ABMD PATHMSD ENDPLUMED UNITS | bias generic colvar setup |
| 24.016 | Cryo-EM guided simulations of ribozyme | bio | metainference, cryo-EM | Giovanni Bussi | PRINT MOLINFO EMMIVOX RESTRAINT BIASVALUE ERMSD INCLUDE GROUP WHOLEMOLECULES | colvar core isdb bias generic |
| 24.004 | Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables | materials | metadynamics, nucleation, machine learning | Ziyue Zou | METAD PRINT LOAD RESTART INCLUDE GROUP | bias generic setup core |
| 24.001 | A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations | bio | OPES, OPES-Flooding, QM/MM, Kinetics, Enzyme Catalysis | Dhiman Ray | UPPER_WALLS DISTANCE FLUSH PRINT COMBINE COMMITTOR OPES_METAD LOWER_WALLS UNITS TORSION CUSTOM | colvar function opes bias setup generic |
| 23.044 | Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition | materials | metadynamics, interlocked molecules | Luigi Leanza | METAD PRINT COORDINATION COMMITTOR HISTOGRAM DUMPGRID ENDPLUMED GROUP CONVERT_TO_FES READ | colvar core bias generic gridtools |
| 23.037 | Estimating binding free energy of solid binding peptides without extensive sampling | bio | metadynamics, solid binding peptides | Xin Qi | UPPER_WALLS DISTANCE PRINT MOLINFO GYRATION PBMETAD LOWER_WALLS COM | bias colvar generic vatom |
| 23.036 | Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? | bio | NaCl, nucleation, metadynamics | Ruiyu Wang | VOLUME METAD Q6 PRINT Q4 COMBINE ENERGY COORDINATIONNUMBER MATHEVAL | colvar function bias generic symfunc |
| 23.021 | Into the Dynamics of Rotaxanes at Atomistic Resolution | materials | metadynamics, rotaxanes, molecular shuttles, molecular machines | Luigi Leanza | METAD UPPER_WALLS DISTANCE PRINT CENTER MATHEVAL FIXEDATOM TORSION CUSTOM | colvar function bias vatom generic |
| 23.020 | FEP simulations of ATOX1 homodimer | chemistry | parallel bias metadynamics, FEP, free-energy of metal ion dissociation | Adriana Pietropaolo | DISTANCE PRINT CONSTANT BIASVALUE PBMETAD MATHEVAL ANGLE WHOLEMOLECULES | bias colvar generic function |
| 23.005 | A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs | bio | metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A | Timothy Clark | METAD REWEIGHT_METAD DISTANCE PRINT MOLINFO RMSD HISTOGRAM DUMPGRID MATHEVAL CONVERT_TO_FES READ WHOLEMOLECULES | colvar function bias generic gridtools |
| 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 METAD PRINT TORSION READ | bias colvar generic |
| 22.042 | Metadynamics of NSP10 and variants | bio | metadynamics, NSP10, crystal structure, variants | Shozeb Haider | METAD TORSION PRINT | bias colvar generic |
| 22.039 | Driving and characterizing nucleation of urea and glycine polymorphs in water | bio | metadynamics, nucleation, amino acids, polymorphism | Eric Beyerle | METAD Q6 PRINT Q4 CENTER COMBINE LOAD COORDINATIONNUMBER INCLUDE GROUP MATHEVAL PAIRENTROPY | function core bias vatom setup generic symfunc gridtools |
| 22.038 | Enhanced Sampling Aided Design of Molecular Photoswitches | chemistry | reaction discovery, OPES explore, graph CV | Umberto Raucci | PYTORCH_MODEL OPES_METAD_EXPLORE PRINT COORDINATION UNITS CUSTOM | colvar function opes pytorch setup generic |
| 22.035 | Deciphering the alphabet of disorder — Glu and Asp act differently on local but not global properties | bio | intrinsically disordered proteins, parallel bias metadynamics, protein | Kresten Lindorff-Larsen | MOLINFO GYRATION PBMETAD TORSION WHOLEMOLECULES | bias generic colvar |
| 22.033 | Reciprocal barrier restraint. Application to PROTAC passive permeability prediction | methods | PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR | Istvan Kolossvary | METAD DISTANCE FLUSH PRINT BIASVALUE UNITS DRR COM CUSTOM | drr colvar function bias vatom setup generic |
| 22.030 | Mixing physics across temperatures with generative artificial intelligence | methods | REMD, Generative AI, DDPM | Yihang Wang | TORSION PRINT WHOLEMOLECULES | colvar generic |
| 22.025 | Bubble nucleation rate predictions in a Lennard-Jones fluid | materials | free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation | Kristof Bal | VOLUME UPPER_WALLS REWEIGHT_BIAS FLUSH PRINT LOAD COORDINATIONNUMBER RESTRAINT BIASVALUE HISTOGRAM ANN DUMPGRID COMMITTOR MOVINGRESTRAINT UNITS CONVERT_TO_FES CUSTOM | colvar function annfunc bias setup generic symfunc gridtools |
| 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 | METAD UPPER_WALLS PRINT GYRATION LOWER_WALLS ENDPLUMED GROUP ALPHABETA WHOLEMOLECULES | colvar core bias multicolvar generic |
| 21.043 | Predicting the Conformational Variability of Oncogenic GTP-bound G12D Mutated KRas-4B Proteins at Cell Membranes | chemistry | well-tempered metadynamics, KRas-4B, anionic membrane, conformational variability | Huixia Lu | METAD PRINT FIT_TO_TEMPLATE FIXEDATOM TORSION | bias generic colvar vatom |
| 21.041 | Nucleating a Different Coordination in a Crystal under Pressure. A Study of the B1−B2 Transition in NaCl by Metadynamics | methods | metadynamics, structural phase transitions, pressure-induced phase transition, martensitic transitions | Matej Badin | VOLUME METAD PRINT COMBINE COORDINATION ENDPLUMED CUSTOM | bias colvar generic function |
| 21.038 | Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics | materials | metadynamics, SGOOP, nucleation, urea | Ziyue Zou | METAD VOLUME PRINT CENTER COMBINE ENERGY LOAD COORDINATIONNUMBER INCLUDE GROUP | colvar function core bias vatom setup generic symfunc |
| 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 | METAD UPPER_WALLS PARABETARMSD RANDOM_EXCHANGES PRINT ANTIBETARMSD MOLINFO ENERGY COORDINATION GYRATION LOWER_WALLS DIHCOR GROUP ALPHARMSD WHOLEMOLECULES | colvar core bias multicolvar generic secondarystructure |
| 21.035 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, interface | Aaron Finney | DISTANCE PRINT LOAD RESTRAINT GROUP FIXEDATOM | colvar core bias vatom setup generic |
| 21.027 | EGFR activating mutations mechanism | bio | metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA | Francesco Gervasio | METAD UPPER_WALLS DISTANCE PRINT MOLINFO ENERGY CONTACTMAP INCLUDE LOWER_WALLS MATHEVAL ALPHARMSD WHOLEMOLECULES | colvar function bias generic secondarystructure |
| 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 | |
| 20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Valerio Rizzi | PYTORCH_MODEL UPPER_WALLS DISTANCE PRINT WHOLEMOLECULES CENTER FIT_TO_TEMPLATE COORDINATION ENERGY OPES_METAD ENDPLUMED GROUP ANGLE FIXEDATOM MATHEVAL | colvar core function opes bias pytorch vatom 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 | PRINT MOLINFO COORDINATION RESTRAINT STATS WHOLEMOLECULES | 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 | UPPER_WALLS REWEIGHT_BIAS Q6 COORDINATION PAIRENTROPY VOLUME COMBINE LOAD COORDINATIONNUMBER CONTACT_MATRIX HISTOGRAM LOWER_WALLS LOCAL_AVERAGE DENSITY CONVERT_TO_FES METAD REWEIGHT_METAD FLUSH SPRINT DUMPGRID DISTANCE PRINT CENTER ENERGY UNITS | colvar function sprint bias volumes adjmat vatom setup generic symfunc gridtools |
| 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 | OPT_AVERAGED_SGD VOLUME UPPER_WALLS OPT_DUMMY Q6 BF_LEGENDRE PRINT RESTART ENVIRONMENTSIMILARITY VES_LINEAR_EXPANSION MATHEVAL TD_WELLTEMPERED | colvar function ves envsim bias setup generic symfunc |
| 19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Valerio Rizzi | METAD FLUSH PRINT GROUP COMBINE COORDINATIONNUMBER RESTART ENDPLUMED UNITS EXTERNAL | function core bias setup generic symfunc |
| 19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Matteo Salvalaglio | METAD REWEIGHT_METAD DISTANCE REWEIGHT_BIAS PRINT COMMITTOR BIASVALUE HISTOGRAM DUMPGRID MATHEVAL CONVERT_TO_FES TORSION READ EXTERNAL | colvar function bias generic gridtools |
| 19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Jakub Rydzewski | PRINT MAZE_OPTIMIZER_BIAS MAZE_LOSS UNITS POSITION MAZE_SIMULATED_ANNEALING | setup generic colvar maze |
| 19.059 | cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide | bio | bias-exchange metadynamics, cis-trans isomerization | Fabrizio Marinelli | METAD RANDOM_EXCHANGES PRINT INCLUDE TORSION | bias generic colvar |
| 19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Gareth Tribello | AROUND METAD UPPER_WALLS PRINT LOWER_WALLS CELL UNITS ENDPLUMED FCCUBIC | colvar volumes bias setup generic symfunc |
| 19.050 | Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes | chemistry | metadynamics, membranes, Willard Chandler surface | Gareth Tribello | METAD UPPER_WALLS REWEIGHT_BIAS PRINT COMBINE HISTOGRAM DUMPGRID DISTANCE_FROM_CONTOUR RESTART CONVERT_TO_FES READ | function contour bias setup generic gridtools |
| 19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | METAD UPPER_WALLS DISTANCE FLUSH PRINT COMBINE ENERGY UNITS | colvar function bias setup generic |
| 19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Paolo Raiteri | METAD UPPER_WALLS DISTANCE PRINT FLUSH RESTART UNITS MATHEVAL | colvar function bias setup generic |
| 19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Silvio Pipolo | METAD UPPER_WALLS PRINT FUNCPATHMSD LOWER_WALLS CELL PIV | colvar piv function bias generic |
| 19.025 | Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide | bio | metainference, NMR, protein dynamics, force-fields | Carlo Camilloni | ENSEMBLE CS2BACKBONE FLUSH PRINT RDC MOLINFO BIASVALUE GYRATION PBMETAD ENDPLUMED JCOUPLING STATS TORSION METAINFERENCE WHOLEMOLECULES | colvar function bias isdb generic |
| 19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Matteo Salvalaglio | METAD VOLUME UPPER_WALLS PRINT COMBINE ENERGY ENDPLUMED LOWER_WALLS CELL MATHEVAL TORSION | bias colvar generic function |
| 19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Carlo Camilloni | UPPER_WALLS DISTANCE ENSEMBLE PRINT RDC CENTER MOLINFO RESTRAINT ALPHABETA PBMETAD ENDPLUMED DIHCOR GROUP STATS DHENERGY TORSION METAINFERENCE WHOLEMOLECULES | colvar function core isdb bias multicolvar vatom generic |
| 19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Max Bonomi | PRINT MOLINFO BIASVALUE EMMI GROUP WHOLEMOLECULES | bias generic core isdb |
| 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 | WHOLEMOLECULES COORDINATION COMBINE CENTER LOWER_WALLS UPPER_WALLS MATHEVAL DISTANCE PRINT GROUP GYRATION METAD | vatom colvar generic bias core function |
| 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 | CUSTOM COMMITTOR FUNNEL MATHEVAL FUNNEL_PS ENDPLUMED CENTER WRAPAROUND METAD COM OPES_METAD WHOLEMOLECULES LOWER_WALLS RMSD PRINT COORDINATION UPPER_WALLS DISTANCE GROUP TORSION | vatom colvar opes generic funnel bias core function |
| 25.011 | Chiral perovskite nucleation | chemistry | metadynamics, chiral perovskites, nucleation | Adriana Pietropaolo | PBMETAD LOWER_WALLS MULTI_RMSD UPPER_WALLS MATHEVAL DISTANCE PRINT RESTART UNITS | colvar generic setup bias function |
| 25.010 | Kinetic rates calculation with Ratchet&Pawl MD | methods | kinetics, ligand binding, ABMD, ratchet&pawl MD | Riccardo Capelli | WHOLEMOLECULES FLUSH COMMITTOR DISTANCE ABMD PRINT GROUP COM | vatom colvar generic bias core |
| 25.000 | Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer | bio | metadynamics, pathCV | Sahithya Sridharan Iyer | WHOLEMOLECULES COM UPPER_WALLS MOLINFO PRINT DISTANCE GROUP METAD RESTART FUNCPATHGENERAL | vatom colvar generic setup bias core function |
| 24.032 | DeepLNE++ | methods | PATHCV, OPES | Thorben Fröhlking | OPES_METAD CUSTOM COORDINATION COMBINE ENERGY LOAD DISTANCE PRINT GROUP TORSION | colvar opes generic setup core function |
| 24.029 | Combination of OPES and OPES-Explore | methods | OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin | Dhiman Ray | CUSTOM FIXEDATOM INCLUDE MATHEVAL UNITS FLUSH ENDPLUMED CENTER FIT_TO_TEMPLATE POSITION ENERGY PYTORCH_MODEL CONTACTMAP METAD OPES_METAD WHOLEMOLECULES OPES_METAD_EXPLORE LOWER_WALLS RMSD PRINT BIASVALUE COORDINATION COMBINE UPPER_WALLS MOLINFO DISTANCE GROUP | vatom colvar opes generic setup bias pytorch core function |
| 24.027 | Proline cis and trans subensembles of a disordered peptide | bio | intrinsically disordered proteins, proline cis trans isomerisation, metadynamics, collective variables | Alice Pettitt | WHOLEMOLECULES COORDINATION FLUSH COMBINE PBMETAD ENDPLUMED ALPHARMSD ANTIBETARMSD MOLINFO INCLUDE DISTANCE PRINT GROUP PARABETARMSD GYRATION TORSION DIHCOR | colvar secondarystructure multicolvar generic bias core function |
| 24.021 | Ab initio machine learning simulation of calcium carbonate from aqueous solutions to the solid state | chemistry | ion pairing, caco3, opes, proton transfer, crystallization | Pablo Piaggi | OPES_METAD COORDINATION ENERGY UPPER_WALLS DISTANCE PRINT | bias colvar generic opes |
| 24.020 | Graph Neural Network-State Predictive Information Bottleneck (GNN-SPIB) approach for learning molecular thermodynamics and kinetics | bio | LJ7, alanine, well-tempered metadynamics, infrequent metadynamics, machine learning | Ziyue Zou, Dedi Wang, Pratyush Tiwary | COMMITTOR LOAD PRINT METAD GROUP TORSION | colvar generic setup bias core |
| 24.017 | Absolute Binding Free Energies with OneOPES | methods | protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy | Francesco Gervasio | CUSTOM OPES_EXPANDED INCLUDE MATHEVAL ECV_MULTITHERMAL WRAPAROUND ENERGY PROJECTION_ON_AXIS CONTACTMAP METAD COM WHOLEMOLECULES OPES_METAD_EXPLORE LOWER_WALLS RMSD CONSTANT PRINT BIASVALUE RESTART COORDINATION UPPER_WALLS MOLINFO GROUP TORSION | vatom colvar opes generic setup bias core function |
| 24.007 | SWISH-X | bio | swish-x, SWISH-X, swish, expanded SWISH | Alberto Borsatto | WHOLEMOLECULES ENERGY OPES_EXPANDED UPPER_WALLS MOLINFO INCLUDE PRINT CONTACTMAP ECV_MULTITHERMAL | bias 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 | WHOLEMOLECULES CENTER LOWER_WALLS CONSTANT UPPER_WALLS MATHEVAL DISTANCE PRINT BIASVALUE METAD | vatom colvar generic bias function |
| 23.034 | Urea nucleation in water: do long-range forces matter? | materials | LMF theory, Metadynamics, Nucleation | Ziyue Zou | CENTER COORDINATIONNUMBER INCLUDE LOAD PRINT GROUP METAD | vatom generic setup bias symfunc core |
| 23.032 | Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics | bio | metadynamics, tSNE, neural network, machine learning, trp-cage, folding | Vojtech Spiwok | WHOLEMOLECULES COMBINE FIT_TO_TEMPLATE POSITION ALPHARMSD ANN MOLINFO PRINT METAD | colvar generic bias annfunc function secondarystructure |
| 23.023 | Rational design of novel biomimetic sequence-defined polymers for mineralization applications | methods | metadynamics, surface binding, biomimetic mineralization | Kaylyn Torkelson | COORDINATION PBMETAD UPPER_WALLS PRINT DISTANCE GYRATION COM | bias vatom generic colvar |
| 23.018 | Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention | materials | metadynamics, surface binding, peptide adsorption | Kaylyn Torkelson | PBMETAD UPPER_WALLS PRINT DISTANCE GYRATION COM | bias vatom generic 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 | OPES_METAD CUSTOM COORDINATION WHOLEMOLECULES FIXEDATOM OPES_METAD_EXPLORE CENTER FIT_TO_TEMPLATE LOWER_WALLS PATH UPPER_WALLS PRINT PYTORCH_MODEL DISTANCE GROUP UNITS TORSION | vatom colvar opes generic setup bias pytorch core function mapping |
| 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 | WHOLEMOLECULES LOWER_WALLS CONSTANT UPPER_WALLS MATHEVAL DISTANCE PRINT BIASVALUE METAD | bias colvar generic function |
| 23.007 | Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains | bio | metadynamics, peptoids, parallel-bias metadynamics | Jim Pfaendtner | WHOLEMOLECULES COORDINATION RESTRAINT PBMETAD INCLUDE PRINT GYRATION TORSION COM | bias vatom generic colvar |
| 22.045 | Binding mode and mechanism of enzymatic polyethylene terephthalate degradation | bio | metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation | Francesco Colizzi | WHOLEMOLECULES LOWER_WALLS MOVINGRESTRAINT UPPER_WALLS PRINT DISTANCE ANGLE METAD COM | bias vatom generic colvar |
| 22.022 | Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir | bio | RMSD, protein-ligand interactions | Isabell Grothaus | PRINT RMSD | generic colvar |
| 22.018 | Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations | bio | ligand binding, docking, EMMI, LAT1 | Max Bonomi | WHOLEMOLECULES EMMIVOX MOLINFO LOAD PRINT BIASVALUE GROUP | generic isdb setup bias core |
| 22.017 | Water regulates the residence time of Benzamidine in Trypsin | bio | ligand binding, water, opes, benzamidine trypsin, unbinding rates, machine learning, Deep-LDA, Deep-TICA | Narjes Ansari | OPES_METAD WHOLEMOLECULES COORDINATION CUSTOM COMMITTOR FIXEDATOM CENTER FIT_TO_TEMPLATE LOWER_WALLS RMSD UPPER_WALLS MATHEVAL DISTANCE PYTORCH_MODEL PRINT GROUP | vatom colvar opes generic bias pytorch core function |
| 21.052 | On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets | materials | Ibuprofen, unbinding, WTmetaD | Matteo Salvalaglio | COMMITTOR ENDPLUMED COORDINATIONNUMBER CENTER DISTANCE PRINT TORSION METAD | vatom colvar generic bias symfunc |
| 21.032 | Metal-coupled folding mechanism to metallothionein | bio | parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination | Manuel-Peris Diaz | WHOLEMOLECULES COORDINATION PBMETAD GROUP UNITS | colvar generic setup bias core |
| 21.025 | Computational and biochemical analysis of type IV pilus dynamics and stability | bio | molecular dynamics, calcium binding, Type IV pilus | Yasaman Karami | UPPER_WALLS DISTANCE LOWER_WALLS PRINT | bias generic colvar |
| 21.012 | NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition | bio | funnel metadynamics | Jim Pfaendtner | LOWER_WALLS FUNNEL UPPER_WALLS PRINT DISTANCE FUNNEL_PS METAD COM | vatom colvar generic funnel bias |
| 20.032 | Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil | materials | clustering, conformational isomers | Matteo Salvalaglio | ENDPLUMED PRINT TORSION | generic colvar |
| 20.024 | Gaussian Mixture Based Enhanced Sampling (GAMBES) | methods | enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias | Jayashrita Debnath | COMBINE LOWER_WALLS ENERGY UPPER_WALLS LOAD PRINT DISTANCE GROUP UNITS DISTANCES TORSION | colvar multicolvar generic setup bias core function |
| 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 | METAINFERENCE INCLUDE FLUSH PBMETAD ENDPLUMED WHOLEMOLECULES ALPHARMSD PRINT PARABETARMSD DIHCOR ENSEMBLE COORDINATION COMBINE CS2BACKBONE ANTIBETARMSD MOLINFO GROUP GYRATION TORSION STATS | colvar multicolvar generic isdb bias core function secondarystructure |
| 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 | CUSTOM COORDINATION PRINT UNITS DISTANCES METAD | colvar multicolvar generic setup bias function |
| 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 | Q6 OPT_DUMMY TD_WELLTEMPERED MATHEVAL LOAD TD_MULTITHERMAL_MULTIBARIC REWEIGHT_BIAS DUMPGRID OPT_AVERAGED_SGD ENERGY VES_LINEAR_EXPANSION BF_LEGENDRE LOWER_WALLS CONVERT_TO_FES HISTOGRAM PRINT RESTART COMBINE VOLUME UPPER_WALLS READ REWEIGHT_TEMP_PRESS CELL | colvar ves generic setup bias symfunc gridtools function |
| 19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | ENERGY UPPER_WALLS MOLINFO PRINT DISTANCE GYRATION METAD COM | bias vatom generic colvar |
| 19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Luigi Bonati | ENVIRONMENTSIMILARITY Q6 ENDPLUMED POSITION ENERGY LOAD PRINT UNITS TORSION | colvar envsim generic setup symfunc |
| 19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Gareth Tribello | ENDPLUMED FCCUBIC UPPER_WALLS PRINT CELL UNITS METAD | colvar generic setup bias symfunc |
| 19.041 | Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces | bio | metadynamics, collective variables, conformational changes, multiple walkers, Well-Tempered MetaD, peptide, binding, phosphorylation, post-transitional motif, sio2, adsorption | Jim Pfaendtner | ENERGY UPPER_WALLS PRINT DISTANCE METAD COM | bias vatom generic colvar |
| 19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Carlo Camilloni | WHOLEMOLECULES FLUSH PBMETAD ENDPLUMED LOWER_WALLS ALPHABETA CS2BACKBONE ANTIBETARMSD UPPER_WALLS MOLINFO PRINT BIASVALUE GROUP RESTART | multicolvar generic isdb setup bias core secondarystructure |
| 19.035 | Dimerization of GPCRs from coarse-grained umbrella sampling | bio | Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization | Davide Provasi | RESTRAINT DISTANCE PRINT GROUP TORSION COM | vatom colvar generic bias core |
| 19.011 | Automatic Gradient Computation for Collective Variables | other | gradient, differentiation, curvature | Toni Giorgino | ENDPLUMED | generic |
| 19.005 | Cmyc small molecule interaction | bio | metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP | Gabriella Heller | WHOLEMOLECULES COORDINATION PBMETAD METAINFERENCE CENTER ALPHABETA CS2BACKBONE MOLINFO INCLUDE PRINT DISTANCE GROUP GYRATION | vatom colvar multicolvar generic isdb bias core |
| 26.012 | Buprenorphine Restricts the Conformational Landscape of the μ-Opioid Receptor | bio | OneOPES, GPCR, MOR, activation, euclidean path, conformational changes, allostery | Simone Aureli | OPES_METAD_EXPLORE ECV_MULTITHERMAL VOLUME OPES_EXPANDED PRINT CUSTOM GROUP CENTER PATH ENERGY UPPER_WALLS DISTANCE COORDINATION RMSD | vatom bias function generic core opes mapping colvar |
| 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 | OPES_METAD_EXPLORE ECV_MULTITHERMAL VOLUME OPES_EXPANDED PRINT LOWER_WALLS CUSTOM GROUP CENTER PATH PATHMSD ENERGY UPPER_WALLS DISTANCE COORDINATION RMSD | vatom bias function generic core opes mapping colvar |
| 25.024 | Sampling glycan-glycan interactions for B22 calculations | bio | B22, glycan, carbohydrates, distance, REST2, metadynamics, RECT, replica exchange | Isabell Louise Grothaus | METAD POSITION PRINT RESTRAINT COM DISTANCE COMBINE | vatom bias function generic colvar |
| 25.015 | Assessment of Force Fields for Describing Conformational Polymorphic Crystals of ROY | materials | Molecular crystal, Force Field, Collective Variable | Pradip Si and Omar Valsson | DUMPMULTICOLVAR DISTANCES PRINT TORSIONS SMAC | multicolvar symfunc generic |
| 25.001 | RNA G-quadruplex folding with ST-metaD protocol | bio | RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | METAD MOLINFO ERMSD WHOLEMOLECULES COMBINE | colvar bias function generic |
| 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 | TORSION COORDINATION ANGLE PRINT CONVERT_TO_FES WHOLEMOLECULES GROUP HISTOGRAM DUMPGRID DISTANCE | gridtools core colvar generic |
| 24.034 | Umbrella sampling of ion in transporter SLC26A7 | bio | umbrella sampling, transporter, ions | Xiaoli Lu | POSITION PRINT UNITS RESTRAINT | setup colvar bias generic |
| 24.026 | Constant pH metadynamics of RNA oligomers | bio | metadynamics, pH, RNA | Giovanni Bussi | TORSION METAD RESTART MOLINFO PRINT PUCKERING | setup colvar bias generic |
| 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 | TORSION PYTORCH_MODEL RESTART FIXEDATOM PRINT LOWER_WALLS FIT_TO_TEMPLATE CUSTOM OPES_METAD GROUP CENTER PATH UPPER_WALLS WHOLEMOLECULES COORDINATION DISTANCE | setup vatom bias function generic core opes pytorch mapping colvar |
| 24.024 | Host-Guest binding free energies à la carte, an automated OneOPES protocol | bio | OneOPES, ligand binding, binding free energy,SAMPL challenge, host-guest | Valerio Rizzi | TORSION OPES_METAD_EXPLORE ECV_MULTITHERMAL FIXEDATOM OPES_EXPANDED ANGLE PRINT ENDPLUMED LOWER_WALLS FIT_TO_TEMPLATE GROUP CENTER ENERGY UPPER_WALLS WHOLEMOLECULES COORDINATION DISTANCE MATHEVAL | vatom bias function generic core opes colvar |
| 23.025 | Probing ion binding to G-quadruplexes and related events | chemistry | metadynamics, repulsive potential, nucleic acids, G-quadruplexes | Marcelo Poleto | WRAPAROUND METAD RESTART UNITS POSITION DISTANCES PRINT LOWER_WALLS DUMPATOMS FIT_TO_TEMPLATE COM GROUP UPPER_WALLS WHOLEMOLECULES FLUSH DISTANCE MATHEVAL | setup vatom bias function generic core multicolvar colvar |
| 23.015 | MPCs aggregation | bio | opes_explore, dimerization, MPCs, self-assembly | Vikas Tiwari | OPES_METAD_EXPLORE METAD PRINT LOWER_WALLS CUSTOM COM GROUP CENTER UPPER_WALLS WHOLEMOLECULES COORDINATION DISTANCE | vatom bias function generic core opes colvar |
| 23.014 | Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 | bio | metadynamics, oligomerization, chemokine receptors, GPCR, membrane | Vittorio Limongelli | TORSION METAD FLUSH PRINT COM UPPER_WALLS WHOLEMOLECULES COMBINE DISTANCE | vatom bias function generic colvar |
| 23.009 | Deep Learning Collective Variables from Transition Path Ensemble | methods | TPI-Deep-TDA, Deep-TDA, Transition Path, OPES, OPES Flooding, Machine Learning, Protein folding, Ligand binding | Dhiman Ray | PYTORCH_MODEL MOLINFO CONTACTMAP OPES_METAD WHOLEMOLECULES DISTANCE INCLUDE RMSD FIXEDATOM ANGLE FIT_TO_TEMPLATE GROUP PRINT LOWER_WALLS CENTER MATHEVAL COMBINE ENDPLUMED CUSTOM ENERGY UPPER_WALLS COORDINATION COMMITTOR | vatom bias function generic core opes pytorch colvar |
| 23.008 | PBMetaD simulations of Histatin5 | bio | metadynamics, IDP, Rg, PPII | Francesco Pesce | TORSION MOLINFO GYRATION PRINT GROUP PBMETAD WHOLEMOLECULES | core colvar bias generic |
| 23.002 | Critical comparison of general-purpose collective variables for crystal nucleation | methods | metadynamics, umbrella sampling, commitor, entropy, PIV | Julien Lam | METAD VOLUME Q4 PRINT RESTRAINT CUSTOM ENERGY PIV PAIRENTROPY UPPER_WALLS LOCAL_AVERAGE Q6 UNITS FUNCPATHMSD | gridtools symfunc setup bias function generic piv colvar |
| 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 | METAD PRINT CUSTOM DRR PATHMSD BIASVALUE FLUSH | drr bias function generic colvar |
| 22.031 | Rare Event Kinetics from Adaptive Bias Enhanced Sampling | methods | OPES Flooding, Kinetics, Rate, OPES, Machine Learning | Dhiman Ray | PYTORCH_MODEL MOLINFO CONTACTMAP OPES_METAD WHOLEMOLECULES UNITS INCLUDE CONSTANT DISTANCE RMSD GROUP BIASVALUE TORSION POSITION PRINT COMBINE ENDPLUMED CUSTOM ENERGY COMMITTOR | setup bias function generic core opes pytorch colvar |
| 22.024 | Conformational Entropy as a Potential Liability of Computationally Designed Antibodies | bio | metadynamics, conformational entropy, antibody, nanobody | Thomas Löhr | TORSION RESTART MOLINFO PRINT ANTIBETARMSD ALPHABETA COM PBMETAD ALPHARMSD WHOLEMOLECULES | setup vatom bias generic secondarystructure multicolvar colvar |
| 22.015 | Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome | bio | photodynamics, bacteriophytochrome, variationally enhanced sampling | Jakub Rydzewski | TORSION OPT_AVERAGED_SGD PRINT VES_LINEAR_EXPANSION TD_UNIFORM BF_FOURIER | ves colvar generic |
| 22.002 | GAMBES_SAMPL5_RATES | other | GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding | Jayashrita Debnath | PYTORCH_MODEL COMMITTOR LOAD COORDINATION FIXEDATOM ANGLE PRINT ENDPLUMED FIT_TO_TEMPLATE GROUP CENTER ENERGY UPPER_WALLS WHOLEMOLECULES FLUSH DISTANCE MATHEVAL | setup vatom bias function generic core pytorch colvar |
| 22.001 | Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials | methods | enhanced sampling, variationally enhanced sampling, ves, metadynamics, bias representation, wavelets, adam | Benjamin Pampel | TD_WELLTEMPERED DISTANCE COORDINATION UNITS INCLUDE VES_OUTPUT_BASISFUNCTIONS OPT_ADAM VES_LINEAR_EXPANSION BF_GAUSSIANS POSITION PRINT FLUSH OPT_AVERAGED_SGD BF_CHEBYSHEV METAD BF_LEGENDRE BF_WAVELETS TD_UNIFORM ENERGY UPPER_WALLS BF_CUBIC_B_SPLINES | setup bias generic ves colvar |
| 21.037 | Molecular Dynamics simulations of RBD/hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain | Max Bonomi | PRINT DISTANCE RMSD | colvar generic |
| 21.029 | Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs | bio | metadynamics, small peptide, machine learning | Pratyush Tiwary | TORSION RESTART EXTERNAL MOLINFO PRINT ENERGY FLUSH | setup colvar bias generic |
| 21.016 | MD SAXS GTPase associated center | bio | metadynamics, RNA, folding, SAXS | Giovanni Bussi | METAD GYRATION MOLINFO PRINT LOWER_WALLS CUSTOM GROUP SAXS UPPER_WALLS ERMSD WHOLEMOLECULES INCLUDE | bias function generic core colvar isdb |
| 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 | OPT_AVERAGED_SGD RESTART VOLUME BF_LEGENDRE ECV_UMBRELLAS_LINE ENVIRONMENTSIMILARITY OPES_EXPANDED PRINT VES_LINEAR_EXPANSION TD_UNIFORM ENERGY ECV_MULTITHERMAL_MULTIBARIC UPPER_WALLS Q6 MATHEVAL | symfunc setup bias function generic envsim opes ves 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 | PRINT COM GROUP WHOLEMOLECULES DISTANCE | core vatom colvar generic |
| 20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Max Bonomi | INCLUDE GYRATION MOLINFO PRINT ALPHABETA PBMETAD WHOLEMOLECULES COORDINATION DIHCOR | multicolvar colvar bias generic |
| 19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | METAD GYRATION MOLINFO PRINT COM ENERGY UPPER_WALLS DISTANCE | vatom colvar bias generic |
| 19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Kim Jelfs | RESTART MOVINGRESTRAINT FLUSH PRINT DISTANCES COM INPLANEDISTANCES | setup vatom bias generic multicolvar |
| 19.056 | maze | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_SIMULATED_ANNEALING POSITION MAZE_LOSS PRINT UNITS MAZE_OPTIMIZER_BIAS | setup colvar generic maze |
| 19.048 | Understanding Ligand Binding Selectivity in a Prototypical GPCR Family | bio | metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | METAD PRINT LOWER_WALLS WHOLEMOLECULES COM CONSTANT UPPER_WALLS BIASVALUE DISTANCE MATHEVAL | vatom bias function generic colvar |
| 19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Matteo Salvalaglio | TORSION METAD PRINT LOWER_WALLS CENTER UPPER_WALLS DISTANCE COMMITTOR | vatom colvar bias generic |
| 19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Matteo Salvalaglio | METAD RESTART GYRATION ENDPLUMED PRINT DISTANCES COORDINATIONNUMBER | symfunc setup bias generic multicolvar colvar |
| 19.013 | RNA FF FITTING | methods | force field, RNA | Giovanni Bussi | TORSION MOLINFO CONSTANT PUCKERING BIASVALUE INCLUDE MATHEVAL | colvar bias function generic |
| 19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Max Bonomi | MOLINFO PRINT EMMI GROUP BIASVALUE | core bias isdb generic |
| 26.013 | Characterizing Partially Unfolded States of the C-Terminal Domain in WT and 3PA Mouse Prion Protein | bio | parallel-bias metadynamics, PBMetaD, metadynamics, mouse prion protein, prion protein, protein folding, partially unfolded states, molecular dynamics | Sonali M. Jadhav | GYRATION DISTANCE INCLUDE MOLINFO CONTACTMAP GROUP PRINT PBMETAD DUMPMASSCHARGE COORDINATION WHOLEMOLECULES ALPHARMSD COM | vatom generic core colvar secondarystructure bias |
| 26.000 | OPES simulations of disordered proteins | bio | OPES, IDPs | Julian Streit | RESTART OPES_EXPANDED ENERGY PRINT ECV_MULTITHERMAL | opes colvar generic setup |
| 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 | CUSTOM CELL MATHEVAL DISTANCE ENERGY INCLUDE POSITION PRINT BIASVALUE COMBINE COORDINATION OPES_METAD LOAD UNITS FLUSH TORSION | opes generic colvar function setup bias |
| 25.009 | Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water | chemistry | metadynamics, nitrate photolysis | Kam-Tung Chan | METAD READ CUSTOM DISTANCE RESTART GROUP PRINT REWEIGHT_METAD COORDINATION DUMPGRID HISTOGRAM UPPER_WALLS FLUSH | generic core gridtools colvar function setup bias |
| 25.008 | Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting | methods | metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting | Dhiman Ray | METAD PYTORCH_MODEL CUSTOM DISTANCE ENERGY LOWER_WALLS MOLINFO POSITION GROUP PRINT BIASVALUE WHOLEMOLECULES UNITS RMSD UPPER_WALLS OPES_METAD ENDPLUMED TORSION | opes pytorch generic core colvar function setup bias |
| 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 | METAD DISTANCE RESTRAINT FIXEDATOM LOWER_WALLS DISTANCES GROUP PRINT FLUSH ANGLE COMBINE COORDINATION UNITS COM UPPER_WALLS COORDINATIONNUMBER | vatom generic symfunc core multicolvar colvar function setup bias |
| 24.028 | All-atom simulations of RNA-membrane interactions | bio | metadynamics, membrane, RNA | Giovanni Bussi | METAD GYRATION MATHEVAL DISTANCE LOWER_WALLS MOLINFO POSITION GROUP PRINT DISTANCES GHOST COMBINE SORT WHOLEMOLECULES UPPER_WALLS CENTER PUCKERING | vatom generic core colvar multicolvar function bias |
| 22.036 | Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction | bio | Well-tempered MetaDynamics with Hamiltonian Replica Exchange | Miroslav Krepl | METAD CUSTOM MOLINFO GROUP PRINT BIASVALUE COMBINE COORDINATION GHBFIX LOAD UPPER_WALLS FLUSH | generic core colvar function setup bias |
| 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 | COMMITTOR METAD CUSTOM CELL MATHEVAL LOWER_WALLS DRMSD PRINT UPPER_WALLS | function bias colvar generic |
| 22.007 | Characterization of a natural variant of human NDP52 and its functional consequences on mitophagy | bio | metadynamics, well-tempered, protein-protein interactions, disordered proteins, mutations autophagy | Elena Papaleo | METAD ALPHABETA DISTANCE MOLINFO PRINT ANGLE COORDINATION WHOLEMOLECULES ALPHARMSD UPPER_WALLS FLUSH TORSION | generic colvar multicolvar secondarystructure bias |
| 21.044 | NaCl nucleation | chemistry | metadynamics, DFS clustering | Aaron Finney | CLUSTER_DISTRIBUTION METAD CONTACT_MATRIX FIXEDATOM GROUP PRINT LOCAL_Q6 INSPHERE COMBINE DUMPGRID Q6 HISTOGRAM DFSCLUSTERING CLUSTER_NATOMS MFILTER_MORE COORDINATIONNUMBER | adjmat vatom generic symfunc core gridtools multicolvar function volumes clusters bias |
| 21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Kristof Bal | COMMITTOR METAD CONVERT_TO_FES MOVINGRESTRAINT FLUSH PRINT REWEIGHT_METAD DUMPGRID LOAD HISTOGRAM UNITS UPPER_WALLS COORDINATIONNUMBER | generic symfunc gridtools setup bias |
| 20.016 | Predicting polymorphism in molecular crystals using orientational entropy | materials | metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy | Pablo Piaggi | METAD INCLUDE GROUP PRINT VOLUME LOAD UPPER_WALLS CENTER | vatom generic core colvar setup bias |
| 20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Jim Pfaendtner | DISTANCE RESTART DISTANCES GROUP PRINT COORDINATION WHOLEMOLECULES CENTER | vatom generic core multicolvar colvar setup |
| 19.075 | PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python | other | Python, automatic differentiation | Toni Giorgino | CUSTOM DISTANCE RESTRAINT GROUP PRINT ANGLE COMBINE CENTER ENDPLUMED TORSION DUMPDERIVATIVES | vatom generic core colvar function bias |
| 19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Carlo Camilloni | DISTANCE RESTRAINT INCLUDE MOLINFO SAXS GROUP PRINT BIASVALUE WHOLEMOLECULES STATS RMSD UPPER_WALLS CENTER ENDPLUMED | vatom generic core colvar function isdb bias |
| 19.003 | EMMI ClpP | bio | metainference, cryo-EM | Max Bonomi | EMMI MOLINFO GROUP PRINT BIASVALUE | core bias isdb generic |
| 25.030 | Committor Regularization | methods | metadynamics, enhanced sampling, mlcvs, committor, machine learning | Florian Dietrich | PRINT UNITS METAD MOVINGRESTRAINT | setup generic bias |
| 25.022 | Imidazole Diffusion in SALEM-2 MOF | materials | OPES, Diffusion, Ring opening, MOFs, Machine Learning Potentials | Sudheesh Kumar Ethirajan | CENTER DISTANCES PRINT UNITS GROUP ENDPLUMED PROJECTION_ON_AXIS OPES_METAD WHOLEMOLECULES MOLINFO DISTANCE | setup core colvar generic opes multicolvar vatom |
| 25.014 | Atomic resolution ensembles of intrinsically disordered proteins with Alphafold | bio | bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement | Vincent Schnapka | BIASVALUE PRINT BAIES GROUP | isdb generic core bias |
| 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 | VOLUME CENTER TORSION READ PRINT GYRATION ENERGY PBMETAD INCLUDE UPDATE_IF RESTART WHOLEMOLECULES DUMPATOMS MOLINFO DISTANCE | setup colvar generic vatom bias |
| 25.003 | Surrogate Model CV | methods | Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding | Sompriya Chatterjee | TORSION COMBINE PRINT CUSTOM GROUP ENDPLUMED ENERGY COMMITTOR OPES_METAD MATHEVAL WHOLEMOLECULES MOLINFO PYTORCH_MODEL DISTANCE | pytorch core function colvar generic opes |
| 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 CENTER DUMPATOMS UPPER_WALLS PRINT GROUP PARABETARMSD ALPHARMSD PBMETAD COM DUMPMASSCHARGE EMMI WHOLEMOLECULES BIASVALUE COORDINATION MOLINFO DISTANCE | core isdb colvar generic secondarystructure vatom bias |
| 24.014 | Learning Collective Variables with Synthetic Data Augmentation through Physics-inspired Geodesic Interpolation | methods | data augmentation, geodesic interpolation, collective variables, protein folding | Juno Nam | DRR RMSD UPPER_WALLS PRINT METAD LOWER_WALLS FLUSH WHOLEMOLECULES COORDINATION MOLINFO PYTORCH_MODEL | pytorch colvar generic drr bias |
| 24.011 | Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble | methods | committor, machine learning | Peilin Kang | RMSD LOWER_WALLS DISTANCE TORSION PRINT CUSTOM CELL INCLUDE BIASVALUE UNITS GROUP LOAD MATHEVAL WHOLEMOLECULES POSITION UPPER_WALLS ENDPLUMED ENERGY COORDINATION MOLINFO | setup core function colvar generic bias |
| 24.005 | Learning Markovian Dynamics with Spectral Maps | methods | spectral map, collective variables, machine learning | Jakub Rydzewski | PRINT UNITS CUSTOM BIASVALUE DISTANCE | setup function colvar generic bias |
| 23.046 | Lasso Peptides - HLDA CV | bio | metadynamics, protein folding, HLDA, harmonic | Gabriel da Hora | COMBINE PRINT METAD UNITS WHOLEMOLECULES DISTANCE | setup function colvar generic bias |
| 23.019 | Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors | bio | binding pathway, binding energy, sketch-map, drug development | Raitis Bobrovs | VSTACK LANDMARK_SELECT_FPS UPPER_WALLS COLLECT_FRAMES PRINT METAD CUSTOM PATHMSD SKETCHMAP VORONOI SKETCHMAP_PROJECTION COM WHOLEMOLECULES TRANSPOSE DISSIMILARITIES DISTANCE | valtools function colvar generic landmarks matrixtools dimred vatom bias |
| 23.006 | Transcription factor unbinding | bio | metadynamics, DNA, conformational changes | Malin Lüking | CONTACTMAP PRINT ANGLE METAD ALPHARMSD COM DUMPFORCES MOLINFO DISTANCE | colvar generic secondarystructure vatom bias |
| 22.040 | From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure | bio | SARS-CoV-2, Spike, Omicron | Miłosz Wieczór | UPPER_WALLS PRINT METAD LOWER_WALLS PCAVARS WHOLEMOLECULES | mapping generic bias |
| 21.051 | Automatic learning of hydrogen-bond fixes in an AMBER RNA force field | methods | force field, RNA | Giovanni Bussi | COMBINE PRINT METAD ERMSD WHOLEMOLECULES BIASVALUE COORDINATION MOLINFO | function colvar generic bias |
| 21.049 | Multiple-path-metadynamics and PathMaps | methods | path-CV, metadynamics, multiple-walker, multiple paths, pathmap | Alberto Pérez-de-Alba-Ortíz | RESTRAINT TORSION COMBINE CONSTANT UPPER_WALLS PRINT UNITS METAD CUSTOM LOWER_WALLS LOAD ENSEMBLE MOVINGRESTRAINT | setup function colvar generic bias |
| 21.040 | A structural ensemble of a tau-microtubule complex reveals regulatory tau phosphorylation and acetylation mechanisms | bio | EMMI, CryoEM, tau-microtubules, post-translational modifications, chemical mutagenesis, structural ensemble, Metainference | Faidon Brotzakis | UPPER_WALLS PRINT GROUP COM RESTART EMMI WHOLEMOLECULES BIASVALUE MOLINFO DISTANCE | setup core isdb colvar generic vatom bias |
| 21.039 | Deep learning the slow modes for rare events sampling | methods | collective variables, machine learning, slow modes, deep-tica, opes | Luigi Bonati | RMSD COMBINE Q6 ENVIRONMENTSIMILARITY DISTANCE TORSION PRINT INCLUDE OPES_EXPANDED ECV_MULTITHERMAL PYTORCH_MODEL VOLUME CONTACTMAP UNITS GROUP FLUSH LOAD OPES_METAD WHOLEMOLECULES ENDPLUMED ENERGY MOLINFO | setup pytorch envsim core function colvar symfunc generic opes |
| 21.020 | Reweighted Jarzynski sampling | methods | free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions | Kristof Bal | RESTRAINT COMBINE CONSTANT METAD ANN TD_WELLTEMPERED DUMPGRID DISTANCE MOVINGRESTRAINT PRINT CUSTOM CONVERT_TO_FES REWEIGHT_BIAS VES_LINEAR_EXPANSION BIASVALUE UNITS COORDINATIONNUMBER FLUSH BF_CHEBYSHEV LOAD OPES_METAD HISTOGRAM OPT_AVERAGED_SGD REWEIGHT_METAD UPPER_WALLS | setup ves annfunc gridtools function colvar symfunc generic opes bias |
| 21.018 | Localized Volume-based Metadynamics | bio | LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification | Riccardo Capelli | RMSD METAD FIXEDATOM DUMPGRID DISTANCE PRINT COM CONVERT_TO_FES READ GROUP FLUSH HISTOGRAM MATHEVAL WHOLEMOLECULES REWEIGHT_METAD POSITION UPPER_WALLS ENDPLUMED COORDINATION | core gridtools function colvar generic vatom bias |
| 21.011 | CmuMD simulations of NaCl(aq) at graphite | chemistry | CmuMD, DFS clustering | Aaron Finney | RESTRAINT DENSITY AROUND MULTICOLVARDENS PRINT GROUP COORDINATIONNUMBER CLUSTER_DISTRIBUTION MFILTER_MORE DFSCLUSTERING FIXEDATOM LOAD CLUSTER_NATOMS CONTACT_MATRIX DUMPGRID | setup clusters core gridtools volumes symfunc generic adjmat multicolvar vatom bias |
| 21.004 | Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy | bio | machine learning, well-tempered metadynamics, path collective variable, potential of mean force, standard binding free energy calculations, host-guest, protein-ligand unbinding | Dorothea Gobbo | UPPER_WALLS PRINT METAD PATHMSD LOWER_WALLS RESTART WHOLEMOLECULES | setup colvar generic bias |
| 20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Faidon Brotzakis | RMSD DISTANCES PRINT GROUP CONVERT_TO_FES HISTOGRAM EMMI WHOLEMOLECULES READ MOLINFO DUMPGRID BIASVALUE | core gridtools isdb colvar generic multicolvar 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 | CONTACTMAP FUNCPATHGENERAL UPPER_WALLS CONSTANT PRINT METAD GROUP LOWER_WALLS INCLUDE COM LOAD PROJECTION_ON_AXIS MATHEVAL WHOLEMOLECULES BIASVALUE MOLINFO DISTANCE | setup core function colvar generic vatom bias |
| 19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Kim E. Jelfs | CENTER UPPER_WALLS PRINT METAD GROUP LOWER_WALLS COM RESTART DISTANCE | setup core colvar generic vatom bias |
| 19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Cristina Paissoni | CENTER COMBINE PRINT ANGLE GROUP ENDPLUMED ALPHABETA INCLUDE PBMETAD ENSEMBLE MATHEVAL WHOLEMOLECULES BIASVALUE STATS SAXS MOLINFO COORDINATION | core isdb function colvar generic multicolvar vatom bias |
| 19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Gareth Tribello | FCCUBIC CENTER FIND_CONTOUR_SURFACE FOURIER_TRANSFORM MULTICOLVARDENS UNITS GROUP DUMPGRID MORE_THAN | setup core gridtools fourier contour symfunc function vatom |
| 19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Elena Papaleo | UPPER_WALLS PRINT METAD GROUP LOWER_WALLS ALPHABETA WHOLEMOLECULES GYRATION MOLINFO | core colvar generic multicolvar bias |
| 19.023 | RECT | methods | metadynamics, replica exchange | Giovanni Bussi | TORSION PRINT METAD WHOLEMOLECULES GYRATION | colvar generic bias |
| 19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Giovanni Bussi | COMBINE DISTANCES UPPER_WALLS ANGLE METAD PRINT LOWER_WALLS FLUSH INCLUDE ERMSD RANDOM_EXCHANGES MOLINFO DISTANCE | function colvar generic multicolvar bias |
| 26.001 | Molecular simulations Alx riboswitch | bio | RNA, riboswitch | Giovanni Bussi | DISTANCE MATHEVAL MOVINGRESTRAINT PRINT RESTRAINT MOLINFO ERMSD | function generic colvar bias |
| 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 | CENTER DISTANCE GYRATION METAD WHOLEMOLECULES GROUP UPPER_WALLS PRINT MOVINGRESTRAINT INCLUDE SAXS MOLINFO | core colvar bias isdb generic vatom |
| 24.031 | DeepLNE | methods | PATHCV, OPES, OneOPES | Thorben Fröhlking | OPES_METAD_EXPLORE ENERGY COORDINATION VOLUME OPES_EXPANDED PYTORCH_MODEL PRINT COMBINE ECV_MULTITHERMAL RESTART MOLINFO ERMSD | opes colvar generic function setup pytorch |
| 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 | ENDPLUMED COORDINATION MATHEVAL UPPER_WALLS TORSION COMMITTOR DISTANCE FIT_TO_TEMPLATE METAD OPES_METAD COMBINE CONTACTMAP CENTER ANGLE FIXEDATOM WHOLEMOLECULES GROUP PRINT CUSTOM RMSD MOLINFO | core opes colvar bias generic function vatom |
| 24.018 | A new route to the prebiotic synthesis of glycine via ab initio-based machine learning calculations | chemistry | prebiotic chemistry, glycine, Strecker synthesis, ab initio calculations, machine learning | Léon HUET | PRINT DISTANCE | colvar generic |
| 24.010 | Oxytocin metadynamics simulation | bio | metadynamics, oxytocin, peptide | Jan Beránek | METAD WHOLEMOLECULES PRINT FLUSH TORSION RESTART | bias colvar setup generic |
| 24.009 | Weighted Shape Gaussian Mixture Models | bio | metadynamics, clustering | Glen Hocky | UNITS METAD GROUP PRINT TORSION | core colvar bias generic setup |
| 24.008 | yCD Metadynamics | bio | volume-based MetaD, path CVs, infrequent MetaD, product release | James McCarty | ENDPLUMED COORDINATION REWEIGHT_METAD MATHEVAL UPPER_WALLS INCLUDE FLUSH PATH COMMITTOR HISTOGRAM DUMPGRID WRAPAROUND DISTANCE FIT_TO_TEMPLATE METAD READ CONVERT_TO_FES CONTACTMAP COM FIXEDATOM WHOLEMOLECULES GROUP PRINT RMSD MOLINFO | mapping core colvar gridtools bias generic function vatom |
| 23.029 | An accurate and efficient SAXS/SANS implementation including solvation layer effects suitable for restrained Molecular Dynamics simulations | bio | SAXS, SANS, SAS, metainference, proteins, nucleic-acid | Federico Ballabio | BIASVALUE CENTER DISTANCE STATS UPPER_WALLS GROUP PRINT WRAPAROUND SAXS RMSD MOLINFO ENSEMBLE | core generic colvar bias isdb vatom function |
| 23.024 | Permutationally Invariant Networks for Enhanced Sampling (PINES) | methods | collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent | Nicholas Herringer | LOAD PRINT PINES PBMETAD | bias pines setup generic |
| 22.029 | Angiotensin-1-7_Metadynamics | bio | Metadynamics, Angiotensin-(1-7), peptide | L.-América Chi | LOWER_WALLS COORDINATION GYRATION METAD UPPER_WALLS GROUP WHOLEMOLECULES PRINT FLUSH | core bias colvar generic |
| 22.027 | Molecular Dynamics simulations of BANAL-236 RBD-hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, BANAL-236, receptor-binding domain | Max Bonomi | PRINT RMSD | colvar generic |
| 22.026 | Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification | materials | Peptoid, silica | Jim Pfaendtner | DISTANCE GYRATION PBMETAD COM UPPER_WALLS PRINT MOLINFO | bias generic colvar vatom |
| 22.016 | Homogeneous ice nucleation in an ab initio machine learning model of water | chemistry | ice, water, nucleation, seeding, environment similarity, interfacial free energy, interfaces | Pablo Piaggi | ENERGY VOLUME HISTOGRAM UPPER_WALLS DUMPGRID PRINT AROUND OPES_METAD CUSTOM RESTART ENVIRONMENTSIMILARITY | envsim opes colvar gridtools bias generic function setup volumes |
| 22.012 | Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT | bio | contact maps, protein-protein interactions | Isabell-Louise Grothaus | CENTER PRINT DISTANCE CONTACTMAP | generic colvar vatom |
| 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 | DISTANCE YANGLES LOWER_WALLS ZANGLES METAD COM UPPER_WALLS WHOLEMOLECULES MATHEVAL XANGLES COMBINE CUSTOM PRINT ALPHABETA TORSION MOLINFO | function colvar bias generic multicolvar vatom |
| 21.050 | N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity | methods | bio | Isabell Louise Grothaus | CENTER PRINT DISTANCE | generic colvar vatom |
| 21.047 | Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations | materials | pair entropy, metadynamics, ves, solids, crystallization | Pablo Piaggi | TD_WELLTEMPERED BF_LEGENDRE ENERGY VES_LINEAR_EXPANSION VOLUME METAD PAIRENTROPY OPT_AVERAGED_SGD PRINT COMBINE RESTART LOAD | colvar gridtools bias generic function setup ves |
| 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 | RANDOM_EXCHANGES ENDPLUMED METAD PBMETAD PRINT INCLUDE TORSION | bias colvar generic |
| 21.019 | Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations | materials | Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen | Matteo Salvalaglio | DISTANCE KDE MATHEVAL PRINT COM TORSIONS | multicolvar generic colvar gridtools vatom function |
| 21.014 | how to determine statistically accurate conformational ensembles | bio | metadynamics, metainference, errors, cv, SAXS, ensemble determination | Cristina Paissoni | CENTER BIASVALUE STATS ANTIBETARMSD GYRATION METAD PBMETAD WHOLEMOLECULES PRINT ALPHABETA CONTACTMAP SAXS TORSION MOLINFO ENSEMBLE | multicolvar generic colvar secondarystructure bias isdb vatom function |
| 21.006 | OPES, On-the-fly Probability Enhanced Sampling Method | methods | opes, alanine dipeptide, well-tempered, multithermal, multiumbrella | Michele Invernizzi | ENDPLUMED ENERGY ECV_UMBRELLAS_LINE OPES_EXPANDED PRINT OPES_METAD TORSION ECV_MULTITHERMAL | opes colvar generic |
| 21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Tarak Karmakar | LOWER_WALLS UPPER_WALLS GROUP PYTORCH_MODEL MATHEVAL OPES_METAD PRINT FLUSH LOAD | core opes bias generic function setup pytorch |
| 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 PRINT DISTANCE METAD | bias colvar generic |
| 20.026 | Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor | bio | Metadynamics, Umbrella sampling | Brandon Peters | REWEIGHT_METAD HISTOGRAM MULTI_RMSD METAD DUMPGRID PRINT CONVERT_TO_FES RESTRAINT | colvar bias gridtools generic |
| 20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Vojtech Spiwok | TORSION PRINT METAD | bias colvar generic |
| 20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Michele Invernizzi | ECV_LINEAR POSITION ENDPLUMED ENERGY ECV_UMBRELLAS_LINE MATHEVAL UPPER_WALLS TORSION LOAD ECV_MULTITHERMAL ENVIRONMENTSIMILARITY OPES_EXPANDED ECV_MULTITHERMAL_MULTIBARIC VOLUME UNITS WHOLEMOLECULES PRINT CUSTOM RMSD Q6 MOLINFO | envsim opes symfunc colvar bias generic function setup |
| 20.015 | Rational design of ASCT2 inhibitors using an integrated experimental-computational approach | bio | ASCT2 transporter, small-molecules, cryo-EM, metainference | Max Bonomi | BIASVALUE WHOLEMOLECULES GROUP PRINT EMMIVOX DUMPATOMS LOAD MOLINFO | core isdb bias generic setup |
| 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 | METAD UPPER_WALLS GROUP WHOLEMOLECULES PRINT RESTART MOLINFO PATHMSD | core colvar bias generic setup |
| 19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Matteo Salvalaglio | CENTER DISTANCE ENDPLUMED GROUP PRINT INCLUDE | core generic colvar vatom |
| 19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Vittorio Limongelli | FUNNEL DISTANCE LOWER_WALLS FUNNEL_PS METAD WHOLEMOLECULES UPPER_WALLS PRINT RMSD COM | funnel colvar generic bias vatom |
| 26.010 | Solvation-Mediated Ammonia Synthesis in a Nanoheterogeneous Liquid Alloy | materials | OPES, Catalysis, Ammonia Synthesis | Axel Tosello Gardini | COORDINATIONNUMBER OPES_METAD_EXPLORE CUSTOM UNITS COORDINATION INCLUDE FLUSH GROUP PRINT DISTANCES OPES_METAD DISTANCE UPPER_WALLS | core generic colvar symfunc bias multicolvar setup function opes |
| 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 | CUSTOM OPES_METAD_EXPLORE COORDINATION GHOST GROUP CENTER LOWER_WALLS RMSD PRINT ENERGY DISTANCES DISTANCE OPES_EXPANDED ECV_MULTITHERMAL PATHMSD UPPER_WALLS | core colvar function bias multicolvar generic vatom opes |
| 24.002 | Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes | chemistry | metadynamics, ligand design, solvent extraction | Xiaoyu Wang | UNITS RESTART METAD TORSION PRINT | setup generic bias colvar |
| 23.045 | Minute-timescale simulations of G Protein Coupled Receptor A2A activation mechanism reveal a receptor pseudo-active state | bio | Path CVs Metadynamics, GPCRs activation transition | Vittorio Limongelli | ALPHARMSD INCLUDE METAD MOLINFO LOWER_WALLS PRINT CONTACTMAP DISTANCE PATHMSD FUNCPATHMSD UPPER_WALLS | colvar secondarystructure bias generic function |
| 23.041 | Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference | methods | EMMIVox, cryo-EM, single-structure refinement, ensemble refinement, Bayesian inference, B-factors, structural ensembles | Samuel Hoff | EMMIVOX INCLUDE WRAPAROUND MOLINFO GROUP PRINT BIASVALUE WHOLEMOLECULES DISTANCE UPPER_WALLS | core generic colvar bias isdb |
| 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 | SHADOW POSITION WRAPAROUND MOLINFO GROUP CENTER METAD FIT_TO_TEMPLATE PRINT WHOLEMOLECULES DISTANCES UPPER_WALLS | core generic colvar bias multicolvar isdb vatom |
| 23.004 | Melting curves of ice polymorphs in the vicinity of the liquid-liquid critical point | chemistry | water, liquid-liquid transition, second critical point, ice, polymorphs, melting curves, environment similarity, opes, density-functional theory, scan, machine learning potential | Pablo Piaggi | DUMPGRID OPES_EXPANDED RESTART LOWER_WALLS HISTOGRAM PRINT ENVIRONMENTSIMILARITY ECV_UMBRELLAS_LINE UPPER_WALLS | gridtools bias envsim generic setup opes |
| 22.003 | Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling | methods | opes, metadynamics, reweighting, alanine, muller | Michele Invernizzi | OPES_METAD_EXPLORE CUSTOM UNITS POSITION ENDPLUMED PBMETAD ECV_UMBRELLAS_FILE METAD LOWER_WALLS TORSION PRINT ENERGY BIASVALUE OPES_METAD OPES_EXPANDED ECV_MULTITHERMAL UPPER_WALLS | colvar bias generic function setup opes |
| 22.000 | Amyloid precursor protein processing by human γ-secretase | bio | Bias Exchange Metadynamics, Helix unfolding, coupled binding | Xiaoli Lu | UNITS COORDINATION ANTIBETARMSD INCLUDE ALPHARMSD METAD MOLINFO RANDOM_EXCHANGES CENTER PRINT CONTACTMAP DISTANCE | generic colvar secondarystructure bias setup vatom |
| 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 | CUSTOM UNITS METAD LOWER_WALLS TORSION PRINT COM DISTANCE UPPER_WALLS | generic colvar bias setup function vatom |
| 21.022 | Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly | materials | parallel bias metadynamics, adsorption, peptide | Xin Qi | UPPER_WALLS PBMETAD MOLINFO LOWER_WALLS PRINT ENERGY COM DISTANCE GYRATION | bias generic colvar vatom |
| 21.017 | All-atom simulations of the Vav1 AD construct | bio | metadynamics, parallel-bias, well-tempered | Simone Orioli | PBMETAD ALPHARMSD RESTART MOLINFO GROUP ALPHABETA METAD REWEIGHT_BIAS CONTACTMAP WHOLEMOLECULES PRINT | core colvar secondarystructure bias multicolvar generic setup |
| 21.015 | Coarse-grained metadynamics and umbrella sampling simulations to investigate interactions of carbohydrate-binding modules with chitin | bio | metadynamics, umbrella sampling, coarse-grained, MARTINI, chitin, carbohydrate-binding module | Gaston Courtade | MATHEVAL RESTRAINT POSITION COORDINATION RESTART METAD CENTER PRINT WHOLEMOLECULES REWEIGHT_BIAS | generic colvar bias setup function vatom |
| 21.013 | Role of vibrational excitation in heterogeneous catalysis | chemistry | catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption | Kristof Bal | COORDINATIONNUMBER UNITS RESTRAINT COORDINATION METAD BF_CHEBYSHEV UPPER_WALLS CONVERT_TO_FES EXTERNAL LOAD FLUSH DISTANCES REWEIGHT_BIAS DISTANCE LOWER_WALLS ANGLES UWALLS TD_GRID VES_LINEAR_EXPANSION OPT_AVERAGED_SGD DUMPGRID REWEIGHT_METAD HISTOGRAM PRINT COMBINE | generic colvar symfunc bias gridtools multicolvar setup function ves |
| 21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Adriana Pietropaolo | MATHEVAL PBMETAD RESTART TORSION PRINT WHOLEMOLECULES BIASVALUE CONSTANT | generic colvar bias setup function |
| 21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Kresten Lindorff-Larsen | PBMETAD ALPHARMSD FLUSH MOLINFO GROUP CENTER PRINT BIASVALUE WHOLEMOLECULES EEFSOLV SAXS GYRATION METAINFERENCE | core colvar secondarystructure bias isdb generic vatom |
| 21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Tarsis Ferreira | COORDINATION REWEIGHT_METAD DUMPGRID INCLUDE METAD GROUP MOLINFO LOWER_WALLS RANDOM_EXCHANGES PUCKERING HISTOGRAM PRINT ENERGY WHOLEMOLECULES DISTANCE UPPER_WALLS | core colvar bias gridtools generic |
| 20.028 | Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane | bio | metadynamics, KRas-4B, anionic membrane | Huixia Lu | RESTART CENTER METAD FIT_TO_TEMPLATE PRINT DISTANCE | generic colvar bias setup vatom |
| 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 | METAD WHOLEMOLECULES UPPER_WALLS ABMD CONVERT_TO_FES FLUSH COM DISTANCE ENDPLUMED LOWER_WALLS CONTACTMAP FUNCPATHMSD DUMPGRID REWEIGHT_METAD READ MOLINFO HISTOGRAM PRINT COMBINE | colvar function bias gridtools generic vatom |
| 19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | GiovanniMaria Piccini | UPPER_WALLS UNITS METAD FLUSH LOWER_WALLS PRINT ENERGY DISTANCE COMBINE | colvar bias generic function setup |
| 19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Glen Hocky | EDS RESTRAINT TORSION PRINT DISTANCE COMBINE | colvar bias eds generic function |
| 19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Michele Invernizzi | UNITS POSITION ENDPLUMED LOAD METAD RESTART TORSION PRINT ENERGY VES_DELTA_F | generic colvar bias setup ves |
| 26.009 | Exploring the Conformational Landscape of HIV-1 TAR RNA by PT-WTE | bio | RNA, PT-WTE, HIV-1 TAR | Stefano Bosio | ENERGY GROUP MOLINFO PRINT METAD WHOLEMOLECULES | generic bias core colvar |
| 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 | DISTANCE LOWER_WALLS REWEIGHT_BIAS MOLINFO FIXEDATOM UPPER_WALLS PRINT DUMPGRID CONVERT_TO_FES METAD HISTOGRAM COM WHOLEMOLECULES | bias colvar vatom generic gridtools |
| 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 | ENERGY GROUP DISTANCE FIT_TO_TEMPLATE CENTER FIXEDATOM UPPER_WALLS PRINT MATHEVAL OPES_METAD_EXPLORE COORDINATION ANGLE WHOLEMOLECULES | bias core colvar function vatom generic opes |
| 25.007 | Shaping the glycan landscape. Hidden relationships between linkage and ring distortion induced by carbohydrate-active enzmyes | bio | REST-RECT, REST2, glycan, enzyme, CAZyme, steered | Isabell Grothaus | TORSION DISTANCE MOVINGRESTRAINT RESTART MOLINFO PRINT METAD RESTRAINT PUCKERING | generic setup bias colvar |
| 24.019 | Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning | bio | OPES, machine learning, protein folding, adaptive sampling | Mingyuan Zhang | TORSION DISTANCE COMBINE MOLINFO PRINT OPES_METAD GYRATION CUSTOM ALPHARMSD COORDINATION WHOLEMOLECULES | secondarystructure colvar function generic opes |
| 24.013 | Estimating Free Energy Surfaces and their Convergence from multiple, independent static and history-dependent biased molecular-dynamics simulations with Mean Force Integration | methods | Mean Force Integration, Convergence, FES, Umbrella Sampling | Matteo Salvalaglio | BIASVALUE ENERGY COMMITTOR TORSION DISTANCE RESTART MOLINFO PRINT COORDINATIONNUMBER MATHEVAL METAD FLUSH RESTRAINT | bias setup colvar symfunc function generic |
| 24.012 | Molecular simulations to investigate the impact of N6-methylation in RNA recognition | bio | metadynamics, alchemistry, RNA modification, RNA:protein interactions | Giovanni Bussi | BIASVALUE GROUP DISTANCE LOWER_WALLS COMBINE MOLINFO CENTER UPPER_WALLS DEBUG PRINT METAD COM COORDINATION GHBFIX | bias core colvar function vatom generic |
| 23.011 | OneOPES, a combined enhanced sampling method to rule them all | bio | OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding | Valerio Rizzi | ENERGY TORSION ENDPLUMED DISTANCE MOLINFO PRINT OPES_METAD_EXPLORE METAD ECV_MULTITHERMAL OPES_EXPANDED | generic bias opes colvar |
| 22.044 | Colloid Crystallisation Analyses | materials | Q4, Q6, Pair Entropy, DFS | Aaron Finney | MFILTER_LESS DFSCLUSTERING Q6 GROUP LOCAL_Q6 MFILTER_MORE PRINT COORDINATIONNUMBER CONTACT_MATRIX CLUSTER_NATOMS LOCAL_Q4 COMBINE LOCAL_AVERAGE Q4 | core multicolvar adjmat clusters symfunc function generic |
| 22.043 | Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES | bio | OPES, RNA, Tetraloop, Folding | Gül Zerze | ENERGY ECV_UMBRELLAS_LINE CONTACTMAP PRINT ECV_MULTITHERMAL OPES_EXPANDED WHOLEMOLECULES | generic opes colvar |
| 22.021 | Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn Løland Bore | ECV_UMBRELLAS_LINE INCLUDE LOWER_WALLS UPPER_WALLS PRINT ENVIRONMENTSIMILARITY OPES_EXPANDED | generic bias envsim opes |
| 22.006 | Peptide framework for screening the effects of amino acids on assembly | bio | metadynamics, peptides | Andrew White | COM REWEIGHT_BIAS INCLUDE GROUP PRINT DUMPGRID CONVERT_TO_FES DISTANCES METAD GYRATION HISTOGRAM COMBINE | bias core multicolvar colvar function vatom generic gridtools |
| 21.028 | From Enhanced Sampling to Reaction Profiles | methods | collective variables, multi-state, machine learning, Deep-TDA | Enrico Trizio | TORSION DISTANCE CENTER FIXEDATOM PRINT COORDINATION WHOLEMOLECULES LOWER_WALLS LOAD PYTORCH_MODEL FIT_TO_TEMPLATE MATHEVAL OPES_METAD DISTANCES UNITS ENDPLUMED GROUP UPPER_WALLS ANGLE | bias core multicolvar setup pytorch colvar function vatom generic opes |
| 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 | TORSION ABMD DISTANCE RESTART MOLINFO CENTER PRINT ERMSD | bias setup colvar vatom generic |
| 20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Matteo Salvalaglio | ENERGY LOWER_WALLS UPPER_WALLS PRINT MATHEVAL CELL METAD VOLUME | generic bias function colvar |
| 20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Carlo Camilloni | ALPHABETA TORSION DISTANCE SAXS MOLINFO CENTER METAINFERENCE ENSEMBLE PRINT PBMETAD WHOLEMOLECULES FLUSH GYRATION STATS | bias multicolvar colvar isdb function vatom generic |
| 20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Pratyush Tiwary | TORSION DISTANCE RESTART MOLINFO UPPER_WALLS PRINT METAD RMSD COMBINE WHOLEMOLECULES | bias setup colvar function generic |
| 20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Luigi Bonati | TORSION ENDPLUMED PYTORCH_MODEL DISTANCE GROUP LOWER_WALLS LOAD UPPER_WALLS PRINT OPES_METAD MATHEVAL FLUSH COM UNITS | bias core setup pytorch colvar function vatom generic opes |
| 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 | READ ENDPLUMED ABMD DISTANCE COM LOWER_WALLS UPPER_WALLS PRINT DUMPGRID REWEIGHT_METAD CONVERT_TO_FES MATHEVAL METAD HISTOGRAM COMBINE | bias colvar function vatom generic gridtools |
| 19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Valerio Rizzi | ENDPLUMED GROUP RESTART UPPER_WALLS PRINT COORDINATIONNUMBER DISTANCES METAD FLUSH COMBINE UNITS | bias core multicolvar setup symfunc function generic |
| 19.080 | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | methods | ves, variationally enhanced sampling, vibrational excitation, chemical reactions | Kristof Bal | TD_GRID VES_LINEAR_EXPANSION DISTANCE COMBINE LOWER_WALLS UPPER_WALLS PRINT EXTERNAL DUMPGRID CONVERT_TO_FES BF_CHEBYSHEV FLUSH TD_WELLTEMPERED OPT_AVERAGED_SGD COORDINATION HISTOGRAM UNITS ANGLE | bias ves setup colvar function generic gridtools |
| 19.076 | Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones | bio | molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics | Salvatore Assenza | ENDPLUMED MOVINGRESTRAINT PRINT GYRATION UNITS | generic bias setup colvar |
| 19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Giovanni Bussi | TORSION MAXENT DISTANCE INCLUDE MOLINFO SORT PRINT MATHEVAL METAD FLUSH COM COORDINATION WHOLEMOLECULES | bias colvar function vatom generic |
| 19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Mattia Bernetti | LOWER_WALLS UPPER_WALLS PRINT PATHMSD METAD WHOLEMOLECULES | generic bias colvar |
| 19.046 | Optimal Collective from short simulations for Benzamidine-Trypsin ligand binding | bio | VAC-MetaD, optimised collective variables, binding free energy, unbinding rates, benzamidine trypsin, Structure Activity Relation | Faidon Brotzakis | ALPHABETA FUNNEL TORSION GROUP DISTANCE LOWER_WALLS COM MOLINFO UPPER_WALLS PRINT REWEIGHT_METAD DISTANCES METAD RMSD COMBINE BRIDGE WHOLEMOLECULES | bias core multicolvar colvar adjmat function vatom generic funnel |
| 19.040 | Optimal Metric for Path Collective Variables | bio | metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path | Francesco Luigi Gervasio | TORSION ENDPLUMED PRINT MATHEVAL METAD | generic bias function colvar |
| 19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Davide Provasi | FUNCPATHMSD ENDPLUMED DISTANCE CONTACTMAP PRINT METAD RMSD COM WHOLEMOLECULES | bias colvar function vatom generic |
| 19.032 | Chemical reaction in solution using path collective variables based on coordination patterns | chemistry | chemical reactions, solutions, metadynamics, coordination patterns | Fabio Pietrucci | RESTART UPPER_WALLS PRINT DISTANCES METAD FLUSH PATH | bias mapping multicolvar setup generic |
| 19.030 | Coarse-Grained MetaDynamics (CG-MetaD) | bio | Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy | Vittorio Limongelli | DISTANCE LOWER_WALLS UPPER_WALLS PRINT METAD COM WHOLEMOLECULES | vatom generic bias colvar |
| 19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Pratyush Tiwary | ALPHABETA COMMITTOR COM DISTANCE TORSION RESTART PRINT EXTERNAL COMBINE WHOLEMOLECULES | bias multicolvar setup colvar function vatom generic |
| 19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Haochuan Chen | TORSION DRR PRINT | generic drr colvar |
| 19.009 | RNA tetraloops folding | bio | metadynamics, RNA, folding | Giovanni Bussi | ENDPLUMED MOLINFO PRINT METAD RMSD ERMSD WHOLEMOLECULES | generic bias colvar |
| 19.004 | MI Ubiquitin | bio | metainference, NMR | Max Bonomi | GROUP MOLINFO METAINFERENCE PRINT CS2BACKBONE RDC WHOLEMOLECULES | generic core isdb |