Browse the eggs in PLUMED-NEST
PLUMED-NEST provides all the data needed to reproduce the results of a PLUMED-enhanced molecular dynamics simulation or analysis contained in a published paper. Furthermore, PLUMED-NEST monitors the compatibility of the provided PLUMED input files with the current and development versions of the code and integrates links from these files to the PLUMED manual.
Here is the list of projects already deposited in PLUMED-NEST, while a complete bibliography can be found here.
| plumID | Name | Category | Keywords | Contributor | Actions | Modules |
|---|---|---|---|---|---|---|
| 25.025 | 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 | COORDINATION PRINT COMMITTOR METAD CENTER FUNNEL OPES_METAD MATHEVAL GROUP CUSTOM FUNNEL_PS UPPER_WALLS WHOLEMOLECULES LOWER_WALLS WRAPAROUND TORSION RMSD COM | core colvar generic opes function funnel vatom bias |
| 25.024 | Sampling glycan-glycan interactions for B22 calculations | bio | B22, glycan, carbohydrates, distance, REST2, metadynamics, RECT, replica exchange | Isabell Louise Grothaus | PRINT METAD POSITION COMBINE RESTRAINT DISTANCE COM | colvar generic function vatom bias |
| 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 | generic bias core isdb |
| 25.013 | Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices | bio | umbrella sampling, temperature ramping | Alexander Berlaga | PRINT PYTORCH_MODEL GYRATION RESTRAINT DISTANCE | generic pytorch 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 | COORDINATION PRINT COMMITTOR OPES_METAD GROUP CUSTOM UPPER_WALLS LOWER_WALLS RESTART DISTANCE UNITS | core colvar generic opes function bias setup |
| 24.031 | DeepLNE | methods | PATHCV, OPES, OneOPES | Thorben Fröhlking | COORDINATION VOLUME PRINT OPES_EXPANDED MOLINFO PYTORCH_MODEL ECV_MULTITHERMAL COMBINE OPES_METAD_EXPLORE ENERGY RESTART ERMSD | colvar generic opes function pytorch setup |
| 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 PRINT OPES_EXPANDED ECV_MULTITHERMAL GROUP CUSTOM COMBINE OPES_METAD_EXPLORE ENERGY RESTART DISTANCE TORSION | core colvar generic opes function setup |
| 24.016 | Cryo-EM guided simulations of ribozyme | bio | metainference, cryo-EM | Giovanni Bussi | PRINT MOLINFO EMMIVOX BIASVALUE INCLUDE GROUP RESTRAINT WHOLEMOLECULES ERMSD | core colvar generic isdb 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 | COORDINATION PRINT METAD MOLINFO PYTORCH_MODEL FLUSH UPPER_WALLS DRR LOWER_WALLS WHOLEMOLECULES RMSD | colvar drr generic pytorch bias |
| 24.005 | Learning Markovian Dynamics with Spectral Maps | methods | spectral map, collective variables, machine learning | Jakub Rydzewski | PRINT BIASVALUE CUSTOM DISTANCE UNITS | colvar generic function bias setup |
| 24.004 | Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables | materials | metadynamics, nucleation, machine learning | Ziyue Zou | METAD PRINT INCLUDE GROUP LOAD RESTART | generic bias core setup |
| 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 | PATHMSD PRINT METAD MOLINFO INCLUDE FUNCPATHMSD ALPHARMSD CONTACTMAP LOWER_WALLS UPPER_WALLS DISTANCE | colvar generic secondarystructure function bias |
| 23.044 | Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition | materials | metadynamics, interlocked molecules | Luigi Leanza | COORDINATION PRINT COMMITTOR METAD CONVERT_TO_FES HISTOGRAM ENDPLUMED GROUP DUMPGRID READ | core colvar gridtools generic bias |
| 23.041 | Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference | methods | EMMIVox, cryo-EM, single-structure refinement, ensemble refinement, Bayesian inference, B-factors, structural ensembles | Samuel Hoff | PRINT MOLINFO EMMIVOX BIASVALUE INCLUDE GROUP UPPER_WALLS WHOLEMOLECULES WRAPAROUND DISTANCE | core colvar generic isdb bias |
| 23.040 | Supramolecular capsules assembly dynamics | chemistry | Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics | Riccardo Capelli | PRINT METAD CENTER GROUP CUSTOM POSITION FLUSH WHOLEMOLECULES DISTANCES COM DISTANCE UNITS | core colvar multicolvar generic function vatom bias setup |
| 23.037 | Estimating binding free energy of solid binding peptides without extensive sampling | bio | metadynamics, solid binding peptides | Xin Qi | PRINT PBMETAD MOLINFO GYRATION UPPER_WALLS LOWER_WALLS DISTANCE COM | vatom generic bias colvar |
| 23.031 | Identifying small molecules binding sites in RNA conformational ensembles with SHAMAN | bio | RNA, metadynamics, probes, mixed-solvent MD, small molecules, binding sites | Max Bonomi | FIT_TO_TEMPLATE PRINT METAD MOLINFO CENTER GROUP SHADOW POSITION UPPER_WALLS WHOLEMOLECULES DISTANCES WRAPAROUND | core colvar multicolvar generic isdb vatom bias |
| 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 | PATHMSD PRINT METAD BIASVALUE CUSTOM FLUSH UPPER_WALLS DRR LOWER_WALLS TIME UNITS | colvar drr generic function bias setup |
| 23.006 | Transcription factor unbinding | bio | metadynamics, DNA, conformational changes | Malin Lüking | PRINT METAD MOLINFO ALPHARMSD CONTACTMAP ANGLE DUMPFORCES DISTANCE COM | colvar generic secondarystructure vatom bias |
| 23.005 | A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs | bio | metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A | Timothy Clark | PRINT METAD HISTOGRAM MOLINFO CONVERT_TO_FES MATHEVAL DUMPGRID READ WHOLEMOLECULES REWEIGHT_METAD RMSD DISTANCE | colvar gridtools generic function bias |
| 23.004 | Melting curves of ice polymorphs in the vicinity of the liquid-liquid critical point | chemistry | water, liquid-liquid transition, second critical point, ice, polymorphs, melting curves, environment similarity, opes, density-functional theory, scan, machine learning potential | Pablo Piaggi | HISTOGRAM PRINT OPES_EXPANDED DUMPGRID ENVIRONMENTSIMILARITY ECV_UMBRELLAS_LINE UPPER_WALLS LOWER_WALLS RESTART | gridtools generic opes envsim bias setup |
| 22.036 | Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction | bio | Well-tempered MetaDynamics with Hamiltonian Replica Exchange | Miroslav Krepl | COORDINATION GHBFIX PRINT METAD MOLINFO BIASVALUE GROUP CUSTOM COMBINE FLUSH UPPER_WALLS LOAD | core colvar generic function bias setup |
| 22.026 | Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification | materials | Peptoid, silica | Jim Pfaendtner | PRINT MOLINFO GYRATION UPPER_WALLS COM DISTANCE PBMETAD | vatom generic bias colvar |
| 22.023 | Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy | bio | CryoEM, MEMMI,EMMI, Metadynamics, Metainference, IAPP, structural ensemble | Faidon Brotzakis | COORDINATION PRINT MOLINFO BIASVALUE GROUP UPPER_WALLS WHOLEMOLECULES RESTART COM TORSION RMSD EMMI PBMETAD | core colvar generic isdb vatom bias setup |
| 22.004 | Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques | chemistry | reaction discovery, OPES, collective variables | Umberto Raucci | COORDINATION PRINT PYTORCH_MODEL OPES_METAD MATHEVAL GROUP CUSTOM OPES_METAD_EXPLORE UPPER_WALLS LOAD COM LOWER_WALLS DISTANCE UNITS | core colvar generic opes function vatom pytorch bias setup |
| 21.040 | A structural ensemble of a tau-microtubule complex reveals regulatory tau phosphorylation and acetylation mechanisms | bio | EMMI, CryoEM, tau-microtubules, post-translational modifications, chemical mutagenesis, structural ensemble, Metainference | Faidon Brotzakis | PRINT MOLINFO BIASVALUE GROUP UPPER_WALLS WHOLEMOLECULES RESTART EMMI DISTANCE COM | core colvar generic isdb vatom bias setup |
| 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 | COORDINATION ANTIBETARMSD PRINT METAD MOLINFO DIHCOR GROUP PARABETARMSD RANDOM_EXCHANGES GYRATION ENERGY UPPER_WALLS WHOLEMOLECULES LOWER_WALLS ALPHARMSD | core colvar multicolvar generic secondarystructure bias |
| 21.020 | Reweighted Jarzynski sampling | methods | free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions | Kristof Bal | HISTOGRAM METAD BIASVALUE REWEIGHT_METAD BF_CHEBYSHEV CONSTANT COMBINE CUSTOM FLUSH ANN MOVINGRESTRAINT OPT_AVERAGED_SGD DISTANCE TD_WELLTEMPERED PRINT COORDINATIONNUMBER CONVERT_TO_FES OPES_METAD DUMPGRID REWEIGHT_BIAS RESTRAINT UPPER_WALLS LOAD VES_LINEAR_EXPANSION UNITS | colvar symfunc gridtools ves generic opes function annfunc bias setup |
| 21.012 | NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition | bio | funnel metadynamics | Jim Pfaendtner | PRINT METAD FUNNEL_PS UPPER_WALLS LOWER_WALLS FUNNEL DISTANCE COM | colvar generic funnel vatom bias |
| 21.011 | CmuMD simulations of NaCl(aq) at graphite | chemistry | CmuMD, DFS clustering | Aaron Finney | DENSITY CLUSTER_DISTRIBUTION COORDINATIONNUMBER PRINT DFSCLUSTERING CLUSTER_NATOMS CONTACT_MATRIX GROUP MULTICOLVARDENS DUMPGRID RESTRAINT LOAD MFILTER_MORE FIXEDATOM AROUND | clusters core volumes symfunc adjmat gridtools multicolvar generic vatom bias setup |
| 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 | COORDINATION PRINT MOLINFO STATS COMBINE RESTRAINT WHOLEMOLECULES | function generic bias colvar |
| 20.027 | Allosteric Regulation of SARS-CoV-2 Protease. Towards Informed Structure-Based Drug Discovery | bio | SARS-CoV2, MPro, Covid-19, Molecular Dynamics, Metadynamics, Computer-Aided Drug Discovery | Khaled Abdel-Maksoud | METAD PRINT DISTANCE TORSION | generic bias colvar |
| 20.014 | amyloid beta small molecule interaction | bio | intrinsically disordered proteins, disordered proteins, IDPs, fuzzy binding, small molecule, drugs, entropy, binding, Alzheimer’s disease, amyloid beta | Gabriella Heller | COORDINATION MOLINFO STATS DIHCOR METAINFERENCE ENDPLUMED ALPHARMSD TORSION GROUP COMBINE CS2BACKBONE PBMETAD ANTIBETARMSD PARABETARMSD FLUSH WHOLEMOLECULES PRINT ENSEMBLE INCLUDE GYRATION | core colvar secondarystructure multicolvar generic isdb function bias |
| 19.081 | Calculation of phase diagrams in the multithermal-multibaric ensemble | methods | VES, variationally enhanced sampling, multithermal-multibaric, energy, Wang Landau, RefCV, kernel, bcc, fcc, sodium, aluminum | Pablo Piaggi | HISTOGRAM ENERGY VOLUME MATHEVAL COMBINE READ BF_LEGENDRE REWEIGHT_TEMP_PRESS OPT_AVERAGED_SGD RESTART OPT_DUMMY CELL TD_WELLTEMPERED Q6 PRINT CONVERT_TO_FES DUMPGRID REWEIGHT_BIAS TD_MULTITHERMAL_MULTIBARIC UPPER_WALLS VES_LINEAR_EXPANSION LOWER_WALLS LOAD | colvar symfunc gridtools ves generic function bias setup |
| 19.075 | PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python | other | Python, automatic differentiation | Toni Giorgino | PRINT CENTER ENDPLUMED GROUP CUSTOM COMBINE RESTRAINT ANGLE DISTANCE DUMPDERIVATIVES TORSION | core colvar generic function vatom bias |
| 19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | PRINT METAD MOLINFO GYRATION ENERGY UPPER_WALLS DISTANCE COM | vatom generic bias colvar |
| 19.050 | Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes | chemistry | metadynamics, membranes, Willard Chandler surface | Gareth Tribello | CONVERT_TO_FES HISTOGRAM METAD PRINT DUMPGRID REWEIGHT_BIAS COMBINE DISTANCE_FROM_CONTOUR READ UPPER_WALLS RESTART | contour gridtools generic function bias setup |
| 19.046 | Optimal Collective from short simulations for Benzamidine-Trypsin ligand binding | bio | VAC-MetaD, optimised collective variables, binding free energy, unbinding rates, benzamidine trypsin, Structure Activity Relation | Faidon Brotzakis | PRINT METAD MOLINFO BRIDGE ALPHABETA GROUP COMBINE UPPER_WALLS WHOLEMOLECULES LOWER_WALLS DISTANCES FUNNEL RMSD REWEIGHT_METAD COM DISTANCE TORSION | core colvar adjmat multicolvar generic function funnel vatom bias |
| 19.030 | Coarse-Grained MetaDynamics (CG-MetaD) | bio | Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy | Vittorio Limongelli | PRINT METAD UPPER_WALLS WHOLEMOLECULES LOWER_WALLS DISTANCE COM | vatom generic bias colvar |
| 19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Gabriele Cesare Sosso | Q6 COMMITTOR CLUSTER_WITHSURFACE DFSCLUSTERING CLUSTER_NATOMS CONTACT_MATRIX ENDPLUMED FLUSH LOCAL_Q6 MFILTER_MORE OUTPUT_CLUSTER | clusters symfunc adjmat multicolvar generic |
| 19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Jim Pfaendtner | COORDINATION EXTERNAL METAD GROUP ENERGY | core bias colvar |
| 19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Haochuan Chen | PRINT DRR TORSION | generic drr colvar |
| 19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Carlo Camilloni | PRINT SAXS MOLINFO CENTER BIASVALUE INCLUDE STATS GROUP ENDPLUMED UPPER_WALLS WHOLEMOLECULES RESTRAINT RMSD DISTANCE | core colvar generic isdb function vatom bias |
| 19.005 | Cmyc small molecule interaction | bio | metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP | Gabriella Heller | COORDINATION PRINT MOLINFO ALPHABETA CENTER INCLUDE METAINFERENCE GROUP GYRATION WHOLEMOLECULES CS2BACKBONE DISTANCE PBMETAD | core colvar multicolvar generic isdb vatom bias |
| 19.003 | EMMI ClpP | bio | metainference, cryo-EM | Max Bonomi | PRINT MOLINFO BIASVALUE GROUP EMMI | generic bias core isdb |
| 19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Max Bonomi | PRINT MOLINFO BIASVALUE GROUP EMMI | generic bias core isdb |
| 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 | DISTANCE OPES_EXPANDED RMSD UPPER_WALLS DISTANCES GHOST CUSTOM CENTER PATHMSD PRINT ENERGY ECV_MULTITHERMAL OPES_METAD_EXPLORE COORDINATION GROUP LOWER_WALLS | colvar bias function core multicolvar generic vatom opes |
| 25.018 | Metainference simulation for dimerization of RNA binding protein | bio | Metainference, Metadynamics, SAXS, protein dimer | Debadutta Patra | DISTANCE SAXS UPPER_WALLS TORSION MOLINFO PBMETAD CENTER METAINFERENCE PRINT ENSEMBLE STATS FLUSH WHOLEMOLECULES GYRATION | isdb colvar bias function generic vatom |
| 25.011 | Chiral perovskite nucleation | chemistry | metadynamics, chiral perovskites, nucleation | Adriana Pietropaolo | DISTANCE UPPER_WALLS UNITS MATHEVAL MULTI_RMSD RESTART PBMETAD PRINT LOWER_WALLS | colvar bias function setup generic |
| 24.029 | Combination of OPES and OPES-Explore | methods | OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin | Dhiman Ray | UNITS MATHEVAL METAD OPES_METAD INCLUDE OPES_METAD_EXPLORE GROUP LOWER_WALLS RMSD UPPER_WALLS FIXEDATOM ENDPLUMED PRINT WHOLEMOLECULES POSITION CUSTOM BIASVALUE CONTACTMAP COORDINATION DISTANCE COMBINE FIT_TO_TEMPLATE MOLINFO CENTER ENERGY PYTORCH_MODEL FLUSH | colvar bias function setup core generic vatom pytorch opes |
| 24.018 | A new route to the prebiotic synthesis of glycine via ab initio-based machine learning calculations | chemistry | prebiotic chemistry, glycine, Strecker synthesis, ab initio calculations, machine learning | Léon HUET | DISTANCE PRINT | colvar generic |
| 24.017 | Absolute Binding Free Energies with OneOPES | methods | protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy | Francesco Gervasio | MATHEVAL METAD RESTART CONSTANT INCLUDE OPES_METAD_EXPLORE GROUP LOWER_WALLS RMSD UPPER_WALLS COM PROJECTION_ON_AXIS PRINT WHOLEMOLECULES OPES_EXPANDED TORSION CUSTOM BIASVALUE CONTACTMAP COORDINATION MOLINFO ECV_MULTITHERMAL WRAPAROUND ENERGY | colvar bias function setup core generic vatom 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 | DISTANCE RESTRAINT MATHEVAL COORDINATIONNUMBER TORSION MOLINFO METAD RESTART PRINT ENERGY BIASVALUE FLUSH COMMITTOR | colvar bias symfunc function setup generic |
| 24.007 | SWISH-X | bio | swish-x, SWISH-X, swish, expanded SWISH | Alberto Borsatto | OPES_EXPANDED UPPER_WALLS MOLINFO ECV_MULTITHERMAL PRINT INCLUDE ENERGY CONTACTMAP WHOLEMOLECULES | colvar generic bias opes |
| 23.046 | Lasso Peptides - HLDA CV | bio | metadynamics, protein folding, HLDA, harmonic | Gabriel da Hora | DISTANCE COMBINE UNITS METAD PRINT WHOLEMOLECULES | colvar bias function setup generic |
| 23.035 | An Extended Metadynamics Protocol for Binding/Unbinding of Peptide Ligands to Class A G-Protein Coupled Receptors | bio | G protein coupled receptor, peptide ligands, metadynamics, multiple-walker | Timothy Clark | DISTANCE UPPER_WALLS MATHEVAL METAD CENTER PRINT CONSTANT BIASVALUE WHOLEMOLECULES LOWER_WALLS | colvar bias function generic vatom |
| 23.019 | Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors | bio | binding pathway, binding energy, sketch-map, drug development | Raitis Bobrovs | DISTANCE SKETCHMAP UPPER_WALLS SKETCHMAP_PROJECTION COLLECT_FRAMES TRANSPOSE DISSIMILARITIES VORONOI COM VSTACK METAD CUSTOM PATHMSD PRINT LANDMARK_SELECT_FPS WHOLEMOLECULES | colvar landmarks bias matrixtools valtools function generic dimred vatom |
| 23.016 | Activation/deactivation free-energy profiles for the β2-adrenergic receptor: Ligand modes of action | bio | G protein coupled receptor, beta-adrenergic, receptor activation, partial agonism, metadynamics | Timothy Clark | DISTANCE RMSD MATHEVAL MOLINFO DUMPGRID METAD PRINT REWEIGHT_METAD READ CONVERT_TO_FES WHOLEMOLECULES HISTOGRAM | colvar bias function generic gridtools |
| 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 | DISTANCE UPPER_WALLS MATHEVAL METAD PRINT CONSTANT BIASVALUE WHOLEMOLECULES LOWER_WALLS | colvar bias generic function |
| 22.044 | Colloid Crystallisation Analyses | materials | Q4, Q6, Pair Entropy, DFS | Aaron Finney | LOCAL_AVERAGE COMBINE Q4 GROUP MFILTER_LESS COORDINATIONNUMBER CLUSTER_NATOMS CONTACT_MATRIX LOCAL_Q6 PRINT LOCAL_Q4 Q6 MFILTER_MORE DFSCLUSTERING | symfunc function adjmat core multicolvar generic clusters |
| 22.037 | Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site | chemistry | metadynamics, DNA, abasic | Mike Jones | DISTANCE PRINT DISTANCES METAD | colvar multicolvar bias generic |
| 22.035 | Deciphering the alphabet of disorder — Glu and Asp act differently on local but not global properties | bio | intrinsically disordered proteins, parallel bias metadynamics, protein | Kresten Lindorff-Larsen | TORSION MOLINFO PBMETAD WHOLEMOLECULES GYRATION | colvar bias generic |
| 22.029 | Angiotensin-1-7_Metadynamics | bio | Metadynamics, Angiotensin-(1-7), peptide | L.-América Chi | LOWER_WALLS UPPER_WALLS METAD PRINT COORDINATION FLUSH WHOLEMOLECULES GROUP GYRATION | colvar core bias generic |
| 22.025 | Bubble nucleation rate predictions in a Lennard-Jones fluid | materials | free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation | Kristof Bal | RESTRAINT UPPER_WALLS UNITS COORDINATIONNUMBER DUMPGRID REWEIGHT_BIAS CUSTOM LOAD VOLUME PRINT COMMITTOR ANN BIASVALUE FLUSH MOVINGRESTRAINT CONVERT_TO_FES HISTOGRAM | colvar bias symfunc function setup generic gridtools annfunc |
| 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 FUNNEL UPPER_WALLS WHOLEMOLECULES COM METAD PATHMSD PRINT FUNNEL_PS LOWER_WALLS | colvar bias funnel generic vatom |
| 22.009 | Glycosylation in calixarenes capsule | chemistry | Metadynamics, glycosylation, supramolecular catalysis | GiovanniMaria Piccini | DISTANCE RMSD COMBINE FIT_TO_TEMPLATE UNITS BRIDGE MATHEVAL DISTANCES UPPER_WALLS GROUP METAD PRINT COORDINATION FLUSH WHOLEMOLECULES ANGLE LOWER_WALLS | colvar bias adjmat function setup core generic multicolvar |
| 22.005 | Collective Variable for Metadynamics Derived from AlphaFold Output | bio | AlphaFold, protein folding, protein structure prediction, metadynamics, deep learning, free energy simulation, collective variable | Vojtech Spiwok | LOAD PRINT WHOLEMOLECULES METAD | setup bias generic |
| 21.045 | QM/MM metadynamics of thiol-disulfide exchange between methylthiolate and dimethyldisulfide in water with an imposed external electrostatic potential (ESP) | chemistry | metadynamics, QM/MM, electrostatic potential, thiol-disulfide exchange | Denis Maag | DISTANCE COMBINE UPPER_WALLS COORDINATIONNUMBER METAD PRINT COORDINATION LOWER_WALLS | colvar bias symfunc function generic |
| 21.038 | Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics | materials | metadynamics, SGOOP, nucleation, urea | Ziyue Zou | COMBINE COORDINATIONNUMBER METAD LOAD CENTER PRINT INCLUDE VOLUME ENERGY GROUP | colvar bias symfunc function setup core generic vatom |
| 21.030 | Thermodynamic Basis for Stabilization of Helical Peptoids by Chiral Sidechains | bio | parallel bias parallel tempered metadynamics in WTE, synthetic foldamers, self-assembly, peptoid secondary structure | Jim Pfaendtner | DISTANCE ALPHABETA TORSION COM METAD PBMETAD PRINT INCLUDE ENERGY COORDINATION GYRATION | colvar bias generic multicolvar vatom |
| 21.028 | From Enhanced Sampling to Reaction Profiles | methods | collective variables, multi-state, machine learning, Deep-TDA | Enrico Trizio | UNITS MATHEVAL LOAD OPES_METAD GROUP LOWER_WALLS UPPER_WALLS FIXEDATOM ENDPLUMED PRINT WHOLEMOLECULES TORSION COORDINATION DISTANCE FIT_TO_TEMPLATE DISTANCES CENTER PYTORCH_MODEL ANGLE | colvar bias function core setup generic multicolvar vatom pytorch opes |
| 21.017 | All-atom simulations of the Vav1 AD construct | bio | metadynamics, parallel-bias, well-tempered | Simone Orioli | ALPHABETA MOLINFO REWEIGHT_BIAS ALPHARMSD PBMETAD RESTART METAD PRINT CONTACTMAP WHOLEMOLECULES GROUP | colvar bias setup core generic multicolvar secondarystructure |
| 20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Matteo Salvalaglio | UPPER_WALLS MATHEVAL METAD CELL VOLUME PRINT ENERGY LOWER_WALLS | colvar bias generic function |
| 20.018 | Free energy barriers from biased molecular dynamics simulations | methods | kinetics, free energy barriers, chemical reactions, nucleation, metadynamics | Kristof Bal | LOCAL_AVERAGE UNITS METAD LOAD PAIRENTROPY LOWER_WALLS UPPER_WALLS COORDINATIONNUMBER VOLUME PRINT REWEIGHT_METAD CONVERT_TO_FES REWEIGHT_BIAS DUMPGRID COORDINATION Q6 SPRINT HISTOGRAM DISTANCE COMBINE DENSITY CONTACT_MATRIX CENTER ENERGY FLUSH | colvar bias symfunc function sprint adjmat setup generic volumes vatom gridtools |
| 20.016 | Predicting polymorphism in molecular crystals using orientational entropy | materials | metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy | Pablo Piaggi | UPPER_WALLS METAD LOAD VOLUME CENTER INCLUDE PRINT GROUP | colvar bias setup core generic vatom |
| 19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Matteo Salvalaglio | DISTANCE MATHEVAL TORSION READ REWEIGHT_BIAS DUMPGRID METAD EXTERNAL PRINT REWEIGHT_METAD BIASVALUE COMMITTOR CONVERT_TO_FES HISTOGRAM | colvar bias function generic gridtools |
| 19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Sandro Bottaro | DISTANCE RMSD TORSION MOLINFO METAD PRINT ERMSD WHOLEMOLECULES | colvar bias generic |
| 19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Kim Jelfs | DISTANCES COM RESTART PRINT INPLANEDISTANCES FLUSH MOVINGRESTRAINT | bias setup generic multicolvar vatom |
| 19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Gareth Tribello | FCCUBIC UPPER_WALLS UNITS ENDPLUMED METAD CELL PRINT | colvar bias symfunc setup generic |
| 19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Vittorio Limongelli | DISTANCE RMSD FUNNEL UPPER_WALLS WHOLEMOLECULES COM METAD PRINT FUNNEL_PS LOWER_WALLS | colvar bias funnel generic vatom |
| 19.025 | Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide | bio | metainference, NMR, protein dynamics, force-fields | Carlo Camilloni | RDC TORSION MOLINFO ENDPLUMED PBMETAD METAINFERENCE PRINT ENSEMBLE STATS CS2BACKBONE BIASVALUE FLUSH JCOUPLING WHOLEMOLECULES GYRATION | isdb colvar bias function generic |
| 19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Riccardo Capelli | UPPER_WALLS FIT_TO_TEMPLATE MATHEVAL POSITION DUMPGRID COM ENDPLUMED METAD WRAPAROUND PRINT REWEIGHT_METAD HISTOGRAM READ COORDINATION FLUSH CONVERT_TO_FES WHOLEMOLECULES GROUP | colvar bias function core generic vatom gridtools |
| 19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Matteo Salvalaglio | COMBINE UPPER_WALLS MATHEVAL TORSION ENDPLUMED METAD VOLUME CELL PRINT ENERGY LOWER_WALLS | colvar bias generic function |
| 19.004 | MI Ubiquitin | bio | metainference, NMR | Max Bonomi | RDC MOLINFO METAINFERENCE PRINT CS2BACKBONE WHOLEMOLECULES GROUP | isdb core generic |
| 19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Michele Invernizzi | UNITS TORSION POSITION ENDPLUMED METAD RESTART VES_DELTA_F PRINT ENERGY LOAD | colvar bias setup generic ves |
| 25.022 | Imidazole Diffusion in SALEM-2 MOF | materials | OPES, Diffusion, Ring opening, MOFs, Machine Learning Potentials | Sudheesh Kumar Ethirajan | MOLINFO WHOLEMOLECULES OPES_METAD GROUP UNITS DISTANCES PROJECTION_ON_AXIS CENTER ENDPLUMED PRINT DISTANCE | colvar vatom core multicolvar opes generic setup |
| 24.012 | Molecular simulations to investigate the impact of N6-methylation in RNA recognition | bio | metadynamics, alchemistry, RNA modification, RNA:protein interactions | Giovanni Bussi | UPPER_WALLS DISTANCE BIASVALUE MOLINFO COMBINE GROUP COM COORDINATION GHBFIX METAD CENTER PRINT DEBUG LOWER_WALLS | function colvar vatom core bias generic |
| 24.003 | Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations | chemistry | steered molecular dynamics, foldamers, peptoids, bio-inspired | Kaylyn Torkelson | WHOLEMOLECULES INCLUDE TORSION MOVINGRESTRAINT COORDINATION ALPHABETA COM GYRATION PRINT DISTANCE | colvar vatom multicolvar bias generic |
| 24.002 | Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes | chemistry | metadynamics, ligand design, solvent extraction | Xiaoyu Wang | RESTART TORSION METAD PRINT UNITS | colvar generic bias setup |
| 23.034 | Urea nucleation in water: do long-range forces matter? | materials | LMF theory, Metadynamics, Nucleation | Ziyue Zou | INCLUDE LOAD GROUP METAD COORDINATIONNUMBER CENTER PRINT | vatom core bias symfunc generic setup |
| 23.032 | Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics | bio | metadynamics, tSNE, neural network, machine learning, trp-cage, folding | Vojtech Spiwok | MOLINFO WHOLEMOLECULES METAD POSITION ANN COMBINE PRINT ALPHARMSD FIT_TO_TEMPLATE | function colvar annfunc bias secondarystructure generic |
| 23.020 | FEP simulations of ATOX1 homodimer | chemistry | parallel bias metadynamics, FEP, free-energy of metal ion dissociation | Adriana Pietropaolo | ANGLE BIASVALUE PBMETAD WHOLEMOLECULES MATHEVAL CONSTANT PRINT DISTANCE | colvar function bias generic |
| 23.015 | MPCs aggregation | bio | opes_explore, dimerization, MPCs, self-assembly | Vikas Tiwari | UPPER_WALLS WHOLEMOLECULES OPES_METAD_EXPLORE GROUP COM COORDINATION CUSTOM METAD CENTER PRINT LOWER_WALLS DISTANCE | function vatom colvar core bias opes generic |
| 22.042 | Metadynamics of NSP10 and variants | bio | metadynamics, NSP10, crystal structure, variants | Shozeb Haider | PRINT TORSION METAD | colvar bias generic |
| 22.041 | Skipping the Replica Exchange Ladder with Normalizing Flows | methods | OPES, alanine, normalizing flows, replica exchange | Michele Invernizzi | OPES_EXPANDED ECV_MULTITHERMAL OPES_METAD TORSION POSITION ENDPLUMED PRINT ENERGY UNITS | opes generic colvar setup |
| 22.034 | Rationalising the difference in crystallisability of two Sulflowers using efficient in silico methods | materials | metadynamics, crystallizability, crystal structure prediction, sulflower, persulforated coronene | Matteo Salvalaglio | UPPER_WALLS COMMITTOR MATHEVAL DRMSD CUSTOM CELL METAD PRINT LOWER_WALLS | colvar function bias generic |
| 22.033 | Reciprocal barrier restraint. Application to PROTAC passive permeability prediction | methods | PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR | Istvan Kolossvary | DISTANCE FLUSH BIASVALUE DRR COM CUSTOM METAD PRINT UNITS | function colvar vatom bias generic setup drr |
| 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 | FLUSH BIASVALUE DRR CUSTOM METAD PATHMSD PRINT | function colvar bias generic drr |
| 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 | WHOLEMOLECULES GROUP TORSION METAD COM PRINT DISTANCE | colvar vatom core bias generic |
| 21.049 | Multiple-path-metadynamics and PathMaps | methods | path-CV, metadynamics, multiple-walker, multiple paths, pathmap | Alberto Pérez-de-Alba-Ortíz | UPPER_WALLS RESTRAINT ENSEMBLE LOAD CONSTANT TORSION MOVINGRESTRAINT CUSTOM METAD COMBINE PRINT LOWER_WALLS UNITS | function colvar bias generic setup |
| 21.047 | Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations | materials | pair entropy, metadynamics, ves, solids, crystallization | Pablo Piaggi | RESTART LOAD PAIRENTROPY BF_LEGENDRE VOLUME TD_WELLTEMPERED VES_LINEAR_EXPANSION OPT_AVERAGED_SGD METAD COMBINE PRINT ENERGY | function gridtools colvar bias ves generic setup |
| 21.046 | Ubiquitin Interacting Motifs, Duality Between Structured and Disordered Motifs | bio | wt metadynamics, ubiquitin, ataxin-3, short linear motifs, ubiquitin binding motif, moonlight functions, intrinsic disorder | Elena Papaleo | UPPER_WALLS WHOLEMOLECULES GYRATION GROUP ALPHABETA METAD ENDPLUMED PRINT LOWER_WALLS | colvar core multicolvar bias generic |
| 21.044 | NaCl nucleation | chemistry | metadynamics, DFS clustering | Aaron Finney | FIXEDATOM MFILTER_MORE GROUP LOCAL_Q6 CLUSTER_NATOMS METAD Q6 CONTACT_MATRIX CLUSTER_DISTRIBUTION DFSCLUSTERING COORDINATIONNUMBER COMBINE DUMPGRID PRINT HISTOGRAM INSPHERE | function gridtools vatom core multicolvar clusters bias symfunc generic volumes adjmat |
| 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 COORDINATION CUSTOM METAD COMBINE ENDPLUMED PRINT | colvar function bias generic |
| 21.025 | Computational and biochemical analysis of type IV pilus dynamics and stability | bio | molecular dynamics, calcium binding, Type IV pilus | Yasaman Karami | UPPER_WALLS PRINT LOWER_WALLS DISTANCE | colvar bias generic |
| 21.015 | Coarse-grained metadynamics and umbrella sampling simulations to investigate interactions of carbohydrate-binding modules with chitin | bio | metadynamics, umbrella sampling, coarse-grained, MARTINI, chitin, carbohydrate-binding module | Gaston Courtade | RESTART RESTRAINT WHOLEMOLECULES MATHEVAL REWEIGHT_BIAS COORDINATION POSITION METAD CENTER PRINT | function colvar vatom bias generic setup |
| 20.032 | Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil | materials | clustering, conformational isomers | Matteo Salvalaglio | ENDPLUMED PRINT TORSION | colvar generic |
| 20.015 | Rational design of ASCT2 inhibitors using an integrated experimental-computational approach | bio | ASCT2 transporter, small-molecules, cryo-EM, metainference | Max Bonomi | BIASVALUE MOLINFO WHOLEMOLECULES LOAD GROUP PRINT EMMIVOX DUMPATOMS | core bias isdb generic setup |
| 20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Carlo Camilloni | FLUSH ENSEMBLE PBMETAD MOLINFO WHOLEMOLECULES METAINFERENCE TORSION SAXS ALPHABETA STATS CENTER GYRATION PRINT DISTANCE | function colvar vatom multicolvar bias isdb generic |
| 20.006 | Class B GPCR activation mechanism | bio | metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | UPPER_WALLS DISTANCE MOLINFO WHOLEMOLECULES MATHEVAL CENTER METAD COMBINE PRINT LOWER_WALLS ENERGY RMSD | function colvar vatom bias generic |
| 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 | MOLINFO REWEIGHT_METAD METAD DUMPGRID HISTOGRAM FLUSH FUNCPATHMSD CONVERT_TO_FES READ CONTACTMAP COM ENDPLUMED ABMD LOWER_WALLS DISTANCE UPPER_WALLS WHOLEMOLECULES COMBINE PRINT | function gridtools colvar vatom bias generic |
| 20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Luigi Bonati | UPPER_WALLS PYTORCH_MODEL FLUSH OPES_METAD MATHEVAL LOAD GROUP UNITS TORSION COM ENDPLUMED PRINT LOWER_WALLS DISTANCE | function colvar vatom core bias pytorch opes generic setup |
| 19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | UPPER_WALLS MOLINFO METAD COM GYRATION PRINT ENERGY DISTANCE | vatom bias colvar generic |
| 19.073 | On the role of enthalpic and entropic contributions on the conformational free energy landscape of MIL-101(Cr) building units | materials | metadynamics, MOF, MIL101Cr, conformational | Matteo Salvalaglio | UPPER_WALLS GYRATION DISTANCES METAD COORDINATIONNUMBER ENDPLUMED PRINT LOWER_WALLS ENERGY | colvar multicolvar bias symfunc generic |
| 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 | RESTART UPPER_WALLS FLUSH GROUP POSITION COORDINATION METAD PRINT LOWER_WALLS UNITS | colvar core bias generic setup |
| 19.040 | Optimal Metric for Path Collective Variables | bio | metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path | Francesco Luigi Gervasio | MATHEVAL TORSION METAD ENDPLUMED PRINT | colvar function bias generic |
| 19.011 | Automatic Gradient Computation for Collective Variables | other | gradient, differentiation, curvature | Toni Giorgino | ENDPLUMED | generic |
| 25.023 | Molecular simulations of Tau-protein oligomers | bio | metadynamics, proteins, aggregation | Giovanni Bussi | CONTACTMAP RESTRAINT RESTART CUSTOM PRINT FLUSH METAD RMSD | bias setup function generic colvar |
| 25.009 | Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water | chemistry | metadynamics, nitrate photolysis | Kam-Tung Chan | READ COORDINATION UPPER_WALLS CUSTOM RESTART PRINT DISTANCE METAD FLUSH REWEIGHT_METAD GROUP DUMPGRID HISTOGRAM | bias setup gridtools function core generic colvar |
| 25.008 | Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting | methods | metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting | Dhiman Ray | POSITION UPPER_WALLS PYTORCH_MODEL CUSTOM PRINT DISTANCE METAD MOLINFO ENDPLUMED OPES_METAD GROUP ENERGY WHOLEMOLECULES BIASVALUE UNITS RMSD LOWER_WALLS TORSION | bias pytorch opes setup function core generic colvar |
| 25.007 | Shaping the glycan landscape. Hidden relationships between linkage and ring distortion induced by carbohydrate-active enzmyes | bio | REST-RECT, REST2, glycan, enzyme, CAZyme, steered | Isabell Grothaus | RESTRAINT RESTART PRINT DISTANCE METAD MOLINFO PUCKERING MOVINGRESTRAINT TORSION | bias generic colvar setup |
| 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 | READ PBMETAD RESTART PRINT DISTANCE MOLINFO DUMPATOMS GYRATION ENERGY WHOLEMOLECULES VOLUME UPDATE_IF CENTER INCLUDE TORSION | bias setup vatom generic colvar |
| 25.001 | RNA G-quadruplex folding with ST-metaD protocol | bio | RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | COMBINE MOLINFO METAD WHOLEMOLECULES ERMSD | bias generic colvar function |
| 24.036 | Leveraging cryptic ligand envelopes through enhanced molecular simulations | bio | HREX, conformational heterogeneity, drug discovery, ligand binding, plitidepsin, aplidin, ligand-target complexes, cryptic ligand envelope | Francesco Colizzi | COORDINATION PRINT DISTANCE ANGLE GROUP WHOLEMOLECULES CONVERT_TO_FES DUMPGRID HISTOGRAM TORSION | core generic colvar gridtools |
| 24.027 | Proline cis and trans subensembles of a disordered peptide | bio | intrinsically disordered proteins, proline cis trans isomerisation, metadynamics, collective variables | Alice Pettitt | PARABETARMSD COMBINE COORDINATION ANTIBETARMSD PBMETAD FLUSH DISTANCE MOLINFO ALPHARMSD GYRATION GROUP PRINT ENDPLUMED WHOLEMOLECULES DIHCOR INCLUDE TORSION | bias secondarystructure multicolvar function core generic colvar |
| 24.026 | Constant pH metadynamics of RNA oligomers | bio | metadynamics, pH, RNA | Giovanni Bussi | RESTART PRINT MOLINFO METAD PUCKERING TORSION | bias generic colvar setup |
| 24.006 | Water vapor condensation | chemistry | metadynamics, homogeneous condensation, chemical potential | Shenghui Zhong | CONTACT_MATRIX UPPER_WALLS PRINT METAD COORDINATIONNUMBER CLUSTER_NATOMS UNITS CLUSTER_PROPERTIES DFSCLUSTERING | bias symfunc setup adjmat clusters generic |
| 23.039 | Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation | chemistry | metadynamics, ligand dissociation | Eric Beyerle | FIXEDATOM COMBINE RESTRAINT UPPER_WALLS PRINT DISTANCE MOLINFO METAD DUMPMASSCHARGE CENTER | bias vatom function generic 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 | MATHEVAL FIT_TO_TEMPLATE WRAPAROUND COM DISTANCE MOLINFO GROUP WHOLEMOLECULES OPES_METAD_EXPLORE COORDINATION UPPER_WALLS PRINT COMMITTOR FLUSH BIASVALUE LOWER_WALLS TORSION ENDPLUMED ENERGY CENTER UNITS POSITION CUSTOM OPES_METAD | bias opes setup vatom function core generic colvar |
| 23.024 | Permutationally Invariant Networks for Enhanced Sampling (PINES) | methods | collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent | Nicholas Herringer | PRINT PBMETAD LOAD | bias generic setup |
| 23.012 | JAK2 2D meta-eABF PMF with statistical analysis | bio | 2D meta-eABF, path CV, PMF | Istvan Kolossvary | UPPER_WALLS DRR CUSTOM BIASVALUE PRINT METAD FLUSH PATHMSD LOWER_WALLS | bias function generic colvar drr |
| 23.002 | Critical comparison of general-purpose collective variables for crystal nucleation | methods | metadynamics, umbrella sampling, commitor, entropy, PIV | Julien Lam | PAIRENTROPY LOCAL_AVERAGE RESTRAINT UPPER_WALLS CUSTOM PRINT METAD ENERGY Q6 UNITS Q4 FUNCPATHMSD VOLUME PIV | bias symfunc setup gridtools function generic colvar piv |
| 22.022 | Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir | bio | RMSD, protein-ligand interactions | Isabell Grothaus | RMSD PRINT | generic colvar |
| 22.018 | Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations | bio | ligand binding, docking, EMMI, LAT1 | Max Bonomi | BIASVALUE PRINT MOLINFO LOAD GROUP WHOLEMOLECULES EMMIVOX | bias setup isdb core generic |
| 22.017 | Water regulates the residence time of Benzamidine in Trypsin | bio | ligand binding, water, opes, benzamidine trypsin, unbinding rates, machine learning, Deep-LDA, Deep-TICA | Narjes Ansari | FIXEDATOM MATHEVAL FIT_TO_TEMPLATE COORDINATION UPPER_WALLS PYTORCH_MODEL CUSTOM PRINT DISTANCE COMMITTOR GROUP OPES_METAD WHOLEMOLECULES CENTER RMSD LOWER_WALLS | bias pytorch opes vatom function core generic colvar |
| 22.003 | Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling | methods | opes, metadynamics, reweighting, alanine, muller | Michele Invernizzi | POSITION ECV_MULTITHERMAL PBMETAD UPPER_WALLS CUSTOM PRINT ENDPLUMED METAD OPES_EXPANDED BIASVALUE OPES_METAD ENERGY ECV_UMBRELLAS_FILE UNITS LOWER_WALLS TORSION OPES_METAD_EXPLORE | bias opes setup function generic colvar |
| 22.000 | Amyloid precursor protein processing by human γ-secretase | bio | Bias Exchange Metadynamics, Helix unfolding, coupled binding | Xiaoli Lu | CONTACTMAP COORDINATION ANTIBETARMSD PRINT DISTANCE MOLINFO ALPHARMSD METAD INCLUDE UNITS RANDOM_EXCHANGES CENTER | bias secondarystructure setup vatom generic colvar |
| 21.043 | Predicting the Conformational Variability of Oncogenic GTP-bound G12D Mutated KRas-4B Proteins at Cell Membranes | chemistry | well-tempered metadynamics, KRas-4B, anionic membrane, conformational variability | Huixia Lu | FIXEDATOM FIT_TO_TEMPLATE PRINT METAD TORSION | vatom generic bias colvar |
| 21.039 | Deep learning the slow modes for rare events sampling | methods | collective variables, machine learning, slow modes, deep-tica, opes | Luigi Bonati | CONTACTMAP DISTANCE MOLINFO GROUP WHOLEMOLECULES VOLUME COMBINE ECV_MULTITHERMAL PRINT FLUSH LOAD RMSD ENVIRONMENTSIMILARITY TORSION ENDPLUMED ENERGY Q6 INCLUDE UNITS PYTORCH_MODEL OPES_EXPANDED OPES_METAD | pytorch envsim symfunc opes setup function core generic 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 | RMSD PRINT DISTANCE | generic colvar |
| 21.022 | Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly | materials | parallel bias metadynamics, adsorption, peptide | Xin Qi | COM PBMETAD UPPER_WALLS PRINT DISTANCE MOLINFO GYRATION ENERGY LOWER_WALLS | vatom generic bias colvar |
| 21.010 | Step by Step Strecker Amino Acid Synthesis from Ab Initio Prebiotic Chemistry | chemistry | Strecker reaction, free energy landscape, ab initio molecular dynamics, glycine, prebiotic synthesis | Théo Magrino | generic | |
| 21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Kristof Bal | UPPER_WALLS FLUSH COMMITTOR PRINT METAD LOAD REWEIGHT_METAD COORDINATIONNUMBER CONVERT_TO_FES UNITS DUMPGRID MOVINGRESTRAINT HISTOGRAM | bias symfunc setup gridtools generic |
| 21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Adriana Pietropaolo | MATHEVAL CONSTANT PBMETAD RESTART BIASVALUE PRINT WHOLEMOLECULES TORSION | bias setup function generic colvar |
| 21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Tarsis Ferreira | COORDINATION UPPER_WALLS RANDOM_EXCHANGES PRINT DISTANCE METAD MOLINFO GROUP REWEIGHT_METAD ENERGY WHOLEMOLECULES PUCKERING INCLUDE DUMPGRID LOWER_WALLS HISTOGRAM | bias gridtools core generic colvar |
| 20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Faidon Brotzakis | READ PRINT BIASVALUE MOLINFO GROUP WHOLEMOLECULES DISTANCES RMSD CONVERT_TO_FES DUMPGRID HISTOGRAM EMMI | bias multicolvar isdb gridtools core generic colvar |
| 20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Adriana Pietropaolo | COORDINATION PBMETAD PRINT WHOLEMOLECULES CENTER | bias generic vatom colvar |
| 20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Vojtech Spiwok | PRINT METAD TORSION | bias generic colvar |
| 20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Pratyush Tiwary | COMBINE UPPER_WALLS RESTART PRINT DISTANCE METAD MOLINFO WHOLEMOLECULES RMSD TORSION | bias setup function generic colvar |
| 19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Valerio Rizzi | COMBINE UPPER_WALLS RESTART FLUSH PRINT METAD ENDPLUMED GROUP COORDINATIONNUMBER DISTANCES UNITS | bias symfunc setup multicolvar function core generic |
| 19.076 | Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones | bio | molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics | Salvatore Assenza | PRINT ENDPLUMED GYRATION UNITS MOVINGRESTRAINT | bias generic colvar setup |
| 19.056 | maze | methods | maze, ligand unbinding | Jakub Rydzewski | POSITION MAZE_SIMULATED_ANNEALING PRINT MAZE_LOSS UNITS MAZE_OPTIMIZER_BIAS | generic setup colvar maze |
| 19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | COMBINE UPPER_WALLS FLUSH DISTANCE METAD PRINT ENERGY UNITS | bias setup function generic colvar |
| 19.041 | Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces | bio | metadynamics, collective variables, conformational changes, multiple walkers, Well-Tempered MetaD, peptide, binding, phosphorylation, post-transitional motif, sio2, adsorption | Jim Pfaendtner | COM UPPER_WALLS PRINT DISTANCE METAD ENERGY | vatom generic bias colvar |
| 19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Silvio Pipolo | UPPER_WALLS CELL PRINT METAD FUNCPATHMSD LOWER_WALLS PIV | bias function generic colvar piv |
| 19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Kresten Lindorff-Larsen | COMBINE ALPHABETA FLUSH COMMITTOR MOLINFO METAD PRINT | bias generic multicolvar function |
| 25.014 | Atomic resolution ensembles of intrinsically disordered proteins with Alphafold | bio | bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement | Vincent Schnapka | PRINT BIASVALUE GROUP BAIES | generic core isdb 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 | COORDINATIONNUMBER UPPER_WALLS CUSTOM DISTANCE PRINT GROUP UNITS COMMITTOR FLUSH ZDISTANCES OPES_METAD FIXEDATOM DISTANCES | bias core function multicolvar vatom generic opes colvar symfunc setup |
| 24.034 | Umbrella sampling of ion in transporter SLC26A7 | bio | umbrella sampling, transporter, ions | Xiaoli Lu | PRINT UNITS POSITION RESTRAINT | colvar generic bias setup |
| 24.033 | Transient interactions between the fuzzy coat and the cross-b core of brain-derived Ab42 filaments | bio | CryoEM, MEMMI, Metadynamics, Metainference, Ab42 Fibrils, structural ensemble | Maria Milanesi | COORDINATION CENTER UPPER_WALLS MOLINFO DISTANCE WHOLEMOLECULES RMSD ALPHARMSD PARABETARMSD BIASVALUE PRINT GROUP DUMPMASSCHARGE EMMI COM DUMPATOMS PBMETAD | bias secondarystructure vatom generic colvar isdb core |
| 24.028 | All-atom simulations of RNA-membrane interactions | bio | metadynamics, membrane, RNA | Giovanni Bussi | CENTER UPPER_WALLS MOLINFO DISTANCE POSITION GYRATION SORT LOWER_WALLS PRINT METAD PUCKERING GROUP GHOST WHOLEMOLECULES COMBINE MATHEVAL DISTANCES | bias function multicolvar vatom generic colvar core |
| 23.036 | Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? | bio | NaCl, nucleation, metadynamics | Ruiyu Wang | COORDINATIONNUMBER Q4 VOLUME ENERGY PRINT METAD COMBINE Q6 MATHEVAL | bias function generic colvar symfunc |
| 23.028 | Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process | chemistry | Ammonia decomposition; Dynamics;OPES; Neural Network potential | Manyi Yang | COORDINATIONNUMBER UPPER_WALLS CUSTOM DISTANCE ENERGY LOWER_WALLS PRINT GROUP UNITS FLUSH DISTANCES ZDISTANCES COM COMMITTOR OPES_METAD FIXEDATOM MATHEVAL | bias core function multicolvar vatom generic opes colvar symfunc setup |
| 23.025 | Probing ion binding to G-quadruplexes and related events | chemistry | metadynamics, repulsive potential, nucleic acids, G-quadruplexes | Marcelo Poleto | WRAPAROUND UPPER_WALLS FIT_TO_TEMPLATE DISTANCE POSITION WHOLEMOLECULES LOWER_WALLS RESTART PRINT METAD GROUP UNITS FLUSH DISTANCES COM MATHEVAL DUMPATOMS | bias multicolvar function vatom generic colvar core setup |
| 23.023 | Rational design of novel biomimetic sequence-defined polymers for mineralization applications | methods | metadynamics, surface binding, biomimetic mineralization | Kaylyn Torkelson | COORDINATION UPPER_WALLS DISTANCE GYRATION PRINT COM PBMETAD | vatom colvar bias generic |
| 23.014 | Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 | bio | metadynamics, oligomerization, chemokine receptors, GPCR, membrane | Vittorio Limongelli | UPPER_WALLS DISTANCE WHOLEMOLECULES COM PRINT METAD FLUSH COMBINE TORSION | bias function 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 | ANGLE UPPER_WALLS DISTANCE MOVINGRESTRAINT WHOLEMOLECULES LOWER_WALLS PRINT METAD COM | vatom colvar bias generic |
| 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 COORDINATION POSITION PRINT VES_LINEAR_EXPANSION OPT_AVERAGED_SGD BF_WAVELETS UPPER_WALLS OPT_ADAM FLUSH BF_CHEBYSHEV DISTANCE ENERGY METAD UNITS TD_UNIFORM INCLUDE BF_GAUSSIANS VES_OUTPUT_BASISFUNCTIONS BF_CUBIC_B_SPLINES BF_LEGENDRE | bias generic colvar ves setup |
| 21.051 | Automatic learning of hydrogen-bond fixes in an AMBER RNA force field | methods | force field, RNA | Giovanni Bussi | COORDINATION MOLINFO WHOLEMOLECULES PRINT BIASVALUE METAD COMBINE ERMSD | function colvar generic bias |
| 21.014 | how to determine statistically accurate conformational ensembles | bio | metadynamics, metainference, errors, cv, SAXS, ensemble determination | Cristina Paissoni | CENTER ALPHABETA ENSEMBLE MOLINFO GYRATION WHOLEMOLECULES PRINT METAD TORSION BIASVALUE ANTIBETARMSD STATS CONTACTMAP PBMETAD SAXS | bias secondarystructure function multicolvar vatom generic colvar isdb |
| 21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Tarak Karmakar | PYTORCH_MODEL UPPER_WALLS LOWER_WALLS PRINT LOAD GROUP FLUSH OPES_METAD MATHEVAL | bias function generic opes pytorch core setup |
| 21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Kresten Lindorff-Larsen | CENTER MOLINFO METAINFERENCE EEFSOLV GYRATION WHOLEMOLECULES ALPHARMSD PRINT BIASVALUE GROUP FLUSH PBMETAD SAXS | bias secondarystructure vatom generic colvar isdb core |
| 20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Cristina Paissoni | CENTER ENSEMBLE MOLINFO DISTANCE WHOLEMOLECULES RESTRAINT PRINT BIASVALUE GROUP STATS INCLUDE SAXS | bias function vatom generic colvar isdb core |
| 20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Valerio Rizzi | COORDINATION PYTORCH_MODEL CENTER UPPER_WALLS ANGLE DISTANCE WHOLEMOLECULES ENERGY PRINT ENDPLUMED GROUP FIT_TO_TEMPLATE OPES_METAD FIXEDATOM MATHEVAL | bias function vatom generic colvar pytorch core opes |
| 19.080 | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | methods | ves, variationally enhanced sampling, vibrational excitation, chemical reactions | Kristof Bal | TD_WELLTEMPERED COORDINATION ANGLE UPPER_WALLS COMBINE EXTERNAL DISTANCE CONVERT_TO_FES TD_GRID PRINT LOWER_WALLS UNITS FLUSH VES_LINEAR_EXPANSION DUMPGRID OPT_AVERAGED_SGD BF_CHEBYSHEV HISTOGRAM | bias function generic gridtools colvar ves setup |
| 19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | GiovanniMaria Piccini | UPPER_WALLS DISTANCE LOWER_WALLS ENERGY PRINT METAD UNITS FLUSH COMBINE | bias function generic colvar setup |
| 19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Gareth Tribello | FCCUBIC CENTER FOURIER_TRANSFORM MORE_THAN GROUP UNITS DUMPGRID MULTICOLVARDENS FIND_CONTOUR_SURFACE | symfunc function vatom contour gridtools fourier core setup |
| 19.049 | Determining the sizes of solid/liquid clusters in MD trajectories of nucleation | methods | nucleation, metadynamics, clustering, Steinhardt order parameters | Gareth Tribello | COORDINATIONNUMBER LOCAL_Q6 DFSCLUSTERING CUSTOM OUTER_PRODUCT SMAC CLUSTER_PROPERTIES OUTPUT_CLUSTER MATRIX_VECTOR_PRODUCT PRINT MORE_THAN METAD CONTACT_MATRIX CLUSTER_NATOMS CLUSTER_DISTRIBUTION ONES Q6 DISTANCES | clusters bias function multicolvar adjmat generic matrixtools symfunc |
| 19.035 | Dimerization of GPCRs from coarse-grained umbrella sampling | bio | Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization | Davide Provasi | DISTANCE RESTRAINT PRINT GROUP COM TORSION | bias vatom generic colvar core |
| 19.009 | RNA tetraloops folding | bio | metadynamics, RNA, folding | Giovanni Bussi | MOLINFO WHOLEMOLECULES RMSD PRINT METAD ENDPLUMED ERMSD | colvar generic bias |
| 25.019 | The Arch from the Stones. Understanding Protein Folding Energy Landscapes via Bio-inspired Collective Variables | bio | protein folding, OPES, OneOPES, binding free energy | Valerio Rizzi | MOLINFO ENERGY DISTANCE GROUP ECV_MULTITHERMAL COMBINE OPES_METAD_EXPLORE CUSTOM OPES_EXPANDED GHOST COORDINATION RMSD PRINT CENTER | generic opes core vatom colvar function |
| 25.010 | Kinetic rates calculation with Ratchet&Pawl MD | methods | kinetics, ligand binding, ABMD, ratchet&pawl MD | Riccardo Capelli | DISTANCE GROUP WHOLEMOLECULES COMMITTOR ABMD FLUSH COM PRINT | generic bias core vatom 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 | MATHEVAL DISTANCE GROUP ENERGY ECV_MULTITHERMAL TORSION WHOLEMOLECULES LOWER_WALLS OPES_METAD_EXPLORE ENDPLUMED OPES_EXPANDED UPPER_WALLS FIT_TO_TEMPLATE COORDINATION FIXEDATOM ANGLE PRINT CENTER | generic bias opes core vatom colvar function |
| 24.008 | yCD Metadynamics | bio | volume-based MetaD, path CVs, infrequent MetaD, product release | James McCarty | REWEIGHT_METAD GROUP ENDPLUMED COM PATH METAD READ WHOLEMOLECULES HISTOGRAM CONTACTMAP RMSD CONVERT_TO_FES MATHEVAL DISTANCE FLUSH DUMPGRID UPPER_WALLS FIT_TO_TEMPLATE COORDINATION FIXEDATOM MOLINFO WRAPAROUND COMMITTOR INCLUDE PRINT | gridtools generic bias core vatom colvar function mapping |
| 23.021 | Into the Dynamics of Rotaxanes at Atomistic Resolution | materials | metadynamics, rotaxanes, molecular shuttles, molecular machines | Luigi Leanza | MATHEVAL DISTANCE METAD TORSION CUSTOM UPPER_WALLS FIXEDATOM PRINT CENTER | generic bias vatom colvar function |
| 23.017 | How and When Does an Enzyme React? Unraveling α-Amylase Catalytic Activity with Enhanced Sampling Techniques | bio | enzymatic reaction discovery, reaction mechanism, catalysis, ligand-binding modes, water, alpha-amylase, sugar, QM/MM MD, OPES, OPES explore, graph CV, machine learning, Deep TDA CV, path CV | Sudip Das | PYTORCH_MODEL CENTER DISTANCE GROUP WHOLEMOLECULES TORSION LOWER_WALLS OPES_METAD_EXPLORE CUSTOM OPES_METAD FIT_TO_TEMPLATE COORDINATION PATH FIXEDATOM UNITS PRINT UPPER_WALLS | generic bias pytorch opes setup core vatom colvar function mapping |
| 23.011 | OneOPES, a combined enhanced sampling method to rule them all | bio | OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding | Valerio Rizzi | MOLINFO ENERGY DISTANCE ECV_MULTITHERMAL METAD TORSION OPES_METAD_EXPLORE ENDPLUMED OPES_EXPANDED PRINT | opes colvar generic bias |
| 23.009 | Deep Learning Collective Variables from Transition Path Ensemble | methods | TPI-Deep-TDA, Deep-TDA, Transition Path, OPES, OPES Flooding, Machine Learning, Protein folding, Ligand binding | Dhiman Ray | PYTORCH_MODEL GROUP CUSTOM ENDPLUMED ANGLE CENTER WHOLEMOLECULES LOWER_WALLS COMBINE CONTACTMAP RMSD MATHEVAL DISTANCE ENERGY OPES_METAD FIT_TO_TEMPLATE COORDINATION UPPER_WALLS FIXEDATOM MOLINFO COMMITTOR INCLUDE PRINT | generic bias pytorch opes core vatom colvar function |
| 23.008 | PBMetaD simulations of Histatin5 | bio | metadynamics, IDP, Rg, PPII | Francesco Pesce | MOLINFO GROUP GYRATION WHOLEMOLECULES TORSION PBMETAD PRINT | core colvar generic bias |
| 23.001 | Quantum phase diagram of water | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn-Løland Bore | ENVIRONMENTSIMILARITY RESTART ECV_UMBRELLAS_LINE LOWER_WALLS OPES_EXPANDED UPPER_WALLS INCLUDE PRINT | generic bias envsim opes setup |
| 22.043 | Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES | bio | OPES, RNA, Tetraloop, Folding | Gül Zerze | ENERGY ECV_MULTITHERMAL ECV_UMBRELLAS_LINE WHOLEMOLECULES CONTACTMAP OPES_EXPANDED PRINT | generic colvar opes |
| 22.021 | Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn Løland Bore | ENVIRONMENTSIMILARITY ECV_UMBRELLAS_LINE LOWER_WALLS OPES_EXPANDED UPPER_WALLS INCLUDE PRINT | generic bias opes envsim |
| 22.013 | Ligand dissociation from PreQ1 riboswitch | bio | ligand, RNA, metadynamics, pRAVE | Yihang Wang | MOLINFO DISTANCE METAD WHOLEMOLECULES COORDINATIONNUMBER COMBINE COMMITTOR COM RMSD PRINT | generic bias symfunc vatom colvar function |
| 21.035 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, interface | Aaron Finney | DISTANCE GROUP RESTRAINT LOAD FIXEDATOM PRINT | generic bias setup core vatom colvar |
| 21.027 | EGFR activating mutations mechanism | bio | metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA | Francesco Gervasio | MATHEVAL MOLINFO ENERGY DISTANCE METAD WHOLEMOLECULES LOWER_WALLS CONTACTMAP ALPHARMSD UPPER_WALLS INCLUDE PRINT | generic bias secondarystructure colvar function |
| 21.018 | Localized Volume-based Metadynamics | bio | LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification | Riccardo Capelli | REWEIGHT_METAD GROUP ENDPLUMED COM METAD READ WHOLEMOLECULES HISTOGRAM RMSD CONVERT_TO_FES POSITION MATHEVAL DISTANCE FLUSH DUMPGRID UPPER_WALLS COORDINATION FIXEDATOM PRINT | gridtools generic bias core vatom colvar function |
| 21.004 | Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy | bio | machine learning, well-tempered metadynamics, path collective variable, potential of mean force, standard binding free energy calculations, host-guest, protein-ligand unbinding | Dorothea Gobbo | PATHMSD RESTART METAD LOWER_WALLS WHOLEMOLECULES UPPER_WALLS PRINT | setup colvar generic bias |
| 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 METAD RESTRAINT HISTOGRAM CONVERT_TO_FES MULTI_RMSD DUMPGRID PRINT | generic gridtools colvar bias |
| 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 | MOLINFO STATS RESTRAINT WHOLEMOLECULES COORDINATION PRINT | colvar function generic bias |
| 20.002 | Exploring conformational dynamics of the extracellular Venus flytrap domain of the GABAB receptor, a path-metadynamics study | bio | Metadynamics, path CVs | Riccardo Ocello | PATHMSD MOLINFO GROUP RESTART METAD WHOLEMOLECULES UPPER_WALLS PRINT | generic bias setup core colvar |
| 19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Jakub Rydzewski | PATHMSD RESTART METAD LOWER_WALLS UPPER_WALLS UNITS PRINT | setup colvar generic bias |
| 19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_SIMULATED_ANNEALING MAZE_OPTIMIZER_BIAS MAZE_LOSS PRINT UNITS POSITION | setup maze colvar generic |
| 19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Mattia Bernetti | PATHMSD METAD WHOLEMOLECULES LOWER_WALLS UPPER_WALLS PRINT | colvar generic bias |
| 19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Davide Provasi | DISTANCE METAD WHOLEMOLECULES CONTACTMAP FUNCPATHMSD COM ENDPLUMED RMSD PRINT | generic bias vatom colvar function |
| 19.032 | Chemical reaction in solution using path collective variables based on coordination patterns | chemistry | chemical reactions, solutions, metadynamics, coordination patterns | Fabio Pietrucci | RESTART DISTANCES METAD FLUSH UPPER_WALLS PATH PRINT | generic bias multicolvar setup mapping |
| 19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Elena Papaleo | MOLINFO GROUP METAD GYRATION WHOLEMOLECULES LOWER_WALLS UPPER_WALLS ALPHABETA PRINT | generic bias multicolvar core colvar |
| 19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Pratyush Tiwary | DISTANCE EXTERNAL RESTART WHOLEMOLECULES TORSION COMBINE COMMITTOR COM ALPHABETA PRINT | generic bias multicolvar setup vatom colvar function |
| 19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Mattia Bernetti | MOLINFO ENERGY METAD GYRATION WHOLEMOLECULES ENDPLUMED ALPHARMSD PRINT | secondarystructure colvar generic 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 | FUNNEL_PS LOWER_WALLS PRINT UPPER_WALLS METAD COM FUNNEL | generic vatom bias funnel |
| 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 | PRINT OPES_METAD_EXPLORE GROUP ENERGY UPPER_WALLS COORDINATION MATHEVAL WHOLEMOLECULES ANGLE FIXEDATOM FIT_TO_TEMPLATE DISTANCE CENTER | generic opes function vatom colvar bias core |
| 25.015 | Assessment of Force Fields for Describing Conformational Polymorphic Crystals of ROY | materials | Molecular crystal, Force Field, Collective Variable | Pradip Si and Omar Valsson | PRINT TORSIONS SMAC DISTANCES DUMPMULTICOLVAR | generic multicolvar symfunc |
| 25.003 | Surrogate Model CV | methods | Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding | Sompriya Chatterjee | PRINT MOLINFO GROUP TORSION ENERGY MATHEVAL COMBINE WHOLEMOLECULES CUSTOM COMMITTOR DISTANCE OPES_METAD PYTORCH_MODEL ENDPLUMED | generic opes function pytorch colvar core |
| 25.002 | M3_PCV-ABMD | chemistry | Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor | Gian Marco Elisi | ABMD PRINT UPPER_WALLS UNITS PATHMSD ENDPLUMED | colvar generic bias setup |
| 24.021 | Ab initio machine learning simulation of calcium carbonate from aqueous solutions to the solid state | chemistry | ion pairing, caco3, opes, proton transfer, crystallization | Pablo Piaggi | PRINT ENERGY UPPER_WALLS COORDINATION DISTANCE OPES_METAD | colvar generic opes bias |
| 24.001 | A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations | bio | OPES, OPES-Flooding, QM/MM, Kinetics, Enzyme Catalysis | Dhiman Ray | FLUSH LOWER_WALLS PRINT TORSION UPPER_WALLS COMBINE CUSTOM UNITS COMMITTOR DISTANCE OPES_METAD | generic function opes setup colvar bias |
| 23.038 | Determinants of Neutral Antagonism and Inverse Agonism in the β2-adrenergic receptor | bio | protein coupled receptor, beta-adrenergic, receptor activation, antagonism, inverse agonism, metadynamics | Timothy Clark | PRINT RMSD METAD MATHEVAL WHOLEMOLECULES DISTANCE MOLINFO | colvar generic bias function |
| 23.029 | An accurate and efficient SAXS/SANS implementation including solvation layer effects suitable for restrained Molecular Dynamics simulations | bio | SAXS, SANS, SAS, metainference, proteins, nucleic-acid | Federico Ballabio | ENSEMBLE WRAPAROUND SAXS PRINT CENTER GROUP STATS RMSD UPPER_WALLS BIASVALUE DISTANCE MOLINFO | generic function isdb vatom colvar bias core |
| 23.022 | A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar | methods | collective variables, machine learning, toy model | Enrico Trizio | POSITION LOWER_WALLS PRINT UPPER_WALLS BIASVALUE CUSTOM UNITS OPES_METAD PYTORCH_MODEL ENDPLUMED | generic function opes pytorch setup colvar bias |
| 23.018 | Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention | materials | metadynamics, surface binding, peptide adsorption | Kaylyn Torkelson | PRINT PBMETAD UPPER_WALLS GYRATION COM DISTANCE | colvar generic vatom bias |
| 23.003 | Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations | methods | metadynamics, alchemical variable, alchemical free energy calculations | Wei-Tse Hsu | READ PRINT EXTRACV METAD TORSION | colvar generic bias |
| 23.000 | Atomistic simulations of RNA tetraloop folding via PTWTE-WTM | bio | parallel tempering, well-tempered metadynamics, well-tempered ensemble, RNA, Tetraloop, Folding | Gül Zerze | LOWER_WALLS PRINT ENERGY UPPER_WALLS METAD WHOLEMOLECULES CONTACTMAP | colvar generic bias |
| 22.040 | From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure | bio | SARS-CoV-2, Spike, Omicron | Miłosz Wieczór | LOWER_WALLS PRINT PCAVARS UPPER_WALLS METAD WHOLEMOLECULES | generic bias mapping |
| 22.024 | Conformational Entropy as a Potential Liability of Computationally Designed Antibodies | bio | metadynamics, conformational entropy, antibody, nanobody | Thomas Löhr | RESTART PRINT PBMETAD ANTIBETARMSD WHOLEMOLECULES ALPHARMSD ALPHABETA COM TORSION MOLINFO | generic multicolvar secondarystructure setup vatom colvar bias |
| 22.015 | Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome | bio | photodynamics, bacteriophytochrome, variationally enhanced sampling | Jakub Rydzewski | PRINT TD_UNIFORM OPT_AVERAGED_SGD VES_LINEAR_EXPANSION BF_FOURIER TORSION | colvar generic ves |
| 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 | LOWER_WALLS PRINT ZANGLES XANGLES YANGLES UPPER_WALLS METAD MATHEVAL WHOLEMOLECULES COMBINE CUSTOM COM ALPHABETA DISTANCE TORSION MOLINFO | generic multicolvar function vatom colvar bias |
| 22.006 | Peptide framework for screening the effects of amino acids on assembly | bio | metadynamics, peptides | Andrew White | CONVERT_TO_FES PRINT REWEIGHT_BIAS GROUP DUMPGRID METAD COMBINE INCLUDE GYRATION COM DISTANCES HISTOGRAM | generic gridtools function multicolvar vatom colvar bias core |
| 21.031 | Photo-switchable sulfonulureas in KATP channel | bio | metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels | Katarzyna Walczewska-Szewc | LOWER_WALLS PRINT UPPER_WALLS METAD WHOLEMOLECULES COM UNITS DISTANCE | generic setup vatom colvar bias |
| 21.016 | MD SAXS GTPase associated center | bio | metadynamics, RNA, folding, SAXS | Giovanni Bussi | LOWER_WALLS SAXS PRINT GROUP UPPER_WALLS METAD ERMSD WHOLEMOLECULES INCLUDE GYRATION CUSTOM MOLINFO | generic function isdb colvar bias core |
| 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 | RESTART PRINT BF_LEGENDRE ENVIRONMENTSIMILARITY ECV_UMBRELLAS_LINE ENERGY TD_UNIFORM VES_LINEAR_EXPANSION OPT_AVERAGED_SGD OPES_EXPANDED MATHEVAL VOLUME Q6 UPPER_WALLS ECV_MULTITHERMAL_MULTIBARIC | generic opes function ves setup envsim colvar bias symfunc |
| 20.034 | Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations | bio | RNA, SARS-CoV-2, partial tempering | Sandro Bottaro | RESTART ABMD PRINT CENTER ERMSD DISTANCE TORSION MOLINFO | generic setup vatom colvar bias |
| 20.024 | Gaussian Mixture Based Enhanced Sampling (GAMBES) | methods | enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias | Jayashrita Debnath | LOAD LOWER_WALLS PRINT GROUP ENERGY UPPER_WALLS COMBINE UNITS DISTANCES DISTANCE TORSION | generic function multicolvar setup colvar bias core |
| 20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Michele Invernizzi | ECV_MULTITHERMAL OPES_EXPANDED ENERGY ECV_UMBRELLAS_LINE WHOLEMOLECULES VOLUME Q6 CUSTOM UNITS TORSION PRINT MATHEVAL MOLINFO LOAD POSITION ECV_LINEAR RMSD ENVIRONMENTSIMILARITY UPPER_WALLS ENDPLUMED ECV_MULTITHERMAL_MULTIBARIC | generic opes function setup envsim colvar bias symfunc |
| 20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Max Bonomi | PRINT PBMETAD COORDINATION INCLUDE WHOLEMOLECULES GYRATION ALPHABETA DIHCOR MOLINFO | colvar generic multicolvar bias |
| 20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Glen Hocky | PRINT GROUP ENERGY MATHEVAL BIASVALUE GYRATION UNITS DISTANCE FISST RESTRAINT | generic function fisst setup colvar bias core |
| 20.008 | Simulating solvation and acidity in complex mixtures with first-principles accuracy. The case of CH3SO3H and H2O2 in phenol | chemistry | proton trasfer, metadynamics | Kevin Rossi | PRINT METAD COORDINATION CUSTOM UNITS DISTANCES | generic function multicolvar setup colvar bias |
| 19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Valerio Rizzi | RESTART FLUSH PRINT GROUP METAD COMBINE EXTERNAL UNITS COORDINATIONNUMBER ENDPLUMED | generic function setup symfunc bias core |
| 19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Giovanni Bussi | LOWER_WALLS COORDINATION WHOLEMOLECULES RESTRAINT DISTANCE ENDPLUMED | colvar generic bias |
| 19.048 | Understanding Ligand Binding Selectivity in a Prototypical GPCR Family | bio | metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | LOWER_WALLS PRINT UPPER_WALLS METAD MATHEVAL WHOLEMOLECULES BIASVALUE COM CONSTANT DISTANCE | generic function vatom colvar bias |
| 19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Carlo Camilloni | RESTART FLUSH LOWER_WALLS PRINT MOLINFO GROUP PBMETAD UPPER_WALLS WHOLEMOLECULES ANTIBETARMSD BIASVALUE ALPHABETA CS2BACKBONE ENDPLUMED | generic multicolvar isdb secondarystructure setup bias core |
| 19.023 | RECT | methods | metadynamics, replica exchange | Giovanni Bussi | PRINT METAD WHOLEMOLECULES GYRATION TORSION | colvar generic bias |
| 19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Adriana Pietropaolo | PRINT METAD MATHEVAL WHOLEMOLECULES BIASVALUE CONSTANT TORSION | colvar generic bias function |
| 19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Matteo Salvalaglio | RESTART PRINT METAD GYRATION DISTANCES COORDINATIONNUMBER ENDPLUMED | generic multicolvar setup colvar bias symfunc |
| 19.013 | RNA FF FITTING | methods | force field, RNA | Giovanni Bussi | MATHEVAL BIASVALUE INCLUDE CONSTANT TORSION PUCKERING MOLINFO | generic function bias colvar |
| 19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Carlo Camilloni | ENSEMBLE PRINT MOLINFO GROUP PBMETAD STATS UPPER_WALLS RDC DHENERGY WHOLEMOLECULES METAINFERENCE RESTRAINT ALPHABETA DIHCOR DISTANCE TORSION ENDPLUMED CENTER | generic function multicolvar core vatom colvar bias isdb |
| 19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Max Bonomi | PRINT GROUP BIASVALUE WHOLEMOLECULES EMMI MOLINFO | isdb generic bias core |
| 19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Giovanni Bussi | FLUSH LOWER_WALLS PRINT UPPER_WALLS METAD ERMSD ANGLE INCLUDE COMBINE RANDOM_EXCHANGES DISTANCES DISTANCE MOLINFO | generic multicolvar function colvar bias |
| 25.016 | Advancing in silico drug design with Bayesian refinement of AlphaFold models | bio | bAIes, AlphaFold, Bayesian refinement, virtual screening, docking, small-molecule, enrichment | Samiran Sen | BAIES PRINT GROUP BIASVALUE | generic core isdb bias |
| 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 | COMBINE LOAD BIASVALUE FLUSH TORSION COORDINATION CELL POSITION UNITS OPES_METAD DISTANCE INCLUDE PRINT ENERGY MATHEVAL CUSTOM | generic bias function colvar opes setup |
| 24.032 | DeepLNE++ | methods | PATHCV, OPES | Thorben Fröhlking | COMBINE GROUP LOAD TORSION COORDINATION OPES_METAD DISTANCE PRINT ENERGY CUSTOM | generic function core colvar opes setup |
| 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 | GROUP ANGLE TORSION OPES_METAD DISTANCE PRINT COMBINE MOLINFO COORDINATION ENDPLUMED CONTACTMAP MATHEVAL CUSTOM UPPER_WALLS CENTER WHOLEMOLECULES FIXEDATOM FIT_TO_TEMPLATE COMMITTOR METAD RMSD | generic vatom bias function core colvar 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 | GROUP LOAD TORSION COMMITTOR METAD PRINT | generic bias core colvar setup |
| 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 | COMBINE ALPHARMSD MOLINFO TORSION COORDINATION GYRATION OPES_METAD DISTANCE PRINT WHOLEMOLECULES CUSTOM | generic secondarystructure function colvar opes |
| 24.011 | Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble | methods | committor, machine learning | Peilin Kang | GROUP BIASVALUE TORSION POSITION DISTANCE PRINT MOLINFO COORDINATION UNITS ENDPLUMED LOWER_WALLS MATHEVAL CUSTOM LOAD CELL UPPER_WALLS INCLUDE ENERGY WHOLEMOLECULES RMSD | generic bias function core colvar setup |
| 24.009 | Weighted Shape Gaussian Mixture Models | bio | metadynamics, clustering | Glen Hocky | GROUP TORSION METAD UNITS PRINT | generic bias core colvar setup |
| 23.026 | Machine Learning Nucleation Collective Variables with Graph Neural Networks | chemistry | Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks | Florian Dietrich | COMBINE GROUP MOVINGRESTRAINT MFILTER_MORE METAD Q6 COORDINATIONNUMBER LOWER_WALLS PRINT LOCAL_Q6 | generic bias function symfunc multicolvar core |
| 22.039 | Driving and characterizing nucleation of urea and glycine polymorphs in water | bio | metadynamics, nucleation, amino acids, polymorphism | Eric Beyerle | Q4 COMBINE GROUP LOAD METAD Q6 PAIRENTROPY INCLUDE COORDINATIONNUMBER PRINT MATHEVAL CENTER | generic vatom bias function gridtools symfunc core setup |
| 22.038 | Enhanced Sampling Aided Design of Molecular Photoswitches | chemistry | reaction discovery, OPES explore, graph CV | Umberto Raucci | COORDINATION UNITS OPES_METAD_EXPLORE PRINT PYTORCH_MODEL CUSTOM | generic function colvar opes pytorch setup |
| 22.031 | Rare Event Kinetics from Adaptive Bias Enhanced Sampling | methods | OPES Flooding, Kinetics, Rate, OPES, Machine Learning | Dhiman Ray | GROUP BIASVALUE TORSION POSITION OPES_METAD DISTANCE PRINT PYTORCH_MODEL COMBINE MOLINFO UNITS ENDPLUMED CONTACTMAP CONSTANT CUSTOM INCLUDE ENERGY WHOLEMOLECULES RMSD COMMITTOR | generic bias function core colvar opes pytorch setup |
| 22.028 | N-glycan conformer distributions in atomistic simulation | bio | REST2, RECT, N-glycan, pucker | Isabell Grothaus | DUMPGRID CONVERT_TO_FES READ MOLINFO TORSION METAD PUCKERING PRINT HISTOGRAM | generic gridtools bias colvar |
| 22.007 | Characterization of a natural variant of human NDP52 and its functional consequences on mitophagy | bio | metadynamics, well-tempered, protein-protein interactions, disordered proteins, mutations autophagy | Elena Papaleo | ALPHARMSD ANGLE TORSION FLUSH MOLINFO COORDINATION METAD ALPHABETA DISTANCE UPPER_WALLS PRINT WHOLEMOLECULES | generic secondarystructure bias multicolvar colvar |
| 21.042 | Peptoid-mediated Au nanocrystal growth | materials | parallel-bias metadynamics, peptoid, Au | Xin Qi | MOLINFO COM GYRATION DISTANCE UPPER_WALLS PRINT PBMETAD | generic bias vatom colvar |
| 21.032 | Metal-coupled folding mechanism to metallothionein | bio | parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination | Manuel-Peris Diaz | GROUP COORDINATION UNITS PBMETAD WHOLEMOLECULES | generic bias core colvar setup |
| 21.026 | Probing allosteric regulations with coevolution-driven molecular simulations | bio | metadynamics, coevolution, allostery, adenylate cyclase | Francesco Colizzi | METAD COM UNITS UPPER_WALLS DISTANCE PRINT PATHMSD WHOLEMOLECULES | generic vatom bias colvar setup |
| 21.013 | Role of vibrational excitation in heterogeneous catalysis | chemistry | catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption | Kristof Bal | CONVERT_TO_FES TD_GRID DISTANCE ANGLES COORDINATIONNUMBER PRINT COMBINE COORDINATION REWEIGHT_BIAS UNITS LOWER_WALLS UWALLS RESTRAINT LOAD UPPER_WALLS HISTOGRAM DISTANCES REWEIGHT_METAD DUMPGRID BF_CHEBYSHEV OPT_AVERAGED_SGD FLUSH METAD EXTERNAL VES_LINEAR_EXPANSION | generic bias gridtools function symfunc multicolvar ves colvar setup |
| 21.006 | OPES, On-the-fly Probability Enhanced Sampling Method | methods | opes, alanine dipeptide, well-tempered, multithermal, multiumbrella | Michele Invernizzi | TORSION ECV_MULTITHERMAL OPES_EXPANDED OPES_METAD ENDPLUMED PRINT ENERGY ECV_UMBRELLAS_LINE | generic colvar opes |
| 21.000 | Uremic toxin time scale dynamics | bio | uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs) | Jim Pfaendtner | GROUP COM DISTANCE PRINT WHOLEMOLECULES | generic core vatom colvar |
| 20.012 | Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies | bio | metadynamics, well-tempered ensemble, ligand binding, binding affinity calculations, novel COLVAR, funnel restraints, Hamiltonian replica-exchange, PathCV, COMetPath, SWISH | Francesco Gervasio | CONSTANT GROUP LOAD BIASVALUE MOLINFO METAD COM DISTANCE UPPER_WALLS INCLUDE WHOLEMOLECULES CONTACTMAP LOWER_WALLS PRINT MATHEVAL PROJECTION_ON_AXIS FUNCPATHGENERAL | generic vatom bias function core colvar setup |
| 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_DUMMY OPT_AVERAGED_SGD VOLUME BF_LEGENDRE Q6 UPPER_WALLS TD_WELLTEMPERED RESTART PRINT ENVIRONMENTSIMILARITY MATHEVAL VES_LINEAR_EXPANSION | generic envsim bias function symfunc ves colvar setup |
| 19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Giovanni Bussi | MAXENT MOLINFO FLUSH TORSION COORDINATION METAD COM SORT DISTANCE INCLUDE PRINT MATHEVAL WHOLEMOLECULES | generic vatom bias function colvar |
| 19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Matteo Salvalaglio | GROUP ENDPLUMED DISTANCE INCLUDE PRINT CENTER | generic core vatom colvar |
| 19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Michele Invernizzi | TORSION POSITION METAD EXTERNAL UNITS OPES_METAD ENDPLUMED PRINT | generic bias colvar opes setup |
| 19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Wei Chen | COMBINE RESTRAINT POSITION ANN COM | vatom bias function colvar annfunc |
| 19.059 | cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide | bio | bias-exchange metadynamics, cis-trans isomerization | Fabrizio Marinelli | RANDOM_EXCHANGES TORSION METAD INCLUDE PRINT | generic bias colvar |
| 19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Cristina Paissoni | COMBINE GROUP ANGLE BIASVALUE MOLINFO ENSEMBLE COORDINATION STATS ALPHABETA SAXS ENDPLUMED INCLUDE PRINT PBMETAD MATHEVAL CENTER WHOLEMOLECULES | generic isdb vatom bias function multicolvar core colvar |
| 19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Glen Hocky | COMBINE RESTRAINT TORSION EDS DISTANCE PRINT | generic bias function eds colvar |
| 25.005 | Mechanism of Nanocluster Formation from Machine-Learned Potential-based Simulations | chemistry | WT-metadynamics, metal nanoclusters, nucleation, neural network potential, deepMD | Vikas Tiwari, Tarak Karmakar | LOWER_WALLS GROUP PRINT COMBINE FIXEDATOM COORDINATIONNUMBER FLUSH DISTANCES UNITS METAD DISTANCE ANGLE COM UPPER_WALLS COORDINATION RESTRAINT | function core bias symfunc setup generic colvar vatom multicolvar |
| 25.000 | Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer | bio | metadynamics, pathCV | Sahithya Sridharan Iyer | DISTANCE PRINT MOLINFO UPPER_WALLS WHOLEMOLECULES FUNCPATHGENERAL GROUP RESTART METAD COM | function core vatom colvar generic setup bias |
| 24.030 | NMR guided simulation of dsRBD | bio | Metainference, NMR, protein dynamics | Debadutta Patra | PRINT DISTANCE MOLINFO WHOLEMOLECULES GROUP METAINFERENCE STATS ENSEMBLE RDC FLUSH ALPHABETA | function core colvar generic multicolvar isdb |
| 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 | FIXEDATOM TORSION DISTANCE PRINT UPPER_WALLS COORDINATION CUSTOM LOWER_WALLS PATH WHOLEMOLECULES GROUP FIT_TO_TEMPLATE RESTART CENTER PYTORCH_MODEL OPES_METAD | mapping function core pytorch vatom opes colvar generic setup bias |
| 24.010 | Oxytocin metadynamics simulation | bio | metadynamics, oxytocin, peptide | Jan Beránek | TORSION PRINT WHOLEMOLECULES RESTART METAD FLUSH | colvar setup generic 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 | FIXEDATOM DISTANCE PRINT UPPER_WALLS GROUP UNITS COORDINATIONNUMBER OPES_METAD FLUSH ZDISTANCES | symfunc core opes vatom colvar generic multicolvar setup bias |
| 23.043 | Modeling the ferroelectric phase transition in barium titanate with DFT accuracy and converged sampling | materials | Barium Titanate, ferroelectric phase transition, Machine Learning, polarization order parameters | Lorenzo Gigli | PRINT SELECT_COMPONENTS SUM METAD TRANSPOSE MATHEVAL FLUSH INCLUDE | valtools function generic matrixtools 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 | PRINT MOLINFO BIASVALUE COORDINATION WHOLEMOLECULES COMBINE METAD ERMSD GHBFIX | colvar function generic bias |
| 23.027 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, DFS, Q3, Pair Entropy | Aaron Finney | FIXEDATOM PRINT CONTACT_MATRIX LOCAL_AVERAGE AROUND LOCAL_Q3 Q3 GROUP LOAD CLUSTER_DISTRIBUTION UNITS DENSITY COORDINATIONNUMBER DUMPGRID DFSCLUSTERING RESTRAINT CLUSTER_NATOMS HISTOGRAM | adjmat symfunc core vatom generic gridtools setup volumes bias clusters |
| 23.007 | Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains | bio | metadynamics, peptoids, parallel-bias metadynamics | Jim Pfaendtner | TORSION PRINT GYRATION COORDINATION WHOLEMOLECULES PBMETAD RESTRAINT COM INCLUDE | vatom colvar generic bias |
| 22.030 | Mixing physics across temperatures with generative artificial intelligence | methods | REMD, Generative AI, DDPM | Yihang Wang | WHOLEMOLECULES TORSION PRINT | 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 |
| 22.016 | 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 | PRINT AROUND CUSTOM UPPER_WALLS ENVIRONMENTSIMILARITY RESTART ENERGY OPES_METAD VOLUME HISTOGRAM DUMPGRID | function opes generic colvar envsim gridtools setup volumes bias |
| 22.012 | Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT | bio | contact maps, protein-protein interactions | Isabell-Louise Grothaus | DISTANCE PRINT CONTACTMAP CENTER | vatom colvar generic |
| 22.008 | Ab initio metadynamics determination of temperature-dependent free-energy landscape in ultrasmall silver clusters | materials | Well tempered metadynamics, ab-initio, ase | Daniel Sucerquia | COM DISTANCE UPPER_WALLS COORDINATION GYRATION LOWER_WALLS COMBINE UNITS METAD COORDINATIONNUMBER FLUSH | function symfunc vatom colvar generic setup bias |
| 22.002 | GAMBES_SAMPL5_RATES | other | GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding | Jayashrita Debnath | FIXEDATOM DISTANCE PRINT UPPER_WALLS COORDINATION ANGLE WHOLEMOLECULES LOAD GROUP CENTER FIT_TO_TEMPLATE ENDPLUMED COMMITTOR PYTORCH_MODEL ENERGY MATHEVAL FLUSH | pytorch core function vatom colvar generic setup bias |
| 21.052 | On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets | materials | Ibuprofen, unbinding, WTmetaD | Matteo Salvalaglio | DISTANCE TORSION PRINT CENTER ENDPLUMED COMMITTOR COORDINATIONNUMBER METAD | symfunc vatom colvar generic bias |
| 21.050 | N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity | methods | bio | Isabell Louise Grothaus | DISTANCE CENTER PRINT | vatom colvar generic |
| 21.048 | Enhancing ligand exploration within a channel pore and fenestrations using metadynamics | bio | well-tempered metadynamics, protein-ligand enhanced sampling, sodium channel, Nav, small molecule drug | Elaine Tao | DISTANCE TORSION PRINT UPPER_WALLS CUSTOM LOWER_WALLS UNITS METAD COM | function vatom colvar generic setup bias |
| 21.034 | Efficient sampling of high-dimensional free energy landscapes using adaptive reinforced dynamics | bio | reinforced dynamics, bias-exchange metadynamics, parallel-bias metadynamics | Dongdong Wang | RANDOM_EXCHANGES TORSION PRINT PBMETAD ENDPLUMED METAD INCLUDE | colvar generic bias |
| 21.033 | Multiple-path-metadynamics applied to DNA base-pairing transitions | bio | path-CV, metadynamics, multiple-walker, dna | Alberto Pérez-de-Alba-Ortíz | PRINT UPPER_WALLS RESTRAINT COMBINE METAD CONSTANT MOVINGRESTRAINT INCLUDE | function generic bias |
| 21.029 | Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs | bio | metadynamics, small peptide, machine learning | Pratyush Tiwary | TORSION PRINT MOLINFO EXTERNAL RESTART ENERGY FLUSH | colvar setup generic bias |
| 21.023 | Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling | methods | enhanced sampling, collective variables, machine learning | Jakub Rydzewski | DISTANCE PRINT BIASVALUE TORSION CUSTOM UNITS METAD ENERGY CONSTANT REWEIGHT_METAD INCLUDE | function colvar generic setup bias |
| 21.019 | Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations | materials | Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen | Matteo Salvalaglio | DISTANCE PRINT TORSIONS KDE MATHEVAL COM | function vatom colvar gridtools generic multicolvar |
| 20.028 | Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane | bio | metadynamics, KRas-4B, anionic membrane | Huixia Lu | DISTANCE PRINT CENTER FIT_TO_TEMPLATE RESTART METAD | vatom colvar generic setup bias |
| 20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Jim Pfaendtner | DISTANCE PRINT COORDINATION WHOLEMOLECULES GROUP CENTER RESTART DISTANCES | core vatom colvar generic multicolvar setup |
| 20.001 | Conformational stability and dynamics in solution and in crystals report similarly on unfolding and aggregation propensity of amyloidogenic proteins | bio | metainference, metadynamics, NMR, protein dynamics, b2m, protein crystals | Carlo Camilloni | PRINT MOLINFO UPPER_WALLS BIASVALUE LOWER_WALLS WHOLEMOLECULES PBMETAD GROUP ENDPLUMED ANTIBETARMSD CS2BACKBONE FLUSH ALPHABETA | secondarystructure core generic multicolvar bias isdb |
| 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 | DISTANCE PRINT UPPER_WALLS LOWER_WALLS ABMD CONVERT_TO_FES COMBINE ENDPLUMED READ METAD HISTOGRAM DUMPGRID MATHEVAL COM REWEIGHT_METAD | function vatom colvar gridtools generic bias |
| 19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Jim Pfaendtner | PRINT GYRATION WHOLEMOLECULES METAD ENERGY | colvar generic bias |
| 19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Kim E. Jelfs | DISTANCE PRINT UPPER_WALLS LOWER_WALLS GROUP CENTER RESTART METAD COM | core vatom colvar generic setup bias |
| 19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Luigi Bonati | PRINT TORSION POSITION ENVIRONMENTSIMILARITY LOAD ENDPLUMED UNITS Q6 ENERGY | symfunc colvar generic envsim setup |
| 19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Gareth Tribello | CELL PRINT AROUND UPPER_WALLS LOWER_WALLS ENDPLUMED UNITS METAD FCCUBIC | symfunc colvar generic setup volumes bias |
| 19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | DISTANCE PRINT UPPER_WALLS COMBINE RESTART UNITS METAD FLUSH DISTANCES | function colvar generic multicolvar setup bias |
| 19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Paolo Raiteri | DISTANCE PRINT UPPER_WALLS RESTART UNITS METAD MATHEVAL FLUSH | function colvar generic setup bias |
| 19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Matteo Salvalaglio | DISTANCE TORSION PRINT UPPER_WALLS LOWER_WALLS CENTER COMMITTOR METAD | vatom colvar generic bias |