Browse the eggs in PLUMED-NEST
PLUMED-NEST provides all the data needed to reproduce the results of a PLUMED-enhanced molecular dynamics simulation or analysis contained in a published paper. Furthermore, PLUMED-NEST monitors the compatibility of the provided PLUMED input files with the current and development versions of the code and integrates links from these files to the PLUMED manual.
Here is the list of projects already deposited in PLUMED-NEST, while a complete bibliography can be found here.
| plumID | Name | Category | Keywords | Contributor | Actions | Modules |
|---|---|---|---|---|---|---|
| 25.005 | Mechanism of Nanocluster Formation from Machine-Learned Potential-based Simulations | chemistry | WT-metadynamics, metal nanoclusters, nucleation, neural network potential, deepMD | Vikas Tiwari, Tarak Karmakar | DISTANCE DISTANCES LOWER_WALLS UPPER_WALLS FIXEDATOM COORDINATION FLUSH COM COMBINE UNITS COORDINATIONNUMBER RESTRAINT GROUP PRINT ANGLE METAD | function core multicolvar generic symfunc setup colvar bias vatom |
| 25.012 | A Machine Learning-Driven, Probability-Based Approach to Enzyme Catalysis | bio | enzyme catalysis, transition state, structure-activity relationship, free energy surface, reaction mechanism, water, alpha-amylase, sugar, QM/MM MD, OPES, committor function, machine learning | Sudip Das | FLUSH DISTANCE UNITS INCLUDE ENERGY BIASVALUE POSITION PRINT MATHEVAL LOAD TORSION OPES_METAD COMBINE COORDINATION CELL CUSTOM | function generic opes colvar bias setup |
| 25.003 | Surrogate Model CV | methods | Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding | Sompriya Chatterjee | GROUP DISTANCE ENERGY ENDPLUMED COMMITTOR PRINT MATHEVAL PYTORCH_MODEL MOLINFO TORSION OPES_METAD COMBINE WHOLEMOLECULES CUSTOM | function core generic pytorch opes 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 | GROUP PARABETARMSD DISTANCE ALPHARMSD BIASVALUE DUMPMASSCHARGE RMSD PRINT CENTER DUMPATOMS COM MOLINFO UPPER_WALLS COORDINATION EMMI WHOLEMOLECULES PBMETAD | core secondarystructure generic isdb colvar bias vatom |
| 24.028 | All-atom simulations of RNA-membrane interactions | bio | metadynamics, membrane, RNA | Giovanni Bussi | GROUP GYRATION DISTANCE DISTANCES SORT PUCKERING GHOST POSITION PRINT CENTER MATHEVAL METAD MOLINFO UPPER_WALLS COMBINE WHOLEMOLECULES LOWER_WALLS | function core multicolvar generic colvar bias 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 | GROUP DISTANCE WHOLEMOLECULES PATH PRINT FIT_TO_TEMPLATE CENTER RESTART UPPER_WALLS CUSTOM TORSION OPES_METAD PYTORCH_MODEL FIXEDATOM COORDINATION LOWER_WALLS | function core mapping generic pytorch opes colvar bias setup vatom |
| 24.020 | Graph Neural Network-State Predictive Information Bottleneck (GNN-SPIB) approach for learning molecular thermodynamics and kinetics | bio | LJ7, alanine, well-tempered metadynamics, infrequent metadynamics, machine learning | Ziyue Zou, Dedi Wang, Pratyush Tiwary | GROUP COMMITTOR PRINT METAD LOAD TORSION | core generic colvar bias setup |
| 24.010 | Oxytocin metadynamics simulation | bio | metadynamics, oxytocin, peptide | Jan Beránek | FLUSH PRINT RESTART METAD TORSION WHOLEMOLECULES | bias generic setup colvar |
| 23.046 | Lasso Peptides - HLDA CV | bio | metadynamics, protein folding, HLDA, harmonic | Gabriel da Hora | DISTANCE UNITS PRINT METAD COMBINE WHOLEMOLECULES | function generic colvar bias setup |
| 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 | DISTANCE RMSD PRINT MATHEVAL METAD MOLINFO WHOLEMOLECULES | function bias 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 | WRAPAROUND COMMITTOR ENERGY ENDPLUMED UNITS POSITION COM MOLINFO OPES_METAD CENTER UPPER_WALLS WHOLEMOLECULES CUSTOM GROUP FLUSH DISTANCE PRINT MATHEVAL BIASVALUE FIT_TO_TEMPLATE TORSION COORDINATION OPES_METAD_EXPLORE LOWER_WALLS | function core generic opes colvar bias setup vatom |
| 23.014 | Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 | bio | metadynamics, oligomerization, chemokine receptors, GPCR, membrane | Vittorio Limongelli | FLUSH DISTANCE PRINT COM METAD TORSION UPPER_WALLS COMBINE WHOLEMOLECULES | function generic colvar bias vatom |
| 23.008 | PBMetaD simulations of Histatin5 | bio | metadynamics, IDP, Rg, PPII | Francesco Pesce | GROUP GYRATION PRINT MOLINFO TORSION WHOLEMOLECULES PBMETAD | bias colvar core generic |
| 22.031 | Rare Event Kinetics from Adaptive Bias Enhanced Sampling | methods | OPES Flooding, Kinetics, Rate, OPES, Machine Learning | Dhiman Ray | COMMITTOR UNITS ENDPLUMED ENERGY INCLUDE POSITION MOLINFO OPES_METAD CONSTANT RMSD CONTACTMAP COMBINE WHOLEMOLECULES CUSTOM GROUP DISTANCE PRINT BIASVALUE TORSION PYTORCH_MODEL | function core generic pytorch opes colvar bias setup |
| 22.023 | Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy | bio | CryoEM, MEMMI,EMMI, Metadynamics, Metainference, IAPP, structural ensemble | Faidon Brotzakis | GROUP BIASVALUE RMSD PRINT COM RESTART MOLINFO TORSION UPPER_WALLS COORDINATION EMMI WHOLEMOLECULES PBMETAD | core generic isdb colvar bias setup vatom |
| 22.013 | Ligand dissociation from PreQ1 riboswitch | bio | ligand, RNA, metadynamics, pRAVE | Yihang Wang | DISTANCE COMMITTOR RMSD PRINT COORDINATIONNUMBER COM METAD MOLINFO COMBINE WHOLEMOLECULES | function symfunc generic colvar bias vatom |
| 21.041 | Nucleating a Different Coordination in a Crystal under Pressure. A Study of the B1−B2 Transition in NaCl by Metadynamics | methods | metadynamics, structural phase transitions, pressure-induced phase transition, martensitic transitions | Matej Badin | ENDPLUMED VOLUME PRINT METAD COMBINE COORDINATION CUSTOM | colvar bias generic function |
| 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 ENDPLUMED RANDOM_EXCHANGES PRINT METAD TORSION PBMETAD | bias generic colvar |
| 21.020 | Reweighted Jarzynski sampling | methods | free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions | Kristof Bal | UNITS MOVINGRESTRAINT RESTRAINT LOAD OPES_METAD CONSTANT OPT_AVERAGED_SGD HISTOGRAM CONVERT_TO_FES ANN REWEIGHT_BIAS UPPER_WALLS COMBINE CUSTOM VES_LINEAR_EXPANSION FLUSH DISTANCE TD_WELLTEMPERED PRINT COORDINATIONNUMBER REWEIGHT_METAD METAD DUMPGRID BF_CHEBYSHEV BIASVALUE | function ves symfunc generic gridtools opes colvar bias setup annfunc |
| 21.016 | MD SAXS GTPase associated center | bio | metadynamics, RNA, folding, SAXS | Giovanni Bussi | GROUP GYRATION INCLUDE PRINT METAD MOLINFO SAXS CUSTOM ERMSD UPPER_WALLS WHOLEMOLECULES LOWER_WALLS | function core generic isdb colvar bias |
| 21.010 | Step by Step Strecker Amino Acid Synthesis from Ab Initio Prebiotic Chemistry | chemistry | Strecker reaction, free energy landscape, ab initio molecular dynamics, glycine, prebiotic synthesis | Théo Magrino | generic | |
| 21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Kresten Lindorff-Larsen | GROUP FLUSH ALPHARMSD GYRATION BIASVALUE PRINT CENTER EEFSOLV MOLINFO SAXS METAINFERENCE WHOLEMOLECULES PBMETAD | core generic secondarystructure isdb colvar bias vatom |
| 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 COM WHOLEMOLECULES | colvar vatom core generic |
| 20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Valerio Rizzi | GROUP DISTANCE ENERGY ENDPLUMED WHOLEMOLECULES ANGLE PRINT CENTER FIT_TO_TEMPLATE MATHEVAL UPPER_WALLS OPES_METAD PYTORCH_MODEL FIXEDATOM COORDINATION | function core generic pytorch opes colvar bias vatom |
| 20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Vojtech Spiwok | METAD PRINT TORSION | bias generic colvar |
| 20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Luigi Bonati | GROUP FLUSH DISTANCE UNITS ENDPLUMED PRINT COM MATHEVAL LOAD UPPER_WALLS TORSION OPES_METAD PYTORCH_MODEL LOWER_WALLS | function core generic pytorch opes colvar bias setup vatom |
| 20.001 | Conformational stability and dynamics in solution and in crystals report similarly on unfolding and aggregation propensity of amyloidogenic proteins | bio | metainference, metadynamics, NMR, protein dynamics, b2m, protein crystals | Carlo Camilloni | GROUP FLUSH ALPHABETA ENDPLUMED BIASVALUE PRINT MOLINFO CS2BACKBONE UPPER_WALLS ANTIBETARMSD WHOLEMOLECULES PBMETAD LOWER_WALLS | core multicolvar generic isdb secondarystructure bias |
| 19.076 | Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones | bio | molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics | Salvatore Assenza | GYRATION UNITS ENDPLUMED PRINT MOVINGRESTRAINT | bias colvar setup generic |
| 19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Giovanni Bussi | DISTANCE ENDPLUMED RESTRAINT COORDINATION WHOLEMOLECULES LOWER_WALLS | bias colvar generic |
| 19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Jakub Rydzewski | PATHMSD UNITS PRINT RESTART METAD UPPER_WALLS LOWER_WALLS | bias colvar setup generic |
| 19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | GYRATION DISTANCE ENERGY PRINT COM METAD MOLINFO UPPER_WALLS | bias colvar vatom generic |
| 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 RANDOM_EXCHANGES PRINT METAD TORSION | bias generic colvar |
| 19.048 | Understanding Ligand Binding Selectivity in a Prototypical GPCR Family | bio | metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | DISTANCE BIASVALUE PRINT COM MATHEVAL METAD UPPER_WALLS WHOLEMOLECULES CONSTANT LOWER_WALLS | function generic colvar bias vatom |
| 19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Carlo Camilloni | GROUP FLUSH ALPHABETA ENDPLUMED BIASVALUE PRINT RESTART MOLINFO CS2BACKBONE UPPER_WALLS ANTIBETARMSD WHOLEMOLECULES PBMETAD LOWER_WALLS | core multicolvar generic isdb secondarystructure bias setup |
| 19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Elena Papaleo | GROUP GYRATION ALPHABETA PRINT METAD MOLINFO UPPER_WALLS WHOLEMOLECULES LOWER_WALLS | core multicolvar generic colvar bias |
| 19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Max Bonomi | GROUP BIASVALUE PRINT MOLINFO EMMI WHOLEMOLECULES | bias generic isdb core |
| 19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Max Bonomi | GROUP BIASVALUE PRINT MOLINFO EMMI | bias generic isdb 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 PRINT UPPER_WALLS WHOLEMOLECULES RMSD MOLINFO METAD LOWER_WALLS | bias colvar pytorch drr 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 | DISTANCE COMBINE DEBUG GHBFIX COORDINATION BIASVALUE PRINT GROUP UPPER_WALLS MOLINFO CENTER METAD COM LOWER_WALLS | bias function colvar vatom core generic |
| 24.011 | Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble | methods | committor, machine learning | Peilin Kang | UNITS LOAD CELL LOWER_WALLS DISTANCE POSITION ENERGY TORSION PRINT CUSTOM INCLUDE WHOLEMOLECULES COORDINATION BIASVALUE MATHEVAL GROUP UPPER_WALLS ENDPLUMED RMSD MOLINFO | bias function setup colvar core generic |
| 24.005 | Learning Markovian Dynamics with Spectral Maps | methods | spectral map, collective variables, machine learning | Jakub Rydzewski | DISTANCE UNITS BIASVALUE PRINT CUSTOM | bias function setup colvar 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 | COMBINE COORDINATION BIASVALUE ERMSD PRINT WHOLEMOLECULES MOLINFO GHBFIX METAD | function bias generic colvar |
| 22.033 | Reciprocal barrier restraint. Application to PROTAC passive permeability prediction | methods | PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR | Istvan Kolossvary | DISTANCE FLUSH UNITS BIASVALUE DRR PRINT CUSTOM METAD COM | bias function setup colvar vatom drr generic |
| 22.026 | Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification | materials | Peptoid, silica | Jim Pfaendtner | DISTANCE PRINT UPPER_WALLS MOLINFO GYRATION PBMETAD COM | vatom bias generic colvar |
| 22.025 | Bubble nucleation rate predictions in a Lennard-Jones fluid | materials | free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation | Kristof Bal | HISTOGRAM COORDINATIONNUMBER VOLUME FLUSH UNITS RESTRAINT BIASVALUE CONVERT_TO_FES DUMPGRID REWEIGHT_BIAS PRINT CUSTOM UPPER_WALLS MOVINGRESTRAINT COMMITTOR LOAD ANN | gridtools annfunc bias symfunc function setup colvar generic |
| 22.022 | Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir | bio | RMSD, protein-ligand interactions | Isabell Grothaus | RMSD PRINT | generic colvar |
| 21.036 | 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 | ALPHARMSD COORDINATION DIHCOR ANTIBETARMSD ENERGY PARABETARMSD PRINT GROUP UPPER_WALLS WHOLEMOLECULES RANDOM_EXCHANGES MOLINFO GYRATION METAD LOWER_WALLS | bias colvar multicolvar secondarystructure core 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 | DISTANCE METAD COORDINATION ENERGY ALPHABETA TORSION INCLUDE PRINT GYRATION PBMETAD COM | bias vatom colvar multicolvar generic |
| 21.028 | From Enhanced Sampling to Reaction Profiles | methods | collective variables, multi-state, machine learning, Deep-TDA | Enrico Trizio | UNITS FIXEDATOM FIT_TO_TEMPLATE OPES_METAD LOAD DISTANCES LOWER_WALLS DISTANCE PYTORCH_MODEL TORSION PRINT WHOLEMOLECULES ANGLE CENTER COORDINATION MATHEVAL GROUP UPPER_WALLS ENDPLUMED | bias function setup opes vatom colvar multicolvar pytorch core generic |
| 20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Matteo Salvalaglio | VOLUME ENERGY MATHEVAL PRINT UPPER_WALLS METAD CELL LOWER_WALLS | function bias generic colvar |
| 20.018 | Free energy barriers from biased molecular dynamics simulations | methods | kinetics, free energy barriers, chemical reactions, nucleation, metadynamics | Kristof Bal | VOLUME UNITS REWEIGHT_METAD LOCAL_AVERAGE SPRINT DENSITY FLUSH CONVERT_TO_FES REWEIGHT_BIAS LOAD LOWER_WALLS DISTANCE COMBINE COORDINATIONNUMBER CONTACT_MATRIX ENERGY PAIRENTROPY PRINT CENTER HISTOGRAM Q6 COORDINATION DUMPGRID UPPER_WALLS METAD | gridtools bias symfunc function setup colvar vatom adjmat sprint volumes generic |
| 20.002 | Exploring conformational dynamics of the extracellular Venus flytrap domain of the GABAB receptor, a path-metadynamics study | bio | Metadynamics, path CVs | Riccardo Ocello | PATHMSD RESTART PRINT GROUP UPPER_WALLS WHOLEMOLECULES MOLINFO METAD | bias setup colvar core generic |
| 19.080 | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | methods | ves, variationally enhanced sampling, vibrational excitation, chemical reactions | Kristof Bal | EXTERNAL DISTANCE HISTOGRAM COMBINE BF_CHEBYSHEV VES_LINEAR_EXPANSION COORDINATION UNITS FLUSH CONVERT_TO_FES DUMPGRID TD_GRID PRINT UPPER_WALLS ANGLE OPT_AVERAGED_SGD TD_WELLTEMPERED LOWER_WALLS | gridtools bias generic function setup colvar ves |
| 19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Giovanni Bussi | DISTANCE COORDINATION FLUSH MAXENT TORSION MATHEVAL INCLUDE PRINT WHOLEMOLECULES MOLINFO METAD COM SORT | bias function vatom colvar generic |
| 19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Wei Chen | COMBINE POSITION RESTRAINT COM ANN | annfunc bias function vatom colvar |
| 19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Kim E. Jelfs | DISTANCE RESTART PRINT GROUP UPPER_WALLS CENTER METAD COM LOWER_WALLS | bias setup colvar vatom core generic |
| 19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Gareth Tribello | METAD UNITS FCCUBIC PRINT UPPER_WALLS ENDPLUMED AROUND CELL LOWER_WALLS | bias symfunc setup colvar volumes generic |
| 19.045 | Adsorption free energy of Ca/CO3 ions on calcite steps in contact with water | materials | metadynamics, well-tempered, multiple walkers, LAMMPS | Marco De La Pierre | COORDINATION POSITION UNITS FLUSH RESTART PRINT GROUP UPPER_WALLS METAD LOWER_WALLS | bias setup colvar core generic |
| 19.044 | Multithermal-multibaric simulations using VES | methods | ves, Wang Landau, multicanonical, water, density anomaly | Pablo Piaggi | HISTOGRAM COMBINE VOLUME READ VES_LINEAR_EXPANSION ENERGY CONVERT_TO_FES RESTART OPT_DUMMY DUMPGRID AVERAGE REWEIGHT_TEMP_PRESS REWEIGHT_BIAS PRINT BF_LEGENDRE OPT_AVERAGED_SGD TD_MULTITHERMAL_MULTIBARIC | gridtools bias generic function setup colvar ves |
| 19.032 | Chemical reaction in solution using path collective variables based on coordination patterns | chemistry | chemical reactions, solutions, metadynamics, coordination patterns | Fabio Pietrucci | DISTANCES FLUSH RESTART PRINT UPPER_WALLS PATH METAD | bias mapping setup multicolvar generic |
| 24.031 | DeepLNE | methods | PATHCV, OPES, OneOPES | Thorben Fröhlking | ECV_MULTITHERMAL VOLUME OPES_EXPANDED ERMSD COMBINE PRINT OPES_METAD_EXPLORE MOLINFO RESTART PYTORCH_MODEL COORDINATION ENERGY | function opes colvar pytorch generic setup |
| 24.029 | Combination of OPES and OPES-Explore | methods | OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin | Dhiman Ray | FIT_TO_TEMPLATE UPPER_WALLS ENDPLUMED ENERGY WHOLEMOLECULES CUSTOM POSITION RMSD UNITS CENTER MATHEVAL INCLUDE BIASVALUE OPES_METAD_EXPLORE MOLINFO FIXEDATOM PYTORCH_MODEL LOWER_WALLS GROUP METAD OPES_METAD COMBINE PRINT DISTANCE COORDINATION FLUSH CONTACTMAP | function bias vatom opes core colvar pytorch generic setup |
| 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 | LOWER_WALLS ECV_MULTITHERMAL GROUP ANGLE TORSION FIT_TO_TEMPLATE WHOLEMOLECULES CENTER MATHEVAL UPPER_WALLS PRINT FIXEDATOM DISTANCE OPES_METAD_EXPLORE OPES_EXPANDED COORDINATION ENDPLUMED ENERGY | function bias vatom core opes colvar generic |
| 24.017 | Absolute Binding Free Energies with OneOPES | methods | protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy | Francesco Gervasio | WRAPAROUND UPPER_WALLS ENERGY WHOLEMOLECULES CUSTOM RMSD PROJECTION_ON_AXIS CONSTANT COM MATHEVAL INCLUDE BIASVALUE OPES_METAD_EXPLORE MOLINFO RESTART LOWER_WALLS ECV_MULTITHERMAL GROUP TORSION METAD PRINT OPES_EXPANDED COORDINATION CONTACTMAP | function bias vatom opes core colvar generic setup |
| 24.016 | Cryo-EM guided simulations of ribozyme | bio | metainference, cryo-EM | Giovanni Bussi | GROUP WHOLEMOLECULES EMMIVOX BIASVALUE INCLUDE ERMSD PRINT MOLINFO RESTRAINT | bias core colvar generic isdb |
| 24.002 | Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes | chemistry | metadynamics, ligand design, solvent extraction | Xiaoyu Wang | UNITS TORSION METAD PRINT RESTART | bias colvar generic setup |
| 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 | LOWER_WALLS UNITS COMMITTOR TORSION CUSTOM OPES_METAD UPPER_WALLS COMBINE PRINT DISTANCE FLUSH | function bias opes colvar generic setup |
| 23.044 | Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition | materials | metadynamics, interlocked molecules | Luigi Leanza | CONVERT_TO_FES GROUP READ METAD ENDPLUMED PRINT DUMPGRID HISTOGRAM COORDINATION COMMITTOR | bias gridtools core colvar generic |
| 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 | GROUP WHOLEMOLECULES EMMIVOX WRAPAROUND DISTANCE BIASVALUE INCLUDE UPPER_WALLS PRINT MOLINFO | bias core colvar generic isdb |
| 23.040 | Supramolecular capsules assembly dynamics | chemistry | Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics | Riccardo Capelli | GROUP UNITS METAD WHOLEMOLECULES CENTER COM DISTANCE PRINT CUSTOM DISTANCES POSITION FLUSH | function bias vatom core colvar generic multicolvar setup |
| 23.020 | FEP simulations of ATOX1 homodimer | chemistry | parallel bias metadynamics, FEP, free-energy of metal ion dissociation | Adriana Pietropaolo | PBMETAD CONSTANT WHOLEMOLECULES MATHEVAL BIASVALUE PRINT DISTANCE ANGLE | function bias colvar generic |
| 23.015 | MPCs aggregation | bio | opes_explore, dimerization, MPCs, self-assembly | Vikas Tiwari | LOWER_WALLS GROUP METAD CENTER WHOLEMOLECULES COM DISTANCE UPPER_WALLS PRINT OPES_METAD_EXPLORE CUSTOM COORDINATION | function vatom bias core opes colvar generic |
| 23.002 | Critical comparison of general-purpose collective variables for crystal nucleation | methods | metadynamics, umbrella sampling, commitor, entropy, PIV | Julien Lam | UNITS LOCAL_AVERAGE Q4 VOLUME METAD FUNCPATHMSD PAIRENTROPY UPPER_WALLS PIV PRINT CUSTOM RESTRAINT Q6 ENERGY | function bias gridtools piv colvar symfunc generic setup |
| 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 | PBMETAD TORSION WHOLEMOLECULES GYRATION MOLINFO | bias colvar generic |
| 22.030 | Mixing physics across temperatures with generative artificial intelligence | methods | REMD, Generative AI, DDPM | Yihang Wang | TORSION WHOLEMOLECULES PRINT | colvar generic |
| 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 | LOWER_WALLS ENVIRONMENTSIMILARITY INCLUDE UPPER_WALLS PRINT OPES_EXPANDED ECV_UMBRELLAS_LINE | bias envsim opes generic |
| 22.019 | Exploring aspartic protease inhibitor binding to design selective antimalarials | bio | ligand binding, loop opening, path CV, funnel metadynamics, drug development | Raitis Bobrovs | LOWER_WALLS FUNNEL_PS METAD WHOLEMOLECULES COM PATHMSD UPPER_WALLS PRINT DISTANCE FUNNEL | vatom bias colvar funnel generic |
| 22.008 | Ab initio metadynamics determination of temperature-dependent free-energy landscape in ultrasmall silver clusters | materials | Well tempered metadynamics, ab-initio, ase | Daniel Sucerquia | LOWER_WALLS UNITS COORDINATIONNUMBER METAD GYRATION COM UPPER_WALLS COMBINE DISTANCE COORDINATION FLUSH | function vatom bias colvar symfunc generic setup |
| 21.027 | EGFR activating mutations mechanism | bio | metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA | Francesco Gervasio | LOWER_WALLS ALPHARMSD METAD WHOLEMOLECULES MATHEVAL DISTANCE INCLUDE UPPER_WALLS CONTACTMAP PRINT MOLINFO ENERGY | function bias secondarystructure colvar generic |
| 21.004 | Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy | bio | machine learning, well-tempered metadynamics, path collective variable, potential of mean force, standard binding free energy calculations, host-guest, protein-ligand unbinding | Dorothea Gobbo | LOWER_WALLS METAD WHOLEMOLECULES PATHMSD UPPER_WALLS PRINT RESTART | bias setup colvar generic |
| 20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Cristina Paissoni | GROUP SAXS STATS CENTER WHOLEMOLECULES INCLUDE BIASVALUE ENSEMBLE PRINT MOLINFO DISTANCE RESTRAINT | function vatom bias core colvar generic isdb |
| 20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Glen Hocky | GROUP UNITS FISST GYRATION MATHEVAL BIASVALUE PRINT DISTANCE RESTRAINT ENERGY | function bias core colvar fisst generic setup |
| 20.015 | Rational design of ASCT2 inhibitors using an integrated experimental-computational approach | bio | ASCT2 transporter, small-molecules, cryo-EM, metainference | Max Bonomi | GROUP WHOLEMOLECULES EMMIVOX DUMPATOMS LOAD BIASVALUE PRINT MOLINFO | bias core generic isdb setup |
| 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 | PARABETARMSD FLUSH ENSEMBLE ENDPLUMED WHOLEMOLECULES GYRATION METAINFERENCE PBMETAD ALPHARMSD CS2BACKBONE INCLUDE DIHCOR MOLINFO GROUP TORSION STATS COMBINE PRINT COORDINATION ANTIBETARMSD | function bias core secondarystructure colvar generic multicolvar isdb |
| 20.013 | Improving accuracy of biased Alchemistic simulations | methods | flying Gaussian method, Alchemistic simulations, thermodynamic integration, reweighting | Vojtech Spiwok | TORSION METAD PRINT | bias colvar generic |
| 19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Sandro Bottaro | RMSD TORSION METAD WHOLEMOLECULES ERMSD PRINT MOLINFO DISTANCE | bias colvar generic |
| 19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Jim Pfaendtner | METAD WHOLEMOLECULES GYRATION PRINT ENERGY | bias colvar generic |
| 19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Gareth Tribello | UNITS FCCUBIC CELL METAD UPPER_WALLS PRINT ENDPLUMED | bias colvar symfunc generic setup |
| 19.046 | Optimal Collective from short simulations for Benzamidine-Trypsin ligand binding | bio | VAC-MetaD, optimised collective variables, binding free energy, unbinding rates, benzamidine trypsin, Structure Activity Relation | Faidon Brotzakis | LOWER_WALLS RMSD GROUP BRIDGE TORSION METAD WHOLEMOLECULES COM DISTANCE ALPHABETA UPPER_WALLS COMBINE PRINT MOLINFO REWEIGHT_METAD FUNNEL DISTANCES | function bias vatom core colvar adjmat funnel generic multicolvar |
| 19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | UNITS METAD UPPER_WALLS COMBINE PRINT DISTANCE FLUSH ENERGY | function bias colvar generic setup |
| 19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Paolo Raiteri | UNITS METAD MATHEVAL UPPER_WALLS PRINT DISTANCE RESTART FLUSH | function bias colvar generic setup |
| 19.025 | Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide | bio | metainference, NMR, protein dynamics, force-fields | Carlo Camilloni | PBMETAD TORSION STATS CS2BACKBONE FLUSH WHOLEMOLECULES GYRATION RDC BIASVALUE METAINFERENCE ENSEMBLE PRINT MOLINFO ENDPLUMED JCOUPLING | function bias colvar generic isdb |
| 19.008 | anncolvar | methods | neural network, dimensionality reduction | Vojtech Spiwok | ALPHARMSD METAD FIT_TO_TEMPLATE WHOLEMOLECULES MATHEVAL COMBINE PRINT MOLINFO POSITION | function bias secondarystructure colvar generic |
| 25.010 | Kinetic rates calculation with Ratchet&Pawl MD | methods | kinetics, ligand binding, ABMD, ratchet&pawl MD | Riccardo Capelli | WHOLEMOLECULES COM ABMD DISTANCE GROUP FLUSH PRINT COMMITTOR | vatom bias generic core colvar |
| 25.008 | Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting | methods | metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting | Dhiman Ray | UNITS WHOLEMOLECULES BIASVALUE MOLINFO CUSTOM RMSD LOWER_WALLS POSITION ENDPLUMED PYTORCH_MODEL METAD GROUP UPPER_WALLS TORSION DISTANCE OPES_METAD ENERGY PRINT | opes bias pytorch function setup generic core colvar |
| 24.034 | Umbrella sampling of ion in transporter SLC26A7 | bio | umbrella sampling, transporter, ions | Xiaoli Lu | UNITS POSITION PRINT RESTRAINT | colvar bias setup generic |
| 24.022 | Integrating Path Sampling with Enhanced Sampling for Rare-event Kinetics | methods | OPES Flooding, Weighted Ensemble, Metadynamics, Kinetics, Infrequent Metadynamics, Integrated Sampling | Dhiman Ray | MOLINFO COORDINATION ANGLE TORSION COMBINE OPES_METAD CENTER FIXEDATOM CONTACTMAP MATHEVAL PRINT WHOLEMOLECULES ENDPLUMED METAD FIT_TO_TEMPLATE CUSTOM RMSD UPPER_WALLS GROUP DISTANCE COMMITTOR | opes bias colvar function generic core vatom |
| 24.007 | SWISH-X | bio | swish-x, SWISH-X, swish, expanded SWISH | Alberto Borsatto | WHOLEMOLECULES MOLINFO UPPER_WALLS ECV_MULTITHERMAL OPES_EXPANDED CONTACTMAP ENERGY PRINT INCLUDE | opes bias colvar generic |
| 23.035 | An Extended Metadynamics Protocol for Binding/Unbinding of Peptide Ligands to Class A G-Protein Coupled Receptors | bio | G protein coupled receptor, peptide ligands, metadynamics, multiple-walker | Timothy Clark | WHOLEMOLECULES BIASVALUE LOWER_WALLS CONSTANT UPPER_WALLS METAD DISTANCE MATHEVAL PRINT CENTER | bias colvar function generic 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 | UNITS BIASVALUE CUSTOM LOWER_WALLS POSITION ENDPLUMED PYTORCH_MODEL UPPER_WALLS OPES_METAD PRINT | opes bias pytorch function setup generic colvar |
| 23.018 | Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention | materials | metadynamics, surface binding, peptide adsorption | Kaylyn Torkelson | COM GYRATION PBMETAD UPPER_WALLS DISTANCE PRINT | colvar bias vatom generic |
| 22.032 | Reciprocal barrier restraint. Application to path-meta-eABF | methods | restraint, upper wall, lower wall, path colvar, meta-eABF, metadynamics, DRR, protein conformational transition, PROTAC | Istvan Kolossvary | BIASVALUE CUSTOM METAD DRR FLUSH PATHMSD PRINT | bias function generic drr colvar |
| 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 | WHOLEMOLECULES CUSTOM RMSD LOWER_WALLS CENTER PYTORCH_MODEL COORDINATION UPPER_WALLS GROUP FIT_TO_TEMPLATE DISTANCE OPES_METAD MATHEVAL PRINT FIXEDATOM COMMITTOR | opes vatom bias pytorch function generic core colvar |
| 22.007 | Characterization of a natural variant of human NDP52 and its functional consequences on mitophagy | bio | metadynamics, well-tempered, protein-protein interactions, disordered proteins, mutations autophagy | Elena Papaleo | WHOLEMOLECULES MOLINFO ALPHABETA DISTANCE COORDINATION ANGLE UPPER_WALLS METAD ALPHARMSD TORSION FLUSH PRINT | bias multicolvar secondarystructure generic colvar |
| 22.006 | Peptide framework for screening the effects of amino acids on assembly | bio | metadynamics, peptides | Andrew White | COM DISTANCES GYRATION CONVERT_TO_FES REWEIGHT_BIAS HISTOGRAM METAD DUMPGRID GROUP COMBINE PRINT INCLUDE | vatom bias multicolvar function generic core colvar gridtools |
| 22.002 | GAMBES_SAMPL5_RATES | other | GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding | Jayashrita Debnath | WHOLEMOLECULES LOAD ENDPLUMED CENTER PYTORCH_MODEL COORDINATION UPPER_WALLS GROUP ANGLE DISTANCE FIT_TO_TEMPLATE MATHEVAL FLUSH ENERGY PRINT FIXEDATOM COMMITTOR | vatom bias pytorch function setup generic core colvar |
| 21.047 | Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations | materials | pair entropy, metadynamics, ves, solids, crystallization | Pablo Piaggi | OPT_AVERAGED_SGD RESTART PAIRENTROPY LOAD VOLUME METAD COMBINE TD_WELLTEMPERED ENERGY BF_LEGENDRE PRINT VES_LINEAR_EXPANSION | bias function setup generic ves colvar gridtools |
| 21.046 | Ubiquitin Interacting Motifs, Duality Between Structured and Disordered Motifs | bio | wt metadynamics, ubiquitin, ataxin-3, short linear motifs, ubiquitin binding motif, moonlight functions, intrinsic disorder | Elena Papaleo | WHOLEMOLECULES GYRATION ALPHABETA LOWER_WALLS ENDPLUMED UPPER_WALLS GROUP METAD PRINT | bias multicolvar generic core colvar |
| 21.037 | Molecular Dynamics simulations of RBD/hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain | Max Bonomi | PRINT RMSD DISTANCE | colvar generic |
| 21.032 | Metal-coupled folding mechanism to metallothionein | bio | parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination | Manuel-Peris Diaz | UNITS WHOLEMOLECULES PBMETAD COORDINATION GROUP | bias setup generic core colvar |
| 21.018 | Localized Volume-based Metadynamics | bio | LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification | Riccardo Capelli | READ COORDINATION FIXEDATOM MATHEVAL PRINT WHOLEMOLECULES COM POSITION REWEIGHT_METAD HISTOGRAM ENDPLUMED METAD DUMPGRID FLUSH RMSD CONVERT_TO_FES UPPER_WALLS GROUP DISTANCE | bias colvar function generic core vatom gridtools |
| 21.013 | Role of vibrational excitation in heterogeneous catalysis | chemistry | catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption | Kristof Bal | BF_CHEBYSHEV TD_GRID ANGLES REWEIGHT_BIAS COORDINATION COMBINE EXTERNAL UNITS OPT_AVERAGED_SGD LOAD PRINT VES_LINEAR_EXPANSION DISTANCES LOWER_WALLS REWEIGHT_METAD HISTOGRAM METAD DUMPGRID FLUSH UWALLS CONVERT_TO_FES RESTRAINT UPPER_WALLS DISTANCE COORDINATIONNUMBER | bias symfunc multicolvar function setup generic ves colvar gridtools |
| 21.011 | CmuMD simulations of NaCl(aq) at graphite | chemistry | CmuMD, DFS clustering | Aaron Finney | DFSCLUSTERING MULTICOLVARDENS CLUSTER_NATOMS LOAD COORDINATIONNUMBER AROUND DENSITY CLUSTER_DISTRIBUTION RESTRAINT GROUP DUMPGRID CONTACT_MATRIX MFILTER_MORE PRINT FIXEDATOM | vatom volumes symfunc bias multicolvar generic core adjmat setup gridtools clusters |
| 21.007 | Sampling enhancement by metadynamics driven by machine learning and de novo protein modelling | bio | metadynamics, machine learning, protein folding | Vojtech Spiwok | WHOLEMOLECULES MOLINFO POSITION FIT_TO_TEMPLATE COMBINE ALPHARMSD MATHEVAL | function colvar generic secondarystructure |
| 21.006 | OPES, On-the-fly Probability Enhanced Sampling Method | methods | opes, alanine dipeptide, well-tempered, multithermal, multiumbrella | Michele Invernizzi | ECV_UMBRELLAS_LINE ENDPLUMED ECV_MULTITHERMAL TORSION OPES_EXPANDED OPES_METAD ENERGY PRINT | opes colvar generic |
| 20.021 | Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins. | bio | phi-values, restrained MD, transition-state, protein folding, disordered proteins, protein evolution | Cristina Paissoni | WHOLEMOLECULES MOLINFO RESTRAINT STATS COORDINATION PRINT | colvar bias function generic |
| 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 | WHOLEMOLECULES COM BIASVALUE MOLINFO LOAD LOWER_WALLS CONSTANT CONTACTMAP PROJECTION_ON_AXIS FUNCPATHGENERAL GROUP UPPER_WALLS METAD DISTANCE MATHEVAL PRINT INCLUDE | vatom bias function setup generic core colvar |
| 20.010 | Phase equilibrium of liquid water and hexagonal ice from enhanced sampling molecular dynamics simulations | materials | water, ice, TIP4P, crystallization, EnvironmentSimilarity, RefCV, kernel, VES, variationally enhanced sampling | Pablo Piaggi | OPT_DUMMY OPT_AVERAGED_SGD RESTART ENVIRONMENTSIMILARITY VOLUME UPPER_WALLS TD_WELLTEMPERED MATHEVAL Q6 PRINT VES_LINEAR_EXPANSION BF_LEGENDRE | envsim bias symfunc function setup generic ves colvar |
| 20.008 | Simulating solvation and acidity in complex mixtures with first-principles accuracy. The case of CH3SO3H and H2O2 in phenol | chemistry | proton trasfer, metadynamics | Kevin Rossi | UNITS DISTANCES CUSTOM COORDINATION METAD PRINT | bias multicolvar function setup generic 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 | READ MOLINFO FUNCPATHMSD COMBINE CONTACTMAP PRINT WHOLEMOLECULES COM LOWER_WALLS ENDPLUMED REWEIGHT_METAD HISTOGRAM METAD DUMPGRID FLUSH ABMD CONVERT_TO_FES UPPER_WALLS DISTANCE | bias colvar function generic vatom gridtools |
| 20.000 | Muscarinic M2 receptor-ligand funnel metadynamics | bio | multiple walker metadynamics, well-tempered metadynamics, funnel metadynamics, MC-HLDA, GPCR, receptor, Adiabatic Bias MD | Riccardo Capelli | ABMD COM READ CONVERT_TO_FES LOWER_WALLS ENDPLUMED REWEIGHT_METAD HISTOGRAM UPPER_WALLS METAD DUMPGRID COMBINE DISTANCE MATHEVAL PRINT | bias colvar function generic vatom gridtools |
| 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 | READ REWEIGHT_BIAS COMBINE REWEIGHT_TEMP_PRESS OPT_AVERAGED_SGD RESTART LOAD TD_WELLTEMPERED MATHEVAL PRINT VES_LINEAR_EXPANSION LOWER_WALLS VOLUME HISTOGRAM DUMPGRID ENERGY TD_MULTITHERMAL_MULTIBARIC BF_LEGENDRE OPT_DUMMY CONVERT_TO_FES UPPER_WALLS CELL Q6 | bias symfunc colvar function generic ves setup gridtools |
| 19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Vittorio Limongelli | WHOLEMOLECULES COM FUNNEL RMSD LOWER_WALLS FUNNEL_PS METAD UPPER_WALLS DISTANCE PRINT | funnel vatom bias generic colvar |
| 19.030 | Coarse-Grained MetaDynamics (CG-MetaD) | bio | Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy | Vittorio Limongelli | WHOLEMOLECULES COM LOWER_WALLS METAD UPPER_WALLS DISTANCE PRINT | colvar bias vatom generic |
| 19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Matteo Salvalaglio | LOWER_WALLS METAD UPPER_WALLS TORSION DISTANCE PRINT CENTER COMMITTOR | vatom bias colvar generic |
| 19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Carlo Camilloni | WHOLEMOLECULES BIASVALUE MOLINFO RMSD ENDPLUMED RESTRAINT STATS UPPER_WALLS GROUP SAXS DISTANCE PRINT CENTER INCLUDE | vatom bias isdb function generic core colvar |
| 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 MOLINFO RMSD ERMSD ENDPLUMED METAD PRINT | bias colvar generic |
| 19.005 | Cmyc small molecule interaction | bio | metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP | Gabriella Heller | WHOLEMOLECULES GYRATION MOLINFO ALPHABETA PBMETAD METAINFERENCE COORDINATION GROUP CS2BACKBONE DISTANCE PRINT CENTER INCLUDE | vatom bias multicolvar isdb generic core colvar |
| 19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Giovanni Bussi | DISTANCES MOLINFO ERMSD LOWER_WALLS DISTANCE RANDOM_EXCHANGES ANGLE UPPER_WALLS METAD COMBINE FLUSH PRINT INCLUDE | bias multicolvar function generic colvar |
| 25.009 | Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water | chemistry | metadynamics, nitrate photolysis | Kam-Tung Chan | COORDINATION PRINT READ REWEIGHT_METAD FLUSH HISTOGRAM RESTART DUMPGRID CUSTOM GROUP UPPER_WALLS DISTANCE METAD | function core gridtools bias setup generic colvar |
| 25.007 | Shaping the glycan landscape. Hidden relationships between linkage and ring distortion induced by carbohydrate-active enzmyes | bio | REST-RECT, REST2, glycan, enzyme, CAZyme, steered | Isabell Grothaus | RESTRAINT PRINT PUCKERING MOLINFO RESTART MOVINGRESTRAINT TORSION DISTANCE METAD | colvar bias setup generic |
| 25.002 | M3_PCV-ABMD | chemistry | Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor | Gian Marco Elisi | PATHMSD ENDPLUMED PRINT ABMD UNITS UPPER_WALLS | colvar bias setup generic |
| 24.036 | Leveraging cryptic ligand envelopes through enhanced molecular simulations | bio | HREX, conformational heterogeneity, drug discovery, ligand binding, plitidepsin, aplidin, ligand-target complexes, cryptic ligand envelope | Francesco Colizzi | COORDINATION CONVERT_TO_FES PRINT HISTOGRAM WHOLEMOLECULES ANGLE DUMPGRID TORSION GROUP DISTANCE | colvar gridtools core generic |
| 24.030 | NMR guided simulation of dsRBD | bio | Metainference, NMR, protein dynamics | Debadutta Patra | PRINT METAINFERENCE FLUSH DISTANCE MOLINFO WHOLEMOLECULES RDC ALPHABETA GROUP ENSEMBLE STATS | function multicolvar core isdb generic colvar |
| 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 | RESTRAINT MATHEVAL COMMITTOR PRINT FLUSH MOLINFO RESTART COORDINATIONNUMBER BIASVALUE ENERGY TORSION DISTANCE METAD | function symfunc bias setup generic colvar |
| 23.039 | Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation | chemistry | metadynamics, ligand dissociation | Eric Beyerle | RESTRAINT PRINT COMBINE MOLINFO CENTER FIXEDATOM DUMPMASSCHARGE UPPER_WALLS DISTANCE METAD | function vatom bias generic colvar |
| 23.037 | Estimating binding free energy of solid binding peptides without extensive sampling | bio | metadynamics, solid binding peptides | Xin Qi | GYRATION PRINT PBMETAD MOLINFO COM LOWER_WALLS UPPER_WALLS DISTANCE | colvar vatom bias generic |
| 23.028 | Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process | chemistry | Ammonia decomposition; Dynamics;OPES; Neural Network potential | Manyi Yang | MATHEVAL ZDISTANCES COMMITTOR PRINT FLUSH UNITS FIXEDATOM CUSTOM COORDINATIONNUMBER COM LOWER_WALLS OPES_METAD ENERGY DISTANCES GROUP UPPER_WALLS DISTANCE | function opes vatom multicolvar core symfunc bias setup generic colvar |
| 23.024 | Permutationally Invariant Networks for Enhanced Sampling (PINES) | methods | collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent | Nicholas Herringer | LOAD PBMETAD PRINT | bias setup 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 | UPPER_WALLS COORDINATION PRINT FIT_TO_TEMPLATE OPES_METAD_EXPLORE CENTER WHOLEMOLECULES FIXEDATOM LOWER_WALLS GROUP OPES_METAD CUSTOM TORSION UNITS PYTORCH_MODEL DISTANCE PATH | function opes vatom core mapping bias setup generic colvar pytorch |
| 23.013 | Path meta-eABF simulation of large scale conformational change in STING protein | methods | meta-eABF, path CV, large scale conformational change, STING protein, reciprocal barrier restraint | Istvan Kolossvary | PATHMSD PRINT TIME FLUSH DRR LOWER_WALLS BIASVALUE CUSTOM UNITS UPPER_WALLS METAD | function drr bias setup generic colvar |
| 23.011 | OneOPES, a combined enhanced sampling method to rule them all | bio | OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding | Valerio Rizzi | ENDPLUMED PRINT ECV_MULTITHERMAL OPES_METAD_EXPLORE MOLINFO OPES_EXPANDED ENERGY TORSION DISTANCE METAD | colvar opes bias generic |
| 23.010 | An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G‑Protein-Coupled Receptor Ligands | bio | GPCR, binding free energy, free energy surface | Timothy Clark | MATHEVAL PRINT WHOLEMOLECULES LOWER_WALLS CONSTANT BIASVALUE UPPER_WALLS DISTANCE METAD | function colvar bias generic |
| 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 | COMMITTOR INCLUDE CONTACTMAP ANGLE ENERGY PYTORCH_MODEL COORDINATION RMSD MATHEVAL ENDPLUMED PRINT COMBINE MOLINFO CENTER WHOLEMOLECULES CUSTOM GROUP UPPER_WALLS DISTANCE FIT_TO_TEMPLATE LOWER_WALLS OPES_METAD FIXEDATOM | function opes vatom core bias generic colvar pytorch |
| 23.006 | Transcription factor unbinding | bio | metadynamics, DNA, conformational changes | Malin Lüking | PRINT ALPHARMSD MOLINFO CONTACTMAP ANGLE METAD COM DISTANCE DUMPFORCES | vatom bias generic colvar secondarystructure |
| 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 MATHEVAL CONVERT_TO_FES PRINT READ REWEIGHT_METAD HISTOGRAM MOLINFO WHOLEMOLECULES DUMPGRID DISTANCE METAD | function gridtools bias generic colvar |
| 22.045 | Binding mode and mechanism of enzymatic polyethylene terephthalate degradation | bio | metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation | Francesco Colizzi | PRINT WHOLEMOLECULES ANGLE MOVINGRESTRAINT LOWER_WALLS COM UPPER_WALLS DISTANCE METAD | colvar vatom bias generic |
| 22.044 | Colloid Crystallisation Analyses | materials | Q4, Q6, Pair Entropy, DFS | Aaron Finney | LOCAL_Q4 Q6 CONTACT_MATRIX PRINT COMBINE MFILTER_MORE MFILTER_LESS LOCAL_Q6 COORDINATIONNUMBER Q4 GROUP CLUSTER_NATOMS DFSCLUSTERING LOCAL_AVERAGE | function adjmat multicolvar core clusters symfunc generic |
| 22.024 | Conformational Entropy as a Potential Liability of Computationally Designed Antibodies | bio | metadynamics, conformational entropy, antibody, nanobody | Thomas Löhr | PRINT PBMETAD ALPHARMSD MOLINFO ANTIBETARMSD WHOLEMOLECULES RESTART COM TORSION ALPHABETA | vatom multicolvar bias setup generic colvar secondarystructure |
| 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 PRINT AROUND HISTOGRAM ENERGY RESTART DUMPGRID OPES_METAD CUSTOM UPPER_WALLS VOLUME | function opes gridtools envsim setup generic bias colvar volumes |
| 22.015 | Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome | bio | photodynamics, bacteriophytochrome, variationally enhanced sampling | Jakub Rydzewski | PRINT OPT_AVERAGED_SGD BF_FOURIER TD_UNIFORM TORSION VES_LINEAR_EXPANSION | ves colvar generic |
| 22.005 | Collective Variable for Metadynamics Derived from AlphaFold Output | bio | AlphaFold, protein folding, protein structure prediction, metadynamics, deep learning, free energy simulation, collective variable | Vojtech Spiwok | LOAD WHOLEMOLECULES PRINT METAD | bias setup generic |
| 22.003 | Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling | methods | opes, metadynamics, reweighting, alanine, muller | Michele Invernizzi | ECV_UMBRELLAS_FILE ENDPLUMED PRINT ECV_MULTITHERMAL PBMETAD POSITION OPES_METAD_EXPLORE CUSTOM LOWER_WALLS OPES_EXPANDED BIASVALUE OPES_METAD ENERGY TORSION UNITS UPPER_WALLS METAD | function opes bias setup generic colvar |
| 21.051 | Automatic learning of hydrogen-bond fixes in an AMBER RNA force field | methods | force field, RNA | Giovanni Bussi | COORDINATION PRINT COMBINE MOLINFO WHOLEMOLECULES BIASVALUE ERMSD METAD | function colvar bias generic |
| 21.042 | Peptoid-mediated Au nanocrystal growth | materials | parallel-bias metadynamics, peptoid, Au | Xin Qi | GYRATION PRINT PBMETAD MOLINFO COM UPPER_WALLS DISTANCE | colvar vatom bias generic |
| 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 | MATHEVAL ENVIRONMENTSIMILARITY Q6 ECV_MULTITHERMAL_MULTIBARIC PRINT OPT_AVERAGED_SGD BF_LEGENDRE RESTART TD_UNIFORM OPES_EXPANDED ECV_UMBRELLAS_LINE VOLUME ENERGY UPPER_WALLS VES_LINEAR_EXPANSION | function opes ves symfunc envsim setup generic bias colvar |
| 20.028 | Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane | bio | metadynamics, KRas-4B, anionic membrane | Huixia Lu | PRINT FIT_TO_TEMPLATE CENTER RESTART DISTANCE METAD | vatom bias setup generic colvar |
| 20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Jim Pfaendtner | COORDINATION PRINT CENTER WHOLEMOLECULES RESTART DISTANCES GROUP DISTANCE | vatom multicolvar core setup generic colvar |
| 20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Pratyush Tiwary | RMSD PRINT COMBINE MOLINFO WHOLEMOLECULES RESTART TORSION UPPER_WALLS DISTANCE METAD | function bias setup generic colvar |
| 19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Valerio Rizzi | ENDPLUMED PRINT COMBINE FLUSH RESTART COORDINATIONNUMBER UNITS DISTANCES GROUP UPPER_WALLS METAD | function multicolvar core symfunc bias setup generic |
| 19.075 | PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python | other | Python, automatic differentiation | Toni Giorgino | RESTRAINT ENDPLUMED PRINT COMBINE DUMPDERIVATIVES CENTER ANGLE CUSTOM TORSION GROUP DISTANCE | function vatom core 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 | GYRATION ENDPLUMED PRINT LOWER_WALLS COORDINATIONNUMBER ENERGY DISTANCES UPPER_WALLS METAD | multicolvar symfunc bias generic colvar |
| 19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Matteo Salvalaglio | MATHEVAL EXTERNAL COMMITTOR CONVERT_TO_FES PRINT READ REWEIGHT_METAD HISTOGRAM REWEIGHT_BIAS DUMPGRID BIASVALUE TORSION DISTANCE METAD | function gridtools bias generic colvar |
| 19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Michele Invernizzi | EXTERNAL ENDPLUMED PRINT POSITION OPES_METAD TORSION UNITS METAD | opes bias setup generic colvar |
| 19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Kim Jelfs | INPLANEDISTANCES PRINT FLUSH MOVINGRESTRAINT RESTART COM DISTANCES | vatom multicolvar bias setup generic |
| 19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | GiovanniMaria Piccini | PRINT COMBINE FLUSH LOWER_WALLS ENERGY UNITS UPPER_WALLS DISTANCE METAD | function bias setup generic colvar |
| 19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Gabriele Cesare Sosso | COMMITTOR Q6 CONTACT_MATRIX ENDPLUMED FLUSH MFILTER_MORE OUTPUT_CLUSTER CLUSTER_WITHSURFACE LOCAL_Q6 CLUSTER_NATOMS DFSCLUSTERING | adjmat multicolvar clusters symfunc generic |
| 19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Jim Pfaendtner | COORDINATION EXTERNAL ENERGY GROUP METAD | colvar bias core |
| 19.023 | RECT | methods | metadynamics, replica exchange | Giovanni Bussi | GYRATION PRINT WHOLEMOLECULES TORSION METAD | colvar bias generic |
| 19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Matteo Salvalaglio | GYRATION ENDPLUMED PRINT RESTART COORDINATIONNUMBER DISTANCES METAD | multicolvar symfunc bias setup generic colvar |
| 19.004 | MI Ubiquitin | bio | metainference, NMR | Max Bonomi | PRINT METAINFERENCE MOLINFO WHOLEMOLECULES RDC GROUP CS2BACKBONE | isdb core generic |
| 19.003 | EMMI ClpP | bio | metainference, cryo-EM | Max Bonomi | PRINT MOLINFO BIASVALUE EMMI GROUP | isdb core bias generic |
| 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 COMBINE OPES_METAD_EXPLORE ECV_MULTITHERMAL OPES_EXPANDED PRINT COORDINATION GROUP CUSTOM RESTART TORSION ENERGY | colvar function setup generic opes core |
| 24.018 | A new route to the prebiotic synthesis of glycine via ab initio-based machine learning calculations | chemistry | prebiotic chemistry, glycine, Strecker synthesis, ab initio calculations, machine learning | Léon HUET | PRINT DISTANCE | generic colvar |
| 24.008 | yCD Metadynamics | bio | volume-based MetaD, path CVs, infrequent MetaD, product release | James McCarty | METAD WHOLEMOLECULES HISTOGRAM WRAPAROUND FLUSH ENDPLUMED INCLUDE PRINT CONTACTMAP PATH CONVERT_TO_FES FIXEDATOM DISTANCE DUMPGRID GROUP FIT_TO_TEMPLATE UPPER_WALLS MOLINFO COM REWEIGHT_METAD RMSD COORDINATION READ MATHEVAL COMMITTOR | gridtools colvar function mapping generic vatom core bias |
| 24.004 | Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables | materials | metadynamics, nucleation, machine learning | Ziyue Zou | METAD INCLUDE PRINT GROUP RESTART LOAD | bias core generic setup |
| 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 METAD FLUSH INCLUDE SUM PRINT SELECT_COMPONENTS MATHEVAL | function valtools generic matrixtools 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 | COMBINE METAD Q6 LOCAL_Q6 MFILTER_MORE COORDINATIONNUMBER PRINT GROUP LOWER_WALLS MOVINGRESTRAINT | function multicolvar generic core bias symfunc |
| 23.007 | Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains | bio | metadynamics, peptoids, parallel-bias metadynamics | Jim Pfaendtner | COM WHOLEMOLECULES INCLUDE RESTRAINT GYRATION PBMETAD PRINT COORDINATION TORSION | vatom bias generic colvar |
| 23.004 | Melting curves of ice polymorphs in the vicinity of the liquid-liquid critical point | chemistry | water, liquid-liquid transition, second critical point, ice, polymorphs, melting curves, environment similarity, opes, density-functional theory, scan, machine learning potential | Pablo Piaggi | HISTOGRAM LOWER_WALLS ECV_UMBRELLAS_LINE ENVIRONMENTSIMILARITY OPES_EXPANDED PRINT DUMPGRID RESTART UPPER_WALLS | gridtools setup generic envsim opes bias |
| 22.036 | Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction | bio | Well-tempered MetaDynamics with Hamiltonian Replica Exchange | Miroslav Krepl | COMBINE METAD FLUSH GHBFIX PRINT COORDINATION GROUP CUSTOM BIASVALUE UPPER_WALLS MOLINFO LOAD | colvar function setup generic core bias |
| 22.028 | N-glycan conformer distributions in atomistic simulation | bio | REST2, RECT, N-glycan, pucker | Isabell Grothaus | METAD READ HISTOGRAM PRINT CONVERT_TO_FES DUMPGRID TORSION PUCKERING MOLINFO | gridtools bias generic colvar |
| 22.011 | Accelerating all-atom simulations and gaining mechanistic understanding of biophysical systems through State Predictive Information Bottleneck | methods | metadynamics, membrane permeation, protein folding | Shams Mehdi | COM DISTANCE WHOLEMOLECULES COMBINE METAD MOLINFO PRINT ZANGLES CUSTOM TORSION LOWER_WALLS ALPHABETA UPPER_WALLS XANGLES MATHEVAL YANGLES | colvar function multicolvar generic vatom bias |
| 21.049 | Multiple-path-metadynamics and PathMaps | methods | path-CV, metadynamics, multiple-walker, multiple paths, pathmap | Alberto Pérez-de-Alba-Ortíz | COMBINE METAD ENSEMBLE RESTRAINT UNITS PRINT CUSTOM TORSION LOWER_WALLS UPPER_WALLS MOVINGRESTRAINT CONSTANT LOAD | colvar setup function generic bias |
| 21.048 | Enhancing ligand exploration within a channel pore and fenestrations using metadynamics | bio | well-tempered metadynamics, protein-ligand enhanced sampling, sodium channel, Nav, small molecule drug | Elaine Tao | COM DISTANCE METAD UNITS PRINT CUSTOM TORSION LOWER_WALLS UPPER_WALLS | colvar setup function generic vatom bias |
| 21.025 | Computational and biochemical analysis of type IV pilus dynamics and stability | bio | molecular dynamics, calcium binding, Type IV pilus | Yasaman Karami | PRINT DISTANCE UPPER_WALLS LOWER_WALLS | bias generic colvar |
| 21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Kristof Bal | REWEIGHT_METAD METAD HISTOGRAM FLUSH COORDINATIONNUMBER UNITS PRINT CONVERT_TO_FES DUMPGRID UPPER_WALLS MOVINGRESTRAINT COMMITTOR LOAD | gridtools setup generic bias symfunc |
| 21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Tarsis Ferreira | REWEIGHT_METAD METAD DISTANCE WHOLEMOLECULES HISTOGRAM LOWER_WALLS INCLUDE PRINT COORDINATION DUMPGRID GROUP ENERGY PUCKERING UPPER_WALLS MOLINFO RANDOM_EXCHANGES | gridtools colvar generic core bias |
| 20.003 | Enhanced sampling of transition states | methods | Variationally Enhanced Sampling, Target distribution, Transition state, Enhanced Sampling, Nucleation, chemical reaction | Jayashrita Debnath | BF_LEGENDRE OPT_AVERAGED_SGD VES_LINEAR_EXPANSION POSITION UNITS PRINT ENERGY LOAD | colvar generic ves setup |
| 19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Matteo Salvalaglio | DISTANCE ENDPLUMED INCLUDE CENTER PRINT GROUP | vatom core generic colvar |
| 19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Jakub Rydzewski | POSITION UNITS MAZE_OPTIMIZER_BIAS PRINT MAZE_SIMULATED_ANNEALING MAZE_LOSS | maze generic colvar setup |
| 19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Luigi Bonati | Q6 ENDPLUMED ENVIRONMENTSIMILARITY POSITION UNITS PRINT ENERGY TORSION LOAD | colvar setup generic envsim symfunc |
| 19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Cristina Paissoni | COMBINE ANGLE WHOLEMOLECULES ENDPLUMED INCLUDE CENTER PBMETAD ENSEMBLE STATS PRINT COORDINATION GROUP SAXS BIASVALUE ALPHABETA MOLINFO MATHEVAL | colvar function isdb multicolvar generic vatom core bias |
| 19.055 | Flying Gaussian method | methods | flying Gaussians, alanine dipeptide, peptide bond, Met-enkephalin | Vojtech Spiwok | COMBINE METAD DISTANCE PRINT TORSION MATHEVAL | bias generic colvar function |
| 19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Gareth Tribello | MULTICOLVARDENS FCCUBIC FOURIER_TRANSFORM CENTER UNITS DUMPGRID GROUP FIND_CONTOUR_SURFACE MORE_THAN | contour gridtools setup function vatom core fourier symfunc |
| 19.041 | Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces | bio | metadynamics, collective variables, conformational changes, multiple walkers, Well-Tempered MetaD, peptide, binding, phosphorylation, post-transitional motif, sio2, adsorption | Jim Pfaendtner | COM DISTANCE METAD PRINT ENERGY UPPER_WALLS | vatom bias generic colvar |
| 19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Davide Provasi | COM DISTANCE WHOLEMOLECULES METAD ENDPLUMED FUNCPATHMSD RMSD CONTACTMAP PRINT | colvar function generic vatom bias |
| 19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Silvio Pipolo | METAD CELL FUNCPATHMSD PRINT LOWER_WALLS UPPER_WALLS PIV | colvar function generic piv bias |
| 19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Haochuan Chen | PRINT TORSION DRR | generic colvar drr |
| 19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Riccardo Capelli | COM METAD WHOLEMOLECULES REWEIGHT_METAD READ HISTOGRAM FLUSH ENDPLUMED POSITION PRINT COORDINATION WRAPAROUND CONVERT_TO_FES GROUP FIT_TO_TEMPLATE DUMPGRID UPPER_WALLS MATHEVAL | gridtools colvar function generic vatom 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 | UPPER_WALLS FIXEDATOM CUSTOM COMMITTOR ZDISTANCES DISTANCE COORDINATIONNUMBER UNITS GROUP DISTANCES OPES_METAD PRINT FLUSH | symfunc colvar multicolvar function vatom setup core generic opes bias |
| 25.001 | RNA G-quadruplex folding with ST-metaD protocol | bio | RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | METAD ERMSD COMBINE MOLINFO WHOLEMOLECULES | bias colvar generic function |
| 24.027 | Proline cis and trans subensembles of a disordered peptide | bio | intrinsically disordered proteins, proline cis trans isomerisation, metadynamics, collective variables | Alice Pettitt | ALPHARMSD PARABETARMSD GYRATION TORSION INCLUDE DIHCOR FLUSH COORDINATION MOLINFO DISTANCE ENDPLUMED ANTIBETARMSD GROUP PBMETAD PRINT COMBINE WHOLEMOLECULES | colvar multicolvar function secondarystructure core generic bias |
| 24.006 | Water vapor condensation | chemistry | metadynamics, homogeneous condensation, chemical potential | Shenghui Zhong | UPPER_WALLS CLUSTER_PROPERTIES METAD DFSCLUSTERING CONTACT_MATRIX COORDINATIONNUMBER UNITS CLUSTER_NATOMS PRINT | symfunc adjmat setup clusters generic bias |
| 24.000 | Ammonia Decomposition on Non-stoichiometric Lithium Imide | chemistry | ammonia decomposition, non-stoichiometric lithium imide, machine learning interatomic potentials, enhanced sampling, heterogeneous catalysis | Francesco Mambretti | UPPER_WALLS FIXEDATOM ZDISTANCES DISTANCE COORDINATIONNUMBER UNITS GROUP OPES_METAD PRINT FLUSH | symfunc colvar multicolvar vatom setup core generic opes bias |
| 23.036 | Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? | bio | NaCl, nucleation, metadynamics | Ruiyu Wang | MATHEVAL Q4 ENERGY METAD COORDINATIONNUMBER Q6 COMBINE PRINT VOLUME | symfunc colvar function generic 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 | SAXS UPPER_WALLS STATS DISTANCE RMSD ENSEMBLE GROUP WRAPAROUND CENTER BIASVALUE MOLINFO PRINT | colvar function vatom isdb core generic bias |
| 22.041 | Skipping the Replica Exchange Ladder with Normalizing Flows | methods | OPES, alanine, normalizing flows, replica exchange | Michele Invernizzi | TORSION ENERGY OPES_EXPANDED ENDPLUMED POSITION UNITS ECV_MULTITHERMAL PRINT OPES_METAD | setup opes 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 | UPPER_WALLS METAD LOWER_WALLS PRINT PCAVARS WHOLEMOLECULES | mapping bias generic |
| 22.039 | Driving and characterizing nucleation of urea and glycine polymorphs in water | bio | metadynamics, nucleation, amino acids, polymorphism | Eric Beyerle | MATHEVAL Q4 INCLUDE PAIRENTROPY METAD COORDINATIONNUMBER GROUP Q6 COMBINE CENTER PRINT LOAD | symfunc function vatom setup core generic bias gridtools |
| 22.038 | Enhanced Sampling Aided Design of Molecular Photoswitches | chemistry | reaction discovery, OPES explore, graph CV | Umberto Raucci | CUSTOM COORDINATION PYTORCH_MODEL UNITS OPES_METAD_EXPLORE PRINT | colvar function setup pytorch generic opes |
| 22.037 | Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site | chemistry | metadynamics, DNA, abasic | Mike Jones | DISTANCES PRINT METAD DISTANCE | generic bias colvar multicolvar |
| 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 | MATHEVAL UPPER_WALLS CUSTOM METAD COMMITTOR LOWER_WALLS CELL PRINT DRMSD | bias colvar generic function |
| 22.029 | Angiotensin-1-7_Metadynamics | bio | Metadynamics, Angiotensin-(1-7), peptide | L.-América Chi | GYRATION UPPER_WALLS METAD COORDINATION GROUP LOWER_WALLS PRINT WHOLEMOLECULES FLUSH | core bias colvar generic |
| 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 CENTER PRINT DISTANCE | colvar generic vatom |
| 21.050 | N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity | methods | bio | Isabell Louise Grothaus | CENTER PRINT DISTANCE | colvar generic vatom |
| 21.045 | QM/MM metadynamics of thiol-disulfide exchange between methylthiolate and dimethyldisulfide in water with an imposed external electrostatic potential (ESP) | chemistry | metadynamics, QM/MM, electrostatic potential, thiol-disulfide exchange | Denis Maag | UPPER_WALLS METAD COORDINATION DISTANCE COORDINATIONNUMBER COMBINE LOWER_WALLS PRINT | symfunc colvar function generic bias |
| 21.038 | Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics | materials | metadynamics, SGOOP, nucleation, urea | Ziyue Zou | INCLUDE METAD ENERGY COORDINATIONNUMBER GROUP COMBINE CENTER PRINT LOAD VOLUME | symfunc colvar function vatom setup core generic bias |
| 21.029 | Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs | bio | metadynamics, small peptide, machine learning | Pratyush Tiwary | TORSION RESTART ENERGY EXTERNAL PRINT MOLINFO FLUSH | setup bias colvar generic |
| 21.024 | Property map collective variable as a useful tool for force field correction | chemistry | molecular mechanics | Vojtech Spiwok | TORSION METAD PROPERTYMAP BIASVALUE PRINT WHOLEMOLECULES | bias 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 | INCLUDE TORSION REWEIGHT_METAD CUSTOM METAD ENERGY DISTANCE UNITS BIASVALUE CONSTANT PRINT | colvar function setup generic bias |
| 21.019 | Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations | materials | Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen | Matteo Salvalaglio | MATHEVAL DISTANCE KDE TORSIONS PRINT COM | colvar multicolvar function vatom generic gridtools |
| 21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Adriana Pietropaolo | MATHEVAL TORSION RESTART PBMETAD BIASVALUE CONSTANT PRINT WHOLEMOLECULES | colvar function setup generic bias |
| 20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Faidon Brotzakis | BIASVALUE DISTANCES EMMI CONVERT_TO_FES RMSD DUMPGRID GROUP HISTOGRAM PRINT MOLINFO READ WHOLEMOLECULES | colvar multicolvar isdb core generic bias gridtools |
| 20.026 | Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor | bio | Metadynamics, Umbrella sampling | Brandon Peters | MULTI_RMSD REWEIGHT_METAD METAD CONVERT_TO_FES RESTRAINT DUMPGRID HISTOGRAM PRINT | bias colvar generic gridtools |
| 20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Max Bonomi | GYRATION INCLUDE DIHCOR COORDINATION ALPHABETA PBMETAD PRINT MOLINFO WHOLEMOLECULES | bias multicolvar colvar generic |
| 20.016 | Predicting polymorphism in molecular crystals using orientational entropy | materials | metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy | Pablo Piaggi | UPPER_WALLS INCLUDE METAD GROUP CENTER PRINT LOAD VOLUME | colvar vatom setup core generic bias |
| 20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Carlo Camilloni | SAXS GYRATION TORSION DISTANCE STATS ALPHABETA PBMETAD CENTER ENSEMBLE MOLINFO PRINT WHOLEMOLECULES METAINFERENCE FLUSH | colvar multicolvar function vatom isdb generic bias |
| 19.079 | Impact of Glutamate Carboxylation in the Adsorption of the alpha-1 Domain of Osteocalcin to Hydroxyapatite and Titania | bio | metadynamics, peptide adsorption, parallel tempering, well-tempered ensemble | Sarah Alamdari | GYRATION UPPER_WALLS ENERGY METAD DISTANCE GROUP PRINT MOLINFO COM | colvar vatom core generic bias |
| 19.078 | Iterative unbiasing of quasi-equilibrium sampling | methods | metadynamics, reweighting | Federico Giberti | MATHEVAL COLLECT_FRAMES METAD DISTANCE COORDINATIONNUMBER UNITS REWEIGHT_BIAS BIASVALUE DUMPATOMS PRINT | landmarks symfunc colvar function setup generic bias |
| 19.056 | maze | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_SIMULATED_ANNEALING POSITION UNITS PRINT MAZE_LOSS MAZE_OPTIMIZER_BIAS | maze setup colvar generic |
| 19.049 | Determining the sizes of solid/liquid clusters in MD trajectories of nucleation | methods | nucleation, metadynamics, clustering, Steinhardt order parameters | Gareth Tribello | OUTPUT_CLUSTER OUTER_PRODUCT CLUSTER_PROPERTIES SMAC ONES CUSTOM METAD DFSCLUSTERING MORE_THAN CLUSTER_DISTRIBUTION CONTACT_MATRIX COORDINATIONNUMBER MATRIX_VECTOR_PRODUCT Q6 CLUSTER_NATOMS DISTANCES LOCAL_Q6 PRINT | symfunc multicolvar function adjmat matrixtools generic clusters bias |
| 19.047 | Close Structure | methods | metadynamics, RMSD, path collective variables, property map | Vojtech Spiwok | METAD PRINT PROPERTYMAP WHOLEMOLECULES | bias colvar generic |
| 19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | UPPER_WALLS RESTART METAD DISTANCE UNITS COMBINE DISTANCES PRINT FLUSH | colvar multicolvar function setup 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 | TORSION DISTANCE RESTRAINT GROUP PRINT COM | colvar vatom core generic bias |
| 19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Pratyush Tiwary | TORSION RESTART EXTERNAL COMMITTOR DISTANCE ALPHABETA COMBINE PRINT COM WHOLEMOLECULES | colvar multicolvar function vatom setup generic bias |
| 19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Matteo Salvalaglio | MATHEVAL UPPER_WALLS CELL TORSION METAD ENERGY ENDPLUMED COMBINE LOWER_WALLS PRINT VOLUME | bias colvar generic function |
| 19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Carlo Camilloni | UPPER_WALLS TORSION DIHCOR STATS DISTANCE ENDPLUMED RDC RESTRAINT ALPHABETA GROUP DHENERGY PBMETAD CENTER ENSEMBLE MOLINFO PRINT METAINFERENCE WHOLEMOLECULES | colvar multicolvar function vatom isdb core generic bias |
| 19.006 | Flying Gaussian proof | methods | flying Gaussians, alanine dipeptide | Vojtech Spiwok | METAD PRINT TORSION | bias colvar generic |
| 19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Michele Invernizzi | VES_DELTA_F TORSION RESTART METAD ENERGY POSITION ENDPLUMED UNITS PRINT LOAD | colvar ves setup generic bias |
| 25.011 | Chiral perovskite nucleation | chemistry | metadynamics, chiral perovskites, nucleation | Adriana Pietropaolo | RESTART UNITS DISTANCE MATHEVAL MULTI_RMSD LOWER_WALLS UPPER_WALLS PRINT PBMETAD | generic bias setup function 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 | CENTER RESTART INCLUDE ENERGY DISTANCE READ TORSION VOLUME GYRATION PRINT PBMETAD | generic bias setup vatom colvar |
| 24.035 | Data efficient machine learning potentials for modeling catalytic reactivity via active learning and enhanced sampling | chemistry | opes, catalysis, ammonia, machine learning potentials | Luigi Bonati | COMMITTOR UNITS OPES_METAD CUSTOM DISTANCE COORDINATION LOWER_WALLS UPPER_WALLS PRINT GROUP RESTART | generic opes bias setup core function colvar |
| 24.026 | Constant pH metadynamics of RNA oligomers | bio | metadynamics, pH, RNA | Giovanni Bussi | MOLINFO METAD TORSION PUCKERING PRINT RESTART | generic colvar setup bias |
| 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 | ENERGY OPES_METAD DISTANCE UPPER_WALLS PRINT COORDINATION | generic opes bias colvar |
| 24.019 | Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning | bio | OPES, machine learning, protein folding, adaptive sampling | Mingyuan Zhang | MOLINFO OPES_METAD ALPHARMSD CUSTOM DISTANCE TORSION WHOLEMOLECULES COMBINE PRINT COORDINATION GYRATION | generic secondarystructure opes function 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 | INCLUDE MOVINGRESTRAINT DISTANCE ALPHABETA TORSION WHOLEMOLECULES COM PRINT COORDINATION GYRATION | generic multicolvar bias vatom 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 | MOLINFO FUNCPATHMSD INCLUDE METAD ALPHARMSD DISTANCE CONTACTMAP LOWER_WALLS PATHMSD PRINT UPPER_WALLS | generic secondarystructure bias function colvar |
| 23.031 | Identifying small molecules binding sites in RNA conformational ensembles with SHAMAN | bio | RNA, metadynamics, probes, mixed-solvent MD, small molecules, binding sites | Max Bonomi | WRAPAROUND MOLINFO FIT_TO_TEMPLATE METAD POSITION DISTANCES SHADOW WHOLEMOLECULES UPPER_WALLS PRINT GROUP CENTER | generic multicolvar bias core isdb vatom colvar |
| 23.025 | Probing ion binding to G-quadruplexes and related events | chemistry | metadynamics, repulsive potential, nucleic acids, G-quadruplexes | Marcelo Poleto | WRAPAROUND FIT_TO_TEMPLATE DUMPATOMS RESTART UNITS METAD FLUSH POSITION DISTANCE DISTANCES MATHEVAL WHOLEMOLECULES LOWER_WALLS COM PRINT GROUP UPPER_WALLS | generic multicolvar bias setup core vatom function colvar |
| 23.016 | Activation/deactivation free-energy profiles for the β2-adrenergic receptor: Ligand modes of action | bio | G protein coupled receptor, beta-adrenergic, receptor activation, partial agonism, metadynamics | Timothy Clark | MOLINFO REWEIGHT_METAD DUMPGRID METAD CONVERT_TO_FES DISTANCE MATHEVAL READ RMSD HISTOGRAM WHOLEMOLECULES PRINT | generic bias gridtools function colvar |
| 23.012 | JAK2 2D meta-eABF PMF with statistical analysis | bio | 2D meta-eABF, path CV, PMF | Istvan Kolossvary | DRR METAD BIASVALUE FLUSH CUSTOM LOWER_WALLS PATHMSD PRINT UPPER_WALLS | generic bias function colvar drr |
| 23.003 | Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations | methods | metadynamics, alchemical variable, alchemical free energy calculations | Wei-Tse Hsu | EXTRACV METAD READ TORSION PRINT | generic bias colvar |
| 23.001 | Quantum phase diagram of water | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn-Løland Bore | ECV_UMBRELLAS_LINE ENVIRONMENTSIMILARITY INCLUDE LOWER_WALLS UPPER_WALLS PRINT OPES_EXPANDED RESTART | generic opes bias setup envsim |
| 22.043 | Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES | bio | OPES, RNA, Tetraloop, Folding | Gül Zerze | ECV_UMBRELLAS_LINE ENERGY CONTACTMAP ECV_MULTITHERMAL WHOLEMOLECULES PRINT OPES_EXPANDED | generic colvar opes |
| 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 |
| 22.009 | Glycosylation in calixarenes capsule | chemistry | Metadynamics, glycosylation, supramolecular catalysis | GiovanniMaria Piccini | FIT_TO_TEMPLATE ANGLE UNITS FLUSH METAD DISTANCE BRIDGE MATHEVAL DISTANCES RMSD GROUP WHOLEMOLECULES COMBINE LOWER_WALLS UPPER_WALLS PRINT COORDINATION | generic multicolvar bias setup adjmat core function colvar |
| 21.052 | On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets | materials | Ibuprofen, unbinding, WTmetaD | Matteo Salvalaglio | COMMITTOR ENDPLUMED METAD DISTANCE COORDINATIONNUMBER TORSION PRINT CENTER | generic symfunc bias vatom colvar |
| 21.043 | Predicting the Conformational Variability of Oncogenic GTP-bound G12D Mutated KRas-4B Proteins at Cell Membranes | chemistry | well-tempered metadynamics, KRas-4B, anionic membrane, conformational variability | Huixia Lu | FIT_TO_TEMPLATE FIXEDATOM METAD TORSION PRINT | generic colvar bias vatom |
| 21.033 | Multiple-path-metadynamics applied to DNA base-pairing transitions | bio | path-CV, metadynamics, multiple-walker, dna | Alberto Pérez-de-Alba-Ortíz | INCLUDE METAD MOVINGRESTRAINT RESTRAINT CONSTANT COMBINE UPPER_WALLS PRINT | generic bias function |
| 21.031 | Photo-switchable sulfonulureas in KATP channel | bio | metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels | Katarzyna Walczewska-Szewc | UNITS METAD DISTANCE WHOLEMOLECULES LOWER_WALLS COM PRINT UPPER_WALLS | generic bias setup vatom colvar |
| 21.021 | ATLAS | methods | Machine Learning, Metadynamics | Federico Giberti | DUMPATOMS UNITS BIASVALUE METAD DISTANCE MATHEVAL COORDINATIONNUMBER TORSION GROUP WHOLEMOLECULES PRINT COORDINATION GYRATION | generic symfunc bias setup core function colvar |
| 21.017 | All-atom simulations of the Vav1 AD construct | bio | metadynamics, parallel-bias, well-tempered | Simone Orioli | MOLINFO RESTART METAD ALPHARMSD REWEIGHT_BIAS ALPHABETA CONTACTMAP WHOLEMOLECULES PRINT GROUP PBMETAD | generic secondarystructure multicolvar bias setup core colvar |
| 21.014 | how to determine statistically accurate conformational ensembles | bio | metadynamics, metainference, errors, cv, SAXS, ensemble determination | Cristina Paissoni | MOLINFO CENTER PBMETAD METAD BIASVALUE ENSEMBLE STATS SAXS ALPHABETA TORSION ANTIBETARMSD CONTACTMAP WHOLEMOLECULES PRINT GYRATION | generic secondarystructure multicolvar bias isdb vatom function 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 TORSION PRINT | generic bias colvar |
| 20.024 | Gaussian Mixture Based Enhanced Sampling (GAMBES) | methods | enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias | Jayashrita Debnath | UNITS ENERGY PRINT DISTANCE DISTANCES TORSION COMBINE LOWER_WALLS UPPER_WALLS LOAD GROUP | generic multicolvar bias setup core function colvar |
| 20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Michele Invernizzi | ECV_UMBRELLAS_LINE POSITION ECV_MULTITHERMAL_MULTIBARIC VOLUME PRINT OPES_EXPANDED ECV_LINEAR UNITS ENDPLUMED WHOLEMOLECULES MOLINFO ENERGY MATHEVAL TORSION RMSD UPPER_WALLS CUSTOM Q6 ECV_MULTITHERMAL ENVIRONMENTSIMILARITY LOAD | generic symfunc opes bias setup envsim function colvar |
| 19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | MOLINFO ENERGY METAD DISTANCE COM UPPER_WALLS PRINT GYRATION | generic bias colvar vatom |
| 19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Mattia Bernetti | METAD WHOLEMOLECULES LOWER_WALLS PATHMSD PRINT UPPER_WALLS | generic colvar bias |
| 19.050 | Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes | chemistry | metadynamics, membranes, Willard Chandler surface | Gareth Tribello | DISTANCE_FROM_CONTOUR METAD REWEIGHT_BIAS CONVERT_TO_FES READ HISTOGRAM DUMPGRID COMBINE UPPER_WALLS PRINT RESTART | generic bias setup contour gridtools function |
| 19.040 | Optimal Metric for Path Collective Variables | bio | metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path | Francesco Luigi Gervasio | ENDPLUMED METAD MATHEVAL TORSION PRINT | generic colvar bias function |
| 19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Mattia Bernetti | MOLINFO ENDPLUMED ENERGY METAD ALPHARMSD WHOLEMOLECULES PRINT GYRATION | generic secondarystructure bias colvar |
| 19.013 | RNA FF FITTING | methods | force field, RNA | Giovanni Bussi | MOLINFO INCLUDE BIASVALUE CONSTANT MATHEVAL TORSION PUCKERING | generic colvar bias function |
| 25.013 | Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices | bio | umbrella sampling, temperature ramping | Alexander Berlaga | RESTRAINT DISTANCE PRINT PYTORCH_MODEL GYRATION | colvar pytorch generic bias |
| 25.000 | Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer | bio | metadynamics, pathCV | Sahithya Sridharan Iyer | DISTANCE PRINT GROUP METAD UPPER_WALLS MOLINFO WHOLEMOLECULES RESTART FUNCPATHGENERAL COM | core generic bias colvar setup vatom function |
| 24.032 | DeepLNE++ | methods | PATHCV, OPES | Thorben Fröhlking | TORSION COMBINE CUSTOM DISTANCE PRINT GROUP OPES_METAD ENERGY COORDINATION LOAD | core generic colvar opes setup function |
| 24.009 | Weighted Shape Gaussian Mixture Models | bio | metadynamics, clustering | Glen Hocky | TORSION PRINT GROUP METAD UNITS | core generic bias colvar setup |
| 23.034 | Urea nucleation in water: do long-range forces matter? | materials | LMF theory, Metadynamics, Nucleation | Ziyue Zou | INCLUDE PRINT GROUP METAD COORDINATIONNUMBER CENTER LOAD | core generic bias setup vatom symfunc |
| 23.032 | Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics | bio | metadynamics, tSNE, neural network, machine learning, trp-cage, folding | Vojtech Spiwok | COMBINE ANN PRINT FIT_TO_TEMPLATE METAD ALPHARMSD WHOLEMOLECULES MOLINFO POSITION | annfunc generic bias colvar function secondarystructure |
| 23.027 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, DFS, Q3, Pair Entropy | Aaron Finney | LOCAL_Q3 RESTRAINT PRINT DFSCLUSTERING FIXEDATOM GROUP CLUSTER_NATOMS LOAD COORDINATIONNUMBER Q3 CLUSTER_DISTRIBUTION DUMPGRID DENSITY CONTACT_MATRIX LOCAL_AVERAGE HISTOGRAM UNITS AROUND | clusters core generic bias gridtools setup adjmat vatom volumes symfunc |
| 23.023 | Rational design of novel biomimetic sequence-defined polymers for mineralization applications | methods | metadynamics, surface binding, biomimetic mineralization | Kaylyn Torkelson | PBMETAD DISTANCE PRINT UPPER_WALLS GYRATION COORDINATION COM | colvar generic bias vatom |
| 23.021 | Into the Dynamics of Rotaxanes at Atomistic Resolution | materials | metadynamics, rotaxanes, molecular shuttles, molecular machines | Luigi Leanza | TORSION CUSTOM DISTANCE PRINT MATHEVAL UPPER_WALLS METAD CENTER FIXEDATOM | generic bias colvar vatom function |
| 23.019 | Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors | bio | binding pathway, binding energy, sketch-map, drug development | Raitis Bobrovs | CUSTOM LANDMARK_SELECT_FPS VSTACK DISSIMILARITIES DISTANCE PRINT SKETCHMAP_PROJECTION VORONOI TRANSPOSE METAD UPPER_WALLS COLLECT_FRAMES PATHMSD WHOLEMOLECULES SKETCHMAP COM | valtools generic bias colvar matrixtools landmarks vatom function dimred |
| 23.000 | Atomistic simulations of RNA tetraloop folding via PTWTE-WTM | bio | parallel tempering, well-tempered metadynamics, well-tempered ensemble, RNA, Tetraloop, Folding | Gül Zerze | LOWER_WALLS PRINT METAD UPPER_WALLS CONTACTMAP ENERGY WHOLEMOLECULES | colvar generic bias |
| 22.042 | Metadynamics of NSP10 and variants | bio | metadynamics, NSP10, crystal structure, variants | Shozeb Haider | PRINT TORSION METAD | 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 | TORSION DISTANCE PRINT GROUP METAD WHOLEMOLECULES COM | core generic bias colvar vatom |
| 22.018 | Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations | bio | ligand binding, docking, EMMI, LAT1 | Max Bonomi | PRINT GROUP EMMIVOX BIASVALUE WHOLEMOLECULES LOAD MOLINFO | core generic bias setup isdb |
| 22.004 | Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques | chemistry | reaction discovery, OPES, collective variables | Umberto Raucci | CUSTOM LOWER_WALLS OPES_METAD_EXPLORE PRINT DISTANCE COM GROUP MATHEVAL PYTORCH_MODEL OPES_METAD UPPER_WALLS COORDINATION LOAD UNITS | core generic bias colvar opes setup vatom function pytorch |
| 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 | BF_CUBIC_B_SPLINES BF_WAVELETS UPPER_WALLS BF_GAUSSIANS VES_LINEAR_EXPANSION COORDINATION POSITION BF_CHEBYSHEV TD_UNIFORM OPT_ADAM DISTANCE METAD ENERGY OPT_AVERAGED_SGD UNITS INCLUDE PRINT TD_WELLTEMPERED BF_LEGENDRE FLUSH VES_OUTPUT_BASISFUNCTIONS | generic ves bias colvar setup |
| 22.000 | Amyloid precursor protein processing by human γ-secretase | bio | Bias Exchange Metadynamics, Helix unfolding, coupled binding | Xiaoli Lu | INCLUDE RANDOM_EXCHANGES DISTANCE PRINT ANTIBETARMSD UNITS CONTACTMAP ALPHARMSD CENTER METAD COORDINATION MOLINFO | generic bias colvar setup vatom secondarystructure |
| 21.044 | NaCl nucleation | chemistry | metadynamics, DFS clustering | Aaron Finney | COMBINE LOCAL_Q6 PRINT DFSCLUSTERING GROUP CLUSTER_NATOMS MFILTER_MORE COORDINATIONNUMBER METAD HISTOGRAM CLUSTER_DISTRIBUTION DUMPGRID Q6 INSPHERE CONTACT_MATRIX FIXEDATOM | clusters core generic bias gridtools adjmat vatom volumes function symfunc multicolvar |
| 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 | DISTANCE PRINT GROUP EMMI COM UPPER_WALLS BIASVALUE WHOLEMOLECULES RESTART MOLINFO | core generic bias colvar setup vatom isdb |
| 21.039 | Deep learning the slow modes for rare events sampling | methods | collective variables, machine learning, slow modes, deep-tica, opes | Luigi Bonati | TORSION OPES_METAD RMSD MOLINFO PYTORCH_MODEL ENDPLUMED OPES_EXPANDED LOAD COMBINE ECV_MULTITHERMAL DISTANCE GROUP ENVIRONMENTSIMILARITY CONTACTMAP ENERGY VOLUME UNITS INCLUDE PRINT FLUSH Q6 WHOLEMOLECULES | core generic colvar opes setup envsim function pytorch symfunc |
| 21.035 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, interface | Aaron Finney | RESTRAINT DISTANCE PRINT FIXEDATOM GROUP LOAD | core generic bias colvar setup vatom |
| 21.026 | Probing allosteric regulations with coevolution-driven molecular simulations | bio | metadynamics, coevolution, allostery, adenylate cyclase | Francesco Colizzi | DISTANCE PRINT COM METAD UPPER_WALLS PATHMSD WHOLEMOLECULES UNITS | generic bias colvar setup vatom |
| 21.022 | Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly | materials | parallel bias metadynamics, adsorption, peptide | Xin Qi | PBMETAD LOWER_WALLS DISTANCE PRINT COM UPPER_WALLS ENERGY GYRATION MOLINFO | colvar generic bias vatom |
| 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 | REWEIGHT_BIAS RESTRAINT PRINT MATHEVAL METAD CENTER WHOLEMOLECULES RESTART COORDINATION POSITION | generic bias colvar setup vatom function |
| 21.012 | NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition | bio | funnel metadynamics | Jim Pfaendtner | LOWER_WALLS DISTANCE PRINT FUNNEL METAD FUNNEL_PS UPPER_WALLS COM | generic bias colvar funnel vatom |
| 21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Tarak Karmakar | LOWER_WALLS PRINT GROUP MATHEVAL OPES_METAD PYTORCH_MODEL UPPER_WALLS FLUSH LOAD | core generic bias opes setup function pytorch |
| 20.034 | Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations | bio | RNA, SARS-CoV-2, partial tempering | Sandro Bottaro | TORSION DISTANCE ERMSD PRINT ABMD CENTER RESTART MOLINFO | generic bias colvar setup vatom |
| 20.032 | Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil | materials | clustering, conformational isomers | Matteo Salvalaglio | PRINT TORSION ENDPLUMED | colvar generic |
| 20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Adriana Pietropaolo | PBMETAD PRINT CENTER WHOLEMOLECULES COORDINATION | colvar generic bias vatom |
| 20.030 | Converging experimental and computational views of the knotting mechanism of the smallest knotted protein | bio | phi-values, transition state, knotted proteins | Cristina Paissoni | RESTRAINT COMBINE PRINT STATS WHOLEMOLECULES COORDINATION MOLINFO | colvar function bias generic |
| 20.006 | Class B GPCR activation mechanism | bio | metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | COMBINE LOWER_WALLS DISTANCE PRINT MATHEVAL METAD UPPER_WALLS RMSD CENTER ENERGY WHOLEMOLECULES MOLINFO | generic bias colvar vatom function |
| 19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Valerio Rizzi | COMBINE PRINT EXTERNAL GROUP ENDPLUMED COORDINATIONNUMBER METAD FLUSH RESTART UNITS | core generic bias setup function symfunc |
| 19.027 | Multithermal-multibaric simulations using VES | methods | ves, Wang Landau, multicanonical, liquid sodium, density anomaly | Pablo Piaggi | REWEIGHT_BIAS COMBINE RESTART PRINT OPT_DUMMY REWEIGHT_TEMP_PRESS BF_LEGENDRE CONVERT_TO_FES TD_MULTICANONICAL AVERAGE DUMPGRID ENERGY READ OPT_AVERAGED_SGD VES_LINEAR_EXPANSION HISTOGRAM UNITS | generic ves bias gridtools setup colvar function |
| 19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Glen Hocky | TORSION COMBINE RESTRAINT EDS DISTANCE PRINT | generic bias colvar eds function |
| 19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Kresten Lindorff-Larsen | COMBINE PRINT FLUSH METAD COMMITTOR ALPHABETA MOLINFO | multicolvar function bias generic |
| 19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Adriana Pietropaolo | TORSION CONSTANT PRINT MATHEVAL METAD BIASVALUE WHOLEMOLECULES | colvar generic function bias |