Browse the eggs in PLUMED-NEST
PLUMED-NEST provides all the data needed to reproduce the results of a PLUMED-enhanced molecular dynamics simulation or analysis contained in a published paper. Furthermore, PLUMED-NEST monitors the compatibility of the provided PLUMED input files with the current and development versions of the code and integrates links from these files to the PLUMED manual.
Here is the list of projects already deposited in PLUMED-NEST, while a complete bibliography can be found here.
| plumID | Name | Category | Keywords | Contributor | Actions | Modules |
|---|---|---|---|---|---|---|
| 25.025 | Enhanced Sampling of Ligand Binding Coupled to RNA Conformational Dynamics | bio | OPES, OPES Flooding , Metadynamics, RNA, Ligand binding, Free Energy, Kinetics, Funnel | Revanth Elangovan and Dhiman Ray | GROUP WRAPAROUND CENTER FUNNEL COMMITTOR UPPER_WALLS CUSTOM METAD RMSD COORDINATION OPES_METAD TORSION WHOLEMOLECULES MATHEVAL LOWER_WALLS FUNNEL_PS COM PRINT | function colvar core bias generic vatom opes funnel |
| 25.015 | Assessment of Force Fields for Describing Conformational Polymorphic Crystals of ROY | materials | Molecular crystal, Force Field, Collective Variable | Pradip Si and Omar Valsson | TORSIONS DUMPMULTICOLVAR SMAC DISTANCES PRINT | generic symfunc multicolvar |
| 25.011 | Chiral perovskite nucleation | chemistry | metadynamics, chiral perovskites, nucleation | Adriana Pietropaolo | PBMETAD DISTANCE MULTI_RMSD RESTART MATHEVAL UNITS LOWER_WALLS UPPER_WALLS PRINT | function colvar bias generic setup |
| 25.010 | Kinetic rates calculation with Ratchet&Pawl MD | methods | kinetics, ligand binding, ABMD, ratchet&pawl MD | Riccardo Capelli | GROUP FLUSH COMMITTOR DISTANCE ABMD WHOLEMOLECULES COM PRINT | colvar core bias generic vatom |
| 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 | DISTANCE METAD MOVINGRESTRAINT RESTART PUCKERING TORSION MOLINFO RESTRAINT PRINT | generic setup bias colvar |
| 25.003 | Surrogate Model CV | methods | Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding | Sompriya Chatterjee | GROUP COMMITTOR ENDPLUMED DISTANCE CUSTOM MOLINFO OPES_METAD TORSION ENERGY PYTORCH_MODEL MATHEVAL WHOLEMOLECULES COMBINE PRINT | function colvar core generic opes pytorch |
| 24.034 | Umbrella sampling of ion in transporter SLC26A7 | bio | umbrella sampling, transporter, ions | Xiaoli Lu | UNITS RESTRAINT POSITION PRINT | generic setup bias colvar |
| 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 | DISTANCE COORDINATION OPES_METAD ENERGY UPPER_WALLS PRINT | generic opes bias colvar |
| 24.009 | Weighted Shape Gaussian Mixture Models | bio | metadynamics, clustering | Glen Hocky | GROUP METAD TORSION UNITS PRINT | colvar core bias generic setup |
| 23.038 | Determinants of Neutral Antagonism and Inverse Agonism in the β2-adrenergic receptor | bio | protein coupled receptor, beta-adrenergic, receptor activation, antagonism, inverse agonism, metadynamics | Timothy Clark | DISTANCE METAD RMSD MOLINFO MATHEVAL WHOLEMOLECULES PRINT | generic function bias colvar |
| 23.023 | Rational design of novel biomimetic sequence-defined polymers for mineralization applications | methods | metadynamics, surface binding, biomimetic mineralization | Kaylyn Torkelson | GYRATION PBMETAD DISTANCE COORDINATION UPPER_WALLS COM PRINT | vatom generic bias colvar |
| 23.022 | A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar | methods | collective variables, machine learning, toy model | Enrico Trizio | BIASVALUE ENDPLUMED CUSTOM POSITION OPES_METAD PYTORCH_MODEL UNITS LOWER_WALLS UPPER_WALLS PRINT | function colvar bias generic opes pytorch setup |
| 23.020 | FEP simulations of ATOX1 homodimer | chemistry | parallel bias metadynamics, FEP, free-energy of metal ion dissociation | Adriana Pietropaolo | ANGLE BIASVALUE PBMETAD DISTANCE MATHEVAL CONSTANT WHOLEMOLECULES PRINT | generic function bias colvar |
| 23.016 | Activation/deactivation free-energy profiles for the β2-adrenergic receptor: Ligand modes of action | bio | G protein coupled receptor, beta-adrenergic, receptor activation, partial agonism, metadynamics | Timothy Clark | DUMPGRID REWEIGHT_METAD HISTOGRAM CONVERT_TO_FES DISTANCE METAD RMSD MOLINFO READ MATHEVAL WHOLEMOLECULES PRINT | gridtools function colvar bias generic |
| 23.005 | A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs | bio | metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A | Timothy Clark | DUMPGRID REWEIGHT_METAD HISTOGRAM CONVERT_TO_FES DISTANCE METAD RMSD MOLINFO READ MATHEVAL WHOLEMOLECULES PRINT | gridtools function colvar bias generic |
| 22.044 | Colloid Crystallisation Analyses | materials | Q4, Q6, Pair Entropy, DFS | Aaron Finney | GROUP LOCAL_Q4 COORDINATIONNUMBER MFILTER_MORE MFILTER_LESS LOCAL_AVERAGE CONTACT_MATRIX Q4 Q6 DFSCLUSTERING CLUSTER_NATOMS COMBINE LOCAL_Q6 PRINT | symfunc clusters function core multicolvar generic adjmat |
| 22.029 | Angiotensin-1-7_Metadynamics | bio | Metadynamics, Angiotensin-(1-7), peptide | L.-América Chi | GROUP FLUSH GYRATION METAD COORDINATION WHOLEMOLECULES LOWER_WALLS UPPER_WALLS PRINT | generic core bias colvar |
| 22.026 | Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification | materials | Peptoid, silica | Jim Pfaendtner | GYRATION PBMETAD DISTANCE MOLINFO UPPER_WALLS COM PRINT | generic vatom bias colvar |
| 22.018 | Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations | bio | ligand binding, docking, EMMI, LAT1 | Max Bonomi | GROUP BIASVALUE LOAD MOLINFO EMMIVOX WHOLEMOLECULES PRINT | isdb core bias generic setup |
| 21.050 | N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity | methods | bio | Isabell Louise Grothaus | CENTER DISTANCE PRINT | vatom generic colvar |
| 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 | PBMETAD ENDPLUMED METAD INCLUDE TORSION RANDOM_EXCHANGES PRINT | generic bias colvar |
| 21.023 | Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling | methods | enhanced sampling, collective variables, machine learning | Jakub Rydzewski | BIASVALUE REWEIGHT_METAD DISTANCE CUSTOM METAD INCLUDE TORSION ENERGY CONSTANT UNITS PRINT | function 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 | |
| 20.032 | Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil | materials | clustering, conformational isomers | Matteo Salvalaglio | ENDPLUMED TORSION PRINT | generic colvar |
| 20.028 | Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane | bio | metadynamics, KRas-4B, anionic membrane | Huixia Lu | CENTER FIT_TO_TEMPLATE DISTANCE METAD RESTART PRINT | colvar bias vatom generic setup |
| 20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Valerio Rizzi | GROUP CENTER FIT_TO_TEMPLATE ENDPLUMED DISTANCE COORDINATION OPES_METAD PYTORCH_MODEL ENERGY WHOLEMOLECULES MATHEVAL ANGLE UPPER_WALLS FIXEDATOM PRINT | function colvar core bias vatom generic opes pytorch |
| 20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Max Bonomi | GYRATION PBMETAD DIHCOR COORDINATION MOLINFO INCLUDE WHOLEMOLECULES ALPHABETA PRINT | generic multicolvar bias colvar |
| 20.014 | amyloid beta small molecule interaction | bio | intrinsically disordered proteins, disordered proteins, IDPs, fuzzy binding, small molecule, drugs, entropy, binding, Alzheimer’s disease, amyloid beta | Gabriella Heller | PBMETAD ENSEMBLE COMBINE STATS GROUP ENDPLUMED COORDINATION ALPHARMSD METAINFERENCE PRINT FLUSH GYRATION MOLINFO INCLUDE TORSION WHOLEMOLECULES PARABETARMSD CS2BACKBONE DIHCOR ANTIBETARMSD | function isdb colvar core bias multicolvar generic secondarystructure |
| 20.006 | Class B GPCR activation mechanism | bio | metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | CENTER LOWER_WALLS DISTANCE METAD RMSD MOLINFO ENERGY MATHEVAL WHOLEMOLECULES COMBINE UPPER_WALLS PRINT | function colvar bias vatom generic |
| 19.080 | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | methods | ves, variationally enhanced sampling, vibrational excitation, chemical reactions | Kristof Bal | DUMPGRID FLUSH VES_LINEAR_EXPANSION HISTOGRAM CONVERT_TO_FES TD_GRID LOWER_WALLS DISTANCE BF_CHEBYSHEV COORDINATION TD_WELLTEMPERED UNITS ANGLE COMBINE UPPER_WALLS EXTERNAL OPT_AVERAGED_SGD PRINT | gridtools ves function colvar bias generic setup |
| 19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_LOSS MAZE_SIMULATED_ANNEALING POSITION MAZE_OPTIMIZER_BIAS UNITS PRINT | setup maze generic colvar |
| 19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | GYRATION DISTANCE METAD MOLINFO ENERGY UPPER_WALLS COM PRINT | generic vatom bias colvar |
| 19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | FLUSH DISTANCE METAD ENERGY UNITS COMBINE UPPER_WALLS PRINT | function colvar bias generic setup |
| 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 | DISTANCE METAD ENERGY UPPER_WALLS COM PRINT | vatom generic bias colvar |
| 19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Vittorio Limongelli | FUNNEL FUNNEL_PS DISTANCE METAD RMSD WHOLEMOLECULES LOWER_WALLS UPPER_WALLS COM PRINT | colvar bias generic vatom funnel |
| 19.023 | RECT | methods | metadynamics, replica exchange | Giovanni Bussi | GYRATION METAD TORSION WHOLEMOLECULES PRINT | generic bias colvar |
| 19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Matteo Salvalaglio | VOLUME ENDPLUMED METAD CELL TORSION ENERGY MATHEVAL LOWER_WALLS COMBINE UPPER_WALLS PRINT | generic function bias colvar |
| 19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Carlo Camilloni | CENTER GROUP BIASVALUE ENDPLUMED DISTANCE SAXS RMSD MOLINFO INCLUDE RESTRAINT WHOLEMOLECULES UPPER_WALLS STATS PRINT | function isdb colvar core bias vatom generic |
| 19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Carlo Camilloni | GROUP CENTER DHENERGY PBMETAD ENDPLUMED DISTANCE DIHCOR RDC MOLINFO TORSION ENSEMBLE RESTRAINT WHOLEMOLECULES ALPHABETA METAINFERENCE UPPER_WALLS STATS PRINT | function isdb colvar core bias multicolvar vatom generic |
| 19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Max Bonomi | GROUP BIASVALUE MOLINFO EMMI WHOLEMOLECULES PRINT | isdb generic core bias |
| 19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Giovanni Bussi | ANGLE FLUSH DISTANCE METAD MOLINFO INCLUDE DISTANCES ERMSD LOWER_WALLS COMBINE UPPER_WALLS RANDOM_EXCHANGES PRINT | function colvar bias multicolvar generic |
| 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 | FLUSH GROUP COORDINATION COM DISTANCE COORDINATIONNUMBER DISTANCES UPPER_WALLS METAD RESTRAINT LOWER_WALLS UNITS FIXEDATOM COMBINE ANGLE PRINT | setup symfunc function vatom bias core multicolvar colvar generic |
| 25.026 | Deciphering the Molecular Mechanisms of Startle Disease - the Role of the Asn46Lys Mutation in the Glycine Receptor | bio | metadynamics, glycine receptors, funnel metadynamics | Jacob Adam Clark | UPPER_WALLS FUNNEL FUNNEL_PS PRINT METAD LOWER_WALLS COM | generic funnel bias vatom |
| 25.021 | All You Need Is Water. Converging Ligand Binding Simulations with Hydration Collective Variables | bio | OPES Explore, ligand binding, binding free energy, water, hydration CVs, SAMPL challenge, host-guest | Valerio Rizzi | UPPER_WALLS FIT_TO_TEMPLATE ANGLE COORDINATION PRINT MATHEVAL GROUP FIXEDATOM CENTER DISTANCE OPES_METAD_EXPLORE ENERGY WHOLEMOLECULES | generic core colvar opes bias function vatom |
| 25.002 | M3_PCV-ABMD | chemistry | Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor | Gian Marco Elisi | UPPER_WALLS UNITS ENDPLUMED PRINT PATHMSD ABMD | colvar setup generic bias |
| 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 | CUSTOM UNITS UPPER_WALLS RESTART COMMITTOR COORDINATION PRINT GROUP LOWER_WALLS DISTANCE OPES_METAD | setup generic core colvar opes bias function |
| 24.032 | DeepLNE++ | methods | PATHCV, OPES | Thorben Fröhlking | CUSTOM LOAD COMBINE COORDINATION PRINT GROUP DISTANCE OPES_METAD TORSION ENERGY | setup generic core colvar opes function |
| 24.016 | Cryo-EM guided simulations of ribozyme | bio | metainference, cryo-EM | Giovanni Bussi | INCLUDE RESTRAINT PRINT EMMIVOX GROUP MOLINFO BIASVALUE WHOLEMOLECULES ERMSD | isdb generic core colvar bias |
| 24.005 | Learning Markovian Dynamics with Spectral Maps | methods | spectral map, collective variables, machine learning | Jakub Rydzewski | CUSTOM UNITS PRINT DISTANCE BIASVALUE | setup generic colvar bias function |
| 23.040 | Supramolecular capsules assembly dynamics | chemistry | Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics | Riccardo Capelli | CUSTOM UNITS POSITION FLUSH DISTANCES PRINT METAD GROUP DISTANCE CENTER COM WHOLEMOLECULES | setup multicolvar generic core colvar bias function vatom |
| 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 CONSTANT PRINT METAD MATHEVAL LOWER_WALLS DISTANCE CENTER BIASVALUE WHOLEMOLECULES | generic colvar bias function vatom |
| 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 | UPPER_WALLS CONTACTMAP PRINT METAD LOWER_WALLS ENERGY WHOLEMOLECULES | colvar generic bias |
| 22.042 | Metadynamics of NSP10 and variants | bio | metadynamics, NSP10, crystal structure, variants | Shozeb Haider | METAD TORSION PRINT | colvar generic bias |
| 22.030 | Mixing physics across temperatures with generative artificial intelligence | methods | REMD, Generative AI, DDPM | Yihang Wang | TORSION WHOLEMOLECULES PRINT | colvar generic |
| 22.024 | Conformational Entropy as a Potential Liability of Computationally Designed Antibodies | bio | metadynamics, conformational entropy, antibody, nanobody | Thomas Löhr | COM ANTIBETARMSD RESTART PRINT ALPHARMSD MOLINFO PBMETAD TORSION ALPHABETA WHOLEMOLECULES | setup multicolvar secondarystructure generic colvar bias vatom |
| 22.023 | Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy | bio | CryoEM, MEMMI,EMMI, Metadynamics, Metainference, IAPP, structural ensemble | Faidon Brotzakis | UPPER_WALLS COM RESTART COORDINATION RMSD PRINT GROUP MOLINFO BIASVALUE PBMETAD TORSION WHOLEMOLECULES EMMI | setup isdb generic core colvar bias vatom |
| 22.004 | Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques | chemistry | reaction discovery, OPES, collective variables | Umberto Raucci | CUSTOM UNITS UPPER_WALLS LOAD COORDINATION PRINT MATHEVAL PYTORCH_MODEL GROUP LOWER_WALLS DISTANCE COM OPES_METAD_EXPLORE OPES_METAD | setup pytorch generic core colvar opes bias function vatom |
| 21.049 | Multiple-path-metadynamics and PathMaps | methods | path-CV, metadynamics, multiple-walker, multiple paths, pathmap | Alberto Pérez-de-Alba-Ortíz | UPPER_WALLS UNITS CUSTOM LOAD COMBINE CONSTANT RESTRAINT PRINT METAD MOVINGRESTRAINT ENSEMBLE LOWER_WALLS TORSION | setup generic colvar bias function |
| 21.039 | Deep learning the slow modes for rare events sampling | methods | collective variables, machine learning, slow modes, deep-tica, opes | Luigi Bonati | ENDPLUMED Q6 LOAD GROUP DISTANCE VOLUME UNITS FLUSH ECV_MULTITHERMAL RMSD COMBINE PYTORCH_MODEL TORSION ENERGY ENVIRONMENTSIMILARITY INCLUDE CONTACTMAP PRINT OPES_EXPANDED MOLINFO OPES_METAD WHOLEMOLECULES | setup symfunc envsim pytorch generic core colvar opes function |
| 21.027 | EGFR activating mutations mechanism | bio | metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA | Francesco Gervasio | UPPER_WALLS CONTACTMAP INCLUDE PRINT MATHEVAL METAD ALPHARMSD MOLINFO LOWER_WALLS DISTANCE ENERGY WHOLEMOLECULES | secondarystructure generic colvar bias function |
| 21.020 | Reweighted Jarzynski sampling | methods | free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions | Kristof Bal | LOAD VES_LINEAR_EXPANSION RESTRAINT MOVINGRESTRAINT BIASVALUE DISTANCE UPPER_WALLS UNITS FLUSH COMBINE CONSTANT BF_CHEBYSHEV DUMPGRID REWEIGHT_METAD COORDINATIONNUMBER OPT_AVERAGED_SGD CONVERT_TO_FES REWEIGHT_BIAS ANN CUSTOM TD_WELLTEMPERED HISTOGRAM PRINT METAD OPES_METAD | setup ves symfunc gridtools annfunc generic colvar opes bias function |
| 21.018 | Localized Volume-based Metadynamics | bio | LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification | Riccardo Capelli | ENDPLUMED GROUP DISTANCE UPPER_WALLS POSITION FLUSH RMSD DUMPGRID FIXEDATOM COORDINATION MATHEVAL REWEIGHT_METAD CONVERT_TO_FES HISTOGRAM READ PRINT METAD COM WHOLEMOLECULES | gridtools generic core colvar bias function vatom |
| 21.012 | NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition | bio | funnel metadynamics | Jim Pfaendtner | UPPER_WALLS FUNNEL FUNNEL_PS PRINT METAD LOWER_WALLS DISTANCE COM | funnel generic colvar bias vatom |
| 20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Adriana Pietropaolo | COORDINATION PRINT CENTER PBMETAD WHOLEMOLECULES | colvar generic bias vatom |
| 20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Cristina Paissoni | STATS INCLUDE RESTRAINT PRINT ENSEMBLE MOLINFO GROUP CENTER DISTANCE BIASVALUE SAXS WHOLEMOLECULES | isdb generic core colvar bias function vatom |
| 20.018 | Free energy barriers from biased molecular dynamics simulations | methods | kinetics, free energy barriers, chemical reactions, nucleation, metadynamics | Kristof Bal | Q6 LOAD DISTANCE CONTACT_MATRIX VOLUME UPPER_WALLS UNITS FLUSH COMBINE LOCAL_AVERAGE DUMPGRID ENERGY DENSITY PAIRENTROPY COORDINATION REWEIGHT_METAD COORDINATIONNUMBER CONVERT_TO_FES REWEIGHT_BIAS HISTOGRAM SPRINT PRINT METAD LOWER_WALLS CENTER | setup adjmat symfunc sprint gridtools generic volumes colvar bias function vatom |
| 20.015 | Rational design of ASCT2 inhibitors using an integrated experimental-computational approach | bio | ASCT2 transporter, small-molecules, cryo-EM, metainference | Max Bonomi | DUMPATOMS LOAD PRINT EMMIVOX MOLINFO GROUP BIASVALUE WHOLEMOLECULES | setup isdb generic core bias |
| 20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Pratyush Tiwary | UPPER_WALLS RESTART COMBINE RMSD PRINT METAD MOLINFO DISTANCE TORSION WHOLEMOLECULES | setup generic colvar bias function |
| 20.001 | Conformational stability and dynamics in solution and in crystals report similarly on unfolding and aggregation propensity of amyloidogenic proteins | bio | metainference, metadynamics, NMR, protein dynamics, b2m, protein crystals | Carlo Camilloni | UPPER_WALLS ENDPLUMED ANTIBETARMSD FLUSH PRINT GROUP MOLINFO LOWER_WALLS BIASVALUE PBMETAD CS2BACKBONE ALPHABETA WHOLEMOLECULES | multicolvar secondarystructure isdb generic core bias |
| 19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Giovanni Bussi | ENDPLUMED RESTRAINT COORDINATION LOWER_WALLS DISTANCE WHOLEMOLECULES | colvar generic bias |
| 19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Kim Jelfs | RESTART FLUSH DISTANCES PRINT MOVINGRESTRAINT COM INPLANEDISTANCES | setup multicolvar generic bias vatom |
| 19.050 | Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes | chemistry | metadynamics, membranes, Willard Chandler surface | Gareth Tribello | UPPER_WALLS REWEIGHT_BIAS HISTOGRAM READ RESTART COMBINE PRINT METAD CONVERT_TO_FES DISTANCE_FROM_CONTOUR DUMPGRID | setup gridtools generic contour bias function |
| 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 | UPPER_WALLS UNITS RESTART POSITION FLUSH COORDINATION PRINT METAD GROUP LOWER_WALLS | setup generic core colvar bias |
| 19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Davide Provasi | ENDPLUMED CONTACTMAP RMSD PRINT METAD FUNCPATHMSD DISTANCE COM WHOLEMOLECULES | generic colvar bias function vatom |
| 19.032 | Chemical reaction in solution using path collective variables based on coordination patterns | chemistry | chemical reactions, solutions, metadynamics, coordination patterns | Fabio Pietrucci | UPPER_WALLS RESTART PATH FLUSH DISTANCES PRINT METAD | setup multicolvar mapping generic bias |
| 19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Kresten Lindorff-Larsen | FLUSH COMMITTOR COMBINE PRINT METAD MOLINFO ALPHABETA | multicolvar generic bias function |
| 19.011 | Automatic Gradient Computation for Collective Variables | other | gradient, differentiation, curvature | Toni Giorgino | ENDPLUMED | generic |
| 19.004 | MI Ubiquitin | bio | metainference, NMR | Max Bonomi | RDC PRINT MOLINFO GROUP METAINFERENCE CS2BACKBONE WHOLEMOLECULES | generic isdb core |
| 25.028 | Designing transferable transition state guided collective variable via interpretable machine learning model for enhanced sampling. A case study on polymer collapse transition | bio | metadynamics, polymer collapse transition, transferable CV,interpretable ML-model | Saikat Dhibar and Biman Jana | COMBINE METAD COORDINATION GYRATION GROUP CENTER WHOLEMOLECULES LOWER_WALLS DISTANCE MATHEVAL UPPER_WALLS PRINT | colvar bias vatom core generic function |
| 25.018 | Metainference simulation for dimerization of RNA binding protein | bio | Metainference, Metadynamics, SAXS, protein dimer | Debadutta Patra | STATS ENSEMBLE PBMETAD GYRATION CENTER WHOLEMOLECULES TORSION DISTANCE SAXS METAINFERENCE UPPER_WALLS FLUSH PRINT MOLINFO | colvar bias vatom generic function isdb |
| 24.025 | Correlating Enzymatic Reactivity for Different Substrates using Transferable Data-Driven Collective Variables | bio | enzymatic reactivity, k_cat, transfer learning, data-driven CVs, catalysis, ligand-binding modes, water, alpha-amylase, sugar, classical MD, OPES, machine learning, Deep TDA CV, path CV | Sudip Das | RESTART GROUP COORDINATION TORSION WHOLEMOLECULES CENTER DISTANCE CUSTOM FIT_TO_TEMPLATE LOWER_WALLS PATH PYTORCH_MODEL UPPER_WALLS PRINT FIXEDATOM OPES_METAD | colvar bias vatom core generic opes setup function mapping pytorch |
| 23.045 | Minute-timescale simulations of G Protein Coupled Receptor A2A activation mechanism reveal a receptor pseudo-active state | bio | Path CVs Metadynamics, GPCRs activation transition | Vittorio Limongelli | ALPHARMSD METAD CONTACTMAP LOWER_WALLS DISTANCE FUNCPATHMSD INCLUDE PATHMSD UPPER_WALLS PRINT MOLINFO | colvar bias function generic secondarystructure |
| 23.036 | Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? | bio | NaCl, nucleation, metadynamics | Ruiyu Wang | ENERGY COMBINE METAD VOLUME COORDINATIONNUMBER Q6 MATHEVAL Q4 PRINT | colvar bias generic symfunc function |
| 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 | BIASVALUE ERMSD COMBINE METAD GHBFIX COORDINATION WHOLEMOLECULES PRINT MOLINFO | generic function colvar 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 | COORDINATION WHOLEMOLECULES CUSTOM BIASVALUE COMMITTOR POSITION OPES_METAD_EXPLORE TORSION MATHEVAL FLUSH PRINT MOLINFO COM ENERGY WRAPAROUND GROUP CENTER LOWER_WALLS FIT_TO_TEMPLATE UPPER_WALLS UNITS DISTANCE ENDPLUMED OPES_METAD | colvar bias vatom generic core opes setup 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 | CONSTANT BIASVALUE METAD WHOLEMOLECULES LOWER_WALLS DISTANCE MATHEVAL UPPER_WALLS PRINT | generic function colvar bias |
| 23.004 | Melting curves of ice polymorphs in the vicinity of the liquid-liquid critical point | chemistry | water, liquid-liquid transition, second critical point, ice, polymorphs, melting curves, environment similarity, opes, density-functional theory, scan, machine learning potential | Pablo Piaggi | DUMPGRID OPES_EXPANDED RESTART HISTOGRAM LOWER_WALLS ECV_UMBRELLAS_LINE UPPER_WALLS ENVIRONMENTSIMILARITY PRINT | envsim bias generic opes setup gridtools |
| 22.043 | Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES | bio | OPES, RNA, Tetraloop, Folding | Gül Zerze | OPES_EXPANDED ENERGY CONTACTMAP ECV_MULTITHERMAL WHOLEMOLECULES ECV_UMBRELLAS_LINE PRINT | generic colvar opes |
| 22.036 | Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction | bio | Well-tempered MetaDynamics with Hamiltonian Replica Exchange | Miroslav Krepl | BIASVALUE COMBINE METAD GHBFIX GROUP COORDINATION CUSTOM LOAD UPPER_WALLS FLUSH PRINT MOLINFO | colvar bias core generic setup function |
| 22.034 | Rationalising the difference in crystallisability of two Sulflowers using efficient in silico methods | materials | metadynamics, crystallizability, crystal structure prediction, sulflower, persulforated coronene | Matteo Salvalaglio | COMMITTOR CELL METAD LOWER_WALLS CUSTOM MATHEVAL UPPER_WALLS DRMSD PRINT | generic function colvar bias |
| 22.028 | N-glycan conformer distributions in atomistic simulation | bio | REST2, RECT, N-glycan, pucker | Isabell Grothaus | DUMPGRID METAD READ TORSION HISTOGRAM CONVERT_TO_FES PUCKERING PRINT MOLINFO | generic gridtools colvar bias |
| 22.027 | Molecular Dynamics simulations of BANAL-236 RBD-hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, BANAL-236, receptor-binding domain | Max Bonomi | PRINT RMSD | generic colvar |
| 22.019 | Exploring aspartic protease inhibitor binding to design selective antimalarials | bio | ligand binding, loop opening, path CV, funnel metadynamics, drug development | Raitis Bobrovs | COM FUNNEL METAD WHOLEMOLECULES LOWER_WALLS DISTANCE PATHMSD FUNNEL_PS UPPER_WALLS PRINT | colvar bias vatom generic funnel |
| 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 | PRINT METAD WHOLEMOLECULES LOAD | setup generic bias |
| 22.003 | Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling | methods | opes, metadynamics, reweighting, alanine, muller | Michele Invernizzi | BIASVALUE OPES_EXPANDED ENERGY METAD OPES_METAD_EXPLORE PBMETAD POSITION ECV_MULTITHERMAL UNITS TORSION LOWER_WALLS ECV_UMBRELLAS_FILE ENDPLUMED CUSTOM UPPER_WALLS PRINT OPES_METAD | colvar bias generic opes setup function |
| 22.000 | Amyloid precursor protein processing by human γ-secretase | bio | Bias Exchange Metadynamics, Helix unfolding, coupled binding | Xiaoli Lu | ALPHARMSD METAD CONTACTMAP COORDINATION UNITS CENTER DISTANCE INCLUDE RANDOM_EXCHANGES PRINT MOLINFO ANTIBETARMSD | colvar bias vatom generic setup secondarystructure |
| 21.044 | NaCl nucleation | chemistry | metadynamics, DFS clustering | Aaron Finney | DUMPGRID CLUSTER_DISTRIBUTION MFILTER_MORE COMBINE METAD DFSCLUSTERING GROUP HISTOGRAM COORDINATIONNUMBER CLUSTER_NATOMS Q6 LOCAL_Q6 INSPHERE PRINT FIXEDATOM CONTACT_MATRIX | bias vatom function volumes adjmat core clusters generic symfunc multicolvar gridtools |
| 21.037 | Molecular Dynamics simulations of RBD/hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain | Max Bonomi | DISTANCE PRINT RMSD | generic colvar |
| 21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Kresten Lindorff-Larsen | BIASVALUE ALPHARMSD EEFSOLV PBMETAD GROUP GYRATION WHOLEMOLECULES CENTER SAXS METAINFERENCE FLUSH PRINT MOLINFO | colvar bias vatom core generic secondarystructure isdb |
| 21.002 | Phase equilibrium of water with hexagonal and cubic ice using the SCAN functional | materials | ice, water, SCAN, OPES, VES, multithermal, crystallization, environment similarity, refcv, reweighting | Pablo Piaggi | OPES_EXPANDED ENERGY OPT_AVERAGED_SGD RESTART ECV_MULTITHERMAL_MULTIBARIC BF_LEGENDRE VOLUME Q6 ECV_UMBRELLAS_LINE MATHEVAL VES_LINEAR_EXPANSION UPPER_WALLS ENVIRONMENTSIMILARITY PRINT TD_UNIFORM | envsim colvar bias ves generic opes setup symfunc function |
| 20.012 | Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies | bio | metadynamics, well-tempered ensemble, ligand binding, binding affinity calculations, novel COLVAR, funnel restraints, Hamiltonian replica-exchange, PathCV, COMetPath, SWISH | Francesco Gervasio | CONSTANT BIASVALUE COM METAD CONTACTMAP GROUP WHOLEMOLECULES LOWER_WALLS DISTANCE PROJECTION_ON_AXIS INCLUDE MATHEVAL LOAD UPPER_WALLS FUNCPATHGENERAL PRINT MOLINFO | colvar bias vatom generic core setup function |
| 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 | TD_WELLTEMPERED OPT_AVERAGED_SGD RESTART BF_LEGENDRE VOLUME ENVIRONMENTSIMILARITY Q6 MATHEVAL VES_LINEAR_EXPANSION UPPER_WALLS OPT_DUMMY PRINT | envsim colvar bias ves generic setup symfunc function |
| 20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Luigi Bonati | COM GROUP UNITS TORSION LOWER_WALLS DISTANCE MATHEVAL LOAD PYTORCH_MODEL UPPER_WALLS PRINT FLUSH ENDPLUMED OPES_METAD | colvar bias vatom core generic opes setup function pytorch |
| 19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Valerio Rizzi | COMBINE METAD RESTART GROUP DISTANCES UNITS COORDINATIONNUMBER UPPER_WALLS PRINT FLUSH ENDPLUMED | bias core generic setup symfunc multicolvar function |
| 19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | COM ENERGY METAD GYRATION DISTANCE UPPER_WALLS PRINT MOLINFO | generic colvar bias vatom |
| 19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Matteo Salvalaglio | BIASVALUE DUMPGRID COMMITTOR REWEIGHT_METAD METAD EXTERNAL READ TORSION HISTOGRAM CONVERT_TO_FES DISTANCE MATHEVAL REWEIGHT_BIAS PRINT | colvar bias function generic gridtools |
| 19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Wei Chen | COM COMBINE POSITION ANN RESTRAINT | colvar bias vatom function annfunc |
| 19.040 | Optimal Metric for Path Collective Variables | bio | metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path | Francesco Luigi Gervasio | METAD TORSION ENDPLUMED MATHEVAL PRINT | generic function colvar bias |
| 19.030 | Coarse-Grained MetaDynamics (CG-MetaD) | bio | Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy | Vittorio Limongelli | COM METAD WHOLEMOLECULES LOWER_WALLS DISTANCE UPPER_WALLS PRINT | generic colvar bias vatom |
| 19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Pratyush Tiwary | COM COMBINE COMMITTOR EXTERNAL RESTART WHOLEMOLECULES TORSION DISTANCE ALPHABETA PRINT | colvar bias vatom generic setup multicolvar function |
| 25.022 | Imidazole Diffusion in SALEM-2 MOF | materials | OPES, Diffusion, Ring opening, MOFs, Machine Learning Potentials | Sudheesh Kumar Ethirajan | OPES_METAD MOLINFO PRINT CENTER DISTANCE DISTANCES GROUP WHOLEMOLECULES PROJECTION_ON_AXIS ENDPLUMED UNITS | vatom multicolvar setup generic opes colvar core |
| 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 | OPES_METAD DISTANCE PRINT TORSION POSITION INCLUDE FLUSH LOAD CELL MATHEVAL COORDINATION COMBINE ENERGY CUSTOM BIASVALUE UNITS | bias setup generic opes colvar function |
| 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 | MOLINFO PRINT CENTER DUMPATOMS DISTANCE TORSION RESTART INCLUDE UPDATE_IF GYRATION WHOLEMOLECULES VOLUME READ ENERGY PBMETAD | vatom bias setup generic colvar |
| 25.001 | RNA G-quadruplex folding with ST-metaD protocol | bio | RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | MOLINFO WHOLEMOLECULES METAD ERMSD COMBINE | colvar function bias 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 | MOLINFO PRINT CENTER DISTANCE UPPER_WALLS GHBFIX GROUP LOWER_WALLS METAD DEBUG COORDINATION COM COMBINE BIASVALUE | vatom bias generic colvar function core |
| 24.007 | SWISH-X | bio | swish-x, SWISH-X, swish, expanded SWISH | Alberto Borsatto | MOLINFO PRINT ECV_MULTITHERMAL UPPER_WALLS OPES_EXPANDED INCLUDE WHOLEMOLECULES ENERGY CONTACTMAP | colvar opes bias generic |
| 24.004 | Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables | materials | metadynamics, nucleation, machine learning | Ziyue Zou | PRINT RESTART INCLUDE GROUP METAD LOAD | core bias generic setup |
| 24.003 | Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations | chemistry | steered molecular dynamics, foldamers, peptoids, bio-inspired | Kaylyn Torkelson | DISTANCE PRINT TORSION INCLUDE ALPHABETA GYRATION WHOLEMOLECULES COM COORDINATION MOVINGRESTRAINT | vatom multicolvar bias generic colvar |
| 24.000 | Ammonia Decomposition on Non-stoichiometric Lithium Imide | chemistry | ammonia decomposition, non-stoichiometric lithium imide, machine learning interatomic potentials, enhanced sampling, heterogeneous catalysis | Francesco Mambretti | OPES_METAD DISTANCE PRINT UPPER_WALLS GROUP FLUSH ZDISTANCES COORDINATIONNUMBER FIXEDATOM UNITS | vatom multicolvar symfunc bias setup generic opes colvar core |
| 23.015 | MPCs aggregation | bio | opes_explore, dimerization, MPCs, self-assembly | Vikas Tiwari | DISTANCE PRINT CENTER UPPER_WALLS LOWER_WALLS GROUP WHOLEMOLECULES METAD COORDINATION COM OPES_METAD_EXPLORE CUSTOM | vatom bias generic opes colvar function core |
| 22.037 | Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site | chemistry | metadynamics, DNA, abasic | Mike Jones | DISTANCE PRINT METAD DISTANCES | multicolvar colvar bias generic |
| 22.025 | Bubble nucleation rate predictions in a Lennard-Jones fluid | materials | free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation | Kristof Bal | PRINT UPPER_WALLS COMMITTOR RESTRAINT FLUSH HISTOGRAM LOAD VOLUME DUMPGRID ANN REWEIGHT_BIAS MOVINGRESTRAINT CUSTOM COORDINATIONNUMBER CONVERT_TO_FES BIASVALUE UNITS | gridtools annfunc bias setup generic colvar function symfunc |
| 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 |
| 22.007 | 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 | MOLINFO PRINT DISTANCE TORSION UPPER_WALLS FLUSH ALPHABETA WHOLEMOLECULES METAD COORDINATION ALPHARMSD ANGLE | secondarystructure multicolvar bias generic colvar |
| 22.002 | GAMBES_SAMPL5_RATES | other | GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding | Jayashrita Debnath | DISTANCE PRINT CENTER UPPER_WALLS COMMITTOR GROUP FLUSH FIT_TO_TEMPLATE WHOLEMOLECULES LOAD MATHEVAL COORDINATION PYTORCH_MODEL ENDPLUMED ENERGY FIXEDATOM ANGLE | pytorch vatom bias setup generic colvar function core |
| 21.031 | Photo-switchable sulfonulureas in KATP channel | bio | metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels | Katarzyna Walczewska-Szewc | DISTANCE PRINT UPPER_WALLS LOWER_WALLS WHOLEMOLECULES METAD COM UNITS | vatom bias setup generic colvar |
| 21.029 | Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs | bio | metadynamics, small peptide, machine learning | Pratyush Tiwary | MOLINFO PRINT TORSION RESTART FLUSH EXTERNAL ENERGY | colvar bias generic setup |
| 21.028 | From Enhanced Sampling to Reaction Profiles | methods | collective variables, multi-state, machine learning, Deep-TDA | Enrico Trizio | MATHEVAL COORDINATION FIXEDATOM DISTANCE TORSION WHOLEMOLECULES LOWER_WALLS FIT_TO_TEMPLATE ENDPLUMED LOAD OPES_METAD PRINT CENTER UPPER_WALLS DISTANCES GROUP PYTORCH_MODEL ANGLE UNITS | pytorch vatom multicolvar bias setup generic opes colvar function core |
| 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 DISTANCE UPPER_WALLS LOWER_WALLS GYRATION COM ENERGY PBMETAD | colvar bias vatom 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 | PRINT CENTER RESTART POSITION RESTRAINT WHOLEMOLECULES METAD MATHEVAL COORDINATION REWEIGHT_BIAS | vatom bias setup generic colvar function |
| 20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Vojtech Spiwok | PRINT METAD TORSION | colvar bias generic |
| 20.021 | Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins. | bio | phi-values, restrained MD, transition-state, protein folding, disordered proteins, protein evolution | Cristina Paissoni | MOLINFO PRINT WHOLEMOLECULES COORDINATION STATS RESTRAINT | colvar function bias generic |
| 20.016 | Predicting polymorphism in molecular crystals using orientational entropy | materials | metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy | Pablo Piaggi | PRINT CENTER UPPER_WALLS GROUP INCLUDE METAD VOLUME LOAD | vatom bias setup generic colvar core |
| 20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Carlo Camilloni | ENSEMBLE MOLINFO PRINT CENTER DISTANCE TORSION METAINFERENCE FLUSH ALPHABETA WHOLEMOLECULES GYRATION STATS SAXS PBMETAD | vatom multicolvar bias generic isdb colvar function |
| 19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Valerio Rizzi | PRINT RESTART GROUP FLUSH EXTERNAL METAD COMBINE ENDPLUMED COORDINATIONNUMBER UNITS | symfunc bias setup generic function core |
| 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 | PRINT DISTANCES LOWER_WALLS UPPER_WALLS METAD GYRATION ENDPLUMED ENERGY COORDINATIONNUMBER | multicolvar bias generic colvar symfunc |
| 19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Matteo Salvalaglio | DISTANCE PRINT CENTER GROUP INCLUDE ENDPLUMED | colvar vatom generic core |
| 19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Cristina Paissoni | ENSEMBLE MOLINFO PRINT CENTER GROUP INCLUDE ANGLE ALPHABETA WHOLEMOLECULES MATHEVAL COORDINATION STATS COMBINE SAXS ENDPLUMED PBMETAD BIASVALUE | vatom multicolvar bias generic isdb colvar function core |
| 19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Gareth Tribello | PRINT UPPER_WALLS LOWER_WALLS METAD CELL AROUND FCCUBIC ENDPLUMED UNITS | bias setup volumes generic colvar symfunc |
| 19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Elena Papaleo | MOLINFO PRINT UPPER_WALLS LOWER_WALLS GROUP ALPHABETA WHOLEMOLECULES GYRATION METAD | multicolvar bias generic colvar core |
| 19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Glen Hocky | DISTANCE PRINT TORSION COMBINE EDS RESTRAINT | eds bias generic colvar function |
| 19.005 | Cmyc small molecule interaction | bio | metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP | Gabriella Heller | MOLINFO PRINT DISTANCE CENTER CS2BACKBONE GROUP INCLUDE METAINFERENCE ALPHABETA WHOLEMOLECULES GYRATION COORDINATION PBMETAD | vatom multicolvar bias generic isdb colvar core |
| 19.003 | EMMI ClpP | bio | metainference, cryo-EM | Max Bonomi | MOLINFO PRINT GROUP EMMI BIASVALUE | isdb bias generic core |
| 19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Max Bonomi | MOLINFO PRINT GROUP EMMI BIASVALUE | isdb bias generic core |
| 25.027 | Enhanced-sampling MD simulations of a protein-peptide complex integrating SAXS and XL-MS experimental information | bio | steered MD, metadynamics, SAXS, XL-MS, ensemble reconstruction | Mattia Bernetti | GYRATION DISTANCE MOLINFO CENTER WHOLEMOLECULES METAD GROUP PRINT SAXS UPPER_WALLS INCLUDE MOVINGRESTRAINT | bias vatom colvar isdb core generic |
| 25.020 | Revealing Water-Mediated Activation Mechanisms in the Beta 1-Adrenergic Receptor via OneOPES-Enhanced Free Energy Landscapes | bio | OneOPES, GPCR, ADRB1, activation, microswitches, conformational changes, allostery | Valerio Rizzi | LOWER_WALLS ENERGY OPES_METAD_EXPLORE COORDINATION DISTANCE GHOST CENTER RMSD OPES_EXPANDED GROUP PRINT UPPER_WALLS PATHMSD CUSTOM DISTANCES ECV_MULTITHERMAL | bias vatom colvar opes function core multicolvar generic |
| 25.014 | Atomic resolution ensembles of intrinsically disordered proteins with Alphafold | bio | bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement | Vincent Schnapka | GROUP BAIES BIASVALUE PRINT | core bias isdb generic |
| 25.013 | Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices | bio | umbrella sampling, temperature ramping | Alexander Berlaga | GYRATION PYTORCH_MODEL DISTANCE PRINT RESTRAINT | bias colvar pytorch generic |
| 24.022 | Integrating Path Sampling with Enhanced Sampling for Rare-event Kinetics | methods | OPES Flooding, Weighted Ensemble, Metadynamics, Kinetics, Infrequent Metadynamics, Integrated Sampling | Dhiman Ray | ENDPLUMED ANGLE DISTANCE MATHEVAL METAD CENTER OPES_METAD PRINT CONTACTMAP FIT_TO_TEMPLATE MOLINFO GROUP TORSION FIXEDATOM COORDINATION RMSD WHOLEMOLECULES COMMITTOR UPPER_WALLS COMBINE CUSTOM | bias vatom colvar opes function core generic |
| 24.011 | Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble | methods | committor, machine learning | Peilin Kang | LOWER_WALLS ENDPLUMED DISTANCE MATHEVAL INCLUDE ENERGY PRINT CELL BIASVALUE MOLINFO GROUP UNITS POSITION LOAD TORSION COORDINATION RMSD WHOLEMOLECULES UPPER_WALLS CUSTOM | bias colvar setup function core generic |
| 24.001 | A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations | bio | OPES, OPES-Flooding, QM/MM, Kinetics, Enzyme Catalysis | Dhiman Ray | LOWER_WALLS FLUSH DISTANCE OPES_METAD COMMITTOR UNITS PRINT UPPER_WALLS COMBINE CUSTOM TORSION | bias colvar opes setup function generic |
| 23.039 | Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation | chemistry | metadynamics, ligand dissociation | Eric Beyerle | DISTANCE MOLINFO CENTER METAD PRINT UPPER_WALLS COMBINE DUMPMASSCHARGE RESTRAINT FIXEDATOM | bias vatom colvar function generic |
| 23.037 | Estimating binding free energy of solid binding peptides without extensive sampling | bio | metadynamics, solid binding peptides | Xin Qi | LOWER_WALLS GYRATION DISTANCE MOLINFO PRINT UPPER_WALLS PBMETAD COM | colvar bias vatom generic |
| 23.032 | Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics | bio | metadynamics, tSNE, neural network, machine learning, trp-cage, folding | Vojtech Spiwok | FIT_TO_TEMPLATE ALPHARMSD MOLINFO WHOLEMOLECULES METAD PRINT ANN POSITION COMBINE | bias secondarystructure annfunc colvar function generic |
| 23.027 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, DFS, Q3, Pair Entropy | Aaron Finney | HISTOGRAM LOCAL_Q3 CLUSTER_NATOMS GROUP UNITS PRINT DENSITY DFSCLUSTERING CONTACT_MATRIX LOAD RESTRAINT COORDINATIONNUMBER CLUSTER_DISTRIBUTION LOCAL_AVERAGE FIXEDATOM AROUND Q3 DUMPGRID | symfunc bias vatom clusters adjmat volumes setup core gridtools 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 | SKETCHMAP LANDMARK_SELECT_FPS DISTANCE DISSIMILARITIES WHOLEMOLECULES METAD PRINT COLLECT_FRAMES UPPER_WALLS PATHMSD TRANSPOSE CUSTOM SKETCHMAP_PROJECTION VSTACK COM VORONOI | landmarks bias vatom valtools matrixtools colvar function dimred generic |
| 23.018 | Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention | materials | metadynamics, surface binding, peptide adsorption | Kaylyn Torkelson | GYRATION DISTANCE PRINT UPPER_WALLS PBMETAD COM | colvar bias vatom generic |
| 23.014 | Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 | bio | metadynamics, oligomerization, chemokine receptors, GPCR, membrane | Vittorio Limongelli | FLUSH DISTANCE WHOLEMOLECULES METAD PRINT UPPER_WALLS COMBINE TORSION COM | bias vatom colvar function generic |
| 23.007 | Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains | bio | metadynamics, peptoids, parallel-bias metadynamics | Jim Pfaendtner | GYRATION COORDINATION WHOLEMOLECULES PRINT INCLUDE TORSION RESTRAINT PBMETAD COM | colvar bias vatom generic |
| 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 | METAD PRINT EXTRACV TORSION READ | colvar bias generic |
| 22.045 | Binding mode and mechanism of enzymatic polyethylene terephthalate degradation | bio | metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation | Francesco Colizzi | LOWER_WALLS ANGLE DISTANCE WHOLEMOLECULES METAD PRINT UPPER_WALLS COM MOVINGRESTRAINT | colvar bias vatom generic |
| 22.041 | Skipping the Replica Exchange Ladder with Normalizing Flows | methods | OPES, alanine, normalizing flows, replica exchange | Michele Invernizzi | ENERGY ENDPLUMED OPES_EXPANDED OPES_METAD PRINT UNITS POSITION TORSION ECV_MULTITHERMAL | colvar opes setup generic |
| 22.035 | Deciphering the alphabet of disorder — Glu and Asp act differently on local but not global properties | bio | intrinsically disordered proteins, parallel bias metadynamics, protein | Kresten Lindorff-Larsen | GYRATION MOLINFO WHOLEMOLECULES TORSION PBMETAD | colvar bias generic |
| 22.032 | Reciprocal barrier restraint. Application to path-meta-eABF | methods | restraint, upper wall, lower wall, path colvar, meta-eABF, metadynamics, DRR, protein conformational transition, PROTAC | Istvan Kolossvary | DRR FLUSH METAD PRINT PATHMSD CUSTOM BIASVALUE | bias colvar drr function generic |
| 22.016 | Homogeneous ice nucleation in an ab initio machine learning model of water | chemistry | ice, water, nucleation, seeding, environment similarity, interfacial free energy, interfaces | Pablo Piaggi | ENERGY HISTOGRAM OPES_METAD PRINT UPPER_WALLS VOLUME CUSTOM DUMPGRID ENVIRONMENTSIMILARITY AROUND RESTART | bias colvar opes envsim volumes setup function gridtools generic |
| 21.052 | On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets | materials | Ibuprofen, unbinding, WTmetaD | Matteo Salvalaglio | ENDPLUMED DISTANCE CENTER METAD COMMITTOR PRINT TORSION COORDINATIONNUMBER | symfunc bias vatom colvar generic |
| 21.041 | Nucleating a Different Coordination in a Crystal under Pressure. A Study of the B1−B2 Transition in NaCl by Metadynamics | methods | metadynamics, structural phase transitions, pressure-induced phase transition, martensitic transitions | Matej Badin | ENDPLUMED COORDINATION METAD PRINT VOLUME CUSTOM COMBINE | colvar 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 | LOWER_WALLS ANTIBETARMSD ENERGY GYRATION ALPHARMSD COORDINATION RANDOM_EXCHANGES MOLINFO WHOLEMOLECULES METAD GROUP PRINT UPPER_WALLS DIHCOR PARABETARMSD | bias secondarystructure colvar core multicolvar generic |
| 21.033 | Multiple-path-metadynamics applied to DNA base-pairing transitions | bio | path-CV, metadynamics, multiple-walker, dna | Alberto Pérez-de-Alba-Ortíz | METAD PRINT INCLUDE UPPER_WALLS COMBINE RESTRAINT CONSTANT MOVINGRESTRAINT | bias function generic |
| 21.016 | MD SAXS GTPase associated center | bio | metadynamics, RNA, folding, SAXS | Giovanni Bussi | LOWER_WALLS GYRATION MOLINFO WHOLEMOLECULES METAD GROUP INCLUDE SAXS UPPER_WALLS PRINT CUSTOM ERMSD | bias colvar isdb function core generic |
| 21.013 | Role of vibrational excitation in heterogeneous catalysis | chemistry | catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption | Kristof Bal | LOWER_WALLS HISTOGRAM FLUSH DISTANCE EXTERNAL OPT_AVERAGED_SGD METAD DISTANCES ANGLES UWALLS REWEIGHT_BIAS TD_GRID PRINT COORDINATIONNUMBER DUMPGRID CONVERT_TO_FES UNITS LOAD BF_CHEBYSHEV RESTRAINT REWEIGHT_METAD COORDINATION VES_LINEAR_EXPANSION UPPER_WALLS COMBINE | symfunc bias function colvar setup generic multicolvar gridtools ves |
| 21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Kristof Bal | REWEIGHT_METAD CONVERT_TO_FES HISTOGRAM FLUSH METAD COMMITTOR UNITS PRINT UPPER_WALLS LOAD COORDINATIONNUMBER MOVINGRESTRAINT DUMPGRID | symfunc bias setup gridtools generic |
| 21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Tarak Karmakar | LOWER_WALLS FLUSH PYTORCH_MODEL OPES_METAD MATHEVAL GROUP PRINT UPPER_WALLS LOAD | bias opes setup function core pytorch generic |
| 20.026 | Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor | bio | Metadynamics, Umbrella sampling | Brandon Peters | REWEIGHT_METAD CONVERT_TO_FES HISTOGRAM METAD PRINT MULTI_RMSD RESTRAINT DUMPGRID | colvar bias gridtools generic |
| 20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Glen Hocky | ENERGY GYRATION DISTANCE MATHEVAL PRINT UNITS GROUP FISST RESTRAINT BIASVALUE | bias fisst colvar setup function core generic |
| 19.075 | PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python | other | Python, automatic differentiation | Toni Giorgino | ENDPLUMED ANGLE DUMPDERIVATIVES DISTANCE CENTER PRINT GROUP COMBINE CUSTOM RESTRAINT TORSION | bias vatom colvar function core generic |
| 19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Jim Pfaendtner | ENERGY GYRATION WHOLEMOLECULES METAD PRINT | colvar bias generic |
| 19.056 | maze | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_LOSS MAZE_SIMULATED_ANNEALING PRINT UNITS POSITION MAZE_OPTIMIZER_BIAS | colvar setup maze generic |
| 19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Gareth Tribello | FCCUBIC MORE_THAN FOURIER_TRANSFORM MULTICOLVARDENS CENTER GROUP UNITS FIND_CONTOUR_SURFACE DUMPGRID | symfunc fourier vatom setup function core contour gridtools |
| 19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | FLUSH DISTANCE METAD PRINT UNITS UPPER_WALLS COMBINE DISTANCES RESTART | bias colvar setup function multicolvar generic |
| 19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Gabriele Cesare Sosso | ENDPLUMED OUTPUT_CLUSTER Q6 LOCAL_Q6 FLUSH CLUSTER_NATOMS COMMITTOR MFILTER_MORE CONTACT_MATRIX DFSCLUSTERING CLUSTER_WITHSURFACE | symfunc clusters adjmat multicolvar generic |
| 19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Michele Invernizzi | ENDPLUMED VES_DELTA_F ENERGY METAD PRINT UNITS POSITION LOAD TORSION RESTART | bias colvar setup generic ves |
| 25.017 | Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity | bio | EMMIVox, cryo-EM, allostery, decamer, filament, ensemble refinement, glutamine synthetase | Samuel Hoff | BIASVALUE GROUP EMMIVOX MOLINFO WHOLEMOLECULES PRINT | isdb generic core bias |
| 25.008 | Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting | methods | metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting | Dhiman Ray | POSITION BIASVALUE METAD DISTANCE RMSD GROUP ENDPLUMED PYTORCH_MODEL UPPER_WALLS MOLINFO WHOLEMOLECULES OPES_METAD UNITS CUSTOM PRINT TORSION ENERGY LOWER_WALLS | function colvar generic core setup pytorch opes bias |
| 25.004 | Machine Learning-Driven Molecular Dynamics Unveil a Bulk Phase Transformation Driving Ammonia Synthesis on Barium Hydride | chemistry | OPES, OPES flooding, Catalysis, Ammonia Synthesis | Axel Tosello Gardini | COORDINATIONNUMBER ZDISTANCES FLUSH GROUP DISTANCE DISTANCES UPPER_WALLS UNITS CUSTOM OPES_METAD FIXEDATOM PRINT COMMITTOR | function colvar core generic symfunc setup vatom opes bias multicolvar |
| 24.030 | NMR guided simulation of dsRBD | bio | Metainference, NMR, protein dynamics | Debadutta Patra | DISTANCE FLUSH STATS GROUP ENSEMBLE WHOLEMOLECULES MOLINFO METAINFERENCE PRINT ALPHABETA RDC | function colvar core generic isdb multicolvar |
| 24.029 | Combination of OPES and OPES-Explore | methods | OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin | Dhiman Ray | FIT_TO_TEMPLATE UPPER_WALLS OPES_METAD_EXPLORE CENTER DISTANCE COMBINE RMSD COORDINATION MATHEVAL FLUSH PYTORCH_MODEL WHOLEMOLECULES OPES_METAD UNITS PRINT CONTACTMAP LOWER_WALLS POSITION INCLUDE BIASVALUE METAD GROUP ENDPLUMED MOLINFO CUSTOM FIXEDATOM ENERGY | function colvar generic core setup vatom pytorch opes bias |
| 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 | FIT_TO_TEMPLATE OPES_EXPANDED MATHEVAL DISTANCE GROUP ENDPLUMED COORDINATION UPPER_WALLS ANGLE WHOLEMOLECULES CENTER FIXEDATOM PRINT TORSION ECV_MULTITHERMAL ENERGY OPES_METAD_EXPLORE LOWER_WALLS | function colvar core generic vatom opes bias |
| 24.017 | Absolute Binding Free Energies with OneOPES | methods | protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy | Francesco Gervasio | UPPER_WALLS OPES_METAD_EXPLORE OPES_EXPANDED RMSD COORDINATION PROJECTION_ON_AXIS MATHEVAL WHOLEMOLECULES PRINT ECV_MULTITHERMAL RESTART CONTACTMAP LOWER_WALLS INCLUDE BIASVALUE METAD GROUP CONSTANT MOLINFO CUSTOM TORSION ENERGY COM WRAPAROUND | function colvar generic core setup vatom opes bias |
| 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 | COORDINATIONNUMBER BIASVALUE MATHEVAL METAD DISTANCE FLUSH MOLINFO PRINT RESTRAINT TORSION ENERGY RESTART COMMITTOR | function colvar generic symfunc setup bias |
| 24.008 | yCD Metadynamics | bio | volume-based MetaD, path CVs, infrequent MetaD, product release | James McCarty | FIT_TO_TEMPLATE CONVERT_TO_FES HISTOGRAM UPPER_WALLS DUMPGRID RMSD DISTANCE COORDINATION REWEIGHT_METAD MATHEVAL FLUSH WHOLEMOLECULES PRINT CONTACTMAP COMMITTOR INCLUDE METAD GROUP READ ENDPLUMED MOLINFO PATH FIXEDATOM COM WRAPAROUND | gridtools function colvar generic core vatom bias mapping |
| 24.006 | Water vapor condensation | chemistry | metadynamics, homogeneous condensation, chemical potential | Shenghui Zhong | COORDINATIONNUMBER METAD UPPER_WALLS UNITS DFSCLUSTERING PRINT CLUSTER_NATOMS CONTACT_MATRIX CLUSTER_PROPERTIES | generic symfunc setup adjmat clusters bias |
| 23.021 | Into the Dynamics of Rotaxanes at Atomistic Resolution | materials | metadynamics, rotaxanes, molecular shuttles, molecular machines | Luigi Leanza | METAD MATHEVAL DISTANCE UPPER_WALLS CUSTOM FIXEDATOM PRINT TORSION CENTER | function colvar generic vatom bias |
| 23.008 | PBMetaD simulations of Histatin5 | bio | metadynamics, IDP, Rg, PPII | Francesco Pesce | PBMETAD GROUP MOLINFO WHOLEMOLECULES GYRATION TORSION PRINT | generic colvar core bias |
| 22.040 | From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure | bio | SARS-CoV-2, Spike, Omicron | Miłosz Wieczór | METAD PCAVARS UPPER_WALLS WHOLEMOLECULES PRINT LOWER_WALLS | mapping generic bias |
| 22.020 | Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix–Junction–Helix RNA | bio | RNA force field, Helix-Junction-Helix RNA, SAXS, Well tempered metadynamics | Weiwei He | METAD DISTANCE GROUP WHOLEMOLECULES PRINT TORSION COM | colvar generic core vatom bias |
| 22.013 | Ligand dissociation from PreQ1 riboswitch | bio | ligand, RNA, metadynamics, pRAVE | Yihang Wang | COORDINATIONNUMBER DISTANCE COMBINE RMSD METAD MOLINFO WHOLEMOLECULES PRINT COM COMMITTOR | function colvar generic symfunc vatom bias |
| 21.047 | Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations | materials | pair entropy, metadynamics, ves, solids, crystallization | Pablo Piaggi | PAIRENTROPY METAD LOAD COMBINE VES_LINEAR_EXPANSION TD_WELLTEMPERED BF_LEGENDRE PRINT ENERGY RESTART OPT_AVERAGED_SGD VOLUME | gridtools function colvar generic setup ves bias |
| 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 | COORDINATIONNUMBER DISTANCE COMBINE METAD COORDINATION UPPER_WALLS PRINT LOWER_WALLS | function colvar generic symfunc 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 | DISTANCE GROUP WHOLEMOLECULES PRINT COM | generic vatom colvar core |
| 20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Michele Invernizzi | LOAD UPPER_WALLS ECV_MULTITHERMAL_MULTIBARIC VOLUME OPES_EXPANDED RMSD ECV_LINEAR MATHEVAL WHOLEMOLECULES UNITS PRINT ECV_MULTITHERMAL POSITION ENVIRONMENTSIMILARITY ECV_UMBRELLAS_LINE Q6 ENDPLUMED MOLINFO CUSTOM TORSION ENERGY | function colvar generic setup symfunc opes bias envsim |
| 19.076 | Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones | bio | molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics | Salvatore Assenza | ENDPLUMED UNITS GYRATION PRINT MOVINGRESTRAINT | setup bias colvar generic |
| 19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Carlo Camilloni | PBMETAD BIASVALUE FLUSH GROUP ENDPLUMED UPPER_WALLS WHOLEMOLECULES MOLINFO CS2BACKBONE PRINT RESTART ALPHABETA ANTIBETARMSD LOWER_WALLS | generic core setup secondarystructure bias isdb multicolvar |
| 19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Paolo Raiteri | METAD MATHEVAL FLUSH DISTANCE UPPER_WALLS UNITS PRINT RESTART | function colvar generic setup bias |
| 19.035 | Dimerization of GPCRs from coarse-grained umbrella sampling | bio | Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization | Davide Provasi | DISTANCE GROUP PRINT RESTRAINT TORSION COM | colvar generic core vatom bias |
| 19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Silvio Pipolo | METAD CELL UPPER_WALLS PIV PRINT FUNCPATHMSD LOWER_WALLS | function colvar generic piv bias |
| 19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Jim Pfaendtner | METAD GROUP EXTERNAL COORDINATION ENERGY | colvar core bias |
| 19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Adriana Pietropaolo | BIASVALUE METAD MATHEVAL CONSTANT WHOLEMOLECULES PRINT TORSION | function generic colvar bias |
| 25.024 | Sampling glycan-glycan interactions for B22 calculations | bio | B22, glycan, carbohydrates, distance, REST2, metadynamics, RECT, replica exchange | Isabell Louise Grothaus | COMBINE COM DISTANCE POSITION METAD RESTRAINT PRINT | bias vatom colvar generic function |
| 25.023 | Molecular simulations of Tau-protein oligomers | bio | metadynamics, proteins, aggregation | Giovanni Bussi | CUSTOM CONTACTMAP RMSD RESTART METAD FLUSH RESTRAINT PRINT | bias colvar generic setup function |
| 25.009 | Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water | chemistry | metadynamics, nitrate photolysis | Kam-Tung Chan | DUMPGRID CUSTOM HISTOGRAM GROUP DISTANCE READ UPPER_WALLS COORDINATION METAD FLUSH REWEIGHT_METAD RESTART PRINT | bias colvar generic core setup gridtools function |
| 24.031 | DeepLNE | methods | PATHCV, OPES, OneOPES | Thorben Fröhlking | COMBINE ENERGY MOLINFO PYTORCH_MODEL OPES_EXPANDED ECV_MULTITHERMAL OPES_METAD_EXPLORE RESTART COORDINATION ERMSD PRINT VOLUME | colvar opes generic pytorch setup function |
| 24.028 | All-atom simulations of RNA-membrane interactions | bio | metadynamics, membrane, RNA | Giovanni Bussi | GYRATION COMBINE PUCKERING WHOLEMOLECULES DISTANCE POSITION MOLINFO MATHEVAL CENTER LOWER_WALLS UPPER_WALLS SORT GHOST METAD GROUP PRINT DISTANCES | bias vatom colvar generic core multicolvar function |
| 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 | CUSTOM COMBINE WHOLEMOLECULES DISTANCE MOLINFO TORSION OPES_METAD COORDINATION PRINT GYRATION ALPHARMSD | secondarystructure colvar opes generic function |
| 24.018 | A new route to the prebiotic synthesis of glycine via ab initio-based machine learning calculations | chemistry | prebiotic chemistry, glycine, Strecker synthesis, ab initio calculations, machine learning | Léon HUET | DISTANCE PRINT | colvar generic |
| 23.046 | Lasso Peptides - HLDA CV | bio | metadynamics, protein folding, HLDA, harmonic | Gabriel da Hora | COMBINE WHOLEMOLECULES DISTANCE METAD UNITS PRINT | bias colvar generic setup function |
| 23.044 | Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition | materials | metadynamics, interlocked molecules | Luigi Leanza | DUMPGRID HISTOGRAM ENDPLUMED COMMITTOR READ COORDINATION METAD GROUP PRINT CONVERT_TO_FES | bias colvar generic core gridtools |
| 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 | WHOLEMOLECULES INCLUDE DISTANCE MOLINFO UPPER_WALLS EMMIVOX GROUP BIASVALUE PRINT WRAPAROUND | isdb bias colvar core generic |
| 23.024 | Permutationally Invariant Networks for Enhanced Sampling (PINES) | methods | collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent | Nicholas Herringer | LOAD PRINT PBMETAD | bias generic setup |
| 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 | CUSTOM COMBINE MATHEVAL MOLINFO OPES_METAD COORDINATION GROUP WHOLEMOLECULES DISTANCE LOWER_WALLS ANGLE RMSD ENERGY ENDPLUMED FIT_TO_TEMPLATE CENTER UPPER_WALLS INCLUDE PRINT FIXEDATOM CONTACTMAP PYTORCH_MODEL COMMITTOR | bias colvar opes vatom core generic pytorch function |
| 22.031 | Rare Event Kinetics from Adaptive Bias Enhanced Sampling | methods | OPES Flooding, Kinetics, Rate, OPES, Machine Learning | Dhiman Ray | CUSTOM COMBINE MOLINFO OPES_METAD GROUP UNITS WHOLEMOLECULES DISTANCE TORSION RMSD ENERGY ENDPLUMED CONSTANT POSITION INCLUDE BIASVALUE PRINT CONTACTMAP PYTORCH_MODEL COMMITTOR | bias colvar opes core generic pytorch setup function |
| 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 | COMBINE COM DISTANCE COORDINATIONNUMBER LOWER_WALLS UPPER_WALLS COORDINATION METAD FLUSH UNITS GYRATION | symfunc bias vatom colvar generic setup function |
| 22.006 | Peptide framework for screening the effects of amino acids on assembly | bio | metadynamics, peptides | Andrew White | DUMPGRID COMBINE HISTOGRAM GROUP COM REWEIGHT_BIAS METAD PRINT INCLUDE GYRATION CONVERT_TO_FES DISTANCES | bias vatom colvar core generic multicolvar gridtools function |
| 21.048 | Enhancing ligand exploration within a channel pore and fenestrations using metadynamics | bio | well-tempered metadynamics, protein-ligand enhanced sampling, sodium channel, Nav, small molecule drug | Elaine Tao | CUSTOM COM DISTANCE TORSION UPPER_WALLS LOWER_WALLS METAD UNITS PRINT | bias vatom colvar generic setup function |
| 21.042 | Peptoid-mediated Au nanocrystal growth | materials | parallel-bias metadynamics, peptoid, Au | Xin Qi | GYRATION COM DISTANCE MOLINFO UPPER_WALLS PRINT PBMETAD | bias vatom colvar generic |
| 21.035 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, interface | Aaron Finney | FIXEDATOM DISTANCE LOAD GROUP RESTRAINT PRINT | bias vatom colvar core generic setup |
| 21.032 | Metal-coupled folding mechanism to metallothionein | bio | parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination | Manuel-Peris Diaz | WHOLEMOLECULES COORDINATION GROUP UNITS PBMETAD | bias colvar core generic setup |
| 21.026 | Probing allosteric regulations with coevolution-driven molecular simulations | bio | metadynamics, coevolution, allostery, adenylate cyclase | Francesco Colizzi | WHOLEMOLECULES DISTANCE COM PATHMSD UPPER_WALLS METAD UNITS PRINT | bias vatom colvar generic setup |
| 21.025 | Computational and biochemical analysis of type IV pilus dynamics and stability | bio | molecular dynamics, calcium binding, Type IV pilus | Yasaman Karami | DISTANCE UPPER_WALLS PRINT LOWER_WALLS | bias colvar generic |
| 21.019 | Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations | materials | Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen | Matteo Salvalaglio | COM DISTANCE MATHEVAL TORSIONS KDE PRINT | vatom colvar generic multicolvar gridtools function |
| 21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Adriana Pietropaolo | WHOLEMOLECULES CONSTANT MATHEVAL TORSION PBMETAD RESTART BIASVALUE PRINT | bias colvar generic setup function |
| 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 | WHOLEMOLECULES PATHMSD MOLINFO UPPER_WALLS RESTART METAD GROUP PRINT | bias colvar core generic setup |
| 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 | BF_LEGENDRE COMBINE HISTOGRAM MATHEVAL CELL RESTART LOAD REWEIGHT_BIAS LOWER_WALLS DUMPGRID ENERGY UPPER_WALLS Q6 TD_WELLTEMPERED PRINT OPT_DUMMY READ TD_MULTITHERMAL_MULTIBARIC OPT_AVERAGED_SGD REWEIGHT_TEMP_PRESS VES_LINEAR_EXPANSION CONVERT_TO_FES VOLUME | symfunc ves bias colvar generic setup gridtools function |
| 19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Michele Invernizzi | ENDPLUMED POSITION TORSION OPES_METAD METAD EXTERNAL UNITS PRINT | bias colvar opes generic setup |
| 19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Gareth Tribello | ENDPLUMED FCCUBIC UPPER_WALLS CELL METAD UNITS PRINT | symfunc bias colvar generic setup |
| 19.049 | Determining the sizes of solid/liquid clusters in MD trajectories of nucleation | methods | nucleation, metadynamics, clustering, Steinhardt order parameters | Gareth Tribello | CUSTOM SMAC LOCAL_Q6 ONES CLUSTER_PROPERTIES COORDINATIONNUMBER CLUSTER_DISTRIBUTION Q6 OUTER_PRODUCT MATRIX_VECTOR_PRODUCT MORE_THAN DFSCLUSTERING METAD OUTPUT_CLUSTER CLUSTER_NATOMS PRINT CONTACT_MATRIX DISTANCES | symfunc clusters bias generic multicolvar adjmat matrixtools function |
| 19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Mattia Bernetti | GYRATION ENERGY ENDPLUMED WHOLEMOLECULES MOLINFO METAD PRINT ALPHARMSD | bias colvar secondarystructure generic |
| 25.016 | Advancing in silico drug design with Bayesian refinement of AlphaFold models | bio | bAIes, AlphaFold, Bayesian refinement, virtual screening, docking, small-molecule, enrichment | Samiran Sen | GROUP BIASVALUE PRINT BAIES | bias generic core isdb |
| 25.000 | Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer | bio | metadynamics, pathCV | Sahithya Sridharan Iyer | MOLINFO WHOLEMOLECULES COM RESTART GROUP FUNCPATHGENERAL METAD UPPER_WALLS PRINT DISTANCE | generic core function colvar bias setup vatom |
| 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 | WHOLEMOLECULES ANGLE COORDINATION GROUP CONVERT_TO_FES HISTOGRAM TORSION PRINT DISTANCE DUMPGRID | generic core colvar gridtools |
| 24.027 | Proline cis and trans subensembles of a disordered peptide | bio | intrinsically disordered proteins, proline cis trans isomerisation, metadynamics, collective variables | Alice Pettitt | MOLINFO FLUSH ENDPLUMED WHOLEMOLECULES GYRATION COORDINATION ALPHARMSD PARABETARMSD COMBINE DIHCOR INCLUDE ANTIBETARMSD PBMETAD GROUP TORSION PRINT DISTANCE | generic secondarystructure core function colvar multicolvar bias |
| 24.026 | Constant pH metadynamics of RNA oligomers | bio | metadynamics, pH, RNA | Giovanni Bussi | MOLINFO PUCKERING RESTART METAD TORSION PRINT | generic bias colvar setup |
| 24.023 | Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21. A Machine-Learning-Aided Enhanced Sampling Study | bio | RNA, miRNA, OneOPES, ligand binding, conformational changes | Valerio Rizzi | COORDINATION CUSTOM ENERGY COMBINE RESTART OPES_EXPANDED GROUP OPES_METAD_EXPLORE TORSION PRINT DISTANCE ECV_MULTITHERMAL | generic core function colvar setup opes |
| 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 FLUSH WHOLEMOLECULES RMSD COORDINATION PYTORCH_MODEL METAD UPPER_WALLS DRR PRINT LOWER_WALLS | generic colvar bias drr pytorch |
| 24.010 | Oxytocin metadynamics simulation | bio | metadynamics, oxytocin, peptide | Jan Beránek | WHOLEMOLECULES FLUSH RESTART METAD TORSION PRINT | generic bias colvar setup |
| 23.034 | Urea nucleation in water: do long-range forces matter? | materials | LMF theory, Metadynamics, Nucleation | Ziyue Zou | INCLUDE CENTER COORDINATIONNUMBER GROUP METAD LOAD PRINT | generic core bias setup vatom symfunc |
| 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 | MOLINFO WHOLEMOLECULES DISTANCES CENTER GROUP SHADOW FIT_TO_TEMPLATE METAD WRAPAROUND UPPER_WALLS POSITION PRINT | generic core colvar multicolvar bias isdb vatom |
| 23.029 | An accurate and efficient SAXS/SANS implementation including solvation layer effects suitable for restrained Molecular Dynamics simulations | bio | SAXS, SANS, SAS, metainference, proteins, nucleic-acid | Federico Ballabio | MOLINFO BIASVALUE RMSD CENTER GROUP SAXS ENSEMBLE WRAPAROUND STATS UPPER_WALLS PRINT DISTANCE | generic core function colvar bias isdb vatom |
| 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 COM OPES_METAD ZDISTANCES ENERGY DISTANCES CUSTOM COORDINATIONNUMBER GROUP COMMITTOR UNITS UPPER_WALLS LOWER_WALLS FIXEDATOM MATHEVAL PRINT DISTANCE | generic core function colvar multicolvar bias setup vatom opes symfunc |
| 23.026 | Machine Learning Nucleation Collective Variables with Graph Neural Networks | chemistry | Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks | Florian Dietrich | COMBINE LOCAL_Q6 COORDINATIONNUMBER GROUP METAD MOVINGRESTRAINT MFILTER_MORE PRINT LOWER_WALLS Q6 | generic core function multicolvar bias symfunc |
| 23.025 | Probing ion binding to G-quadruplexes and related events | chemistry | metadynamics, repulsive potential, nucleic acids, G-quadruplexes | Marcelo Poleto | WHOLEMOLECULES FLUSH COM DISTANCES DUMPATOMS RESTART GROUP FIT_TO_TEMPLATE METAD WRAPAROUND UNITS UPPER_WALLS DISTANCE POSITION MATHEVAL PRINT LOWER_WALLS | generic core function colvar multicolvar bias setup vatom |
| 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 | WHOLEMOLECULES OPES_METAD COORDINATION CUSTOM PYTORCH_MODEL PATH CENTER OPES_METAD_EXPLORE GROUP FIT_TO_TEMPLATE DISTANCE UNITS UPPER_WALLS LOWER_WALLS TORSION PRINT FIXEDATOM | generic core function colvar bias setup vatom opes mapping pytorch |
| 23.013 | Path meta-eABF simulation of large scale conformational change in STING protein | methods | meta-eABF, path CV, large scale conformational change, STING protein, reciprocal barrier restraint | Istvan Kolossvary | BIASVALUE FLUSH CUSTOM METAD TIME UNITS UPPER_WALLS DRR PATHMSD PRINT LOWER_WALLS | generic function colvar bias setup drr |
| 23.012 | JAK2 2D meta-eABF PMF with statistical analysis | bio | 2D meta-eABF, path CV, PMF | Istvan Kolossvary | BIASVALUE FLUSH CUSTOM METAD UPPER_WALLS DRR PATHMSD PRINT LOWER_WALLS | generic function colvar bias drr |
| 23.006 | Transcription factor unbinding | bio | metadynamics, DNA, conformational changes | Malin Lüking | MOLINFO ANGLE COM CONTACTMAP DUMPFORCES ALPHARMSD METAD PRINT DISTANCE | generic secondarystructure colvar bias vatom |
| 23.001 | Quantum phase diagram of water | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn-Løland Bore | ECV_UMBRELLAS_LINE INCLUDE RESTART ENVIRONMENTSIMILARITY OPES_EXPANDED UPPER_WALLS PRINT LOWER_WALLS | generic envsim bias setup opes |
| 22.033 | Reciprocal barrier restraint. Application to PROTAC passive permeability prediction | methods | PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR | Istvan Kolossvary | BIASVALUE FLUSH COM CUSTOM METAD UNITS DRR PRINT DISTANCE | generic function colvar bias setup vatom drr |
| 22.021 | Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn Løland Bore | ECV_UMBRELLAS_LINE INCLUDE ENVIRONMENTSIMILARITY OPES_EXPANDED UPPER_WALLS PRINT LOWER_WALLS | generic bias opes envsim |
| 22.015 | Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome | bio | photodynamics, bacteriophytochrome, variationally enhanced sampling | Jakub Rydzewski | VES_LINEAR_EXPANSION OPT_AVERAGED_SGD TD_UNIFORM BF_FOURIER TORSION PRINT | generic colvar ves |
| 22.011 | Accelerating all-atom simulations and gaining mechanistic understanding of biophysical systems through State Predictive Information Bottleneck | methods | metadynamics, membrane permeation, protein folding | Shams Mehdi | MOLINFO WHOLEMOLECULES COM CUSTOM ZANGLES COMBINE METAD DISTANCE UPPER_WALLS XANGLES TORSION ALPHABETA YANGLES MATHEVAL PRINT LOWER_WALLS | generic function colvar multicolvar bias vatom |
| 22.009 | Glycosylation in calixarenes capsule | chemistry | Metadynamics, glycosylation, supramolecular catalysis | GiovanniMaria Piccini | WHOLEMOLECULES ANGLE RMSD FLUSH COORDINATION DISTANCES COMBINE BRIDGE GROUP FIT_TO_TEMPLATE METAD DISTANCE UNITS UPPER_WALLS MATHEVAL PRINT LOWER_WALLS | generic core function colvar adjmat multicolvar bias setup |
| 21.051 | Automatic learning of hydrogen-bond fixes in an AMBER RNA force field | methods | force field, RNA | Giovanni Bussi | MOLINFO BIASVALUE WHOLEMOLECULES COORDINATION COMBINE ERMSD METAD PRINT | generic bias function colvar |
| 21.046 | Ubiquitin Interacting Motifs, Duality Between Structured and Disordered Motifs | bio | wt metadynamics, ubiquitin, ataxin-3, short linear motifs, ubiquitin binding motif, moonlight functions, intrinsic disorder | Elena Papaleo | WHOLEMOLECULES ENDPLUMED GYRATION GROUP METAD UPPER_WALLS ALPHABETA PRINT LOWER_WALLS | generic core colvar multicolvar bias |
| 21.030 | Thermodynamic Basis for Stabilization of Helical Peptoids by Chiral Sidechains | bio | parallel bias parallel tempered metadynamics in WTE, synthetic foldamers, self-assembly, peptoid secondary structure | Jim Pfaendtner | COM GYRATION COORDINATION ENERGY PBMETAD INCLUDE METAD ALPHABETA TORSION PRINT DISTANCE | generic colvar multicolvar bias vatom |
| 21.014 | how to determine statistically accurate conformational ensembles | bio | metadynamics, metainference, errors, cv, SAXS, ensemble determination | Cristina Paissoni | MOLINFO WHOLEMOLECULES BIASVALUE CONTACTMAP GYRATION PBMETAD ANTIBETARMSD CENTER SAXS METAD ENSEMBLE STATS ALPHABETA TORSION PRINT | generic secondarystructure function colvar multicolvar bias isdb vatom |
| 21.006 | OPES, On-the-fly Probability Enhanced Sampling Method | methods | opes, alanine dipeptide, well-tempered, multithermal, multiumbrella | Michele Invernizzi | ENDPLUMED OPES_METAD ECV_UMBRELLAS_LINE ENERGY OPES_EXPANDED TORSION PRINT ECV_MULTITHERMAL | generic opes colvar |
| 21.004 | Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy | bio | machine learning, well-tempered metadynamics, path collective variable, potential of mean force, standard binding free energy calculations, host-guest, protein-ligand unbinding | Dorothea Gobbo | WHOLEMOLECULES RESTART METAD UPPER_WALLS PATHMSD PRINT LOWER_WALLS | generic bias colvar setup |
| 20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Faidon Brotzakis | MOLINFO WHOLEMOLECULES RMSD BIASVALUE DISTANCES DUMPGRID GROUP EMMI READ CONVERT_TO_FES PRINT HISTOGRAM | generic gridtools core colvar multicolvar bias isdb |
| 20.027 | Allosteric Regulation of SARS-CoV-2 Protease. Towards Informed Structure-Based Drug Discovery | bio | SARS-CoV2, MPro, Covid-19, Molecular Dynamics, Metadynamics, Computer-Aided Drug Discovery | Khaled Abdel-Maksoud | METAD PRINT DISTANCE TORSION | generic bias colvar |
| 20.024 | Gaussian Mixture Based Enhanced Sampling (GAMBES) | methods | enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias | Jayashrita Debnath | DISTANCES ENERGY COMBINE GROUP DISTANCE UNITS UPPER_WALLS TORSION LOAD PRINT LOWER_WALLS | generic core function colvar multicolvar bias setup |
| 20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Matteo Salvalaglio | ENERGY CELL METAD UPPER_WALLS VOLUME MATHEVAL PRINT LOWER_WALLS | generic bias function colvar |
| 20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Jim Pfaendtner | WHOLEMOLECULES DISTANCES COORDINATION RESTART CENTER GROUP PRINT DISTANCE | generic core colvar multicolvar setup vatom |
| 20.008 | Simulating solvation and acidity in complex mixtures with first-principles accuracy. The case of CH3SO3H and H2O2 in phenol | chemistry | proton trasfer, metadynamics | Kevin Rossi | COORDINATION CUSTOM DISTANCES METAD UNITS PRINT | generic function colvar multicolvar bias setup |
| 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 COM ABMD DUMPGRID COMBINE REWEIGHT_METAD METAD CONVERT_TO_FES UPPER_WALLS READ LOWER_WALLS MATHEVAL PRINT DISTANCE HISTOGRAM | generic gridtools function colvar bias vatom |
| 19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Sandro Bottaro | MOLINFO WHOLEMOLECULES RMSD ERMSD METAD TORSION PRINT DISTANCE | generic bias colvar |
| 19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Jakub Rydzewski | RESTART METAD UNITS UPPER_WALLS PATHMSD PRINT LOWER_WALLS | generic bias colvar setup |
| 19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Mattia Bernetti | WHOLEMOLECULES METAD UPPER_WALLS PATHMSD PRINT LOWER_WALLS | generic bias colvar |
| 19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Kim E. Jelfs | COM RESTART CENTER GROUP METAD DISTANCE UPPER_WALLS PRINT LOWER_WALLS | generic core colvar bias setup vatom |
| 19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | GiovanniMaria Piccini | FLUSH ENERGY COMBINE METAD DISTANCE UNITS UPPER_WALLS PRINT LOWER_WALLS | generic function colvar bias setup |
| 19.046 | Optimal Collective from short simulations for Benzamidine-Trypsin ligand binding | bio | VAC-MetaD, optimised collective variables, binding free energy, unbinding rates, benzamidine trypsin, Structure Activity Relation | Faidon Brotzakis | MOLINFO WHOLEMOLECULES RMSD COM DISTANCES COMBINE REWEIGHT_METAD BRIDGE GROUP METAD UPPER_WALLS LOWER_WALLS ALPHABETA TORSION FUNNEL PRINT DISTANCE | generic core function colvar adjmat funnel multicolvar bias vatom |
| 19.025 | Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide | bio | metainference, NMR, protein dynamics, force-fields | Carlo Camilloni | MOLINFO BIASVALUE JCOUPLING WHOLEMOLECULES GYRATION PBMETAD FLUSH ENDPLUMED METAINFERENCE RDC ENSEMBLE STATS TORSION CS2BACKBONE PRINT | generic function colvar bias isdb |
| 19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Haochuan Chen | TORSION PRINT DRR | generic drr colvar |
| 19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Riccardo Capelli | WHOLEMOLECULES FLUSH ENDPLUMED COM COORDINATION DUMPGRID REWEIGHT_METAD GROUP FIT_TO_TEMPLATE METAD WRAPAROUND UPPER_WALLS READ POSITION CONVERT_TO_FES MATHEVAL PRINT HISTOGRAM | generic gridtools core function colvar bias vatom |
| 19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Matteo Salvalaglio | CENTER METAD COMMITTOR UPPER_WALLS LOWER_WALLS TORSION PRINT DISTANCE | generic vatom bias colvar |
| 19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Matteo Salvalaglio | ENDPLUMED GYRATION DISTANCES RESTART COORDINATIONNUMBER METAD PRINT | generic colvar multicolvar bias setup symfunc |
| 25.019 | The Arch from the Stones. Understanding Protein Folding Energy Landscapes via Bio-inspired Collective Variables | bio | protein folding, OPES, OneOPES, binding free energy | Valerio Rizzi | GROUP COORDINATION ECV_MULTITHERMAL MOLINFO COMBINE CENTER ENERGY OPES_EXPANDED DISTANCE CUSTOM GHOST PRINT OPES_METAD_EXPLORE RMSD | vatom generic core colvar opes function |
| 24.033 | Transient interactions between the fuzzy coat and the cross-b core of brain-derived Ab42 filaments | bio | CryoEM, MEMMI, Metadynamics, Metainference, Ab42 Fibrils, structural ensemble | Maria Milanesi | GROUP COORDINATION PARABETARMSD MOLINFO ALPHARMSD EMMI COM BIASVALUE RMSD DISTANCE CENTER DUMPMASSCHARGE PRINT DUMPATOMS WHOLEMOLECULES UPPER_WALLS PBMETAD | vatom isdb generic core secondarystructure bias 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 | COMMITTOR GROUP LOAD METAD PRINT TORSION | generic core bias colvar setup |
| 24.002 | Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes | chemistry | metadynamics, ligand design, solvent extraction | Xiaoyu Wang | RESTART METAD PRINT UNITS TORSION | setup bias colvar generic |
| 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 | FLUSH INCLUDE TRANSPOSE MATHEVAL METAD PRINT SUM SELECT_COMPONENTS | generic matrixtools bias valtools function |
| 23.011 | OneOPES, a combined enhanced sampling method to rule them all | bio | OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding | Valerio Rizzi | ECV_MULTITHERMAL MOLINFO ENERGY OPES_EXPANDED DISTANCE METAD PRINT OPES_METAD_EXPLORE ENDPLUMED TORSION | bias opes colvar generic |
| 23.002 | Critical comparison of general-purpose collective variables for crystal nucleation | methods | metadynamics, umbrella sampling, commitor, entropy, PIV | Julien Lam | Q4 VOLUME ENERGY FUNCPATHMSD CUSTOM METAD Q6 PRINT PIV UPPER_WALLS RESTRAINT PAIRENTROPY UNITS LOCAL_AVERAGE | generic gridtools symfunc bias colvar setup function piv |
| 22.039 | Driving and characterizing nucleation of urea and glycine polymorphs in water | bio | metadynamics, nucleation, amino acids, polymorphism | Eric Beyerle | GROUP INCLUDE LOAD Q4 COMBINE CENTER COORDINATIONNUMBER MATHEVAL Q6 METAD PRINT PAIRENTROPY | vatom generic core gridtools symfunc bias setup function |
| 22.038 | Enhanced Sampling Aided Design of Molecular Photoswitches | chemistry | reaction discovery, OPES explore, graph CV | Umberto Raucci | COORDINATION CUSTOM PRINT OPES_METAD_EXPLORE UNITS PYTORCH_MODEL | generic colvar pytorch setup opes function |
| 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 | GROUP COMMITTOR COORDINATION CENTER LOWER_WALLS WHOLEMOLECULES MATHEVAL DISTANCE CUSTOM FIT_TO_TEMPLATE FIXEDATOM OPES_METAD PRINT RMSD UPPER_WALLS PYTORCH_MODEL | vatom generic core bias colvar pytorch opes function |
| 22.012 | Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT | bio | contact maps, protein-protein interactions | Isabell-Louise Grothaus | CONTACTMAP CENTER PRINT DISTANCE | vatom colvar generic |
| 21.043 | Predicting the Conformational Variability of Oncogenic GTP-bound G12D Mutated KRas-4B Proteins at Cell Membranes | chemistry | well-tempered metadynamics, KRas-4B, anionic membrane, conformational variability | Huixia Lu | FIT_TO_TEMPLATE FIXEDATOM METAD PRINT TORSION | vatom bias colvar generic |
| 21.040 | A structural ensemble of a tau-microtubule complex reveals regulatory tau phosphorylation and acetylation mechanisms | bio | EMMI, CryoEM, tau-microtubules, post-translational modifications, chemical mutagenesis, structural ensemble, Metainference | Faidon Brotzakis | GROUP MOLINFO BIASVALUE EMMI COM RESTART DISTANCE PRINT WHOLEMOLECULES UPPER_WALLS | vatom isdb generic core bias colvar setup |
| 21.038 | Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics | materials | metadynamics, SGOOP, nucleation, urea | Ziyue Zou | GROUP INCLUDE LOAD COMBINE CENTER VOLUME ENERGY COORDINATIONNUMBER METAD PRINT | vatom generic core symfunc bias colvar setup function |
| 21.017 | All-atom simulations of the Vav1 AD construct | bio | metadynamics, parallel-bias, well-tempered | Simone Orioli | GROUP MOLINFO CONTACTMAP ALPHARMSD RESTART REWEIGHT_BIAS METAD PRINT WHOLEMOLECULES PBMETAD ALPHABETA | multicolvar generic core secondarystructure bias colvar setup |
| 21.011 | CmuMD simulations of NaCl(aq) at graphite | chemistry | CmuMD, DFS clustering | Aaron Finney | GROUP AROUND CLUSTER_DISTRIBUTION RESTRAINT LOAD MFILTER_MORE COORDINATIONNUMBER DUMPGRID MULTICOLVARDENS FIXEDATOM DFSCLUSTERING DENSITY PRINT CLUSTER_NATOMS CONTACT_MATRIX | vatom multicolvar generic clusters core gridtools volumes symfunc bias adjmat setup |
| 21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Tarsis Ferreira | GROUP COORDINATION PUCKERING INCLUDE MOLINFO LOWER_WALLS ENERGY DUMPGRID RANDOM_EXCHANGES DISTANCE METAD PRINT REWEIGHT_METAD WHOLEMOLECULES UPPER_WALLS HISTOGRAM | generic core gridtools bias colvar |
| 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 | MOLINFO CENTER RESTART DISTANCE PRINT ABMD ERMSD TORSION | vatom generic bias colvar 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 | COMBINE COM METAD WHOLEMOLECULES FLUSH MOLINFO FUNCPATHMSD LOWER_WALLS ENDPLUMED UPPER_WALLS HISTOGRAM CONTACTMAP DUMPGRID PRINT CONVERT_TO_FES DISTANCE READ ABMD REWEIGHT_METAD | vatom generic gridtools bias colvar function |
| 19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Giovanni Bussi | COORDINATION INCLUDE SORT FLUSH MOLINFO MAXENT COM MATHEVAL DISTANCE METAD PRINT WHOLEMOLECULES TORSION | vatom generic bias colvar function |
| 19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Luigi Bonati | LOAD ENVIRONMENTSIMILARITY ENERGY Q6 PRINT ENDPLUMED POSITION UNITS TORSION | generic symfunc colvar envsim setup |
| 19.059 | cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide | bio | bias-exchange metadynamics, cis-trans isomerization | Fabrizio Marinelli | INCLUDE RANDOM_EXCHANGES METAD PRINT 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 COM MATHEVAL CONSTANT DISTANCE METAD PRINT WHOLEMOLECULES UPPER_WALLS | vatom generic bias colvar function |
| 19.013 | RNA FF FITTING | methods | force field, RNA | Giovanni Bussi | INCLUDE PUCKERING BIASVALUE MOLINFO MATHEVAL CONSTANT TORSION | bias colvar generic function |
| 19.009 | RNA tetraloops folding | bio | metadynamics, RNA, folding | Giovanni Bussi | MOLINFO WHOLEMOLECULES METAD PRINT ENDPLUMED ERMSD RMSD | bias colvar generic |