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 | COMBINE COORDINATIONNUMBER COM PRINT UNITS DISTANCES LOWER_WALLS GROUP UPPER_WALLS FLUSH RESTRAINT COORDINATION METAD DISTANCE ANGLE FIXEDATOM | core setup vatom function colvar generic symfunc bias multicolvar |
| 25.009 | Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water | chemistry | metadynamics, nitrate photolysis | Kam-Tung Chan | DUMPGRID GROUP COORDINATION CUSTOM PRINT UPPER_WALLS REWEIGHT_METAD FLUSH METAD DISTANCE READ HISTOGRAM RESTART | bias generic setup colvar core function gridtools |
| 24.028 | All-atom simulations of RNA-membrane interactions | bio | metadynamics, membrane, RNA | Giovanni Bussi | MOLINFO POSITION PRINT GYRATION LOWER_WALLS COMBINE SORT GHOST UPPER_WALLS CENTER DISTANCES MATHEVAL METAD PUCKERING DISTANCE WHOLEMOLECULES GROUP | vatom bias multicolvar generic colvar core function |
| 24.002 | Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes | chemistry | metadynamics, ligand design, solvent extraction | Xiaoyu Wang | UNITS PRINT METAD RESTART TORSION | bias setup generic colvar |
| 23.039 | Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation | chemistry | metadynamics, ligand dissociation | Eric Beyerle | MOLINFO FIXEDATOM PRINT COMBINE DUMPMASSCHARGE UPPER_WALLS CENTER METAD DISTANCE RESTRAINT | vatom bias generic colvar function |
| 23.031 | Identifying small molecules binding sites in RNA conformational ensembles with SHAMAN | bio | RNA, metadynamics, probes, mixed-solvent MD, small molecules, binding sites | Max Bonomi | SHADOW MOLINFO POSITION PRINT FIT_TO_TEMPLATE UPPER_WALLS WRAPAROUND CENTER DISTANCES METAD WHOLEMOLECULES GROUP | vatom isdb bias multicolvar generic colvar core |
| 23.025 | Probing ion binding to G-quadruplexes and related events | chemistry | metadynamics, repulsive potential, nucleic acids, G-quadruplexes | Marcelo Poleto | UNITS DUMPATOMS POSITION FIT_TO_TEMPLATE LOWER_WALLS PRINT UPPER_WALLS WRAPAROUND DISTANCES MATHEVAL FLUSH METAD DISTANCE WHOLEMOLECULES GROUP COM RESTART | vatom colvar bias multicolvar generic setup core function |
| 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 | BIASVALUE LOWER_WALLS PRINT UPPER_WALLS CONSTANT MATHEVAL METAD DISTANCE WHOLEMOLECULES | bias function generic colvar |
| 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 | CUSTOM LOWER_WALLS PRINT COMMITTOR UPPER_WALLS MATHEVAL CELL METAD DRMSD | bias generic colvar function |
| 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 | PRINT METAD DISTANCE WHOLEMOLECULES GROUP COM TORSION | vatom bias generic colvar core |
| 22.018 | Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations | bio | ligand binding, docking, EMMI, LAT1 | Max Bonomi | MOLINFO PRINT EMMIVOX BIASVALUE WHOLEMOLECULES GROUP LOAD | isdb bias generic setup core |
| 22.017 | Water regulates the residence time of Benzamidine in Trypsin | bio | ligand binding, water, opes, benzamidine trypsin, unbinding rates, machine learning, Deep-LDA, Deep-TICA | Narjes Ansari | FIXEDATOM COORDINATION CUSTOM FIT_TO_TEMPLATE LOWER_WALLS PYTORCH_MODEL PRINT COMMITTOR UPPER_WALLS RMSD CENTER MATHEVAL DISTANCE WHOLEMOLECULES GROUP OPES_METAD | pytorch vatom opes bias generic colvar core function |
| 22.002 | GAMBES_SAMPL5_RATES | other | GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding | Jayashrita Debnath | ENDPLUMED FIXEDATOM COORDINATION FIT_TO_TEMPLATE PRINT PYTORCH_MODEL COMMITTOR UPPER_WALLS CENTER MATHEVAL FLUSH ENERGY ANGLE DISTANCE WHOLEMOLECULES GROUP LOAD | pytorch vatom bias generic setup colvar core function |
| 22.000 | Amyloid precursor protein processing by human γ-secretase | bio | Bias Exchange Metadynamics, Helix unfolding, coupled binding | Xiaoli Lu | UNITS MOLINFO DISTANCE COORDINATION PRINT INCLUDE RANDOM_EXCHANGES CENTER METAD ALPHARMSD ANTIBETARMSD CONTACTMAP | vatom secondarystructure colvar bias generic setup |
| 21.048 | Enhancing ligand exploration within a channel pore and fenestrations using metadynamics | bio | well-tempered metadynamics, protein-ligand enhanced sampling, sodium channel, Nav, small molecule drug | Elaine Tao | UNITS CUSTOM LOWER_WALLS PRINT UPPER_WALLS METAD DISTANCE COM TORSION | vatom colvar bias generic setup function |
| 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 | BIASVALUE MOLINFO PRINT EMMI UPPER_WALLS DISTANCE WHOLEMOLECULES GROUP COM RESTART | vatom isdb bias generic setup colvar core |
| 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 |
| 21.031 | Photo-switchable sulfonulureas in KATP channel | bio | metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels | Katarzyna Walczewska-Szewc | UNITS LOWER_WALLS PRINT UPPER_WALLS METAD DISTANCE WHOLEMOLECULES COM | vatom colvar bias generic setup |
| 21.010 | Step by Step Strecker Amino Acid Synthesis from Ab Initio Prebiotic Chemistry | chemistry | Strecker reaction, free energy landscape, ab initio molecular dynamics, glycine, prebiotic synthesis | Théo Magrino | generic | |
| 21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Kristof Bal | UNITS DUMPGRID CONVERT_TO_FES PRINT COMMITTOR COORDINATIONNUMBER UPPER_WALLS MOVINGRESTRAINT FLUSH REWEIGHT_METAD METAD HISTOGRAM LOAD | symfunc bias generic setup gridtools |
| 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 | PRINT METAD DISTANCE TORSION | bias colvar generic |
| 20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Michele Invernizzi | ENDPLUMED MOLINFO ECV_LINEAR ENVIRONMENTSIMILARITY UPPER_WALLS ENERGY Q6 TORSION CUSTOM OPES_EXPANDED UNITS VOLUME POSITION ECV_MULTITHERMAL WHOLEMOLECULES PRINT ECV_MULTITHERMAL_MULTIBARIC RMSD ECV_UMBRELLAS_LINE MATHEVAL LOAD | envsim symfunc opes bias generic setup colvar function |
| 20.016 | Predicting polymorphism in molecular crystals using orientational entropy | materials | metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy | Pablo Piaggi | VOLUME PRINT INCLUDE UPPER_WALLS CENTER METAD GROUP LOAD | vatom bias generic setup colvar core |
| 20.013 | Improving accuracy of biased Alchemistic simulations | methods | flying Gaussian method, Alchemistic simulations, thermodynamic integration, reweighting | Vojtech Spiwok | PRINT METAD TORSION | bias colvar generic |
| 20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Pratyush Tiwary | MOLINFO PRINT COMBINE RMSD UPPER_WALLS METAD DISTANCE WHOLEMOLECULES RESTART TORSION | colvar bias generic setup function |
| 19.078 | Iterative unbiasing of quasi-equilibrium sampling | methods | metadynamics, reweighting | Federico Giberti | UNITS DUMPATOMS DISTANCE PRINT COLLECT_FRAMES COORDINATIONNUMBER MATHEVAL METAD BIASVALUE REWEIGHT_BIAS | symfunc colvar bias generic setup landmarks function |
| 19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Michele Invernizzi | UNITS ENDPLUMED POSITION PRINT EXTERNAL METAD OPES_METAD TORSION | opes colvar bias generic setup |
| 19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Mattia Bernetti | LOWER_WALLS PRINT UPPER_WALLS METAD WHOLEMOLECULES PATHMSD | bias colvar 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 | PRINT INCLUDE RANDOM_EXCHANGES METAD TORSION | bias colvar generic |
| 19.048 | Understanding Ligand Binding Selectivity in a Prototypical GPCR Family | bio | metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | BIASVALUE LOWER_WALLS PRINT UPPER_WALLS CONSTANT MATHEVAL METAD DISTANCE WHOLEMOLECULES COM | vatom bias generic colvar function |
| 19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Pratyush Tiwary | EXTERNAL PRINT COMMITTOR COMBINE ALPHABETA DISTANCE WHOLEMOLECULES COM RESTART TORSION | vatom bias multicolvar generic setup colvar function |
| 19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Carlo Camilloni | BIASVALUE MOLINFO ENDPLUMED PRINT INCLUDE SAXS STATS UPPER_WALLS RMSD CENTER DISTANCE WHOLEMOLECULES GROUP RESTRAINT | vatom isdb bias generic colvar core function |
| 19.003 | EMMI ClpP | bio | metainference, cryo-EM | Max Bonomi | MOLINFO PRINT EMMI BIASVALUE GROUP | isdb bias core generic |
| 24.032 | DeepLNE++ | methods | PATHCV, OPES | Thorben Fröhlking | ENERGY COORDINATION LOAD COMBINE CUSTOM TORSION DISTANCE GROUP PRINT OPES_METAD | colvar opes setup core function generic |
| 24.029 | Combination of OPES and OPES-Explore | methods | OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin | Dhiman Ray | COORDINATION MATHEVAL PYTORCH_MODEL OPES_METAD_EXPLORE DISTANCE PRINT ENERGY UNITS WHOLEMOLECULES COMBINE CONTACTMAP FIT_TO_TEMPLATE UPPER_WALLS RMSD MOLINFO FLUSH LOWER_WALLS CUSTOM POSITION GROUP FIXEDATOM CENTER OPES_METAD METAD ENDPLUMED BIASVALUE INCLUDE | colvar vatom opes setup core bias function generic pytorch |
| 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 | COORDINATION WHOLEMOLECULES PYTORCH_MODEL PATH LOWER_WALLS CUSTOM TORSION FIT_TO_TEMPLATE GROUP DISTANCE FIXEDATOM RESTART CENTER PRINT UPPER_WALLS OPES_METAD | colvar vatom opes setup core mapping bias function generic pytorch |
| 24.022 | Integrating Path Sampling with Enhanced Sampling for Rare-event Kinetics | methods | OPES Flooding, Weighted Ensemble, Metadynamics, Kinetics, Infrequent Metadynamics, Integrated Sampling | Dhiman Ray | MATHEVAL COORDINATION DISTANCE PRINT ANGLE WHOLEMOLECULES COMBINE CONTACTMAP FIT_TO_TEMPLATE UPPER_WALLS RMSD MOLINFO COMMITTOR CUSTOM FIXEDATOM GROUP CENTER OPES_METAD METAD ENDPLUMED TORSION | colvar vatom opes core bias function generic |
| 23.037 | Estimating binding free energy of solid binding peptides without extensive sampling | bio | metadynamics, solid binding peptides | Xin Qi | MOLINFO PBMETAD LOWER_WALLS DISTANCE PRINT UPPER_WALLS COM GYRATION | colvar bias vatom generic |
| 23.036 | Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? | bio | NaCl, nucleation, metadynamics | Ruiyu Wang | ENERGY COORDINATIONNUMBER MATHEVAL VOLUME METAD Q6 COMBINE PRINT Q4 | symfunc colvar bias function generic |
| 23.019 | Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors | bio | binding pathway, binding energy, sketch-map, drug development | Raitis Bobrovs | DISSIMILARITIES COLLECT_FRAMES METAD WHOLEMOLECULES SKETCHMAP_PROJECTION SKETCHMAP LANDMARK_SELECT_FPS PATHMSD VORONOI CUSTOM PRINT DISTANCE VSTACK UPPER_WALLS COM TRANSPOSE | landmarks colvar vatom bias dimred function generic matrixtools valtools |
| 23.005 | A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs | bio | metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A | Timothy Clark | MATHEVAL READ METAD HISTOGRAM WHOLEMOLECULES MOLINFO REWEIGHT_METAD CONVERT_TO_FES DISTANCE PRINT DUMPGRID RMSD | colvar bias function generic gridtools |
| 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 | OPES_EXPANDED HISTOGRAM ENVIRONMENTSIMILARITY ECV_UMBRELLAS_LINE LOWER_WALLS PRINT RESTART UPPER_WALLS DUMPGRID | opes envsim setup bias generic gridtools |
| 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 | ENERGY METAD WHOLEMOLECULES CONTACTMAP LOWER_WALLS PRINT UPPER_WALLS | 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 | ANGLE METAD WHOLEMOLECULES LOWER_WALLS MOVINGRESTRAINT DISTANCE PRINT UPPER_WALLS COM | vatom bias generic colvar |
| 22.039 | Driving and characterizing nucleation of urea and glycine polymorphs in water | bio | metadynamics, nucleation, amino acids, polymorphism | Eric Beyerle | COORDINATIONNUMBER MATHEVAL METAD LOAD Q6 COMBINE PRINT GROUP PAIRENTROPY CENTER Q4 INCLUDE | symfunc vatom setup core bias function generic gridtools |
| 22.033 | Reciprocal barrier restraint. Application to PROTAC passive permeability prediction | methods | PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR | Istvan Kolossvary | UNITS METAD FLUSH CUSTOM DRR DISTANCE PRINT BIASVALUE COM | colvar vatom drr setup bias function generic |
| 22.025 | Bubble nucleation rate predictions in a Lennard-Jones fluid | materials | free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation | Kristof Bal | COORDINATIONNUMBER UNITS VOLUME LOAD HISTOGRAM CONVERT_TO_FES ANN FLUSH COMMITTOR RESTRAINT CUSTOM REWEIGHT_BIAS MOVINGRESTRAINT PRINT BIASVALUE UPPER_WALLS DUMPGRID | symfunc colvar annfunc setup bias function generic gridtools |
| 21.047 | Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations | materials | pair entropy, metadynamics, ves, solids, crystallization | Pablo Piaggi | ENERGY VES_LINEAR_EXPANSION VOLUME LOAD METAD OPT_AVERAGED_SGD COMBINE PAIRENTROPY BF_LEGENDRE TD_WELLTEMPERED PRINT RESTART | colvar ves setup bias function generic gridtools |
| 21.045 | QM/MM metadynamics of thiol-disulfide exchange between methylthiolate and dimethyldisulfide in water with an imposed external electrostatic potential (ESP) | chemistry | metadynamics, QM/MM, electrostatic potential, thiol-disulfide exchange | Denis Maag | COORDINATION COORDINATIONNUMBER METAD COMBINE LOWER_WALLS DISTANCE PRINT UPPER_WALLS | symfunc colvar bias function generic |
| 21.038 | Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics | materials | metadynamics, SGOOP, nucleation, urea | Ziyue Zou | ENERGY COORDINATIONNUMBER METAD LOAD VOLUME COMBINE PRINT GROUP CENTER INCLUDE | symfunc colvar vatom setup core bias function generic |
| 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 | ENERGY COORDINATION RANDOM_EXCHANGES METAD WHOLEMOLECULES MOLINFO LOWER_WALLS PARABETARMSD ALPHARMSD PRINT GROUP ANTIBETARMSD UPPER_WALLS GYRATION DIHCOR | colvar core secondarystructure multicolvar bias generic |
| 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 | METAD RANDOM_EXCHANGES PBMETAD ENDPLUMED TORSION PRINT INCLUDE | colvar bias generic |
| 21.016 | MD SAXS GTPase associated center | bio | metadynamics, RNA, folding, SAXS | Giovanni Bussi | METAD WHOLEMOLECULES MOLINFO SAXS LOWER_WALLS CUSTOM PRINT GROUP ERMSD UPPER_WALLS GYRATION INCLUDE | colvar isdb core bias function generic |
| 21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Tarak Karmakar | MATHEVAL LOAD FLUSH PYTORCH_MODEL LOWER_WALLS PRINT GROUP UPPER_WALLS OPES_METAD | opes setup core bias function generic pytorch |
| 20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Cristina Paissoni | WHOLEMOLECULES MOLINFO SAXS BIASVALUE ENSEMBLE RESTRAINT DISTANCE GROUP PRINT STATS CENTER INCLUDE | colvar isdb vatom core 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 | MATHEVAL METAD LOAD WHOLEMOLECULES CONSTANT MOLINFO CONTACTMAP LOWER_WALLS PROJECTION_ON_AXIS DISTANCE GROUP PRINT BIASVALUE FUNCPATHGENERAL UPPER_WALLS COM INCLUDE | colvar vatom setup core bias function generic |
| 20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Jim Pfaendtner | COORDINATION WHOLEMOLECULES DISTANCES DISTANCE GROUP PRINT RESTART CENTER | colvar vatom setup core multicolvar generic |
| 20.006 | Class B GPCR activation mechanism | bio | metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | ENERGY MATHEVAL METAD WHOLEMOLECULES MOLINFO COMBINE LOWER_WALLS PRINT DISTANCE CENTER UPPER_WALLS RMSD | colvar vatom bias function generic |
| 19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | ENERGY METAD MOLINFO DISTANCE PRINT UPPER_WALLS COM GYRATION | vatom bias generic colvar |
| 19.075 | PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python | other | Python, automatic differentiation | Toni Giorgino | ANGLE COMBINE ENDPLUMED RESTRAINT CUSTOM TORSION DISTANCE DUMPDERIVATIVES PRINT GROUP CENTER | colvar vatom core bias function generic |
| 19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Matteo Salvalaglio | ENDPLUMED PRINT DISTANCE GROUP CENTER INCLUDE | core colvar vatom generic |
| 19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | ENERGY UNITS METAD COMBINE FLUSH DISTANCE PRINT UPPER_WALLS | colvar setup bias function generic |
| 19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Carlo Camilloni | WHOLEMOLECULES MOLINFO PBMETAD ALPHABETA FLUSH CS2BACKBONE ENDPLUMED LOWER_WALLS PRINT GROUP RESTART BIASVALUE UPPER_WALLS ANTIBETARMSD | isdb setup core multicolvar secondarystructure bias generic |
| 19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Davide Provasi | METAD WHOLEMOLECULES CONTACTMAP ENDPLUMED DISTANCE PRINT FUNCPATHMSD COM RMSD | colvar vatom bias function generic |
| 19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Silvio Pipolo | PIV METAD LOWER_WALLS CELL PRINT FUNCPATHMSD UPPER_WALLS | piv colvar bias function generic |
| 19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Adriana Pietropaolo | MATHEVAL METAD CONSTANT WHOLEMOLECULES TORSION PRINT BIASVALUE | colvar bias function generic |
| 19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Matteo Salvalaglio | ENERGY MATHEVAL METAD VOLUME COMBINE ENDPLUMED LOWER_WALLS CELL TORSION PRINT UPPER_WALLS | bias generic function colvar |
| 19.009 | RNA tetraloops folding | bio | metadynamics, RNA, folding | Giovanni Bussi | METAD WHOLEMOLECULES MOLINFO ENDPLUMED PRINT ERMSD RMSD | colvar bias generic |
| 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 | RESTART LOWER_WALLS GROUP PRINT COORDINATION CUSTOM UNITS UPPER_WALLS DISTANCE OPES_METAD COMMITTOR | function colvar core bias setup generic opes |
| 24.033 | Transient interactions between the fuzzy coat and the cross-b core of brain-derived Ab42 filaments | bio | CryoEM, MEMMI, Metadynamics, Metainference, Ab42 Fibrils, structural ensemble | Maria Milanesi | ALPHARMSD EMMI PBMETAD DUMPMASSCHARGE MOLINFO PARABETARMSD GROUP PRINT COORDINATION DISTANCE CENTER WHOLEMOLECULES DUMPATOMS RMSD UPPER_WALLS BIASVALUE COM | colvar isdb secondarystructure core vatom bias generic |
| 24.026 | Constant pH metadynamics of RNA oligomers | bio | metadynamics, pH, RNA | Giovanni Bussi | TORSION PUCKERING RESTART MOLINFO PRINT METAD | bias colvar generic setup |
| 24.018 | A new route to the prebiotic synthesis of glycine via ab initio-based machine learning calculations | chemistry | prebiotic chemistry, glycine, Strecker synthesis, ab initio calculations, machine learning | Léon HUET | PRINT DISTANCE | colvar generic |
| 24.013 | 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 | TORSION FLUSH RESTART MOLINFO PRINT METAD MATHEVAL RESTRAINT DISTANCE COORDINATIONNUMBER BIASVALUE COMMITTOR ENERGY | function colvar bias setup generic symfunc |
| 24.011 | Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble | methods | committor, machine learning | Peilin Kang | COORDINATION ENDPLUMED CUSTOM MATHEVAL UNITS UPPER_WALLS MOLINFO LOAD WHOLEMOLECULES ENERGY PRINT RMSD BIASVALUE TORSION LOWER_WALLS GROUP POSITION DISTANCE CELL INCLUDE | function colvar core bias setup generic |
| 24.010 | Oxytocin metadynamics simulation | bio | metadynamics, oxytocin, peptide | Jan Beránek | TORSION FLUSH RESTART PRINT METAD WHOLEMOLECULES | bias colvar generic setup |
| 24.006 | Water vapor condensation | chemistry | metadynamics, homogeneous condensation, chemical potential | Shenghui Zhong | PRINT METAD CLUSTER_PROPERTIES DFSCLUSTERING CLUSTER_NATOMS UNITS CONTACT_MATRIX UPPER_WALLS COORDINATIONNUMBER | clusters bias setup generic symfunc adjmat |
| 24.005 | Learning Markovian Dynamics with Spectral Maps | methods | spectral map, collective variables, machine learning | Jakub Rydzewski | PRINT CUSTOM UNITS DISTANCE BIASVALUE | function colvar bias setup generic |
| 23.029 | An accurate and efficient SAXS/SANS implementation including solvation layer effects suitable for restrained Molecular Dynamics simulations | bio | SAXS, SANS, SAS, metainference, proteins, nucleic-acid | Federico Ballabio | SAXS WRAPAROUND MOLINFO GROUP PRINT CENTER DISTANCE UPPER_WALLS STATS RMSD BIASVALUE ENSEMBLE | function colvar isdb core vatom bias generic |
| 23.013 | Path meta-eABF simulation of large scale conformational change in STING protein | methods | meta-eABF, path CV, large scale conformational change, STING protein, reciprocal barrier restraint | Istvan Kolossvary | FLUSH LOWER_WALLS PRINT METAD CUSTOM DRR UNITS UPPER_WALLS BIASVALUE TIME PATHMSD | function colvar drr bias setup generic |
| 23.012 | JAK2 2D meta-eABF PMF with statistical analysis | bio | 2D meta-eABF, path CV, PMF | Istvan Kolossvary | FLUSH LOWER_WALLS PRINT METAD CUSTOM DRR UPPER_WALLS BIASVALUE PATHMSD | function colvar drr bias generic |
| 22.030 | Mixing physics across temperatures with generative artificial intelligence | methods | REMD, Generative AI, DDPM | Yihang Wang | WHOLEMOLECULES PRINT TORSION | colvar generic |
| 22.029 | Angiotensin-1-7_Metadynamics | bio | Metadynamics, Angiotensin-(1-7), peptide | L.-América Chi | FLUSH LOWER_WALLS GROUP PRINT COORDINATION METAD WHOLEMOLECULES GYRATION UPPER_WALLS | bias colvar generic core |
| 22.024 | Conformational Entropy as a Potential Liability of Computationally Designed Antibodies | bio | metadynamics, conformational entropy, antibody, nanobody | Thomas Löhr | ALPHARMSD TORSION PBMETAD RESTART MOLINFO PRINT COM WHOLEMOLECULES ANTIBETARMSD ALPHABETA | colvar secondarystructure vatom bias setup generic multicolvar |
| 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 PRINT OPES_EXPANDED ECV_UMBRELLAS_LINE UPPER_WALLS ENVIRONMENTSIMILARITY INCLUDE | bias generic envsim opes |
| 22.016 | Homogeneous ice nucleation in an ab initio machine learning model of water | chemistry | ice, water, nucleation, seeding, environment similarity, interfacial free energy, interfaces | Pablo Piaggi | RESTART PRINT AROUND HISTOGRAM CUSTOM ENVIRONMENTSIMILARITY UPPER_WALLS VOLUME DUMPGRID OPES_METAD ENERGY | function colvar volumes bias setup generic envsim opes gridtools |
| 22.008 | Ab initio metadynamics determination of temperature-dependent free-energy landscape in ultrasmall silver clusters | materials | Well tempered metadynamics, ab-initio, ase | Daniel Sucerquia | FLUSH COMBINE LOWER_WALLS COORDINATION METAD GYRATION UNITS UPPER_WALLS DISTANCE COORDINATIONNUMBER COM | function colvar vatom bias setup generic symfunc |
| 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 | TORSION PRINT METAD FIT_TO_TEMPLATE FIXEDATOM | bias colvar generic vatom |
| 21.032 | Metal-coupled folding mechanism to metallothionein | bio | parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination | Manuel-Peris Diaz | PBMETAD GROUP COORDINATION WHOLEMOLECULES UNITS | colvar core bias setup generic |
| 21.025 | Computational and biochemical analysis of type IV pilus dynamics and stability | bio | molecular dynamics, calcium binding, Type IV pilus | Yasaman Karami | PRINT LOWER_WALLS UPPER_WALLS DISTANCE | bias colvar generic |
| 21.015 | Coarse-grained metadynamics and umbrella sampling simulations to investigate interactions of carbohydrate-binding modules with chitin | bio | metadynamics, umbrella sampling, coarse-grained, MARTINI, chitin, carbohydrate-binding module | Gaston Courtade | RESTART PRINT COORDINATION CENTER POSITION METAD MATHEVAL REWEIGHT_BIAS WHOLEMOLECULES RESTRAINT | function colvar vatom bias setup generic |
| 21.011 | CmuMD simulations of NaCl(aq) at graphite | chemistry | CmuMD, DFS clustering | Aaron Finney | CLUSTER_DISTRIBUTION MFILTER_MORE GROUP PRINT AROUND LOAD FIXEDATOM DENSITY DFSCLUSTERING RESTRAINT CLUSTER_NATOMS MULTICOLVARDENS CONTACT_MATRIX COORDINATIONNUMBER DUMPGRID | volumes core vatom clusters bias setup generic symfunc adjmat multicolvar gridtools |
| 20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Faidon Brotzakis | EMMI BIASVALUE MOLINFO READ PRINT GROUP HISTOGRAM WHOLEMOLECULES DISTANCES CONVERT_TO_FES RMSD DUMPGRID | colvar isdb core bias generic multicolvar gridtools |
| 20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Adriana Pietropaolo | PBMETAD PRINT COORDINATION CENTER WHOLEMOLECULES | bias colvar generic vatom |
| 20.024 | Gaussian Mixture Based Enhanced Sampling (GAMBES) | methods | enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias | Jayashrita Debnath | TORSION COMBINE GROUP PRINT LOWER_WALLS LOAD DISTANCES UNITS UPPER_WALLS DISTANCE ENERGY | function colvar core bias setup generic multicolvar |
| 20.018 | Free energy barriers from biased molecular dynamics simulations | methods | kinetics, free energy barriers, chemical reactions, nucleation, metadynamics | Kristof Bal | REWEIGHT_METAD COORDINATION PAIRENTROPY HISTOGRAM LOCAL_AVERAGE UNITS UPPER_WALLS FLUSH REWEIGHT_BIAS LOAD CONTACT_MATRIX VOLUME ENERGY PRINT METAD CENTER DENSITY CONVERT_TO_FES SPRINT COMBINE LOWER_WALLS Q6 DISTANCE COORDINATIONNUMBER DUMPGRID | function colvar volumes vatom sprint bias symfunc setup generic adjmat gridtools |
| 20.003 | Enhanced sampling of transition states | methods | Variationally Enhanced Sampling, Target distribution, Transition state, Enhanced Sampling, Nucleation, chemical reaction | Jayashrita Debnath | VES_LINEAR_EXPANSION BF_LEGENDRE PRINT POSITION LOAD UNITS OPT_AVERAGED_SGD ENERGY | colvar ves generic setup |
| 20.002 | Exploring conformational dynamics of the extracellular Venus flytrap domain of the GABAB receptor, a path-metadynamics study | bio | Metadynamics, path CVs | Riccardo Ocello | RESTART MOLINFO GROUP PRINT METAD WHOLEMOLECULES UPPER_WALLS PATHMSD | colvar core bias setup generic |
| 19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Giovanni Bussi | TORSION FLUSH MOLINFO PRINT COORDINATION METAD SORT MATHEVAL WHOLEMOLECULES DISTANCE MAXENT COM INCLUDE | function colvar vatom bias generic |
| 19.050 | Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes | chemistry | metadynamics, membranes, Willard Chandler surface | Gareth Tribello | RESTART COMBINE READ PRINT METAD REWEIGHT_BIAS HISTOGRAM DISTANCE_FROM_CONTOUR CONVERT_TO_FES UPPER_WALLS DUMPGRID | function bias setup generic contour gridtools |
| 19.044 | Multithermal-multibaric simulations using VES | methods | ves, Wang Landau, multicanonical, water, density anomaly | Pablo Piaggi | VES_LINEAR_EXPANSION RESTART BF_LEGENDRE COMBINE READ PRINT TD_MULTITHERMAL_MULTIBARIC REWEIGHT_BIAS HISTOGRAM OPT_DUMMY REWEIGHT_TEMP_PRESS CONVERT_TO_FES VOLUME DUMPGRID AVERAGE OPT_AVERAGED_SGD ENERGY | function colvar bias setup generic ves gridtools |
| 19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | FLUSH RESTART COMBINE PRINT METAD DISTANCES UNITS UPPER_WALLS DISTANCE | function colvar bias setup generic multicolvar |
| 19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Matteo Salvalaglio | TORSION LOWER_WALLS PRINT METAD CENTER UPPER_WALLS DISTANCE COMMITTOR | bias colvar generic vatom |
| 19.011 | Automatic Gradient Computation for Collective Variables | other | gradient, differentiation, curvature | Toni Giorgino | ENDPLUMED | generic |
| 19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Max Bonomi | EMMI MOLINFO GROUP PRINT WHOLEMOLECULES BIASVALUE | isdb generic core bias |
| 25.011 | Chiral perovskite nucleation | chemistry | metadynamics, chiral perovskites, nucleation | Adriana Pietropaolo | LOWER_WALLS PBMETAD PRINT MATHEVAL UNITS RESTART UPPER_WALLS MULTI_RMSD DISTANCE | bias colvar generic function setup |
| 25.010 | Kinetic rates calculation with Ratchet&Pawl MD | methods | kinetics, ligand binding, ABMD, ratchet&pawl MD | Riccardo Capelli | ABMD COMMITTOR COM PRINT GROUP WHOLEMOLECULES FLUSH DISTANCE | bias colvar core vatom generic |
| 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 | MOLINFO MOVINGRESTRAINT RESTRAINT DISTANCE METAD TORSION RESTART PUCKERING PRINT | bias generic colvar setup |
| 25.006 | Characterizing the conformational ensemble of PROTAC degraders in solutions via atomistic simulations | methods | Enhanced sampling, Atomistic simulations, Conformational ensemble, PROTACs, Targeted Protein Degradation, Chamelonic molecules | Shikshya Bhusal, Omar Valsson | CENTER GYRATION PBMETAD DISTANCE ENERGY TORSION RESTART INCLUDE VOLUME READ PRINT | colvar bias vatom generic setup |
| 25.001 | RNA G-quadruplex folding with ST-metaD protocol | bio | RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | MOLINFO ERMSD COMBINE WHOLEMOLECULES METAD | colvar generic function bias |
| 24.031 | DeepLNE | methods | PATHCV, OPES, OneOPES | Thorben Fröhlking | MOLINFO COORDINATION OPES_METAD_EXPLORE OPES_EXPANDED ERMSD ECV_MULTITHERMAL PYTORCH_MODEL ENERGY RESTART COMBINE VOLUME PRINT | colvar opes pytorch generic function setup |
| 24.030 | NMR guided simulation of dsRBD | bio | Metainference, NMR, protein dynamics | Debadutta Patra | MOLINFO RDC ALPHABETA METAINFERENCE STATS DISTANCE ENSEMBLE GROUP WHOLEMOLECULES FLUSH PRINT | colvar core isdb multicolvar generic function |
| 24.021 | Ab initio machine learning simulation of calcium carbonate from aqueous solutions to the solid state | chemistry | ion pairing, caco3, opes, proton transfer, crystallization | Pablo Piaggi | COORDINATION DISTANCE ENERGY UPPER_WALLS OPES_METAD PRINT | opes colvar generic bias |
| 24.009 | Weighted Shape Gaussian Mixture Models | bio | metadynamics, clustering | Glen Hocky | PRINT UNITS TORSION GROUP METAD | colvar bias core generic setup |
| 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 | MOLINFO WRAPAROUND EMMIVOX DISTANCE BIASVALUE GROUP INCLUDE UPPER_WALLS WHOLEMOLECULES PRINT | colvar bias core isdb generic |
| 23.040 | Supramolecular capsules assembly dynamics | chemistry | Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics | Riccardo Capelli | POSITION CENTER COM PRINT DISTANCES UNITS METAD GROUP CUSTOM WHOLEMOLECULES FLUSH DISTANCE | colvar bias core vatom multicolvar generic function setup |
| 23.021 | Into the Dynamics of Rotaxanes at Atomistic Resolution | materials | metadynamics, rotaxanes, molecular shuttles, molecular machines | Luigi Leanza | CENTER PRINT MATHEVAL FIXEDATOM METAD TORSION CUSTOM UPPER_WALLS DISTANCE | bias colvar vatom generic function |
| 22.044 | Colloid Crystallisation Analyses | materials | Q4, Q6, Pair Entropy, DFS | Aaron Finney | LOCAL_AVERAGE CONTACT_MATRIX COORDINATIONNUMBER LOCAL_Q6 Q6 CLUSTER_NATOMS DFSCLUSTERING GROUP COMBINE Q4 MFILTER_LESS MFILTER_MORE PRINT LOCAL_Q4 | core adjmat multicolvar function generic symfunc clusters |
| 22.043 | Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES | bio | OPES, RNA, Tetraloop, Folding | Gül Zerze | CONTACTMAP OPES_EXPANDED ECV_MULTITHERMAL ENERGY ECV_UMBRELLAS_LINE WHOLEMOLECULES PRINT | opes colvar generic |
| 22.041 | Skipping the Replica Exchange Ladder with Normalizing Flows | methods | OPES, alanine, normalizing flows, replica exchange | Michele Invernizzi | POSITION OPES_EXPANDED ENDPLUMED ECV_MULTITHERMAL ENERGY TORSION UNITS OPES_METAD PRINT | opes colvar generic setup |
| 22.022 | Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir | bio | RMSD, protein-ligand interactions | Isabell Grothaus | PRINT RMSD | 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 DISTANCE CENTER PRINT | colvar generic vatom |
| 22.006 | Peptide framework for screening the effects of amino acids on assembly | bio | metadynamics, peptides | Andrew White | COM GYRATION PRINT CONVERT_TO_FES HISTOGRAM METAD REWEIGHT_BIAS COMBINE INCLUDE DUMPGRID GROUP DISTANCES | colvar bias core vatom multicolvar generic gridtools function |
| 22.005 | Collective Variable for Metadynamics Derived from AlphaFold Output | bio | AlphaFold, protein folding, protein structure prediction, metadynamics, deep learning, free energy simulation, collective variable | Vojtech Spiwok | WHOLEMOLECULES LOAD PRINT METAD | setup generic bias |
| 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 | POSITION BF_WAVELETS BF_CHEBYSHEV TD_UNIFORM BF_LEGENDRE PRINT BF_CUBIC_B_SPLINES UNITS UPPER_WALLS OPT_ADAM VES_OUTPUT_BASISFUNCTIONS ENERGY INCLUDE FLUSH DISTANCE OPT_AVERAGED_SGD VES_LINEAR_EXPANSION COORDINATION TD_WELLTEMPERED BF_GAUSSIANS METAD | bias colvar generic setup ves |
| 21.044 | NaCl nucleation | chemistry | metadynamics, DFS clustering | Aaron Finney | CONTACT_MATRIX COORDINATIONNUMBER INSPHERE PRINT LOCAL_Q6 Q6 FIXEDATOM HISTOGRAM CLUSTER_NATOMS DFSCLUSTERING GROUP COMBINE MFILTER_MORE DUMPGRID CLUSTER_DISTRIBUTION METAD | bias volumes core adjmat vatom multicolvar generic gridtools function symfunc clusters |
| 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 | ALPHABETA COORDINATION COM GYRATION PBMETAD PRINT ENERGY TORSION METAD INCLUDE DISTANCE | bias colvar vatom multicolvar generic |
| 21.020 | Reweighted Jarzynski sampling | methods | free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions | Kristof Bal | MOVINGRESTRAINT BF_CHEBYSHEV RESTRAINT CONSTANT PRINT COORDINATIONNUMBER UNITS BIASVALUE CUSTOM UPPER_WALLS OPES_METAD ANN HISTOGRAM COMBINE FLUSH DISTANCE OPT_AVERAGED_SGD LOAD REWEIGHT_METAD TD_WELLTEMPERED VES_LINEAR_EXPANSION CONVERT_TO_FES REWEIGHT_BIAS DUMPGRID METAD | bias colvar opes generic function annfunc gridtools setup ves symfunc |
| 21.014 | how to determine statistically accurate conformational ensembles | bio | metadynamics, metainference, errors, cv, SAXS, ensemble determination | Cristina Paissoni | MOLINFO ALPHABETA CENTER CONTACTMAP GYRATION PBMETAD PRINT ANTIBETARMSD STATS TORSION SAXS BIASVALUE ENSEMBLE WHOLEMOLECULES METAD | bias colvar secondarystructure vatom isdb multicolvar generic function |
| 20.015 | Rational design of ASCT2 inhibitors using an integrated experimental-computational approach | bio | ASCT2 transporter, small-molecules, cryo-EM, metainference | Max Bonomi | MOLINFO LOAD EMMIVOX BIASVALUE DUMPATOMS GROUP WHOLEMOLECULES PRINT | bias core isdb generic setup |
| 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 | CONTACTMAP PRINT COM FUNCPATHMSD UPPER_WALLS LOWER_WALLS HISTOGRAM COMBINE WHOLEMOLECULES FLUSH DISTANCE MOLINFO ABMD REWEIGHT_METAD ENDPLUMED CONVERT_TO_FES DUMPGRID READ METAD | colvar bias vatom generic function gridtools |
| 19.076 | Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones | bio | molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics | Salvatore Assenza | MOVINGRESTRAINT GYRATION ENDPLUMED UNITS PRINT | bias generic colvar setup |
| 19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Sandro Bottaro | MOLINFO PRINT ERMSD DISTANCE METAD TORSION WHOLEMOLECULES RMSD | colvar generic bias |
| 19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Jakub Rydzewski | LOWER_WALLS PRINT UNITS RESTART PATHMSD UPPER_WALLS METAD | bias generic colvar setup |
| 19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Cristina Paissoni | MOLINFO CENTER ALPHABETA COORDINATION PBMETAD MATHEVAL STATS ENDPLUMED BIASVALUE SAXS GROUP INCLUDE ANGLE COMBINE ENSEMBLE WHOLEMOLECULES PRINT | bias colvar core vatom isdb multicolvar generic function |
| 19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Gareth Tribello | LOWER_WALLS PRINT FCCUBIC CELL ENDPLUMED UNITS UPPER_WALLS AROUND METAD | bias colvar volumes generic setup symfunc |
| 19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Elena Papaleo | MOLINFO ALPHABETA LOWER_WALLS GYRATION PRINT GROUP UPPER_WALLS WHOLEMOLECULES METAD | colvar bias core multicolvar generic |
| 19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Carlo Camilloni | MOLINFO DHENERGY RDC ALPHABETA CENTER PBMETAD PRINT METAINFERENCE STATS ENDPLUMED RESTRAINT TORSION ENSEMBLE GROUP UPPER_WALLS WHOLEMOLECULES DIHCOR DISTANCE | colvar bias core vatom isdb multicolvar generic function |
| 19.008 | anncolvar | methods | neural network, dimensionality reduction | Vojtech Spiwok | MOLINFO POSITION ALPHARMSD PRINT MATHEVAL COMBINE FIT_TO_TEMPLATE WHOLEMOLECULES METAD | colvar bias secondarystructure generic function |
| 19.004 | MI Ubiquitin | bio | metainference, NMR | Max Bonomi | MOLINFO RDC METAINFERENCE GROUP CS2BACKBONE WHOLEMOLECULES PRINT | core generic isdb |
| 25.000 | Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer | bio | metadynamics, pathCV | Sahithya Sridharan Iyer | GROUP FUNCPATHGENERAL UPPER_WALLS RESTART COM METAD DISTANCE MOLINFO PRINT WHOLEMOLECULES | function vatom colvar setup core generic bias |
| 24.027 | Proline cis and trans subensembles of a disordered peptide | bio | intrinsically disordered proteins, proline cis trans isomerisation, metadynamics, collective variables | Alice Pettitt | ENDPLUMED GROUP INCLUDE COORDINATION GYRATION PARABETARMSD COMBINE ANTIBETARMSD DISTANCE TORSION FLUSH MOLINFO ALPHARMSD PBMETAD PRINT DIHCOR WHOLEMOLECULES | function colvar multicolvar core generic secondarystructure bias |
| 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 | CUSTOM GROUP ECV_MULTITHERMAL COORDINATION RESTART COMBINE DISTANCE TORSION ENERGY PRINT OPES_EXPANDED OPES_METAD_EXPLORE | function colvar setup core opes generic |
| 24.016 | Cryo-EM guided simulations of ribozyme | bio | metainference, cryo-EM | Giovanni Bussi | GROUP EMMIVOX INCLUDE ERMSD RESTRAINT MOLINFO PRINT BIASVALUE WHOLEMOLECULES | colvar isdb core generic bias |
| 24.008 | yCD Metadynamics | bio | volume-based MetaD, path CVs, infrequent MetaD, product release | James McCarty | INCLUDE HISTOGRAM DUMPGRID PATH METAD WHOLEMOLECULES GROUP FIXEDATOM RMSD UPPER_WALLS COORDINATION COM MOLINFO FIT_TO_TEMPLATE ENDPLUMED PRINT CONTACTMAP REWEIGHT_METAD MATHEVAL CONVERT_TO_FES READ DISTANCE WRAPAROUND FLUSH COMMITTOR | vatom function colvar mapping core generic gridtools bias |
| 23.044 | Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition | materials | metadynamics, interlocked molecules | Luigi Leanza | ENDPLUMED GROUP COORDINATION HISTOGRAM CONVERT_TO_FES DUMPGRID READ METAD PRINT COMMITTOR | colvar core generic gridtools bias |
| 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 | UPPER_WALLS MATHEVAL CENTER METAD CONSTANT DISTANCE LOWER_WALLS PRINT BIASVALUE WHOLEMOLECULES | function vatom colvar generic bias |
| 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 | CUSTOM GROUP FIXEDATOM OPES_METAD COORDINATION UPPER_WALLS UNITS CENTER PATH TORSION DISTANCE LOWER_WALLS PRINT PYTORCH_MODEL FIT_TO_TEMPLATE OPES_METAD_EXPLORE WHOLEMOLECULES | function vatom colvar setup mapping core opes generic pytorch bias |
| 23.011 | OneOPES, a combined enhanced sampling method to rule them all | bio | OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding | Valerio Rizzi | ENDPLUMED ECV_MULTITHERMAL TORSION ENERGY DISTANCE METAD MOLINFO PRINT OPES_EXPANDED OPES_METAD_EXPLORE | opes 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 | ANGLE INCLUDE CENTER WHOLEMOLECULES GROUP CUSTOM FIXEDATOM COORDINATION UPPER_WALLS RMSD ENERGY MOLINFO FIT_TO_TEMPLATE ENDPLUMED PRINT PYTORCH_MODEL CONTACTMAP OPES_METAD MATHEVAL COMBINE DISTANCE LOWER_WALLS COMMITTOR | vatom function colvar core opes generic pytorch bias |
| 22.038 | Enhanced Sampling Aided Design of Molecular Photoswitches | chemistry | reaction discovery, OPES explore, graph CV | Umberto Raucci | CUSTOM COORDINATION UNITS PRINT PYTORCH_MODEL OPES_METAD_EXPLORE | function colvar setup opes generic pytorch |
| 22.031 | Rare Event Kinetics from Adaptive Bias Enhanced Sampling | methods | OPES Flooding, Kinetics, Rate, OPES, Machine Learning | Dhiman Ray | INCLUDE TORSION WHOLEMOLECULES CUSTOM GROUP RMSD UNITS CONSTANT ENERGY MOLINFO BIASVALUE ENDPLUMED PRINT PYTORCH_MODEL CONTACTMAP POSITION OPES_METAD COMBINE DISTANCE COMMITTOR | function colvar setup core opes generic pytorch bias |
| 22.026 | Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification | materials | Peptoid, silica | Jim Pfaendtner | UPPER_WALLS COM GYRATION DISTANCE MOLINFO PBMETAD PRINT | vatom colvar bias generic |
| 22.015 | Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome | bio | photodynamics, bacteriophytochrome, variationally enhanced sampling | Jakub Rydzewski | BF_FOURIER VES_LINEAR_EXPANSION OPT_AVERAGED_SGD TORSION PRINT TD_UNIFORM | ves colvar generic |
| 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 | CUSTOM YANGLES UPPER_WALLS XANGLES MATHEVAL COM COMBINE DISTANCE LOWER_WALLS METAD MOLINFO ZANGLES PRINT TORSION ALPHABETA WHOLEMOLECULES | function vatom colvar multicolvar generic bias |
| 22.009 | Glycosylation in calixarenes capsule | chemistry | Metadynamics, glycosylation, supramolecular catalysis | GiovanniMaria Piccini | GROUP WHOLEMOLECULES ANGLE RMSD COORDINATION MATHEVAL UPPER_WALLS UNITS COMBINE DISTANCE LOWER_WALLS METAD PRINT DISTANCES FLUSH FIT_TO_TEMPLATE BRIDGE | function colvar multicolvar setup core adjmat generic bias |
| 21.052 | On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets | materials | Ibuprofen, unbinding, WTmetaD | Matteo Salvalaglio | ENDPLUMED CENTER METAD TORSION DISTANCE COORDINATIONNUMBER PRINT COMMITTOR | vatom colvar symfunc generic bias |
| 21.042 | Peptoid-mediated Au nanocrystal growth | materials | parallel-bias metadynamics, peptoid, Au | Xin Qi | UPPER_WALLS COM GYRATION DISTANCE MOLINFO PBMETAD PRINT | vatom colvar bias generic |
| 21.029 | Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs | bio | metadynamics, small peptide, machine learning | Pratyush Tiwary | RESTART EXTERNAL TORSION ENERGY FLUSH PRINT MOLINFO | setup colvar bias generic |
| 21.024 | Property map collective variable as a useful tool for force field correction | chemistry | molecular mechanics | Vojtech Spiwok | TORSION METAD PRINT PROPERTYMAP BIASVALUE WHOLEMOLECULES | colvar bias generic |
| 21.019 | Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations | materials | Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen | Matteo Salvalaglio | KDE MATHEVAL COM DISTANCE TORSIONS PRINT | function vatom colvar multicolvar generic gridtools |
| 21.017 | All-atom simulations of the Vav1 AD construct | bio | metadynamics, parallel-bias, well-tempered | Simone Orioli | GROUP REWEIGHT_BIAS RESTART METAD ALPHABETA MOLINFO ALPHARMSD PBMETAD CONTACTMAP PRINT WHOLEMOLECULES | colvar multicolvar setup core generic secondarystructure bias |
| 21.004 | Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy | bio | machine learning, well-tempered metadynamics, path collective variable, potential of mean force, standard binding free energy calculations, host-guest, protein-ligand unbinding | Dorothea Gobbo | UPPER_WALLS RESTART METAD PATHMSD LOWER_WALLS PRINT WHOLEMOLECULES | setup colvar bias generic |
| 20.030 | Converging experimental and computational views of the knotting mechanism of the smallest knotted protein | bio | phi-values, transition state, knotted proteins | Cristina Paissoni | COORDINATION RESTRAINT COMBINE STATS MOLINFO PRINT WHOLEMOLECULES | function colvar bias generic |
| 20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Max Bonomi | INCLUDE COORDINATION GYRATION ALPHABETA MOLINFO PRINT PBMETAD DIHCOR WHOLEMOLECULES | bias colvar multicolvar generic |
| 20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Glen Hocky | GROUP FISST MATHEVAL RESTRAINT UNITS GYRATION DISTANCE ENERGY PRINT BIASVALUE | function colvar setup core generic bias fisst |
| 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 | CS2BACKBONE METAINFERENCE INCLUDE TORSION PBMETAD WHOLEMOLECULES GROUP COORDINATION GYRATION ANTIBETARMSD STATS MOLINFO ALPHARMSD ENDPLUMED PARABETARMSD PRINT ENSEMBLE DIHCOR COMBINE FLUSH | function colvar multicolvar isdb core generic secondarystructure bias |
| 20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Carlo Camilloni | METAINFERENCE CENTER GYRATION SAXS TORSION DISTANCE ALPHABETA STATS MOLINFO PBMETAD ENSEMBLE FLUSH PRINT WHOLEMOLECULES | vatom function colvar multicolvar isdb generic bias |
| 20.008 | Simulating solvation and acidity in complex mixtures with first-principles accuracy. The case of CH3SO3H and H2O2 in phenol | chemistry | proton trasfer, metadynamics | Kevin Rossi | CUSTOM COORDINATION UNITS METAD PRINT DISTANCES | function colvar multicolvar setup generic bias |
| 20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Luigi Bonati | ENDPLUMED GROUP OPES_METAD LOAD UPPER_WALLS MATHEVAL COM UNITS TORSION DISTANCE LOWER_WALLS PRINT PYTORCH_MODEL FLUSH | function vatom colvar setup core opes generic pytorch bias |
| 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 | ENDPLUMED ABMD REWEIGHT_METAD UPPER_WALLS MATHEVAL HISTOGRAM COM CONVERT_TO_FES DUMPGRID READ COMBINE DISTANCE LOWER_WALLS METAD PRINT | function vatom colvar generic gridtools bias |
| 19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Valerio Rizzi | ENDPLUMED GROUP UPPER_WALLS RESTART UNITS COMBINE METAD COORDINATIONNUMBER PRINT DISTANCES FLUSH | function symfunc multicolvar setup core generic bias |
| 19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Jim Pfaendtner | GYRATION METAD ENERGY PRINT WHOLEMOLECULES | colvar bias generic |
| 19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Kim E. Jelfs | GROUP UPPER_WALLS RESTART COM CENTER METAD DISTANCE LOWER_WALLS PRINT | vatom colvar setup core generic bias |
| 19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Luigi Bonati | ENDPLUMED LOAD UNITS TORSION ENERGY Q6 PRINT ENVIRONMENTSIMILARITY POSITION | colvar setup envsim symfunc generic |
| 19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Kim Jelfs | MOVINGRESTRAINT RESTART COM INPLANEDISTANCES FLUSH PRINT DISTANCES | vatom multicolvar setup generic bias |
| 19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Gareth Tribello | ENDPLUMED CELL UPPER_WALLS FCCUBIC UNITS METAD PRINT | colvar setup symfunc generic bias |
| 19.049 | Determining the sizes of solid/liquid clusters in MD trajectories of nucleation | methods | nucleation, metadynamics, clustering, Steinhardt order parameters | Gareth Tribello | OUTER_PRODUCT CUSTOM CLUSTER_NATOMS SMAC MATRIX_VECTOR_PRODUCT LOCAL_Q6 ONES OUTPUT_CLUSTER METAD DFSCLUSTERING Q6 CONTACT_MATRIX PRINT CLUSTER_DISTRIBUTION COORDINATIONNUMBER CLUSTER_PROPERTIES DISTANCES MORE_THAN | function multicolvar matrixtools adjmat clusters symfunc generic bias |
| 19.047 | Close Structure | methods | metadynamics, RMSD, path collective variables, property map | Vojtech Spiwok | METAD PRINT WHOLEMOLECULES PROPERTYMAP | colvar bias generic |
| 19.041 | Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces | bio | metadynamics, collective variables, conformational changes, multiple walkers, Well-Tempered MetaD, peptide, binding, phosphorylation, post-transitional motif, sio2, adsorption | Jim Pfaendtner | UPPER_WALLS COM METAD ENERGY DISTANCE PRINT | vatom colvar bias generic |
| 19.040 | Optimal Metric for Path Collective Variables | bio | metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path | Francesco Luigi Gervasio | ENDPLUMED MATHEVAL TORSION METAD PRINT | function colvar bias generic |
| 19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Jim Pfaendtner | GROUP COORDINATION EXTERNAL METAD ENERGY | bias colvar core |
| 19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Mattia Bernetti | ENDPLUMED GYRATION METAD ENERGY MOLINFO ALPHARMSD PRINT WHOLEMOLECULES | secondarystructure colvar bias generic |
| 19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Kresten Lindorff-Larsen | COMBINE METAD ALPHABETA FLUSH MOLINFO PRINT COMMITTOR | function multicolvar bias generic |
| 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 POSITION COMBINE CUSTOM ENERGY PRINT CELL MATHEVAL OPES_METAD INCLUDE BIASVALUE TORSION UNITS DISTANCE LOAD COORDINATION | opes function generic colvar setup bias |
| 24.004 | Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables | materials | metadynamics, nucleation, machine learning | Ziyue Zou | PRINT INCLUDE RESTART METAD GROUP LOAD | generic setup core bias |
| 24.003 | Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations | chemistry | steered molecular dynamics, foldamers, peptoids, bio-inspired | Kaylyn Torkelson | WHOLEMOLECULES ALPHABETA PRINT GYRATION MOVINGRESTRAINT INCLUDE TORSION DISTANCE COM COORDINATION | generic colvar vatom bias multicolvar |
| 24.001 | A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations | bio | OPES, OPES-Flooding, QM/MM, Kinetics, Enzyme Catalysis | Dhiman Ray | FLUSH CUSTOM PRINT COMBINE COMMITTOR UPPER_WALLS OPES_METAD TORSION UNITS DISTANCE LOWER_WALLS | opes function generic colvar setup 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 | FLUSH COORDINATIONNUMBER PRINT UPPER_WALLS ZDISTANCES OPES_METAD FIXEDATOM UNITS DISTANCE GROUP | core opes generic colvar vatom setup bias symfunc multicolvar |
| 23.032 | Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics | bio | metadynamics, tSNE, neural network, machine learning, trp-cage, folding | Vojtech Spiwok | WHOLEMOLECULES MOLINFO COMBINE PRINT ALPHARMSD ANN METAD FIT_TO_TEMPLATE POSITION | function generic colvar secondarystructure annfunc bias |
| 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 | MOLINFO WRAPAROUND COMMITTOR BIASVALUE POSITION CENTER COORDINATION ENERGY UPPER_WALLS ENDPLUMED TORSION UNITS DISTANCE WHOLEMOLECULES FLUSH PRINT CUSTOM LOWER_WALLS FIT_TO_TEMPLATE COM OPES_METAD_EXPLORE MATHEVAL OPES_METAD GROUP | core opes function generic colvar vatom setup bias |
| 23.028 | Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process | chemistry | Ammonia decomposition; Dynamics;OPES; Neural Network potential | Manyi Yang | FLUSH COORDINATIONNUMBER PRINT CUSTOM ENERGY COMMITTOR UPPER_WALLS MATHEVAL OPES_METAD ZDISTANCES DISTANCES FIXEDATOM UNITS DISTANCE GROUP LOWER_WALLS COM | core opes function generic colvar vatom setup bias symfunc multicolvar |
| 23.020 | FEP simulations of ATOX1 homodimer | chemistry | parallel bias metadynamics, FEP, free-energy of metal ion dissociation | Adriana Pietropaolo | WHOLEMOLECULES PRINT PBMETAD MATHEVAL BIASVALUE CONSTANT DISTANCE ANGLE | generic colvar function bias |
| 23.007 | Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains | bio | metadynamics, peptoids, parallel-bias metadynamics | Jim Pfaendtner | WHOLEMOLECULES PRINT GYRATION PBMETAD INCLUDE TORSION RESTRAINT COM COORDINATION | generic colvar vatom bias |
| 23.006 | Transcription factor unbinding | bio | metadynamics, DNA, conformational changes | Malin Lüking | MOLINFO PRINT ALPHARMSD CONTACTMAP DUMPFORCES METAD DISTANCE ANGLE COM | generic colvar vatom secondarystructure bias |
| 22.037 | Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site | chemistry | metadynamics, DNA, abasic | Mike Jones | DISTANCE DISTANCES PRINT METAD | generic colvar bias multicolvar |
| 22.019 | Exploring aspartic protease inhibitor binding to design selective antimalarials | bio | ligand binding, loop opening, path CV, funnel metadynamics, drug development | Raitis Bobrovs | WHOLEMOLECULES FUNNEL_PS PRINT PATHMSD UPPER_WALLS FUNNEL METAD DISTANCE LOWER_WALLS COM | generic funnel colvar vatom bias |
| 21.039 | Deep learning the slow modes for rare events sampling | methods | collective variables, machine learning, slow modes, deep-tica, opes | Luigi Bonati | MOLINFO PYTORCH_MODEL LOAD ENERGY ENDPLUMED TORSION ECV_MULTITHERMAL UNITS DISTANCE WHOLEMOLECULES FLUSH PRINT VOLUME COMBINE OPES_EXPANDED Q6 CONTACTMAP ENVIRONMENTSIMILARITY OPES_METAD INCLUDE RMSD GROUP | core opes function generic colvar setup envsim symfunc pytorch |
| 21.035 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, interface | Aaron Finney | PRINT FIXEDATOM RESTRAINT DISTANCE GROUP LOAD | core generic colvar vatom setup bias |
| 21.033 | Multiple-path-metadynamics applied to DNA base-pairing transitions | bio | path-CV, metadynamics, multiple-walker, dna | Alberto Pérez-de-Alba-Ortíz | COMBINE PRINT MOVINGRESTRAINT UPPER_WALLS RESTRAINT INCLUDE METAD CONSTANT | generic bias function |
| 21.028 | From Enhanced Sampling to Reaction Profiles | methods | collective variables, multi-state, machine learning, Deep-TDA | Enrico Trizio | PYTORCH_MODEL LOAD COORDINATION CENTER UPPER_WALLS ENDPLUMED TORSION FIXEDATOM UNITS DISTANCE WHOLEMOLECULES PRINT DISTANCES LOWER_WALLS FIT_TO_TEMPLATE GROUP MATHEVAL OPES_METAD ANGLE | core opes function generic colvar vatom setup bias pytorch multicolvar |
| 21.023 | Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling | methods | enhanced sampling, collective variables, machine learning | Jakub Rydzewski | CUSTOM PRINT ENERGY INCLUDE BIASVALUE TORSION METAD CONSTANT DISTANCE UNITS REWEIGHT_METAD | function generic colvar setup bias |
| 21.007 | Sampling enhancement by metadynamics driven by machine learning and de novo protein modelling | bio | metadynamics, machine learning, protein folding | Vojtech Spiwok | MOLINFO WHOLEMOLECULES COMBINE ALPHARMSD MATHEVAL FIT_TO_TEMPLATE POSITION | generic secondarystructure function colvar |
| 21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Tarsis Ferreira | MOLINFO WHOLEMOLECULES RANDOM_EXCHANGES PUCKERING PRINT ENERGY REWEIGHT_METAD DUMPGRID UPPER_WALLS HISTOGRAM INCLUDE METAD LOWER_WALLS DISTANCE GROUP COORDINATION | core generic colvar bias gridtools |
| 20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Valerio Rizzi | WHOLEMOLECULES DISTANCE PRINT PYTORCH_MODEL ENERGY UPPER_WALLS MATHEVAL OPES_METAD ANGLE ENDPLUMED COORDINATION FIXEDATOM FIT_TO_TEMPLATE GROUP CENTER | core opes function generic colvar vatom bias pytorch |
| 20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Vojtech Spiwok | PRINT TORSION METAD | generic colvar bias |
| 20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Matteo Salvalaglio | PRINT ENERGY CELL UPPER_WALLS MATHEVAL VOLUME METAD LOWER_WALLS | generic colvar function bias |
| 19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Matteo Salvalaglio | PRINT READ REWEIGHT_BIAS DUMPGRID COMMITTOR EXTERNAL MATHEVAL HISTOGRAM TORSION BIASVALUE METAD DISTANCE CONVERT_TO_FES REWEIGHT_METAD | function generic colvar bias gridtools |
| 19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_LOSS PRINT MAZE_OPTIMIZER_BIAS UNITS MAZE_SIMULATED_ANNEALING POSITION | generic setup colvar maze |
| 19.056 | maze | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_LOSS PRINT MAZE_OPTIMIZER_BIAS UNITS MAZE_SIMULATED_ANNEALING POSITION | generic setup colvar maze |
| 19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Gareth Tribello | MORE_THAN DUMPGRID FOURIER_TRANSFORM MULTICOLVARDENS FIND_CONTOUR_SURFACE FCCUBIC UNITS GROUP CENTER | fourier core function vatom setup gridtools symfunc contour |
| 19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Vittorio Limongelli | WHOLEMOLECULES FUNNEL_PS PRINT UPPER_WALLS RMSD FUNNEL METAD DISTANCE LOWER_WALLS COM | generic funnel colvar vatom bias |
| 19.032 | Chemical reaction in solution using path collective variables based on coordination patterns | chemistry | chemical reactions, solutions, metadynamics, coordination patterns | Fabio Pietrucci | FLUSH PRINT UPPER_WALLS DISTANCES RESTART METAD PATH | generic setup mapping bias multicolvar |
| 19.025 | Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide | bio | metainference, NMR, protein dynamics, force-fields | Carlo Camilloni | MOLINFO WHOLEMOLECULES FLUSH PRINT GYRATION METAINFERENCE STATS PBMETAD ENSEMBLE ENDPLUMED TORSION BIASVALUE RDC JCOUPLING CS2BACKBONE | function generic colvar isdb bias |
| 19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Haochuan Chen | DRR TORSION PRINT | generic colvar drr |
| 19.013 | RNA FF FITTING | methods | force field, RNA | Giovanni Bussi | MOLINFO PUCKERING MATHEVAL INCLUDE TORSION BIASVALUE CONSTANT | generic colvar bias function |
| 19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Michele Invernizzi | PRINT ENERGY ENDPLUMED TORSION RESTART METAD VES_DELTA_F LOAD UNITS POSITION | generic colvar ves setup bias |
| 25.002 | M3_PCV-ABMD | chemistry | Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor | Gian Marco Elisi | UPPER_WALLS PATHMSD ENDPLUMED PRINT UNITS ABMD | setup colvar generic bias |
| 24.034 | Umbrella sampling of ion in transporter SLC26A7 | bio | umbrella sampling, transporter, ions | Xiaoli Lu | PRINT UNITS RESTRAINT POSITION | colvar setup generic bias |
| 24.019 | Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning | bio | OPES, machine learning, protein folding, adaptive sampling | Mingyuan Zhang | COMBINE ALPHARMSD OPES_METAD COORDINATION GYRATION DISTANCE TORSION CUSTOM WHOLEMOLECULES PRINT MOLINFO | function opes colvar secondarystructure 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 | COMBINE PRINT BIASVALUE CENTER COORDINATION COM LOWER_WALLS GROUP DISTANCE DEBUG GHBFIX METAD UPPER_WALLS MOLINFO | core function colvar generic bias vatom |
| 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 BIASVALUE COORDINATION GHBFIX ERMSD WHOLEMOLECULES METAD PRINT MOLINFO | colvar generic bias function |
| 23.024 | Permutationally Invariant Networks for Enhanced Sampling (PINES) | methods | collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent | Nicholas Herringer | LOAD PBMETAD PRINT | setup generic bias |
| 23.023 | Rational design of novel biomimetic sequence-defined polymers for mineralization applications | methods | metadynamics, surface binding, biomimetic mineralization | Kaylyn Torkelson | PRINT COORDINATION COM GYRATION PBMETAD DISTANCE UPPER_WALLS | colvar generic bias vatom |
| 23.016 | Activation/deactivation free-energy profiles for the β2-adrenergic receptor: Ligand modes of action | bio | G protein coupled receptor, beta-adrenergic, receptor activation, partial agonism, metadynamics | Timothy Clark | REWEIGHT_METAD MATHEVAL DISTANCE DUMPGRID METAD WHOLEMOLECULES CONVERT_TO_FES RMSD PRINT READ HISTOGRAM MOLINFO | gridtools function colvar generic bias |
| 23.015 | MPCs aggregation | bio | opes_explore, dimerization, MPCs, self-assembly | Vikas Tiwari | PRINT CENTER OPES_METAD_EXPLORE COORDINATION COM LOWER_WALLS GROUP DISTANCE CUSTOM METAD WHOLEMOLECULES UPPER_WALLS | core function opes colvar generic bias vatom |
| 23.003 | Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations | methods | metadynamics, alchemical variable, alchemical free energy calculations | Wei-Tse Hsu | TORSION METAD PRINT READ EXTRACV | colvar generic bias |
| 23.002 | Critical comparison of general-purpose collective variables for crystal nucleation | methods | metadynamics, umbrella sampling, commitor, entropy, PIV | Julien Lam | ENERGY FUNCPATHMSD PRINT Q4 RESTRAINT VOLUME PAIRENTROPY CUSTOM Q6 METAD PIV UPPER_WALLS UNITS LOCAL_AVERAGE | setup gridtools piv function colvar symfunc generic bias |
| 22.036 | Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction | bio | Well-tempered MetaDynamics with Hamiltonian Replica Exchange | Miroslav Krepl | COMBINE PRINT BIASVALUE COORDINATION GROUP LOAD CUSTOM GHBFIX METAD UPPER_WALLS MOLINFO FLUSH | core setup function colvar generic bias |
| 22.028 | N-glycan conformer distributions in atomistic simulation | bio | REST2, RECT, N-glycan, pucker | Isabell Grothaus | MOLINFO TORSION METAD CONVERT_TO_FES DUMPGRID PRINT READ HISTOGRAM PUCKERING | gridtools colvar generic bias |
| 22.023 | Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy | bio | CryoEM, MEMMI,EMMI, Metadynamics, Metainference, IAPP, structural ensemble | Faidon Brotzakis | PRINT BIASVALUE COORDINATION COM GROUP PBMETAD RESTART TORSION EMMI WHOLEMOLECULES RMSD UPPER_WALLS MOLINFO | core setup colvar isdb generic bias vatom |
| 22.013 | Ligand dissociation from PreQ1 riboswitch | bio | ligand, RNA, metadynamics, pRAVE | Yihang Wang | COMMITTOR COMBINE COORDINATIONNUMBER COM DISTANCE METAD WHOLEMOLECULES RMSD PRINT MOLINFO | function colvar symfunc generic bias vatom |
| 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 | PRINT ALPHARMSD COORDINATION DISTANCE TORSION ANGLE WHOLEMOLECULES METAD ALPHABETA UPPER_WALLS MOLINFO FLUSH | colvar secondarystructure generic bias multicolvar |
| 21.051 | Automatic learning of hydrogen-bond fixes in an AMBER RNA force field | methods | force field, RNA | Giovanni Bussi | COMBINE BIASVALUE COORDINATION ERMSD METAD WHOLEMOLECULES PRINT MOLINFO | colvar generic bias function |
| 21.049 | Multiple-path-metadynamics and PathMaps | methods | path-CV, metadynamics, multiple-walker, multiple paths, pathmap | Alberto Pérez-de-Alba-Ortíz | COMBINE PRINT RESTRAINT ENSEMBLE LOWER_WALLS CONSTANT TORSION LOAD CUSTOM METAD UPPER_WALLS UNITS MOVINGRESTRAINT | setup function colvar generic bias |
| 21.013 | Role of vibrational excitation in heterogeneous catalysis | chemistry | catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption | Kristof Bal | REWEIGHT_METAD COMBINE LOWER_WALLS DISTANCES ANGLES UWALLS COORDINATIONNUMBER COORDINATION TD_GRID DISTANCE LOAD CONVERT_TO_FES UNITS OPT_AVERAGED_SGD EXTERNAL VES_LINEAR_EXPANSION REWEIGHT_BIAS BF_CHEBYSHEV PRINT HISTOGRAM FLUSH RESTRAINT METAD DUMPGRID UPPER_WALLS | setup ves gridtools function colvar symfunc generic bias multicolvar |
| 21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Kresten Lindorff-Larsen | ALPHARMSD BIASVALUE EEFSOLV CENTER GYRATION GROUP PBMETAD METAINFERENCE WHOLEMOLECULES PRINT SAXS MOLINFO FLUSH | core colvar isdb secondarystructure generic bias vatom |
| 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 | ENERGY ECV_MULTITHERMAL_MULTIBARIC MATHEVAL OPT_AVERAGED_SGD VOLUME VES_LINEAR_EXPANSION UPPER_WALLS RESTART ECV_UMBRELLAS_LINE Q6 BF_LEGENDRE PRINT ENVIRONMENTSIMILARITY OPES_EXPANDED TD_UNIFORM | setup ves function opes colvar envsim symfunc generic bias |
| 21.000 | Uremic toxin time scale dynamics | bio | uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs) | Jim Pfaendtner | COM GROUP DISTANCE WHOLEMOLECULES PRINT | core colvar generic vatom |
| 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 | CENTER DISTANCE RESTART TORSION ERMSD PRINT MOLINFO ABMD | setup colvar generic bias vatom |
| 20.028 | Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane | bio | metadynamics, KRas-4B, anionic membrane | Huixia Lu | FIT_TO_TEMPLATE CENTER DISTANCE RESTART METAD PRINT | setup colvar generic bias 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 | PRINT BIASVALUE LOWER_WALLS ANTIBETARMSD GROUP PBMETAD CS2BACKBONE WHOLEMOLECULES ENDPLUMED ALPHABETA UPPER_WALLS MOLINFO FLUSH | core isdb secondarystructure generic bias multicolvar |
| 19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Valerio Rizzi | COMBINE COORDINATIONNUMBER EXTERNAL GROUP RESTART METAD ENDPLUMED PRINT UNITS FLUSH | core setup function symfunc 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 | ENERGY PRINT COM GYRATION GROUP DISTANCE METAD UPPER_WALLS MOLINFO | core colvar generic bias vatom |
| 19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Giovanni Bussi | RESTRAINT COORDINATION LOWER_WALLS DISTANCE WHOLEMOLECULES ENDPLUMED | colvar generic bias |
| 19.073 | On the role of enthalpic and entropic contributions on the conformational free energy landscape of MIL-101(Cr) building units | materials | metadynamics, MOF, MIL101Cr, conformational | Matteo Salvalaglio | ENERGY PRINT COORDINATIONNUMBER LOWER_WALLS GYRATION METAD ENDPLUMED DISTANCES UPPER_WALLS | colvar symfunc generic bias multicolvar |
| 19.055 | Flying Gaussian method | methods | flying Gaussians, alanine dipeptide, peptide bond, Met-enkephalin | Vojtech Spiwok | COMBINE MATHEVAL DISTANCE TORSION METAD PRINT | colvar generic bias function |
| 19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | GiovanniMaria Piccini | ENERGY COMBINE PRINT LOWER_WALLS DISTANCE METAD UPPER_WALLS UNITS FLUSH | setup function colvar generic bias |
| 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 | REWEIGHT_METAD COMBINE PRINT COM LOWER_WALLS GROUP DISTANCE TORSION ALPHABETA FUNNEL METAD WHOLEMOLECULES DISTANCES BRIDGE RMSD UPPER_WALLS MOLINFO | core funnel function colvar generic bias multicolvar vatom adjmat |
| 19.035 | Dimerization of GPCRs from coarse-grained umbrella sampling | bio | Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization | Davide Provasi | RESTRAINT COM GROUP DISTANCE TORSION PRINT | core colvar generic bias vatom |
| 19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Riccardo Capelli | REWEIGHT_METAD PRINT FIT_TO_TEMPLATE MATHEVAL COORDINATION COM GROUP WRAPAROUND METAD WHOLEMOLECULES CONVERT_TO_FES ENDPLUMED DUMPGRID UPPER_WALLS READ HISTOGRAM FLUSH POSITION | core gridtools function colvar generic bias vatom |
| 19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Max Bonomi | BIASVALUE GROUP EMMI PRINT MOLINFO | core generic bias isdb |
| 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 | COMMITTOR FLUSH UNITS ZDISTANCES DISTANCE CUSTOM COORDINATIONNUMBER OPES_METAD UPPER_WALLS FIXEDATOM GROUP DISTANCES PRINT | symfunc opes multicolvar setup colvar vatom core generic function bias |
| 25.003 | Surrogate Model CV | methods | Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding | Sompriya Chatterjee | GROUP COMMITTOR PYTORCH_MODEL MOLINFO ENERGY DISTANCE MATHEVAL COMBINE OPES_METAD CUSTOM ENDPLUMED WHOLEMOLECULES TORSION PRINT | pytorch opes colvar generic function core |
| 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 COORDINATION OPES_METAD_EXPLORE ENERGY DISTANCE MATHEVAL UPPER_WALLS FIT_TO_TEMPLATE ANGLE FIXEDATOM ENDPLUMED ECV_MULTITHERMAL OPES_EXPANDED CENTER GROUP TORSION PRINT WHOLEMOLECULES | opes colvar vatom core generic function bias |
| 24.007 | SWISH-X | bio | swish-x, SWISH-X, swish, expanded SWISH | Alberto Borsatto | MOLINFO ENERGY ECV_MULTITHERMAL OPES_EXPANDED WHOLEMOLECULES UPPER_WALLS PRINT CONTACTMAP INCLUDE | colvar opes generic bias |
| 23.043 | Modeling the ferroelectric phase transition in barium titanate with DFT accuracy and converged sampling | materials | Barium Titanate, ferroelectric phase transition, Machine Learning, polarization order parameters | Lorenzo Gigli | SELECT_COMPONENTS TRANSPOSE SUM FLUSH MATHEVAL METAD PRINT INCLUDE | valtools generic matrixtools function bias |
| 23.038 | Determinants of Neutral Antagonism and Inverse Agonism in the β2-adrenergic receptor | bio | protein coupled receptor, beta-adrenergic, receptor activation, antagonism, inverse agonism, metadynamics | Timothy Clark | MOLINFO RMSD DISTANCE MATHEVAL METAD WHOLEMOLECULES PRINT | function colvar generic bias |
| 23.034 | Urea nucleation in water: do long-range forces matter? | materials | LMF theory, Metadynamics, Nucleation | Ziyue Zou | LOAD COORDINATIONNUMBER METAD CENTER GROUP PRINT INCLUDE | symfunc setup vatom core generic bias |
| 23.027 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, DFS, Q3, Pair Entropy | Aaron Finney | DUMPGRID DENSITY AROUND DFSCLUSTERING Q3 HISTOGRAM LOAD CONTACT_MATRIX UNITS RESTRAINT CLUSTER_DISTRIBUTION COORDINATIONNUMBER FIXEDATOM LOCAL_Q3 CLUSTER_NATOMS GROUP PRINT LOCAL_AVERAGE | symfunc setup clusters vatom bias core volumes generic gridtools adjmat |
| 23.026 | Machine Learning Nucleation Collective Variables with Graph Neural Networks | chemistry | Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks | Florian Dietrich | LOCAL_Q6 LOWER_WALLS COMBINE COORDINATIONNUMBER Q6 METAD MOVINGRESTRAINT GROUP PRINT MFILTER_MORE | symfunc multicolvar core generic function bias |
| 23.022 | A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar | methods | collective variables, machine learning, toy model | Enrico Trizio | PYTORCH_MODEL BIASVALUE LOWER_WALLS UNITS CUSTOM OPES_METAD ENDPLUMED POSITION UPPER_WALLS PRINT | pytorch opes setup colvar generic function bias |
| 23.014 | Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 | bio | metadynamics, oligomerization, chemokine receptors, GPCR, membrane | Vittorio Limongelli | FLUSH COMBINE DISTANCE COM UPPER_WALLS METAD WHOLEMOLECULES TORSION PRINT | colvar vatom generic function bias |
| 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 DRR FLUSH PATHMSD CUSTOM METAD PRINT | drr colvar generic function bias |
| 22.004 | Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques | chemistry | reaction discovery, OPES, collective variables | Umberto Raucci | PYTORCH_MODEL LOAD OPES_METAD_EXPLORE UNITS COORDINATION LOWER_WALLS COM CUSTOM DISTANCE MATHEVAL OPES_METAD GROUP UPPER_WALLS PRINT | pytorch opes setup colvar vatom core generic function bias |
| 21.050 | N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity | methods | bio | Isabell Louise Grothaus | CENTER PRINT DISTANCE | colvar vatom generic |
| 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 | GYRATION LOWER_WALLS ALPHABETA ENDPLUMED METAD GROUP UPPER_WALLS PRINT WHOLEMOLECULES | multicolvar colvar core generic bias |
| 21.041 | Nucleating a Different Coordination in a Crystal under Pressure. A Study of the B1−B2 Transition in NaCl by Metadynamics | methods | metadynamics, structural phase transitions, pressure-induced phase transition, martensitic transitions | Matej Badin | COORDINATION COMBINE CUSTOM VOLUME ENDPLUMED METAD PRINT | function colvar generic bias |
| 21.027 | EGFR activating mutations mechanism | bio | metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA | Francesco Gervasio | MOLINFO LOWER_WALLS ENERGY DISTANCE MATHEVAL METAD ALPHARMSD WHOLEMOLECULES UPPER_WALLS PRINT CONTACTMAP INCLUDE | secondarystructure colvar generic function bias |
| 21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Adriana Pietropaolo | BIASVALUE PBMETAD PRINT MATHEVAL RESTART WHOLEMOLECULES TORSION CONSTANT | setup colvar generic function bias |
| 20.032 | Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil | materials | clustering, conformational isomers | Matteo Salvalaglio | TORSION ENDPLUMED PRINT | colvar generic |
| 20.026 | Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor | bio | Metadynamics, Umbrella sampling | Brandon Peters | DUMPGRID MULTI_RMSD REWEIGHT_METAD CONVERT_TO_FES HISTOGRAM RESTRAINT METAD PRINT | generic colvar gridtools bias |
| 20.010 | Phase equilibrium of liquid water and hexagonal ice from enhanced sampling molecular dynamics simulations | materials | water, ice, TIP4P, crystallization, EnvironmentSimilarity, RefCV, kernel, VES, variationally enhanced sampling | Pablo Piaggi | ENVIRONMENTSIMILARITY VES_LINEAR_EXPANSION TD_WELLTEMPERED OPT_DUMMY MATHEVAL OPT_AVERAGED_SGD VOLUME Q6 RESTART UPPER_WALLS PRINT BF_LEGENDRE | symfunc ves setup colvar envsim generic function bias |
| 19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Wei Chen | RESTRAINT ANN COMBINE COM POSITION | annfunc colvar vatom function bias |
| 19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | GYRATION MOLINFO DISTANCE COM METAD UPPER_WALLS ENERGY PRINT | colvar vatom generic bias |
| 19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Paolo Raiteri | FLUSH UNITS DISTANCE MATHEVAL METAD RESTART UPPER_WALLS PRINT | setup colvar generic function bias |
| 19.030 | Coarse-Grained MetaDynamics (CG-MetaD) | bio | Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy | Vittorio Limongelli | LOWER_WALLS DISTANCE COM METAD WHOLEMOLECULES UPPER_WALLS PRINT | generic colvar vatom bias |
| 19.023 | RECT | methods | metadynamics, replica exchange | Giovanni Bussi | GYRATION METAD WHOLEMOLECULES TORSION PRINT | generic colvar bias |
| 19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Glen Hocky | RESTRAINT COMBINE DISTANCE EDS TORSION PRINT | colvar eds generic function bias |
| 19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Matteo Salvalaglio | GYRATION COORDINATIONNUMBER ENDPLUMED METAD RESTART DISTANCES PRINT | symfunc multicolvar setup colvar generic bias |
| 19.006 | Flying Gaussian proof | methods | flying Gaussians, alanine dipeptide | Vojtech Spiwok | TORSION PRINT METAD | colvar generic bias |
| 19.005 | Cmyc small molecule interaction | bio | metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP | Gabriella Heller | PBMETAD GYRATION MOLINFO COORDINATION DISTANCE CS2BACKBONE ALPHABETA WHOLEMOLECULES CENTER GROUP METAINFERENCE PRINT INCLUDE | multicolvar colvar vatom core generic bias isdb |
| 19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Giovanni Bussi | RANDOM_EXCHANGES DISTANCES FLUSH MOLINFO LOWER_WALLS COMBINE DISTANCE ANGLE ERMSD METAD UPPER_WALLS PRINT INCLUDE | multicolvar colvar generic function bias |
| 25.008 | Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting | methods | metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting | Dhiman Ray | MOLINFO ENDPLUMED GROUP PRINT WHOLEMOLECULES RMSD BIASVALUE PYTORCH_MODEL ENERGY OPES_METAD UPPER_WALLS DISTANCE LOWER_WALLS POSITION CUSTOM METAD UNITS TORSION | bias setup core opes function colvar generic pytorch |
| 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 | HISTOGRAM GROUP PRINT WHOLEMOLECULES COORDINATION ANGLE DISTANCE DUMPGRID CONVERT_TO_FES TORSION | gridtools generic core colvar |
| 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 PRINT METAD LOAD COMMITTOR TORSION | setup bias core 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 | RMSD OPES_EXPANDED COM COORDINATION PROJECTION_ON_AXIS CUSTOM MOLINFO WRAPAROUND WHOLEMOLECULES CONSTANT BIASVALUE MATHEVAL CONTACTMAP PRINT ECV_MULTITHERMAL ENERGY RESTART METAD OPES_METAD_EXPLORE TORSION GROUP LOWER_WALLS UPPER_WALLS INCLUDE | bias setup core opes function generic colvar vatom |
| 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 | MOLINFO RMSD PRINT DRR WHOLEMOLECULES COORDINATION PYTORCH_MODEL FLUSH LOWER_WALLS METAD UPPER_WALLS | bias drr colvar generic pytorch |
| 23.046 | Lasso Peptides - HLDA CV | bio | metadynamics, protein folding, HLDA, harmonic | Gabriel da Hora | COMBINE WHOLEMOLECULES PRINT DISTANCE METAD UNITS | setup bias function colvar generic |
| 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 CONTACTMAP PRINT UPPER_WALLS DISTANCE LOWER_WALLS ALPHARMSD PATHMSD METAD INCLUDE FUNCPATHMSD | bias secondarystructure function colvar generic |
| 23.018 | Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention | materials | metadynamics, surface binding, peptide adsorption | Kaylyn Torkelson | PRINT COM DISTANCE GYRATION UPPER_WALLS PBMETAD | generic bias vatom colvar |
| 23.008 | PBMetaD simulations of Histatin5 | bio | metadynamics, IDP, Rg, PPII | Francesco Pesce | MOLINFO GROUP WHOLEMOLECULES PRINT GYRATION PBMETAD TORSION | generic bias core colvar |
| 23.001 | Quantum phase diagram of water | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn-Løland Bore | OPES_EXPANDED PRINT ENVIRONMENTSIMILARITY UPPER_WALLS LOWER_WALLS ECV_UMBRELLAS_LINE RESTART INCLUDE | bias setup opes generic envsim |
| 22.042 | Metadynamics of NSP10 and variants | bio | metadynamics, NSP10, crystal structure, variants | Shozeb Haider | PRINT TORSION METAD | generic bias colvar |
| 22.040 | From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure | bio | SARS-CoV-2, Spike, Omicron | Miłosz Wieczór | WHOLEMOLECULES PRINT LOWER_WALLS PCAVARS METAD UPPER_WALLS | generic mapping bias |
| 22.035 | Deciphering the alphabet of disorder — Glu and Asp act differently on local but not global properties | bio | intrinsically disordered proteins, parallel bias metadynamics, protein | Kresten Lindorff-Larsen | MOLINFO WHOLEMOLECULES GYRATION PBMETAD TORSION | generic bias colvar |
| 22.027 | Molecular Dynamics simulations of BANAL-236 RBD-hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, BANAL-236, receptor-binding domain | Max Bonomi | RMSD PRINT | generic colvar |
| 22.003 | Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling | methods | opes, metadynamics, reweighting, alanine, muller | Michele Invernizzi | ENDPLUMED OPES_EXPANDED PRINT ECV_UMBRELLAS_FILE ECV_MULTITHERMAL BIASVALUE OPES_METAD ENERGY UPPER_WALLS LOWER_WALLS POSITION CUSTOM METAD UNITS PBMETAD OPES_METAD_EXPLORE TORSION | bias setup opes function colvar generic |
| 21.026 | Probing allosteric regulations with coevolution-driven molecular simulations | bio | metadynamics, coevolution, allostery, adenylate cyclase | Francesco Colizzi | WHOLEMOLECULES PRINT COM UPPER_WALLS DISTANCE PATHMSD METAD UNITS | bias setup colvar generic vatom |
| 21.022 | Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly | materials | parallel bias metadynamics, adsorption, peptide | Xin Qi | MOLINFO PRINT COM ENERGY LOWER_WALLS DISTANCE GYRATION UPPER_WALLS PBMETAD | generic bias vatom colvar |
| 21.021 | ATLAS | methods | Machine Learning, Metadynamics | Federico Giberti | GROUP PRINT DUMPATOMS WHOLEMOLECULES COORDINATION BIASVALUE MATHEVAL DISTANCE GYRATION METAD UNITS COORDINATIONNUMBER TORSION | bias setup core symfunc function colvar generic |
| 21.018 | Localized Volume-based Metadynamics | bio | LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification | Riccardo Capelli | RMSD HISTOGRAM FIXEDATOM COM COORDINATION DISTANCE FLUSH WHOLEMOLECULES READ MATHEVAL ENDPLUMED PRINT DUMPGRID METAD CONVERT_TO_FES GROUP POSITION UPPER_WALLS REWEIGHT_METAD | gridtools bias core function colvar generic vatom |
| 21.012 | NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition | bio | funnel metadynamics | Jim Pfaendtner | PRINT COM FUNNEL DISTANCE FUNNEL_PS LOWER_WALLS METAD UPPER_WALLS | bias funnel colvar generic vatom |
| 21.006 | OPES, On-the-fly Probability Enhanced Sampling Method | methods | opes, alanine dipeptide, well-tempered, multithermal, multiumbrella | Michele Invernizzi | ENDPLUMED OPES_EXPANDED PRINT ECV_MULTITHERMAL OPES_METAD ENERGY ECV_UMBRELLAS_LINE TORSION | generic opes colvar |
| 20.021 | Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins. | bio | phi-values, restrained MD, transition-state, protein folding, disordered proteins, protein evolution | Cristina Paissoni | MOLINFO WHOLEMOLECULES PRINT STATS COORDINATION RESTRAINT | generic bias colvar function |
| 19.081 | Calculation of phase diagrams in the multithermal-multibaric ensemble | methods | VES, variationally enhanced sampling, multithermal-multibaric, energy, Wang Landau, RefCV, kernel, bcc, fcc, sodium, aluminum | Pablo Piaggi | HISTOGRAM TD_WELLTEMPERED OPT_DUMMY BF_LEGENDRE VOLUME REWEIGHT_TEMP_PRESS READ MATHEVAL REWEIGHT_BIAS COMBINE PRINT ENERGY Q6 CELL DUMPGRID RESTART LOAD CONVERT_TO_FES TD_MULTITHERMAL_MULTIBARIC OPT_AVERAGED_SGD VES_LINEAR_EXPANSION LOWER_WALLS UPPER_WALLS | gridtools bias setup symfunc function ves colvar generic |
| 19.080 | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | methods | ves, variationally enhanced sampling, vibrational excitation, chemical reactions | Kristof Bal | HISTOGRAM TD_WELLTEMPERED COMBINE PRINT OPT_AVERAGED_SGD COORDINATION TD_GRID UPPER_WALLS ANGLE BF_CHEBYSHEV FLUSH DISTANCE VES_LINEAR_EXPANSION DUMPGRID EXTERNAL LOWER_WALLS UNITS CONVERT_TO_FES | gridtools bias setup function ves colvar 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 | GROUP PRINT COORDINATION UPPER_WALLS FLUSH LOWER_WALLS POSITION RESTART METAD UNITS | setup bias core colvar generic |
| 19.027 | Multithermal-multibaric simulations using VES | methods | ves, Wang Landau, multicanonical, liquid sodium, density anomaly | Pablo Piaggi | AVERAGE COMBINE HISTOGRAM PRINT TD_MULTICANONICAL OPT_AVERAGED_SGD REWEIGHT_TEMP_PRESS OPT_DUMMY READ ENERGY BF_LEGENDRE DUMPGRID VES_LINEAR_EXPANSION REWEIGHT_BIAS RESTART UNITS CONVERT_TO_FES | gridtools bias setup function ves colvar generic |
| 19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Gabriele Cesare Sosso | MFILTER_MORE ENDPLUMED LOCAL_Q6 OUTPUT_CLUSTER Q6 CONTACT_MATRIX DFSCLUSTERING CLUSTER_WITHSURFACE FLUSH CLUSTER_NATOMS COMMITTOR | symfunc adjmat multicolvar generic clusters |