Browse the eggs in PLUMED-NEST
PLUMED-NEST provides all the data needed to reproduce the results of a PLUMED-enhanced molecular dynamics simulation or analysis contained in a published paper. Furthermore, PLUMED-NEST monitors the compatibility of the provided PLUMED input files with the current and development versions of the code and integrates links from these files to the PLUMED manual.
Here is the list of projects already deposited in PLUMED-NEST, while a complete bibliography can be found here.
| plumID | Name | Category | Keywords | Contributor | Actions | Modules |
|---|---|---|---|---|---|---|
| 26.004 | Resolving the ambiguous binding site of quercetin at the calcineurin subunit junction using funnel metadynamics with deep learning collective variables | bio | metadynamics, funnel metadynamics, DeepTICA | Jason Loo | FUNNEL PRINT WRAPAROUND FUNNEL_PS LOWER_WALLS UPPER_WALLS GROUP WHOLEMOLECULES RMSD PYTORCH_MODEL DISTANCE METAD COORDINATION ENERGY MATHEVAL COM | generic vatom pytorch colvar funnel function bias core |
| 25.024 | Sampling glycan-glycan interactions for B22 calculations | bio | B22, glycan, carbohydrates, distance, REST2, metadynamics, RECT, replica exchange | Isabell Louise Grothaus | PRINT COMBINE RESTRAINT POSITION DISTANCE METAD COM | generic vatom colvar function 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 | UNITS INCLUDE BIASVALUE PRINT LOAD CUSTOM TORSION COMBINE OPES_METAD POSITION FLUSH CELL DISTANCE COORDINATION ENERGY MATHEVAL | generic colvar opes function bias setup |
| 25.009 | Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water | chemistry | metadynamics, nitrate photolysis | Kam-Tung Chan | DUMPGRID RESTART PRINT UPPER_WALLS COORDINATION CUSTOM REWEIGHT_METAD HISTOGRAM GROUP FLUSH DISTANCE METAD READ | generic colvar function bias setup gridtools core |
| 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 | UNITS RESTART PRINT LOWER_WALLS UPPER_WALLS CUSTOM GROUP OPES_METAD COMMITTOR DISTANCE COORDINATION | generic colvar opes function bias setup core |
| 24.026 | Constant pH metadynamics of RNA oligomers | bio | metadynamics, pH, RNA | Giovanni Bussi | MOLINFO RESTART PRINT TORSION PUCKERING METAD | generic bias colvar 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 | COMBINE OPES_METAD WHOLEMOLECULES CENTER COMMITTOR CONTACTMAP FIT_TO_TEMPLATE DISTANCE METAD COORDINATION MATHEVAL UPPER_WALLS CUSTOM TORSION MOLINFO PRINT ENDPLUMED FIXEDATOM GROUP ANGLE RMSD | generic vatom colvar opes function bias core |
| 24.005 | Learning Markovian Dynamics with Spectral Maps | methods | spectral map, collective variables, machine learning | Jakub Rydzewski | UNITS BIASVALUE PRINT CUSTOM DISTANCE | generic colvar function bias setup |
| 23.019 | Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors | bio | binding pathway, binding energy, sketch-map, drug development | Raitis Bobrovs | TRANSPOSE VORONOI PRINT PATHMSD UPPER_WALLS SKETCHMAP_PROJECTION CUSTOM COLLECT_FRAMES LANDMARK_SELECT_FPS SKETCHMAP WHOLEMOLECULES DISSIMILARITIES DISTANCE METAD VSTACK COM | generic vatom matrixtools colvar function bias landmarks dimred valtools |
| 23.015 | MPCs aggregation | bio | opes_explore, dimerization, MPCs, self-assembly | Vikas Tiwari | PRINT UPPER_WALLS LOWER_WALLS CUSTOM OPES_METAD_EXPLORE GROUP WHOLEMOLECULES CENTER DISTANCE METAD COORDINATION COM | generic vatom colvar opes function bias core |
| 23.011 | OneOPES, a combined enhanced sampling method to rule them all | bio | OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding | Valerio Rizzi | MOLINFO PRINT ECV_MULTITHERMAL ENDPLUMED TORSION OPES_METAD_EXPLORE OPES_EXPANDED DISTANCE METAD ENERGY | generic bias colvar opes |
| 23.003 | Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations | methods | metadynamics, alchemical variable, alchemical free energy calculations | Wei-Tse Hsu | PRINT TORSION METAD READ EXTRACV | generic bias colvar |
| 22.043 | Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES | bio | OPES, RNA, Tetraloop, Folding | Gül Zerze | PRINT ECV_MULTITHERMAL ECV_UMBRELLAS_LINE WHOLEMOLECULES OPES_EXPANDED CONTACTMAP ENERGY | generic colvar opes |
| 22.041 | Skipping the Replica Exchange Ladder with Normalizing Flows | methods | OPES, alanine, normalizing flows, replica exchange | Michele Invernizzi | UNITS ECV_MULTITHERMAL PRINT ENDPLUMED TORSION OPES_METAD POSITION OPES_EXPANDED ENERGY | generic colvar setup opes |
| 22.019 | Exploring aspartic protease inhibitor binding to design selective antimalarials | bio | ligand binding, loop opening, path CV, funnel metadynamics, drug development | Raitis Bobrovs | FUNNEL PRINT PATHMSD FUNNEL_PS LOWER_WALLS UPPER_WALLS WHOLEMOLECULES DISTANCE METAD COM | generic vatom colvar funnel bias |
| 22.005 | Collective Variable for Metadynamics Derived from AlphaFold Output | bio | AlphaFold, protein folding, protein structure prediction, metadynamics, deep learning, free energy simulation, collective variable | Vojtech Spiwok | METAD WHOLEMOLECULES PRINT LOAD | generic bias setup |
| 22.000 | Amyloid precursor protein processing by human γ-secretase | bio | Bias Exchange Metadynamics, Helix unfolding, coupled binding | Xiaoli Lu | INCLUDE UNITS MOLINFO RANDOM_EXCHANGES PRINT CONTACTMAP ANTIBETARMSD CENTER DISTANCE METAD COORDINATION ALPHARMSD | generic vatom secondarystructure colvar bias setup |
| 21.039 | Deep learning the slow modes for rare events sampling | methods | collective variables, machine learning, slow modes, deep-tica, opes | Luigi Bonati | COMBINE OPES_METAD WHOLEMOLECULES OPES_EXPANDED PYTORCH_MODEL VOLUME CONTACTMAP DISTANCE ENVIRONMENTSIMILARITY Q6 INCLUDE UNITS ECV_MULTITHERMAL TORSION MOLINFO PRINT LOAD ENDPLUMED GROUP FLUSH RMSD ENERGY | generic pytorch colvar envsim opes function setup symfunc core |
| 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 | INCLUDE RANDOM_EXCHANGES PRINT ENDPLUMED TORSION PBMETAD METAD | generic bias colvar |
| 21.025 | Computational and biochemical analysis of type IV pilus dynamics and stability | bio | molecular dynamics, calcium binding, Type IV pilus | Yasaman Karami | DISTANCE UPPER_WALLS PRINT LOWER_WALLS | generic bias colvar |
| 21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Tarak Karmakar | PRINT LOAD UPPER_WALLS LOWER_WALLS GROUP OPES_METAD FLUSH PYTORCH_MODEL MATHEVAL | generic pytorch opes function bias setup core |
| 21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Kresten Lindorff-Larsen | MOLINFO BIASVALUE PRINT GROUP WHOLEMOLECULES CENTER PBMETAD FLUSH METAINFERENCE EEFSOLV GYRATION ALPHARMSD SAXS | generic isdb vatom secondarystructure colvar bias core |
| 20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Max Bonomi | INCLUDE MOLINFO PRINT DIHCOR ALPHABETA WHOLEMOLECULES PBMETAD GYRATION COORDINATION | generic multicolvar bias colvar |
| 20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Matteo Salvalaglio | PRINT UPPER_WALLS LOWER_WALLS VOLUME CELL METAD ENERGY MATHEVAL | generic function bias colvar |
| 20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Pratyush Tiwary | MOLINFO RESTART PRINT UPPER_WALLS TORSION COMBINE WHOLEMOLECULES RMSD DISTANCE METAD | generic colvar function bias setup |
| 20.002 | Exploring conformational dynamics of the extracellular Venus flytrap domain of the GABAB receptor, a path-metadynamics study | bio | Metadynamics, path CVs | Riccardo Ocello | MOLINFO RESTART PRINT PATHMSD UPPER_WALLS GROUP WHOLEMOLECULES METAD | generic colvar bias setup core |
| 19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Sandro Bottaro | MOLINFO ERMSD PRINT TORSION WHOLEMOLECULES RMSD DISTANCE METAD | generic bias colvar |
| 19.046 | Optimal Collective from short simulations for Benzamidine-Trypsin ligand binding | bio | VAC-MetaD, optimised collective variables, binding free energy, unbinding rates, benzamidine trypsin, Structure Activity Relation | Faidon Brotzakis | BRIDGE MOLINFO FUNNEL PRINT UPPER_WALLS LOWER_WALLS TORSION REWEIGHT_METAD COMBINE DISTANCES GROUP ALPHABETA WHOLEMOLECULES RMSD DISTANCE METAD COM | generic vatom multicolvar colvar funnel function bias adjmat core |
| 19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | UNITS PRINT UPPER_WALLS COMBINE FLUSH DISTANCE METAD ENERGY | generic colvar function bias setup |
| 19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Riccardo Capelli | DUMPGRID PRINT WRAPAROUND UPPER_WALLS ENDPLUMED REWEIGHT_METAD FIT_TO_TEMPLATE GROUP HISTOGRAM WHOLEMOLECULES POSITION FLUSH READ METAD COORDINATION CONVERT_TO_FES MATHEVAL COM | generic vatom colvar function bias gridtools core |
| 19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Max Bonomi | MOLINFO BIASVALUE PRINT GROUP EMMI | generic bias isdb core |
| 26.001 | Molecular simulations Alx riboswitch | bio | RNA, riboswitch | Giovanni Bussi | MOVINGRESTRAINT PRINT ERMSD DISTANCE MATHEVAL MOLINFO RESTRAINT | bias function colvar generic |
| 25.003 | Surrogate Model CV | methods | Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding | Sompriya Chatterjee | COMMITTOR WHOLEMOLECULES ENERGY TORSION PRINT GROUP ENDPLUMED CUSTOM DISTANCE OPES_METAD PYTORCH_MODEL MOLINFO MATHEVAL COMBINE | function pytorch core colvar opes generic |
| 24.028 | All-atom simulations of RNA-membrane interactions | bio | metadynamics, membrane, RNA | Giovanni Bussi | WHOLEMOLECULES GHOST CENTER POSITION GROUP PRINT GYRATION DISTANCES DISTANCE SORT METAD LOWER_WALLS UPPER_WALLS MATHEVAL MOLINFO PUCKERING COMBINE | multicolvar function bias vatom core colvar generic |
| 24.020 | Graph Neural Network-State Predictive Information Bottleneck (GNN-SPIB) approach for learning molecular thermodynamics and kinetics | bio | LJ7, alanine, well-tempered metadynamics, infrequent metadynamics, machine learning | Ziyue Zou, Dedi Wang, Pratyush Tiwary | COMMITTOR TORSION PRINT GROUP METAD LOAD | bias core setup colvar generic |
| 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 | COMMITTOR ENERGY PRINT TORSION FLUSH DISTANCE COORDINATIONNUMBER METAD MATHEVAL RESTART MOLINFO BIASVALUE RESTRAINT | symfunc bias function setup colvar generic |
| 23.038 | Determinants of Neutral Antagonism and Inverse Agonism in the β2-adrenergic receptor | bio | protein coupled receptor, beta-adrenergic, receptor activation, antagonism, inverse agonism, metadynamics | Timothy Clark | WHOLEMOLECULES PRINT DISTANCE METAD MATHEVAL MOLINFO RMSD | bias function colvar generic |
| 23.023 | Rational design of novel biomimetic sequence-defined polymers for mineralization applications | methods | metadynamics, surface binding, biomimetic mineralization | Kaylyn Torkelson | PRINT GYRATION DISTANCE COORDINATION PBMETAD COM UPPER_WALLS | vatom bias colvar generic |
| 23.007 | Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains | bio | metadynamics, peptoids, parallel-bias metadynamics | Jim Pfaendtner | WHOLEMOLECULES TORSION GYRATION PRINT COORDINATION INCLUDE PBMETAD COM RESTRAINT | vatom bias colvar generic |
| 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 | WHOLEMOLECULES ENERGY PRINT LOWER_WALLS METAD CONTACTMAP UPPER_WALLS | bias colvar generic |
| 22.040 | From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure | bio | SARS-CoV-2, Spike, Omicron | Miłosz Wieczór | WHOLEMOLECULES PRINT LOWER_WALLS METAD PCAVARS UPPER_WALLS | mapping bias generic |
| 22.028 | N-glycan conformer distributions in atomistic simulation | bio | REST2, RECT, N-glycan, pucker | Isabell Grothaus | CONVERT_TO_FES HISTOGRAM PRINT TORSION READ METAD DUMPGRID MOLINFO PUCKERING | bias colvar gridtools generic |
| 22.026 | Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification | materials | Peptoid, silica | Jim Pfaendtner | PRINT GYRATION DISTANCE PBMETAD COM MOLINFO UPPER_WALLS | vatom bias colvar generic |
| 22.025 | Bubble nucleation rate predictions in a Lennard-Jones fluid | materials | free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation | Kristof Bal | COMMITTOR REWEIGHT_BIAS CONVERT_TO_FES HISTOGRAM ANN MOVINGRESTRAINT PRINT UNITS FLUSH CUSTOM COORDINATIONNUMBER VOLUME UPPER_WALLS DUMPGRID BIASVALUE LOAD RESTRAINT | gridtools symfunc bias function setup colvar annfunc generic |
| 22.007 | Characterization of a natural variant of human NDP52 and its functional consequences on mitophagy | bio | metadynamics, well-tempered, protein-protein interactions, disordered proteins, mutations autophagy | Elena Papaleo | WHOLEMOLECULES ALPHABETA TORSION PRINT ALPHARMSD FLUSH DISTANCE COORDINATION METAD MOLINFO UPPER_WALLS ANGLE | multicolvar bias colvar secondarystructure generic |
| 21.052 | On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets | materials | Ibuprofen, unbinding, WTmetaD | Matteo Salvalaglio | COMMITTOR CENTER TORSION PRINT DISTANCE COORDINATIONNUMBER METAD ENDPLUMED | symfunc bias vatom colvar generic |
| 21.023 | Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling | methods | enhanced sampling, collective variables, machine learning | Jakub Rydzewski | ENERGY PRINT UNITS TORSION CUSTOM DISTANCE METAD REWEIGHT_METAD INCLUDE BIASVALUE CONSTANT | function bias setup colvar generic |
| 21.022 | Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly | materials | parallel bias metadynamics, adsorption, peptide | Xin Qi | ENERGY PRINT GYRATION DISTANCE LOWER_WALLS PBMETAD COM MOLINFO UPPER_WALLS | vatom bias generic 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 | |
| 20.018 | Free energy barriers from biased molecular dynamics simulations | methods | kinetics, free energy barriers, chemical reactions, nucleation, metadynamics | Kristof Bal | DENSITY Q6 FLUSH DISTANCE COORDINATIONNUMBER LOWER_WALLS COMBINE REWEIGHT_BIAS PAIRENTROPY CONTACT_MATRIX UNITS SPRINT COORDINATION VOLUME REWEIGHT_METAD LOCAL_AVERAGE DUMPGRID LOAD HISTOGRAM CENTER PRINT CONVERT_TO_FES ENERGY METAD UPPER_WALLS | gridtools symfunc bias function vatom sprint setup volumes colvar adjmat generic |
| 20.016 | Predicting polymorphism in molecular crystals using orientational entropy | materials | metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy | Pablo Piaggi | CENTER GROUP PRINT VOLUME METAD INCLUDE UPPER_WALLS LOAD | bias vatom core setup colvar generic |
| 19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Valerio Rizzi | GROUP UNITS PRINT FLUSH COORDINATIONNUMBER METAD EXTERNAL ENDPLUMED RESTART COMBINE | symfunc bias function core setup generic |
| 19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | ENERGY PRINT GYRATION DISTANCE METAD COM MOLINFO UPPER_WALLS | vatom bias generic colvar |
| 19.073 | On the role of enthalpic and entropic contributions on the conformational free energy landscape of MIL-101(Cr) building units | materials | metadynamics, MOF, MIL101Cr, conformational | Matteo Salvalaglio | ENERGY PRINT GYRATION DISTANCES COORDINATIONNUMBER LOWER_WALLS METAD ENDPLUMED UPPER_WALLS | multicolvar symfunc bias colvar generic |
| 19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Cristina Paissoni | WHOLEMOLECULES ALPHABETA CENTER ANGLE GROUP PRINT SAXS STATS COORDINATION PBMETAD ENSEMBLE INCLUDE MATHEVAL MOLINFO BIASVALUE ENDPLUMED COMBINE | multicolvar isdb function bias vatom core colvar generic |
| 19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Silvio Pipolo | PRINT FUNCPATHMSD PIV METAD LOWER_WALLS UPPER_WALLS CELL | function piv bias colvar generic |
| 19.011 | Automatic Gradient Computation for Collective Variables | other | gradient, differentiation, curvature | Toni Giorgino | ENDPLUMED | generic |
| 19.009 | RNA tetraloops folding | bio | metadynamics, RNA, folding | Giovanni Bussi | WHOLEMOLECULES PRINT ERMSD METAD ENDPLUMED MOLINFO RMSD | bias colvar generic |
| 25.028 | Designing transferable transition state guided collective variable via interpretable machine learning model for enhanced sampling. A case study on polymer collapse transition | bio | metadynamics, polymer collapse transition, transferable CV,interpretable ML-model | Saikat Dhibar and Biman Jana | DISTANCE MATHEVAL WHOLEMOLECULES UPPER_WALLS CENTER GYRATION METAD LOWER_WALLS GROUP PRINT COORDINATION COMBINE | generic function colvar core vatom bias |
| 25.027 | Enhanced-sampling MD simulations of a protein-peptide complex integrating SAXS and XL-MS experimental information | bio | steered MD, metadynamics, SAXS, XL-MS, ensemble reconstruction | Mattia Bernetti | SAXS DISTANCE WHOLEMOLECULES INCLUDE UPPER_WALLS GYRATION METAD GROUP PRINT MOVINGRESTRAINT MOLINFO CENTER | isdb generic colvar core vatom bias |
| 25.025 | Enhanced Sampling of Ligand Binding Coupled to RNA Conformational Dynamics | bio | OPES, OPES Flooding , Metadynamics, RNA, Ligand binding, Free Energy, Kinetics, Funnel | Revanth Elangovan and Dhiman Ray | RMSD FUNNEL PRINT FUNNEL_PS ENDPLUMED COMMITTOR DISTANCE MATHEVAL WRAPAROUND LOWER_WALLS COORDINATION COM CENTER UPPER_WALLS CUSTOM GROUP OPES_METAD WHOLEMOLECULES METAD TORSION | funnel generic function colvar core vatom bias opes |
| 25.018 | Metainference simulation for dimerization of RNA binding protein | bio | Metainference, Metadynamics, SAXS, protein dimer | Debadutta Patra | SAXS FLUSH STATS DISTANCE WHOLEMOLECULES METAINFERENCE UPPER_WALLS GYRATION TORSION PRINT ENSEMBLE PBMETAD MOLINFO CENTER | isdb generic colvar function vatom bias |
| 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 | SMAC DUMPMULTICOLVAR DISTANCES PRINT TORSIONS | multicolvar symfunc generic |
| 25.001 | RNA G-quadruplex folding with ST-metaD protocol | bio | RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | ERMSD WHOLEMOLECULES METAD MOLINFO COMBINE | function bias generic colvar |
| 24.016 | Cryo-EM guided simulations of ribozyme | bio | metainference, cryo-EM | Giovanni Bussi | EMMIVOX ERMSD WHOLEMOLECULES INCLUDE GROUP PRINT RESTRAINT BIASVALUE MOLINFO | isdb generic core colvar bias |
| 24.008 | yCD Metadynamics | bio | volume-based MetaD, path CVs, infrequent MetaD, product release | James McCarty | REWEIGHT_METAD PATH RMSD PRINT ENDPLUMED COMMITTOR DISTANCE MATHEVAL INCLUDE WRAPAROUND COORDINATION COM CONTACTMAP CONVERT_TO_FES FIT_TO_TEMPLATE UPPER_WALLS GROUP HISTOGRAM MOLINFO FIXEDATOM READ FLUSH WHOLEMOLECULES DUMPGRID METAD | gridtools mapping generic function colvar core vatom bias |
| 24.007 | SWISH-X | bio | swish-x, SWISH-X, swish, expanded SWISH | Alberto Borsatto | ECV_MULTITHERMAL INCLUDE WHOLEMOLECULES UPPER_WALLS PRINT MOLINFO CONTACTMAP ENERGY OPES_EXPANDED | bias opes generic colvar |
| 23.039 | Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation | chemistry | metadynamics, ligand dissociation | Eric Beyerle | DUMPMASSCHARGE FIXEDATOM DISTANCE UPPER_WALLS METAD PRINT RESTRAINT COMBINE MOLINFO CENTER | generic function colvar vatom bias |
| 23.026 | Machine Learning Nucleation Collective Variables with Graph Neural Networks | chemistry | Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks | Florian Dietrich | LOCAL_Q6 COORDINATIONNUMBER MFILTER_MORE METAD LOWER_WALLS GROUP MOVINGRESTRAINT PRINT Q6 COMBINE | multicolvar generic core function bias symfunc |
| 23.013 | Path meta-eABF simulation of large scale conformational change in STING protein | methods | meta-eABF, path CV, large scale conformational change, STING protein, reciprocal barrier restraint | Istvan Kolossvary | UNITS FLUSH TIME DRR UPPER_WALLS CUSTOM METAD LOWER_WALLS PRINT PATHMSD BIASVALUE | generic function colvar bias drr setup |
| 23.006 | Transcription factor unbinding | bio | metadynamics, DNA, conformational changes | Malin Lüking | ANGLE DISTANCE ALPHARMSD METAD PRINT COM MOLINFO CONTACTMAP DUMPFORCES | secondarystructure generic colvar vatom bias |
| 22.044 | Colloid Crystallisation Analyses | materials | Q4, Q6, Pair Entropy, DFS | Aaron Finney | LOCAL_Q6 COORDINATIONNUMBER Q4 MFILTER_MORE MFILTER_LESS LOCAL_Q4 LOCAL_AVERAGE GROUP PRINT Q6 CONTACT_MATRIX COMBINE CLUSTER_NATOMS DFSCLUSTERING | multicolvar clusters adjmat generic core function symfunc |
| 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 DRR CUSTOM METAD PRINT PATHMSD BIASVALUE | generic function colvar bias drr |
| 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 | OPT_AVERAGED_SGD BF_CUBIC_B_SPLINES OPT_ADAM PRINT UNITS VES_LINEAR_EXPANSION DISTANCE INCLUDE TD_UNIFORM COORDINATION UPPER_WALLS BF_LEGENDRE ENERGY BF_GAUSSIANS BF_CHEBYSHEV FLUSH METAD BF_WAVELETS POSITION TD_WELLTEMPERED VES_OUTPUT_BASISFUNCTIONS | generic colvar ves bias setup |
| 21.049 | Multiple-path-metadynamics and PathMaps | methods | path-CV, metadynamics, multiple-walker, multiple paths, pathmap | Alberto Pérez-de-Alba-Ortíz | UNITS LOAD CONSTANT RESTRAINT UPPER_WALLS CUSTOM METAD LOWER_WALLS MOVINGRESTRAINT TORSION PRINT ENSEMBLE COMBINE | generic colvar function bias setup |
| 21.038 | Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics | materials | metadynamics, SGOOP, nucleation, urea | Ziyue Zou | LOAD COORDINATIONNUMBER VOLUME INCLUDE METAD GROUP PRINT COMBINE CENTER ENERGY | generic colvar core function vatom bias symfunc 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 | WHOLEMOLECULES UPPER_WALLS ALPHARMSD DIHCOR METAD ANTIBETARMSD PARABETARMSD LOWER_WALLS GROUP GYRATION PRINT COORDINATION RANDOM_EXCHANGES MOLINFO ENERGY | secondarystructure multicolvar generic core colvar bias |
| 21.029 | Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs | bio | metadynamics, small peptide, machine learning | Pratyush Tiwary | FLUSH EXTERNAL TORSION PRINT RESTART MOLINFO ENERGY | setup bias generic colvar |
| 21.027 | EGFR activating mutations mechanism | bio | metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA | Francesco Gervasio | DISTANCE MATHEVAL INCLUDE WHOLEMOLECULES UPPER_WALLS ALPHARMSD METAD LOWER_WALLS PRINT MOLINFO CONTACTMAP ENERGY | secondarystructure generic function colvar 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 MATHEVAL KDE PRINT COM TORSIONS | gridtools multicolvar generic function colvar vatom |
| 21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Adriana Pietropaolo | CONSTANT MATHEVAL WHOLEMOLECULES RESTART TORSION PRINT PBMETAD BIASVALUE | generic colvar function bias setup |
| 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 | WHOLEMOLECULES UPPER_WALLS METAD LOWER_WALLS PRINT PATHMSD RESTART | setup bias generic colvar |
| 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 CONVERT_TO_FES DUMPGRID METAD HISTOGRAM MULTI_RMSD PRINT RESTRAINT | gridtools bias generic colvar |
| 20.024 | Gaussian Mixture Based Enhanced Sampling (GAMBES) | methods | enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias | Jayashrita Debnath | UNITS LOAD DISTANCE UPPER_WALLS LOWER_WALLS GROUP DISTANCES TORSION PRINT COMBINE ENERGY | multicolvar generic colvar core function bias setup |
| 20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Vojtech Spiwok | METAD TORSION PRINT | bias generic colvar |
| 20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Luigi Bonati | UNITS LOAD OPES_METAD FLUSH DISTANCE MATHEVAL UPPER_WALLS LOWER_WALLS GROUP PYTORCH_MODEL TORSION PRINT COM ENDPLUMED | generic function colvar core vatom bias opes setup pytorch |
| 19.076 | Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones | bio | molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics | Salvatore Assenza | UNITS GYRATION PRINT MOVINGRESTRAINT ENDPLUMED | generic bias setup colvar |
| 19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Matteo Salvalaglio | DISTANCE INCLUDE GROUP PRINT ENDPLUMED CENTER | vatom core generic colvar |
| 19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Jakub Rydzewski | UNITS MAZE_OPTIMIZER_BIAS MAZE_LOSS POSITION PRINT MAZE_SIMULATED_ANNEALING | generic colvar setup maze |
| 19.050 | Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes | chemistry | metadynamics, membranes, Willard Chandler surface | Gareth Tribello | READ DISTANCE_FROM_CONTOUR CONVERT_TO_FES DUMPGRID UPPER_WALLS METAD REWEIGHT_BIAS HISTOGRAM PRINT RESTART COMBINE | gridtools generic function bias contour setup |
| 19.049 | Determining the sizes of solid/liquid clusters in MD trajectories of nucleation | methods | nucleation, metadynamics, clustering, Steinhardt order parameters | Gareth Tribello | LOCAL_Q6 COORDINATIONNUMBER OUTPUT_CLUSTER MATRIX_VECTOR_PRODUCT MORE_THAN CLUSTER_PROPERTIES CUSTOM ONES METAD SMAC DISTANCES PRINT Q6 CONTACT_MATRIX OUTER_PRODUCT CLUSTER_DISTRIBUTION CLUSTER_NATOMS DFSCLUSTERING | multicolvar clusters matrixtools generic function adjmat bias symfunc |
| 19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Vittorio Limongelli | DISTANCE WHOLEMOLECULES RMSD UPPER_WALLS FUNNEL METAD LOWER_WALLS PRINT COM FUNNEL_PS | funnel generic colvar vatom bias |
| 19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Haochuan Chen | DRR PRINT TORSION | generic drr colvar |
| 19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Kresten Lindorff-Larsen | FLUSH COMMITTOR METAD PRINT ALPHABETA MOLINFO COMBINE | multicolvar bias generic function |
| 19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Adriana Pietropaolo | CONSTANT MATHEVAL WHOLEMOLECULES METAD TORSION PRINT BIASVALUE | colvar bias generic function |
| 19.004 | MI Ubiquitin | bio | metainference, NMR | Max Bonomi | RDC WHOLEMOLECULES METAINFERENCE GROUP PRINT CS2BACKBONE MOLINFO | isdb generic core |
| 25.023 | Molecular simulations of Tau-protein oligomers | bio | metadynamics, proteins, aggregation | Giovanni Bussi | PRINT RESTART CONTACTMAP CONVERT_TO_FES CUSTOM RESTRAINT FLUSH DUMPGRID RMSD HISTOGRAM REWEIGHT_BIAS METAD | colvar setup function bias generic gridtools |
| 25.022 | Imidazole Diffusion in SALEM-2 MOF | materials | OPES, Diffusion, Ring opening, MOFs, Machine Learning Potentials | Sudheesh Kumar Ethirajan | PRINT MOLINFO OPES_METAD ENDPLUMED GROUP UNITS CENTER WHOLEMOLECULES DISTANCE PROJECTION_ON_AXIS DISTANCES | core colvar opes setup multicolvar vatom generic |
| 24.012 | Molecular simulations to investigate the impact of N6-methylation in RNA recognition | bio | metadynamics, alchemistry, RNA modification, RNA:protein interactions | Giovanni Bussi | PRINT DEBUG MOLINFO GHBFIX BIASVALUE GROUP COM CENTER LOWER_WALLS COMBINE COORDINATION DISTANCE UPPER_WALLS METAD | core colvar function bias vatom generic |
| 24.002 | Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes | chemistry | metadynamics, ligand design, solvent extraction | Xiaoyu Wang | PRINT RESTART TORSION UNITS METAD | setup bias generic colvar |
| 23.045 | Minute-timescale simulations of G Protein Coupled Receptor A2A activation mechanism reveal a receptor pseudo-active state | bio | Path CVs Metadynamics, GPCRs activation transition | Vittorio Limongelli | PRINT INCLUDE CONTACTMAP MOLINFO FUNCPATHMSD PATHMSD LOWER_WALLS ALPHARMSD DISTANCE UPPER_WALLS METAD | colvar function bias secondarystructure generic |
| 23.034 | Urea nucleation in water: do long-range forces matter? | materials | LMF theory, Metadynamics, Nucleation | Ziyue Zou | PRINT INCLUDE LOAD GROUP COORDINATIONNUMBER CENTER METAD | core symfunc setup bias vatom generic |
| 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 GHBFIX BIASVALUE WHOLEMOLECULES COMBINE COORDINATION ERMSD METAD | bias generic function colvar |
| 23.025 | Probing ion binding to G-quadruplexes and related events | chemistry | metadynamics, repulsive potential, nucleic acids, G-quadruplexes | Marcelo Poleto | PRINT LOWER_WALLS UPPER_WALLS POSITION RESTART WRAPAROUND DUMPATOMS GROUP FLUSH FIT_TO_TEMPLATE UNITS COM MATHEVAL DISTANCE DISTANCES WHOLEMOLECULES METAD | core colvar setup multicolvar function bias vatom generic |
| 23.024 | Permutationally Invariant Networks for Enhanced Sampling (PINES) | methods | collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent | Nicholas Herringer | PRINT LOAD PBMETAD | setup bias generic |
| 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 | PRINT UPPER_WALLS FIXEDATOM OPES_METAD_EXPLORE CUSTOM TORSION GROUP OPES_METAD PATH FIT_TO_TEMPLATE UNITS CENTER LOWER_WALLS PYTORCH_MODEL DISTANCE WHOLEMOLECULES COORDINATION | core colvar opes setup mapping function bias pytorch vatom generic |
| 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 | PRINT OPES_EXPANDED LOWER_WALLS RESTART ENVIRONMENTSIMILARITY DUMPGRID HISTOGRAM ECV_UMBRELLAS_LINE UPPER_WALLS | opes setup bias generic envsim gridtools |
| 22.015 | Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome | bio | photodynamics, bacteriophytochrome, variationally enhanced sampling | Jakub Rydzewski | PRINT BF_FOURIER OPT_AVERAGED_SGD TORSION VES_LINEAR_EXPANSION TD_UNIFORM | ves generic colvar |
| 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 | CONTACTMAP DISTANCE PRINT CENTER | vatom generic colvar |
| 22.008 | Ab initio metadynamics determination of temperature-dependent free-energy landscape in ultrasmall silver clusters | materials | Well tempered metadynamics, ab-initio, ase | Daniel Sucerquia | FLUSH UNITS COORDINATIONNUMBER COM LOWER_WALLS COMBINE COORDINATION DISTANCE GYRATION UPPER_WALLS METAD | symfunc colvar setup function bias vatom generic |
| 21.040 | A structural ensemble of a tau-microtubule complex reveals regulatory tau phosphorylation and acetylation mechanisms | bio | EMMI, CryoEM, tau-microtubules, post-translational modifications, chemical mutagenesis, structural ensemble, Metainference | Faidon Brotzakis | PRINT RESTART MOLINFO BIASVALUE GROUP EMMI COM WHOLEMOLECULES DISTANCE UPPER_WALLS | core colvar setup bias isdb vatom generic |
| 21.030 | Thermodynamic Basis for Stabilization of Helical Peptoids by Chiral Sidechains | bio | parallel bias parallel tempered metadynamics in WTE, synthetic foldamers, self-assembly, peptoid secondary structure | Jim Pfaendtner | PRINT ENERGY INCLUDE ALPHABETA TORSION METAD PBMETAD COM DISTANCE GYRATION COORDINATION | colvar multicolvar bias vatom generic |
| 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 FIXEDATOM COM UPPER_WALLS METAD READ FLUSH ENDPLUMED RMSD DISTANCE COORDINATION PRINT POSITION DUMPGRID MATHEVAL WHOLEMOLECULES CONVERT_TO_FES GROUP HISTOGRAM | core colvar function bias vatom generic gridtools |
| 21.013 | Role of vibrational excitation in heterogeneous catalysis | chemistry | catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption | Kristof Bal | REWEIGHT_METAD TD_GRID UWALLS COORDINATIONNUMBER UPPER_WALLS METAD OPT_AVERAGED_SGD FLUSH UNITS LOWER_WALLS COMBINE DISTANCE REWEIGHT_BIAS COORDINATION PRINT BF_CHEBYSHEV RESTRAINT EXTERNAL DUMPGRID ANGLES CONVERT_TO_FES LOAD HISTOGRAM VES_LINEAR_EXPANSION DISTANCES | symfunc colvar setup multicolvar function bias ves generic gridtools |
| 20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Faidon Brotzakis | PRINT READ CONVERT_TO_FES MOLINFO BIASVALUE GROUP EMMI DUMPGRID HISTOGRAM RMSD WHOLEMOLECULES DISTANCES | core colvar multicolvar bias isdb generic gridtools |
| 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 | PRINT STATS MOLINFO RESTRAINT WHOLEMOLECULES COMBINE COORDINATION | bias generic function colvar |
| 20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Cristina Paissoni | PRINT STATS INCLUDE MOLINFO RESTRAINT SAXS GROUP BIASVALUE ENSEMBLE CENTER WHOLEMOLECULES DISTANCE | core colvar function bias isdb vatom generic |
| 20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Glen Hocky | PRINT ENERGY RESTRAINT BIASVALUE GROUP UNITS MATHEVAL DISTANCE FISST GYRATION | core colvar setup function fisst bias generic |
| 19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Matteo Salvalaglio | COMMITTOR PRINT REWEIGHT_METAD READ CONVERT_TO_FES BIASVALUE TORSION EXTERNAL DUMPGRID HISTOGRAM MATHEVAL DISTANCE REWEIGHT_BIAS METAD | colvar function bias generic gridtools |
| 19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Jim Pfaendtner | PRINT ENERGY WHOLEMOLECULES GYRATION METAD | bias generic colvar |
| 19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Kim Jelfs | MOVINGRESTRAINT PRINT RESTART DISTANCES FLUSH COM INPLANEDISTANCES | setup multicolvar bias vatom generic |
| 19.041 | Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces | bio | metadynamics, collective variables, conformational changes, multiple walkers, Well-Tempered MetaD, peptide, binding, phosphorylation, post-transitional motif, sio2, adsorption | Jim Pfaendtner | PRINT ENERGY COM DISTANCE UPPER_WALLS METAD | bias vatom generic colvar |
| 19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Matteo Salvalaglio | PRINT MATHEVAL ENERGY TORSION ENDPLUMED VOLUME LOWER_WALLS COMBINE CELL UPPER_WALLS METAD | bias generic function colvar |
| 19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Matteo Salvalaglio | COMMITTOR PRINT TORSION CENTER LOWER_WALLS DISTANCE UPPER_WALLS METAD | bias vatom generic colvar |
| 19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Carlo Camilloni | PRINT STATS UPPER_WALLS RDC MOLINFO DIHCOR RESTRAINT ALPHABETA GROUP TORSION DHENERGY PBMETAD ENDPLUMED ENSEMBLE CENTER WHOLEMOLECULES DISTANCE METAINFERENCE | core colvar multicolvar function bias isdb vatom generic |
| 19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Michele Invernizzi | PRINT POSITION ENERGY RESTART LOAD TORSION ENDPLUMED UNITS VES_DELTA_F METAD | colvar setup bias ves generic |
| 26.000 | OPES simulations of disordered proteins | bio | OPES, IDPs | Julian Streit | RESTART ECV_MULTITHERMAL OPES_EXPANDED ENERGY PRINT | setup generic opes colvar |
| 25.030 | Committor Regularization | methods | metadynamics, enhanced sampling, mlcvs, committor, machine learning | Florian Dietrich | METAD MOVINGRESTRAINT PRINT UNITS | setup generic bias |
| 25.029 | Energetic Constraints in the Enzymatic Depolymerization of Crystalline PET from enhanced molecular simulations | bio | HREX-Metadynamics, PETase, crystalline PET, amorphous PET, conformational ensembles, substrate binding, chain detachment | Ania Di Pede-Mattatelli and Francesco Colizzi | UPPER_WALLS DUMPGRID METAD FIXEDATOM CONVERT_TO_FES HISTOGRAM MOLINFO REWEIGHT_BIAS WHOLEMOLECULES COM DISTANCE PRINT LOWER_WALLS | generic bias gridtools colvar vatom |
| 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 | GROUP EMMIVOX BIASVALUE MOLINFO WHOLEMOLECULES PRINT | core isdb generic bias |
| 25.014 | Atomic resolution ensembles of intrinsically disordered proteins with Alphafold | bio | bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement | Vincent Schnapka | BAIES GROUP PRINT BIASVALUE | core isdb generic bias |
| 25.013 | Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices | bio | umbrella sampling, temperature ramping | Alexander Berlaga | GYRATION PYTORCH_MODEL DISTANCE PRINT RESTRAINT | pytorch colvar generic bias |
| 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 | GROUP DUMPGRID ANGLE CONVERT_TO_FES TORSION HISTOGRAM COORDINATION WHOLEMOLECULES DISTANCE PRINT | core generic gridtools colvar |
| 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 | UPPER_WALLS GROUP EMMI PARABETARMSD DUMPMASSCHARGE COM CENTER ALPHARMSD DUMPATOMS PBMETAD MOLINFO COORDINATION BIASVALUE WHOLEMOLECULES DISTANCE RMSD PRINT | generic bias core secondarystructure isdb colvar vatom |
| 24.032 | DeepLNE++ | methods | PATHCV, OPES | Thorben Fröhlking | COMBINE CUSTOM GROUP TORSION COORDINATION DISTANCE ENERGY PRINT LOAD OPES_METAD | generic setup core opes function colvar |
| 24.009 | Weighted Shape Gaussian Mixture Models | bio | metadynamics, clustering | Glen Hocky | GROUP METAD TORSION UNITS PRINT | generic bias setup core colvar |
| 24.004 | Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables | materials | metadynamics, nucleation, machine learning | Ziyue Zou | RESTART INCLUDE GROUP METAD PRINT LOAD | setup core generic bias |
| 23.027 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, DFS, Q3, Pair Entropy | Aaron Finney | CONTACT_MATRIX COORDINATIONNUMBER GROUP DUMPGRID LOCAL_Q3 LOCAL_AVERAGE DFSCLUSTERING FIXEDATOM DENSITY CLUSTER_NATOMS UNITS HISTOGRAM AROUND Q3 CLUSTER_DISTRIBUTION PRINT LOAD RESTRAINT | generic bias setup adjmat core gridtools volumes symfunc clusters vatom |
| 23.022 | A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar | methods | collective variables, machine learning, toy model | Enrico Trizio | UPPER_WALLS CUSTOM POSITION ENDPLUMED UNITS PYTORCH_MODEL BIASVALUE OPES_METAD PRINT LOWER_WALLS | generic pytorch bias setup opes function colvar |
| 23.020 | FEP simulations of ATOX1 homodimer | chemistry | parallel bias metadynamics, FEP, free-energy of metal ion dissociation | Adriana Pietropaolo | MATHEVAL ANGLE PBMETAD BIASVALUE WHOLEMOLECULES DISTANCE PRINT CONSTANT | function generic colvar 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 | CONTACTMAP UPPER_WALLS CUSTOM WHOLEMOLECULES COMMITTOR RMSD PRINT OPES_METAD INCLUDE GROUP COORDINATION CENTER DISTANCE ENERGY MATHEVAL MOLINFO LOWER_WALLS FIT_TO_TEMPLATE COMBINE ENDPLUMED ANGLE PYTORCH_MODEL FIXEDATOM | generic pytorch bias core opes function colvar vatom |
| 23.001 | Quantum phase diagram of water | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn-Løland Bore | RESTART UPPER_WALLS INCLUDE ENVIRONMENTSIMILARITY ECV_UMBRELLAS_LINE OPES_EXPANDED PRINT LOWER_WALLS | generic bias setup opes envsim |
| 22.045 | Binding mode and mechanism of enzymatic polyethylene terephthalate degradation | bio | metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation | Francesco Colizzi | UPPER_WALLS METAD ANGLE WHOLEMOLECULES COM DISTANCE MOVINGRESTRAINT PRINT LOWER_WALLS | generic colvar bias vatom |
| 22.038 | Enhanced Sampling Aided Design of Molecular Photoswitches | chemistry | reaction discovery, OPES explore, graph CV | Umberto Raucci | CUSTOM UNITS PYTORCH_MODEL COORDINATION PRINT OPES_METAD_EXPLORE | pytorch generic setup opes function colvar |
| 22.037 | Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site | chemistry | metadynamics, DNA, abasic | Mike Jones | METAD DISTANCE PRINT DISTANCES | multicolvar generic colvar bias |
| 22.033 | Reciprocal barrier restraint. Application to PROTAC passive permeability prediction | methods | PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR | Istvan Kolossvary | CUSTOM METAD DRR UNITS BIASVALUE COM DISTANCE FLUSH PRINT | generic bias setup drr function colvar vatom |
| 22.030 | Mixing physics across temperatures with generative artificial intelligence | methods | REMD, Generative AI, DDPM | Yihang Wang | PRINT TORSION WHOLEMOLECULES | generic colvar |
| 22.027 | Molecular Dynamics simulations of BANAL-236 RBD-hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, BANAL-236, receptor-binding domain | Max Bonomi | RMSD PRINT | generic colvar |
| 22.023 | 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 | RESTART UPPER_WALLS GROUP EMMI TORSION PBMETAD BIASVALUE MOLINFO COORDINATION WHOLEMOLECULES COM RMSD PRINT | generic bias setup core isdb colvar vatom |
| 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 |
| 22.004 | Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques | chemistry | reaction discovery, OPES, collective variables | Umberto Raucci | MATHEVAL UPPER_WALLS CUSTOM GROUP LOWER_WALLS UNITS PYTORCH_MODEL COORDINATION COM DISTANCE PRINT LOAD OPES_METAD OPES_METAD_EXPLORE | pytorch generic bias setup core opes function colvar vatom |
| 21.050 | N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity | methods | bio | Isabell Louise Grothaus | CENTER DISTANCE PRINT | generic colvar vatom |
| 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 GROUP METAD ENDPLUMED GYRATION ALPHABETA WHOLEMOLECULES PRINT LOWER_WALLS | generic multicolvar bias core colvar |
| 21.044 | NaCl nucleation | chemistry | metadynamics, DFS clustering | Aaron Finney | CONTACT_MATRIX COORDINATIONNUMBER COMBINE GROUP MFILTER_MORE DUMPGRID DFSCLUSTERING METAD LOCAL_Q6 CLUSTER_NATOMS HISTOGRAM CLUSTER_DISTRIBUTION Q6 FIXEDATOM INSPHERE PRINT | generic multicolvar bias adjmat core gridtools volumes function symfunc clusters vatom |
| 21.043 | Predicting the Conformational Variability of Oncogenic GTP-bound G12D Mutated KRas-4B Proteins at Cell Membranes | chemistry | well-tempered metadynamics, KRas-4B, anionic membrane, conformational variability | Huixia Lu | METAD TORSION FIXEDATOM PRINT FIT_TO_TEMPLATE | generic colvar bias vatom |
| 20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Jim Pfaendtner | RESTART GROUP DISTANCES COORDINATION WHOLEMOLECULES CENTER DISTANCE PRINT | generic multicolvar setup core colvar vatom |
| 20.008 | Simulating solvation and acidity in complex mixtures with first-principles accuracy. The case of CH3SO3H and H2O2 in phenol | chemistry | proton trasfer, metadynamics | Kevin Rossi | CUSTOM METAD UNITS DISTANCES COORDINATION PRINT | generic multicolvar bias setup function colvar |
| 20.001 | Conformational stability and dynamics in solution and in crystals report similarly on unfolding and aggregation propensity of amyloidogenic proteins | bio | metainference, metadynamics, NMR, protein dynamics, b2m, protein crystals | Carlo Camilloni | CS2BACKBONE UPPER_WALLS GROUP ENDPLUMED ANTIBETARMSD PBMETAD MOLINFO ALPHABETA BIASVALUE WHOLEMOLECULES FLUSH PRINT LOWER_WALLS | generic multicolvar bias core secondarystructure isdb |
| 19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Giovanni Bussi | ENDPLUMED LOWER_WALLS COORDINATION WHOLEMOLECULES DISTANCE RESTRAINT | generic colvar bias |
| 19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Giovanni Bussi | MATHEVAL INCLUDE MAXENT METAD SORT TORSION MOLINFO COORDINATION WHOLEMOLECULES COM DISTANCE FLUSH PRINT | generic bias function colvar vatom |
| 19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Jakub Rydzewski | RESTART UPPER_WALLS METAD UNITS PATHMSD PRINT LOWER_WALLS | setup generic colvar bias |
| 19.059 | cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide | bio | bias-exchange metadynamics, cis-trans isomerization | Fabrizio Marinelli | INCLUDE METAD TORSION RANDOM_EXCHANGES PRINT | generic colvar bias |
| 19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | RESTART COMBINE UPPER_WALLS METAD DISTANCES UNITS DISTANCE FLUSH PRINT | generic multicolvar bias setup function colvar |
| 19.023 | RECT | methods | metadynamics, replica exchange | Giovanni Bussi | METAD TORSION GYRATION WHOLEMOLECULES PRINT | generic colvar bias |
| 19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Matteo Salvalaglio | RESTART COORDINATIONNUMBER METAD ENDPLUMED GYRATION DISTANCES PRINT | generic multicolvar bias setup symfunc colvar |
| 19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Max Bonomi | GROUP EMMI BIASVALUE MOLINFO WHOLEMOLECULES PRINT | core isdb generic bias |
| 19.003 | EMMI ClpP | bio | metainference, cryo-EM | Max Bonomi | GROUP EMMI MOLINFO BIASVALUE PRINT | core isdb 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 | COM PRINT FUNNEL_PS METAD UPPER_WALLS FUNNEL LOWER_WALLS | vatom bias funnel generic |
| 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 | OPES_METAD_EXPLORE ANGLE FIT_TO_TEMPLATE WHOLEMOLECULES CENTER ENERGY PRINT COORDINATION MATHEVAL UPPER_WALLS GROUP DISTANCE FIXEDATOM | colvar bias opes generic vatom function core |
| 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 | OPES_METAD_EXPLORE PATHMSD RMSD CENTER ENERGY CUSTOM PRINT ECV_MULTITHERMAL COORDINATION GHOST UPPER_WALLS GROUP DISTANCE DISTANCES OPES_EXPANDED LOWER_WALLS | colvar bias opes vatom generic function core multicolvar |
| 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 | PRINT TORSION RESTART PUCKERING METAD RESTRAINT MOLINFO DISTANCE MOVINGRESTRAINT | generic setup colvar bias |
| 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 ANTIBETARMSD WHOLEMOLECULES INCLUDE PRINT FLUSH TORSION ALPHARMSD COORDINATION DIHCOR ENDPLUMED GROUP MOLINFO DISTANCE GYRATION PBMETAD COMBINE | colvar bias generic function multicolvar core secondarystructure |
| 24.017 | Absolute Binding Free Energies with OneOPES | methods | protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy | Francesco Gervasio | WRAPAROUND PROJECTION_ON_AXIS WHOLEMOLECULES BIASVALUE CUSTOM RESTART RMSD CONSTANT INCLUDE ECV_MULTITHERMAL COORDINATION CONTACTMAP UPPER_WALLS LOWER_WALLS COM TORSION MOLINFO OPES_METAD_EXPLORE ENERGY PRINT MATHEVAL METAD GROUP OPES_EXPANDED | colvar bias opes generic setup function vatom core |
| 24.011 | Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble | methods | committor, machine learning | Peilin Kang | BIASVALUE WHOLEMOLECULES CUSTOM POSITION RMSD INCLUDE COORDINATION UNITS UPPER_WALLS DISTANCE LOWER_WALLS TORSION LOAD MOLINFO ENDPLUMED PRINT ENERGY MATHEVAL GROUP CELL | colvar bias generic setup function core |
| 22.042 | Metadynamics of NSP10 and variants | bio | metadynamics, NSP10, crystal structure, variants | Shozeb Haider | PRINT TORSION METAD | generic colvar bias |
| 22.039 | Driving and characterizing nucleation of urea and glycine polymorphs in water | bio | metadynamics, nucleation, amino acids, polymorphism | Eric Beyerle | PAIRENTROPY PRINT INCLUDE CENTER COORDINATIONNUMBER LOAD MATHEVAL METAD GROUP Q4 COMBINE Q6 | bias generic setup vatom function core gridtools symfunc |
| 21.042 | Peptoid-mediated Au nanocrystal growth | materials | parallel-bias metadynamics, peptoid, Au | Xin Qi | COM PRINT UPPER_WALLS MOLINFO DISTANCE GYRATION PBMETAD | vatom colvar bias generic |
| 21.028 | From Enhanced Sampling to Reaction Profiles | methods | collective variables, multi-state, machine learning, Deep-TDA | Enrico Trizio | WHOLEMOLECULES FIXEDATOM CENTER COORDINATION UNITS UPPER_WALLS OPES_METAD DISTANCE LOWER_WALLS ANGLE FIT_TO_TEMPLATE TORSION LOAD ENDPLUMED PRINT MATHEVAL GROUP DISTANCES PYTORCH_MODEL | colvar bias opes generic setup vatom function core multicolvar pytorch |
| 21.017 | All-atom simulations of the Vav1 AD construct | bio | metadynamics, parallel-bias, well-tempered | Simone Orioli | ALPHABETA WHOLEMOLECULES PRINT ALPHARMSD RESTART CONTACTMAP METAD GROUP MOLINFO PBMETAD REWEIGHT_BIAS | colvar bias generic setup multicolvar core secondarystructure |
| 21.012 | NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition | bio | funnel metadynamics | Jim Pfaendtner | COM PRINT FUNNEL_PS METAD UPPER_WALLS DISTANCE FUNNEL LOWER_WALLS | colvar bias vatom generic funnel |
| 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 | BF_LEGENDRE OPT_AVERAGED_SGD ECV_UMBRELLAS_LINE PRINT ENERGY RESTART TD_UNIFORM MATHEVAL UPPER_WALLS ENVIRONMENTSIMILARITY VOLUME ECV_MULTITHERMAL_MULTIBARIC Q6 OPES_EXPANDED VES_LINEAR_EXPANSION | ves colvar bias opes generic setup function envsim symfunc |
| 20.032 | Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil | materials | clustering, conformational isomers | Matteo Salvalaglio | ENDPLUMED PRINT TORSION | generic colvar |
| 20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Adriana Pietropaolo | WHOLEMOLECULES CENTER PRINT COORDINATION PBMETAD | generic colvar bias vatom |
| 20.015 | Rational design of ASCT2 inhibitors using an integrated experimental-computational approach | bio | ASCT2 transporter, small-molecules, cryo-EM, metainference | Max Bonomi | WHOLEMOLECULES EMMIVOX BIASVALUE PRINT LOAD DUMPATOMS GROUP MOLINFO | bias isdb generic setup core |
| 20.012 | Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies | bio | metadynamics, well-tempered ensemble, ligand binding, binding affinity calculations, novel COLVAR, funnel restraints, Hamiltonian replica-exchange, PathCV, COMetPath, SWISH | Francesco Gervasio | COM CONSTANT WHOLEMOLECULES INCLUDE PROJECTION_ON_AXIS BIASVALUE PRINT LOAD MATHEVAL UPPER_WALLS GROUP METAD DISTANCE CONTACTMAP MOLINFO FUNCPATHGENERAL LOWER_WALLS | colvar bias vatom setup generic function core |
| 20.010 | Phase equilibrium of liquid water and hexagonal ice from enhanced sampling molecular dynamics simulations | materials | water, ice, TIP4P, crystallization, EnvironmentSimilarity, RefCV, kernel, VES, variationally enhanced sampling | Pablo Piaggi | BF_LEGENDRE OPT_AVERAGED_SGD PRINT RESTART MATHEVAL UPPER_WALLS ENVIRONMENTSIMILARITY TD_WELLTEMPERED VOLUME OPT_DUMMY Q6 VES_LINEAR_EXPANSION | ves colvar bias generic setup function envsim symfunc |
| 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 | CONVERT_TO_FES COM ENDPLUMED PRINT REWEIGHT_METAD MATHEVAL UPPER_WALLS METAD DISTANCE READ HISTOGRAM COMBINE DUMPGRID ABMD LOWER_WALLS | colvar bias vatom function generic gridtools |
| 19.075 | PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python | other | Python, automatic differentiation | Toni Giorgino | DUMPDERIVATIVES ANGLE ENDPLUMED PRINT CENTER CUSTOM TORSION RESTRAINT GROUP DISTANCE COMBINE | colvar bias generic function vatom core |
| 19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Wei Chen | POSITION COM RESTRAINT ANN COMBINE | colvar bias annfunc vatom function |
| 19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | COM PRINT ENERGY METAD UPPER_WALLS MOLINFO DISTANCE GYRATION | vatom colvar bias generic |
| 19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Gareth Tribello | CENTER MULTICOLVARDENS MORE_THAN FCCUBIC UNITS GROUP FIND_CONTOUR_SURFACE FOURIER_TRANSFORM DUMPGRID | vatom setup function core contour symfunc gridtools fourier |
| 19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Gareth Tribello | ENDPLUMED PRINT FCCUBIC UNITS METAD AROUND UPPER_WALLS CELL LOWER_WALLS | colvar bias generic setup symfunc volumes |
| 19.048 | Understanding Ligand Binding Selectivity in a Prototypical GPCR Family | bio | metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | COM CONSTANT WHOLEMOLECULES BIASVALUE PRINT MATHEVAL METAD UPPER_WALLS DISTANCE LOWER_WALLS | colvar bias vatom function generic |
| 19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Davide Provasi | FUNCPATHMSD COM RMSD WHOLEMOLECULES PRINT ENDPLUMED CONTACTMAP METAD DISTANCE | colvar bias function generic vatom |
| 19.030 | Coarse-Grained MetaDynamics (CG-MetaD) | bio | Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy | Vittorio Limongelli | COM WHOLEMOLECULES PRINT METAD UPPER_WALLS DISTANCE LOWER_WALLS | vatom colvar bias generic |
| 19.005 | Cmyc small molecule interaction | bio | metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP | Gabriella Heller | ALPHABETA WHOLEMOLECULES INCLUDE PRINT CS2BACKBONE CENTER COORDINATION GROUP MOLINFO PBMETAD GYRATION DISTANCE METAINFERENCE | colvar bias isdb generic vatom multicolvar core |
| 19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Giovanni Bussi | ANGLE ERMSD PRINT INCLUDE FLUSH METAD UPPER_WALLS MOLINFO DISTANCE DISTANCES COMBINE RANDOM_EXCHANGES LOWER_WALLS | colvar bias generic function multicolvar |
| 26.007 | Metadynamics Simulations Reveal the Protonation-Dependent Conformational Landscape of GSK-3β Dual Inhibitors | chemistry | metadynamics, ligand unbinding, path CVs, funnel metadynamics | Gian Marco Elisi | DISTANCE FUNNEL_PS FUNNEL UNITS WHOLEMOLECULES COM MATHEVAL UPPER_WALLS ANGLE ENDPLUMED METAD MOLINFO PRINT LOWER_WALLS COMBINE RMSD PATHMSD | generic funnel function setup bias colvar vatom |
| 25.016 | Advancing in silico drug design with Bayesian refinement of AlphaFold models | bio | bAIes, AlphaFold, Bayesian refinement, virtual screening, docking, small-molecule, enrichment | Samiran Sen | PRINT BAIES GROUP BIASVALUE | generic isdb core 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 | DISTANCE COMMITTOR FLUSH FIXEDATOM UNITS CUSTOM OPES_METAD ZDISTANCES UPPER_WALLS GROUP COORDINATIONNUMBER PRINT DISTANCES | opes generic symfunc function core setup bias colvar multicolvar vatom |
| 24.030 | NMR guided simulation of dsRBD | bio | Metainference, NMR, protein dynamics | Debadutta Patra | DISTANCE FLUSH ENSEMBLE WHOLEMOLECULES ALPHABETA STATS GROUP METAINFERENCE RDC MOLINFO PRINT | generic function isdb colvar multicolvar core |
| 24.029 | Combination of OPES and OPES-Explore | methods | OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin | Dhiman Ray | FIXEDATOM UNITS ENDPLUMED COMBINE RMSD POSITION COORDINATION CONTACTMAP CENTER MOLINFO PRINT LOWER_WALLS DISTANCE GROUP METAD PYTORCH_MODEL FLUSH WHOLEMOLECULES OPES_METAD ENERGY CUSTOM BIASVALUE INCLUDE MATHEVAL UPPER_WALLS OPES_METAD_EXPLORE FIT_TO_TEMPLATE | opes generic function core setup bias colvar pytorch vatom |
| 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 | DISTANCE PYTORCH_MODEL COORDINATION PATH FIXEDATOM WHOLEMOLECULES CUSTOM OPES_METAD CENTER UPPER_WALLS GROUP TORSION LOWER_WALLS PRINT RESTART FIT_TO_TEMPLATE | mapping opes generic vatom function core setup bias colvar pytorch |
| 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 | DISTANCE COORDINATION RESTART ECV_MULTITHERMAL OPES_EXPANDED CUSTOM ENERGY GROUP TORSION PRINT OPES_METAD_EXPLORE COMBINE | opes generic function setup colvar core |
| 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 | PYTORCH_MODEL COORDINATION FLUSH DRR MOLINFO WHOLEMOLECULES UPPER_WALLS METAD LOWER_WALLS PRINT RMSD | generic bias colvar drr pytorch |
| 24.010 | Oxytocin metadynamics simulation | bio | metadynamics, oxytocin, peptide | Jan Beránek | FLUSH WHOLEMOLECULES METAD TORSION PRINT RESTART | generic setup bias colvar |
| 23.046 | Lasso Peptides - HLDA CV | bio | metadynamics, protein folding, HLDA, harmonic | Gabriel da Hora | DISTANCE UNITS WHOLEMOLECULES METAD PRINT COMBINE | generic function setup colvar 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 | TRANSPOSE FLUSH SELECT_COMPONENTS MATHEVAL INCLUDE METAD PRINT SUM | generic function valtools matrixtools 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 | DISTANCE EMMIVOX WHOLEMOLECULES BIASVALUE INCLUDE UPPER_WALLS GROUP MOLINFO PRINT WRAPAROUND | generic bias isdb 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 | Q4 VOLUME ENERGY MATHEVAL COORDINATIONNUMBER METAD PRINT COMBINE Q6 | generic symfunc function colvar bias |
| 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 | DISTANCE ENSEMBLE SAXS BIASVALUE STATS CENTER UPPER_WALLS GROUP MOLINFO PRINT RMSD WRAPAROUND | generic vatom function core isdb colvar bias |
| 23.021 | Into the Dynamics of Rotaxanes at Atomistic Resolution | materials | metadynamics, rotaxanes, molecular shuttles, molecular machines | Luigi Leanza | DISTANCE FIXEDATOM CUSTOM CENTER UPPER_WALLS MATHEVAL METAD TORSION PRINT | generic function bias colvar 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 CONVERT_TO_FES DUMPGRID WHOLEMOLECULES READ MATHEVAL REWEIGHT_METAD METAD MOLINFO PRINT HISTOGRAM RMSD | generic gridtools function colvar bias |
| 22.034 | Rationalising the difference in crystallisability of two Sulflowers using efficient in silico methods | materials | metadynamics, crystallizability, crystal structure prediction, sulflower, persulforated coronene | Matteo Salvalaglio | COMMITTOR DRMSD CUSTOM MATHEVAL UPPER_WALLS METAD LOWER_WALLS PRINT CELL | function generic bias colvar |
| 22.031 | Rare Event Kinetics from Adaptive Bias Enhanced Sampling | methods | OPES Flooding, Kinetics, Rate, OPES, Machine Learning | Dhiman Ray | UNITS ENDPLUMED COMBINE POSITION RMSD COMMITTOR CONTACTMAP MOLINFO CONSTANT PRINT DISTANCE GROUP TORSION PYTORCH_MODEL CUSTOM OPES_METAD ENERGY BIASVALUE WHOLEMOLECULES INCLUDE | opes generic function setup bias colvar pytorch core |
| 22.029 | Angiotensin-1-7_Metadynamics | bio | Metadynamics, Angiotensin-(1-7), peptide | L.-América Chi | COORDINATION FLUSH WHOLEMOLECULES GYRATION UPPER_WALLS GROUP METAD LOWER_WALLS PRINT | core generic bias colvar |
| 22.018 | Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations | bio | ligand binding, docking, EMMI, LAT1 | Max Bonomi | LOAD EMMIVOX WHOLEMOLECULES BIASVALUE GROUP MOLINFO PRINT | generic setup bias isdb core |
| 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 | ENVIRONMENTSIMILARITY DUMPGRID VOLUME ENERGY OPES_METAD CUSTOM UPPER_WALLS AROUND HISTOGRAM PRINT RESTART | opes generic gridtools function volumes setup envsim colvar bias |
| 21.047 | Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations | materials | pair entropy, metadynamics, ves, solids, crystallization | Pablo Piaggi | PAIRENTROPY LOAD TD_WELLTEMPERED VOLUME ENERGY OPT_AVERAGED_SGD BF_LEGENDRE METAD PRINT RESTART COMBINE VES_LINEAR_EXPANSION | generic gridtools function setup colvar bias ves |
| 21.032 | Metal-coupled folding mechanism to metallothionein | bio | parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination | Manuel-Peris Diaz | COORDINATION PBMETAD UNITS WHOLEMOLECULES GROUP | generic setup bias colvar core |
| 21.031 | Photo-switchable sulfonulureas in KATP channel | bio | metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels | Katarzyna Walczewska-Szewc | DISTANCE UNITS WHOLEMOLECULES COM UPPER_WALLS METAD LOWER_WALLS PRINT | generic setup bias colvar vatom |
| 21.026 | Probing allosteric regulations with coevolution-driven molecular simulations | bio | metadynamics, coevolution, allostery, adenylate cyclase | Francesco Colizzi | DISTANCE UNITS WHOLEMOLECULES COM UPPER_WALLS METAD PRINT PATHMSD | generic setup bias colvar vatom |
| 21.020 | Reweighted Jarzynski sampling | methods | free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions | Kristof Bal | TD_WELLTEMPERED UNITS REWEIGHT_METAD COMBINE COORDINATIONNUMBER RESTRAINT PRINT CONSTANT OPT_AVERAGED_SGD VES_LINEAR_EXPANSION CONVERT_TO_FES DISTANCE MOVINGRESTRAINT METAD REWEIGHT_BIAS LOAD FLUSH DUMPGRID CUSTOM OPES_METAD BIASVALUE UPPER_WALLS BF_CHEBYSHEV HISTOGRAM ANN | opes generic symfunc gridtools function annfunc setup colvar bias ves |
| 21.016 | MD SAXS GTPase associated center | bio | metadynamics, RNA, folding, SAXS | Giovanni Bussi | ERMSD WHOLEMOLECULES SAXS CUSTOM GYRATION INCLUDE UPPER_WALLS GROUP METAD MOLINFO PRINT LOWER_WALLS | generic function core isdb colvar bias |
| 21.011 | CmuMD simulations of NaCl(aq) at graphite | chemistry | CmuMD, DFS clustering | Aaron Finney | CONTACT_MATRIX DENSITY LOAD DUMPGRID DFSCLUSTERING FIXEDATOM RESTRAINT MULTICOLVARDENS CLUSTER_DISTRIBUTION MFILTER_MORE GROUP AROUND COORDINATIONNUMBER CLUSTER_NATOMS PRINT | generic symfunc gridtools core volumes setup bias clusters adjmat multicolvar vatom |
| 19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Valerio Rizzi | RESTART FLUSH UNITS UPPER_WALLS GROUP ENDPLUMED COORDINATIONNUMBER METAD PRINT DISTANCES COMBINE | generic symfunc function setup bias multicolvar core |
| 19.080 | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | methods | ves, variationally enhanced sampling, vibrational excitation, chemical reactions | Kristof Bal | DISTANCE CONVERT_TO_FES COORDINATION EXTERNAL TD_WELLTEMPERED FLUSH DUMPGRID TD_GRID UNITS OPT_AVERAGED_SGD UPPER_WALLS BF_CHEBYSHEV ANGLE HISTOGRAM LOWER_WALLS PRINT COMBINE VES_LINEAR_EXPANSION | generic gridtools function setup colvar bias ves |
| 19.056 | maze | methods | maze, ligand unbinding | Jakub Rydzewski | UNITS MAZE_OPTIMIZER_BIAS MAZE_SIMULATED_ANNEALING MAZE_LOSS PRINT POSITION | maze generic setup colvar |
| 19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Carlo Camilloni | PBMETAD FLUSH ANTIBETARMSD WHOLEMOLECULES CS2BACKBONE BIASVALUE ALPHABETA UPPER_WALLS GROUP ENDPLUMED LOWER_WALLS MOLINFO PRINT RESTART | generic core setup isdb secondarystructure multicolvar bias |
| 19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Carlo Camilloni | DISTANCE SAXS WHOLEMOLECULES RESTRAINT BIASVALUE CENTER STATS INCLUDE UPPER_WALLS GROUP ENDPLUMED MOLINFO PRINT RMSD | generic vatom function core isdb colvar bias |
| 26.005 | Cryptic pocket discovery in Alzheimer disease risk proteins BIN1, PICALM, and CD2AP via well-tempered metadynamics | methods | cryptic pockets, Alzheimer disease, BIN1, PICALM, CD2AP, well-tempered metadynamics, endocytosis, clathrin-mediated trafficking, virtual screening | Cagrı Ozkurt | ANGLE DISTANCE PRINT WHOLEMOLECULES METAD | colvar bias generic |
| 25.011 | Chiral perovskite nucleation | chemistry | metadynamics, chiral perovskites, nucleation | Adriana Pietropaolo | DISTANCE MATHEVAL PBMETAD PRINT MULTI_RMSD LOWER_WALLS UNITS RESTART UPPER_WALLS | setup bias generic function colvar |
| 25.010 | Kinetic rates calculation with Ratchet&Pawl MD | methods | kinetics, ligand binding, ABMD, ratchet&pawl MD | Riccardo Capelli | ABMD GROUP DISTANCE COMMITTOR PRINT WHOLEMOLECULES COM FLUSH | bias generic vatom core colvar |
| 25.008 | Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting | methods | metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting | Dhiman Ray | ENERGY CUSTOM PYTORCH_MODEL GROUP LOWER_WALLS DISTANCE PRINT WHOLEMOLECULES OPES_METAD TORSION METAD BIASVALUE POSITION RMSD ENDPLUMED UNITS MOLINFO UPPER_WALLS | setup bias generic function opes core pytorch colvar |
| 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 UPDATE_IF ENERGY DISTANCE PRINT WHOLEMOLECULES PBMETAD VOLUME CENTER DUMPATOMS GYRATION INCLUDE TORSION MOLINFO RESTART | setup bias generic vatom colvar |
| 24.003 | Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations | chemistry | steered molecular dynamics, foldamers, peptoids, bio-inspired | Kaylyn Torkelson | DISTANCE PRINT WHOLEMOLECULES MOVINGRESTRAINT COORDINATION COM GYRATION INCLUDE ALPHABETA TORSION | multicolvar bias generic vatom colvar |
| 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 GROUP COORDINATIONNUMBER DISTANCE PRINT OPES_METAD ZDISTANCES UNITS UPPER_WALLS FLUSH | setup multicolvar bias generic vatom opes core colvar symfunc |
| 23.044 | Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition | materials | metadynamics, interlocked molecules | Luigi Leanza | READ CONVERT_TO_FES HISTOGRAM GROUP COMMITTOR PRINT COORDINATION METAD DUMPGRID ENDPLUMED | bias core gridtools colvar generic |
| 23.037 | Estimating binding free energy of solid binding peptides without extensive sampling | bio | metadynamics, solid binding peptides | Xin Qi | DISTANCE PRINT PBMETAD COM GYRATION LOWER_WALLS MOLINFO UPPER_WALLS | vatom colvar bias generic |
| 23.032 | Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics | bio | metadynamics, tSNE, neural network, machine learning, trp-cage, folding | Vojtech Spiwok | ALPHARMSD ANN PRINT WHOLEMOLECULES FIT_TO_TEMPLATE METAD POSITION MOLINFO COMBINE | annfunc bias generic function secondarystructure 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 | GROUP DISTANCES PRINT WHOLEMOLECULES FIT_TO_TEMPLATE SHADOW CENTER METAD POSITION WRAPAROUND MOLINFO UPPER_WALLS | multicolvar isdb bias vatom core colvar generic |
| 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 | COM BIASVALUE UPPER_WALLS GROUP COORDINATION LOWER_WALLS TORSION MOLINFO OPES_METAD_EXPLORE DISTANCE MATHEVAL PRINT WHOLEMOLECULES POSITION ENDPLUMED ENERGY CUSTOM COMMITTOR FIT_TO_TEMPLATE OPES_METAD UNITS CENTER WRAPAROUND FLUSH | setup bias generic vatom function opes core colvar |
| 23.018 | Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention | materials | metadynamics, surface binding, peptide adsorption | Kaylyn Torkelson | DISTANCE PRINT PBMETAD COM GYRATION UPPER_WALLS | 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 | DISTANCE PRINT WHOLEMOLECULES COM COMBINE METAD TORSION UPPER_WALLS FLUSH | bias generic vatom function colvar |
| 23.008 | PBMetaD simulations of Histatin5 | bio | metadynamics, IDP, Rg, PPII | Francesco Pesce | GROUP PBMETAD WHOLEMOLECULES PRINT GYRATION TORSION MOLINFO | colvar generic core bias |
| 23.002 | Critical comparison of general-purpose collective variables for crystal nucleation | methods | metadynamics, umbrella sampling, commitor, entropy, PIV | Julien Lam | ENERGY FUNCPATHMSD CUSTOM Q6 LOCAL_AVERAGE PRINT VOLUME PIV METAD Q4 UNITS UPPER_WALLS RESTRAINT PAIRENTROPY | setup piv bias generic function gridtools colvar symfunc |
| 22.036 | Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction | bio | Well-tempered MetaDynamics with Hamiltonian Replica Exchange | Miroslav Krepl | CUSTOM GROUP GHBFIX PRINT COORDINATION LOAD COMBINE METAD BIASVALUE MOLINFO UPPER_WALLS FLUSH | setup bias generic function core colvar |
| 22.021 | Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn Løland Bore | ENVIRONMENTSIMILARITY PRINT ECV_UMBRELLAS_LINE INCLUDE LOWER_WALLS OPES_EXPANDED UPPER_WALLS | envsim opes generic bias |
| 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 CUSTOM PYTORCH_MODEL GROUP DISTANCE MATHEVAL PRINT WHOLEMOLECULES COMMITTOR COORDINATION FIT_TO_TEMPLATE OPES_METAD CENTER LOWER_WALLS RMSD UPPER_WALLS | bias generic vatom function opes core pytorch colvar |
| 22.013 | Ligand dissociation from PreQ1 riboswitch | bio | ligand, RNA, metadynamics, pRAVE | Yihang Wang | COORDINATIONNUMBER DISTANCE COMMITTOR PRINT WHOLEMOLECULES COM METAD RMSD MOLINFO COMBINE | bias generic vatom function colvar symfunc |
| 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 | XANGLES CUSTOM DISTANCE MATHEVAL PRINT WHOLEMOLECULES ZANGLES COM YANGLES METAD LOWER_WALLS ALPHABETA TORSION MOLINFO UPPER_WALLS COMBINE | multicolvar bias generic vatom function colvar |
| 22.006 | Peptide framework for screening the effects of amino acids on assembly | bio | metadynamics, peptides | Andrew White | REWEIGHT_BIAS CONVERT_TO_FES HISTOGRAM GROUP DISTANCES PRINT COM METAD INCLUDE GYRATION DUMPGRID COMBINE | multicolvar bias vatom function gridtools core colvar generic |
| 22.003 | Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling | methods | opes, metadynamics, reweighting, alanine, muller | Michele Invernizzi | ENERGY OPES_METAD_EXPLORE CUSTOM LOWER_WALLS ECV_MULTITHERMAL PRINT PBMETAD OPES_METAD ECV_UMBRELLAS_FILE TORSION METAD BIASVALUE POSITION OPES_EXPANDED ENDPLUMED UNITS UPPER_WALLS | setup bias generic function opes colvar |
| 21.048 | Enhancing ligand exploration within a channel pore and fenestrations using metadynamics | bio | well-tempered metadynamics, protein-ligand enhanced sampling, sodium channel, Nav, small molecule drug | Elaine Tao | CUSTOM DISTANCE PRINT COM METAD LOWER_WALLS TORSION UNITS UPPER_WALLS | setup bias generic vatom function colvar |
| 21.041 | Nucleating a Different Coordination in a Crystal under Pressure. A Study of the B1−B2 Transition in NaCl by Metadynamics | methods | metadynamics, structural phase transitions, pressure-induced phase transition, martensitic transitions | Matej Badin | CUSTOM PRINT VOLUME COORDINATION METAD ENDPLUMED COMBINE | function colvar generic bias |
| 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 | colvar generic |
| 21.035 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, interface | Aaron Finney | FIXEDATOM GROUP DISTANCE PRINT LOAD RESTRAINT | setup bias generic vatom core colvar |
| 21.033 | Multiple-path-metadynamics applied to DNA base-pairing transitions | bio | path-CV, metadynamics, multiple-walker, dna | Alberto Pérez-de-Alba-Ortíz | PRINT CONSTANT MOVINGRESTRAINT METAD INCLUDE UPPER_WALLS RESTRAINT COMBINE | function generic bias |
| 21.014 | how to determine statistically accurate conformational ensembles | bio | metadynamics, metainference, errors, cv, SAXS, ensemble determination | Cristina Paissoni | CONTACTMAP ENSEMBLE PRINT WHOLEMOLECULES ALPHABETA PBMETAD CENTER METAD GYRATION STATS ANTIBETARMSD BIASVALUE TORSION MOLINFO SAXS | multicolvar bias generic vatom function isdb secondarystructure colvar |
| 21.000 | Uremic toxin time scale dynamics | bio | uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs) | Jim Pfaendtner | GROUP DISTANCE PRINT WHOLEMOLECULES COM | vatom colvar core generic |
| 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 | ABMD DISTANCE PRINT ERMSD CENTER RESTART TORSION MOLINFO | setup bias generic vatom colvar |
| 20.014 | amyloid beta small molecule interaction | bio | intrinsically disordered proteins, disordered proteins, IDPs, fuzzy binding, small molecule, drugs, entropy, binding, Alzheimer’s disease, amyloid beta | Gabriella Heller | ALPHARMSD ENSEMBLE GYRATION GROUP DIHCOR FLUSH PBMETAD COORDINATION INCLUDE TORSION CS2BACKBONE MOLINFO METAINFERENCE PRINT WHOLEMOLECULES STATS ANTIBETARMSD ENDPLUMED PARABETARMSD COMBINE | multicolvar bias generic isdb function core secondarystructure colvar |
| 19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Michele Invernizzi | EXTERNAL PRINT OPES_METAD TORSION METAD POSITION ENDPLUMED UNITS | setup bias generic opes colvar |
| 19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Luigi Bonati | ENERGY ENDPLUMED ENVIRONMENTSIMILARITY PRINT LOAD POSITION TORSION UNITS Q6 | envsim setup generic colvar symfunc |
| 19.040 | Optimal Metric for Path Collective Variables | bio | metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path | Francesco Luigi Gervasio | MATHEVAL PRINT TORSION METAD ENDPLUMED | function colvar generic bias |
| 19.035 | Dimerization of GPCRs from coarse-grained umbrella sampling | bio | Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization | Davide Provasi | GROUP DISTANCE PRINT COM TORSION RESTRAINT | bias generic vatom core colvar |
| 19.032 | Chemical reaction in solution using path collective variables based on coordination patterns | chemistry | chemical reactions, solutions, metadynamics, coordination patterns | Fabio Pietrucci | DISTANCES PRINT PATH METAD RESTART UPPER_WALLS FLUSH | setup multicolvar bias mapping generic |
| 19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Pratyush Tiwary | EXTERNAL DISTANCE COMMITTOR PRINT WHOLEMOLECULES COM RESTART ALPHABETA TORSION COMBINE | setup multicolvar bias generic vatom function colvar |
| 19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Gabriele Cesare Sosso | CLUSTER_NATOMS OUTPUT_CLUSTER LOCAL_Q6 COMMITTOR CONTACT_MATRIX FLUSH CLUSTER_WITHSURFACE DFSCLUSTERING MFILTER_MORE ENDPLUMED Q6 | multicolvar adjmat clusters generic symfunc |
| 19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Jim Pfaendtner | ENERGY EXTERNAL GROUP COORDINATION METAD | core colvar bias |
| 19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Mattia Bernetti | ENERGY ALPHARMSD PRINT WHOLEMOLECULES METAD GYRATION ENDPLUMED MOLINFO | secondarystructure colvar bias generic |
| 26.002 | A Transferable and Robust Computational Framework for Class A GPCR Activation Free Energies | bio | OneOPES, GPCR, ADRB1, activation, euclidean path, microswitches, conformational changes, allostery | Valerio Rizzi | RMSD ECV_MULTITHERMAL GROUP ENERGY PATH PATHMSD VOLUME CENTER COORDINATION OPES_METAD_EXPLORE UPPER_WALLS PRINT DISTANCE OPES_EXPANDED CUSTOM LOWER_WALLS | bias core vatom mapping generic function colvar opes |
| 25.019 | The Arch from the Stones. Understanding Protein Folding Energy Landscapes via Bio-inspired Collective Variables | bio | protein folding, OPES, OneOPES, binding free energy | Valerio Rizzi | GHOST RMSD ECV_MULTITHERMAL GROUP ENERGY COORDINATION CENTER OPES_METAD_EXPLORE PRINT CUSTOM DISTANCE OPES_EXPANDED COMBINE MOLINFO | core vatom generic function colvar opes |
| 25.002 | M3_PCV-ABMD | chemistry | Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor | Gian Marco Elisi | ENDPLUMED ABMD PATHMSD PRINT UPPER_WALLS UNITS | colvar generic bias setup |
| 24.031 | DeepLNE | methods | PATHCV, OPES, OneOPES | Thorben Fröhlking | ECV_MULTITHERMAL ERMSD RESTART ENERGY VOLUME COMBINE COORDINATION OPES_METAD_EXPLORE PRINT OPES_EXPANDED PYTORCH_MODEL MOLINFO | generic setup function pytorch colvar opes |
| 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 | ALPHARMSD OPES_METAD TORSION GYRATION COORDINATION PRINT CUSTOM DISTANCE COMBINE MOLINFO WHOLEMOLECULES | generic function secondarystructure colvar opes |
| 24.006 | Water vapor condensation | chemistry | metadynamics, homogeneous condensation, chemical potential | Shenghui Zhong | CONTACT_MATRIX CLUSTER_NATOMS CLUSTER_PROPERTIES METAD DFSCLUSTERING PRINT UPPER_WALLS UNITS COORDINATIONNUMBER | bias clusters generic setup adjmat symfunc |
| 24.001 | A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations | bio | OPES, OPES-Flooding, QM/MM, Kinetics, Enzyme Catalysis | Dhiman Ray | OPES_METAD COMMITTOR TORSION COMBINE PRINT FLUSH UPPER_WALLS UNITS DISTANCE CUSTOM LOWER_WALLS | bias generic setup function colvar opes |
| 23.040 | Supramolecular capsules assembly dynamics | chemistry | Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics | Riccardo Capelli | GROUP METAD POSITION PRINT CENTER FLUSH UNITS DISTANCE COM DISTANCES CUSTOM WHOLEMOLECULES | bias core vatom generic setup multicolvar function colvar |
| 23.035 | An Extended Metadynamics Protocol for Binding/Unbinding of Peptide Ligands to Class A G-Protein Coupled Receptors | bio | G protein coupled receptor, peptide ligands, metadynamics, multiple-walker | Timothy Clark | BIASVALUE METAD LOWER_WALLS MATHEVAL CENTER CONSTANT PRINT UPPER_WALLS DISTANCE WHOLEMOLECULES | bias vatom generic function colvar |
| 23.028 | Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process | chemistry | Ammonia decomposition; Dynamics;OPES; Neural Network potential | Manyi Yang | OPES_METAD COMMITTOR GROUP ENERGY FIXEDATOM MATHEVAL PRINT FLUSH UPPER_WALLS UNITS DISTANCE ZDISTANCES COM DISTANCES CUSTOM COORDINATIONNUMBER LOWER_WALLS | bias core vatom generic setup multicolvar symfunc function colvar opes |
| 23.005 | A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs | bio | metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A | Timothy Clark | RMSD REWEIGHT_METAD READ DUMPGRID METAD CONVERT_TO_FES MATHEVAL HISTOGRAM PRINT DISTANCE MOLINFO WHOLEMOLECULES | bias generic gridtools function colvar |
| 22.035 | Deciphering the alphabet of disorder — Glu and Asp act differently on local but not global properties | bio | intrinsically disordered proteins, parallel bias metadynamics, protein | Kresten Lindorff-Larsen | TORSION GYRATION PBMETAD MOLINFO WHOLEMOLECULES | colvar generic bias |
| 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 | GROUP TORSION METAD PRINT DISTANCE COM WHOLEMOLECULES | bias core vatom generic colvar |
| 22.002 | GAMBES_SAMPL5_RATES | other | GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding | Jayashrita Debnath | ENDPLUMED COMMITTOR GROUP FIT_TO_TEMPLATE LOAD ENERGY FIXEDATOM MATHEVAL CENTER COORDINATION ANGLE UPPER_WALLS PRINT DISTANCE FLUSH PYTORCH_MODEL WHOLEMOLECULES | bias core vatom generic setup function pytorch colvar |
| 21.051 | Automatic learning of hydrogen-bond fixes in an AMBER RNA force field | methods | force field, RNA | Giovanni Bussi | ERMSD BIASVALUE METAD COORDINATION PRINT COMBINE MOLINFO WHOLEMOLECULES | colvar generic bias function |
| 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 | METAD COORDINATION PRINT UPPER_WALLS DISTANCE COMBINE COORDINATIONNUMBER LOWER_WALLS | bias generic symfunc function colvar |
| 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 | RESTRAINT RESTART METAD POSITION MATHEVAL COORDINATION PRINT CENTER REWEIGHT_BIAS WHOLEMOLECULES | bias vatom generic setup function colvar |
| 21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Kristof Bal | COMMITTOR REWEIGHT_METAD DUMPGRID LOAD METAD CONVERT_TO_FES MOVINGRESTRAINT HISTOGRAM PRINT FLUSH UPPER_WALLS UNITS COORDINATIONNUMBER | bias generic setup symfunc gridtools |
| 21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Tarsis Ferreira | PUCKERING RANDOM_EXCHANGES GROUP REWEIGHT_METAD DUMPGRID METAD ENERGY HISTOGRAM WHOLEMOLECULES PRINT COORDINATION INCLUDE UPPER_WALLS DISTANCE MOLINFO LOWER_WALLS | bias core generic gridtools colvar |
| 20.028 | Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane | bio | metadynamics, KRas-4B, anionic membrane | Huixia Lu | FIT_TO_TEMPLATE RESTART METAD CENTER PRINT DISTANCE | bias vatom generic setup 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 | DISTANCE METAD PRINT TORSION | colvar generic bias |
| 20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Valerio Rizzi | ENDPLUMED OPES_METAD GROUP FIT_TO_TEMPLATE ENERGY FIXEDATOM MATHEVAL CENTER COORDINATION ANGLE UPPER_WALLS PRINT DISTANCE PYTORCH_MODEL WHOLEMOLECULES | bias core vatom generic function pytorch colvar opes |
| 20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Michele Invernizzi | RMSD TORSION LOAD ENERGY OPES_EXPANDED CUSTOM WHOLEMOLECULES ENVIRONMENTSIMILARITY ECV_UMBRELLAS_LINE POSITION MATHEVAL UNITS ENDPLUMED Q6 VOLUME PRINT UPPER_WALLS MOLINFO ECV_MULTITHERMAL ECV_LINEAR ECV_MULTITHERMAL_MULTIBARIC | bias generic setup symfunc function colvar opes envsim |
| 20.021 | Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins. | bio | phi-values, restrained MD, transition-state, protein folding, disordered proteins, protein evolution | Cristina Paissoni | RESTRAINT PRINT COORDINATION STATS MOLINFO WHOLEMOLECULES | colvar generic bias function |
| 20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Carlo Camilloni | TORSION SAXS GYRATION PBMETAD ALPHABETA CENTER FLUSH PRINT DISTANCE ENSEMBLE STATS METAINFERENCE MOLINFO WHOLEMOLECULES | bias vatom generic multicolvar function isdb colvar |
| 20.006 | Class B GPCR activation mechanism | bio | metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | RMSD METAD ENERGY LOWER_WALLS MATHEVAL PRINT CENTER UPPER_WALLS DISTANCE COMBINE MOLINFO WHOLEMOLECULES | bias vatom generic function colvar |
| 20.005 | Muscarinic M2 receptor/ligand Frequency-Adaptive Metadynamics and QM/MM calculations | bio | Frequency-adaptive metadynamics, multiple-walkers metadynamics, well-tempered metadynamics, GPCR, receptor, Adiabatic Bias MD | Riccardo Capelli | ABMD FLUSH COM COMBINE WHOLEMOLECULES LOWER_WALLS READ ENDPLUMED REWEIGHT_METAD DUMPGRID HISTOGRAM FUNCPATHMSD PRINT UPPER_WALLS MOLINFO METAD CONVERT_TO_FES CONTACTMAP DISTANCE | bias vatom generic gridtools function colvar |
| 19.081 | Calculation of phase diagrams in the multithermal-multibaric ensemble | methods | VES, variationally enhanced sampling, multithermal-multibaric, energy, Wang Landau, RefCV, kernel, bcc, fcc, sodium, aluminum | Pablo Piaggi | OPT_AVERAGED_SGD TD_MULTITHERMAL_MULTIBARIC CELL LOAD ENERGY REWEIGHT_BIAS COMBINE LOWER_WALLS READ MATHEVAL TD_WELLTEMPERED BF_LEGENDRE OPT_DUMMY Q6 DUMPGRID HISTOGRAM VOLUME PRINT UPPER_WALLS REWEIGHT_TEMP_PRESS RESTART VES_LINEAR_EXPANSION CONVERT_TO_FES | bias generic setup ves symfunc function gridtools colvar |
| 19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | GiovanniMaria Piccini | METAD ENERGY PRINT FLUSH UPPER_WALLS UNITS DISTANCE COMBINE LOWER_WALLS | bias generic setup function colvar |
| 19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Gareth Tribello | FCCUBIC ENDPLUMED CELL METAD PRINT UPPER_WALLS UNITS | bias generic setup symfunc colvar |
| 19.045 | Adsorption free energy of Ca/CO3 ions on calcite steps in contact with water | materials | metadynamics, well-tempered, multiple walkers, LAMMPS | Marco De La Pierre | GROUP RESTART METAD POSITION COORDINATION PRINT FLUSH UPPER_WALLS UNITS LOWER_WALLS | bias core generic setup colvar |
| 19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Elena Papaleo | GROUP METAD GYRATION WHOLEMOLECULES ALPHABETA PRINT UPPER_WALLS MOLINFO LOWER_WALLS | bias core generic multicolvar colvar |
| 19.025 | Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide | bio | metainference, NMR, protein dynamics, force-fields | Carlo Camilloni | ENDPLUMED TORSION GYRATION RDC PBMETAD JCOUPLING WHOLEMOLECULES PRINT FLUSH CS2BACKBONE ENSEMBLE STATS METAINFERENCE MOLINFO BIASVALUE | bias generic function isdb colvar |
| 26.006 | Metadynamics simulations of buried phosphorylation sites and proline isomerisation | bio | metadynamics | Julian Streit | TORSION PRINT WHOLEMOLECULES MOLINFO METAD COORDINATION | bias generic colvar |
| 25.005 | Mechanism of Nanocluster Formation from Machine-Learned Potential-based Simulations | chemistry | WT-metadynamics, metal nanoclusters, nucleation, neural network potential, deepMD | Vikas Tiwari, Tarak Karmakar | ANGLE GROUP FIXEDATOM FLUSH PRINT UNITS UPPER_WALLS COMBINE RESTRAINT DISTANCE METAD COORDINATION COM DISTANCES LOWER_WALLS COORDINATIONNUMBER | setup function multicolvar colvar core bias vatom symfunc generic |
| 25.000 | Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer | bio | metadynamics, pathCV | Sahithya Sridharan Iyer | FUNCPATHGENERAL RESTART GROUP PRINT WHOLEMOLECULES UPPER_WALLS MOLINFO DISTANCE METAD COM | vatom setup function bias colvar core generic |
| 24.034 | Umbrella sampling of ion in transporter SLC26A7 | bio | umbrella sampling, transporter, ions | Xiaoli Lu | RESTRAINT PRINT UNITS POSITION | setup bias generic 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 TORSION ANGLE ENERGY GROUP ENDPLUMED OPES_EXPANDED PRINT WHOLEMOLECULES ECV_MULTITHERMAL UPPER_WALLS FIT_TO_TEMPLATE DISTANCE OPES_METAD_EXPLORE COORDINATION CENTER LOWER_WALLS FIXEDATOM | vatom function colvar bias core opes generic |
| 24.021 | Ab initio machine learning simulation of calcium carbonate from aqueous solutions to the solid state | chemistry | ion pairing, caco3, opes, proton transfer, crystallization | Pablo Piaggi | OPES_METAD PRINT UPPER_WALLS DISTANCE COORDINATION ENERGY | bias opes generic colvar |
| 24.018 | A new route to the prebiotic synthesis of glycine via ab initio-based machine learning calculations | chemistry | prebiotic chemistry, glycine, Strecker synthesis, ab initio calculations, machine learning | Léon HUET | PRINT DISTANCE | generic colvar |
| 23.012 | JAK2 2D meta-eABF PMF with statistical analysis | bio | 2D meta-eABF, path CV, PMF | Istvan Kolossvary | PATHMSD FLUSH PRINT DRR UPPER_WALLS BIASVALUE METAD CUSTOM LOWER_WALLS | function bias drr colvar generic |
| 23.010 | An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G‑Protein-Coupled Receptor Ligands | bio | GPCR, binding free energy, free energy surface | Timothy Clark | MATHEVAL PRINT WHOLEMOLECULES UPPER_WALLS BIASVALUE DISTANCE METAD LOWER_WALLS CONSTANT | function bias generic colvar |
| 22.024 | Conformational Entropy as a Potential Liability of Computationally Designed Antibodies | bio | metadynamics, conformational entropy, antibody, nanobody | Thomas Löhr | TORSION ANTIBETARMSD RESTART ALPHABETA PRINT WHOLEMOLECULES ALPHARMSD PBMETAD MOLINFO COM | vatom setup multicolvar secondarystructure bias colvar generic |
| 22.009 | Glycosylation in calixarenes capsule | chemistry | Metadynamics, glycosylation, supramolecular catalysis | GiovanniMaria Piccini | MATHEVAL ANGLE GROUP FLUSH PRINT UNITS WHOLEMOLECULES UPPER_WALLS COMBINE FIT_TO_TEMPLATE DISTANCE BRIDGE METAD COORDINATION DISTANCES LOWER_WALLS RMSD | setup function multicolvar adjmat colvar bias core generic |
| 21.006 | OPES, On-the-fly Probability Enhanced Sampling Method | methods | opes, alanine dipeptide, well-tempered, multithermal, multiumbrella | Michele Invernizzi | TORSION ENDPLUMED OPES_EXPANDED PRINT ECV_MULTITHERMAL ECV_UMBRELLAS_LINE OPES_METAD ENERGY | opes generic colvar |
| 19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Mattia Bernetti | PATHMSD PRINT WHOLEMOLECULES UPPER_WALLS METAD LOWER_WALLS | bias generic colvar |
| 19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Kim E. Jelfs | RESTART GROUP PRINT UPPER_WALLS DISTANCE METAD COM CENTER LOWER_WALLS | vatom setup bias core colvar generic |
| 19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Paolo Raiteri | MATHEVAL RESTART FLUSH PRINT UNITS UPPER_WALLS DISTANCE METAD | setup function bias colvar generic |
| 19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Glen Hocky | TORSION PRINT COMBINE RESTRAINT DISTANCE EDS | function eds bias colvar generic |
| 19.013 | RNA FF FITTING | methods | force field, RNA | Giovanni Bussi | MATHEVAL TORSION INCLUDE BIASVALUE MOLINFO PUCKERING CONSTANT | function bias generic colvar |