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 |
|---|---|---|---|---|---|---|
| 25.018 | Metainference simulation for dimerization of RNA binding protein | bio | Metainference, Metadynamics, SAXS, protein dimer | Debadutta Patra | PBMETAD SAXS STATS TORSION UPPER_WALLS PRINT DISTANCE WHOLEMOLECULES METAINFERENCE FLUSH ENSEMBLE MOLINFO CENTER GYRATION | generic bias isdb vatom colvar function |
| 25.017 | Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity | bio | EMMIVox, cryo-EM, allostery, decamer, filament, ensemble refinement, glutamine synthetase | Samuel Hoff | PRINT WHOLEMOLECULES MOLINFO EMMIVOX BIASVALUE GROUP | generic core isdb bias |
| 25.004 | Machine Learning-Driven Molecular Dynamics Unveil a Bulk Phase Transformation Driving Ammonia Synthesis on Barium Hydride | chemistry | OPES, OPES flooding, Catalysis, Ammonia Synthesis | Axel Tosello Gardini | DISTANCES COMMITTOR PRINT COORDINATIONNUMBER UPPER_WALLS DISTANCE UNITS FLUSH OPES_METAD CUSTOM FIXEDATOM GROUP ZDISTANCES | generic core bias setup multicolvar symfunc opes vatom colvar function |
| 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 TORSION PRINT DISTANCE OPES_METAD_EXPLORE ECV_MULTITHERMAL ENERGY COMBINE RESTART GROUP OPES_EXPANDED | generic core setup opes colvar 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 | ALPHARMSD COORDINATION CUSTOM TORSION PRINT DISTANCE WHOLEMOLECULES OPES_METAD COMBINE MOLINFO GYRATION | generic secondarystructure opes colvar function |
| 24.009 | Weighted Shape Gaussian Mixture Models | bio | metadynamics, clustering | Glen Hocky | TORSION PRINT UNITS GROUP METAD | generic core bias setup colvar |
| 24.007 | SWISH-X | bio | swish-x, SWISH-X, swish, expanded SWISH | Alberto Borsatto | INCLUDE CONTACTMAP PRINT UPPER_WALLS WHOLEMOLECULES ECV_MULTITHERMAL ENERGY MOLINFO OPES_EXPANDED | opes colvar generic bias |
| 24.006 | Water vapor condensation | chemistry | metadynamics, homogeneous condensation, chemical potential | Shenghui Zhong | CLUSTER_PROPERTIES CLUSTER_NATOMS DFSCLUSTERING UPPER_WALLS COORDINATIONNUMBER PRINT UNITS CONTACT_MATRIX METAD | generic bias setup adjmat symfunc clusters |
| 24.004 | Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables | materials | metadynamics, nucleation, machine learning | Ziyue Zou | INCLUDE RESTART PRINT LOAD GROUP METAD | bias generic core setup |
| 23.043 | Modeling the ferroelectric phase transition in barium titanate with DFT accuracy and converged sampling | materials | Barium Titanate, ferroelectric phase transition, Machine Learning, polarization order parameters | Lorenzo Gigli | INCLUDE PRINT SELECT_COMPONENTS FLUSH MATHEVAL SUM METAD TRANSPOSE | generic valtools bias matrixtools function |
| 23.020 | FEP simulations of ATOX1 homodimer | chemistry | parallel bias metadynamics, FEP, free-energy of metal ion dissociation | Adriana Pietropaolo | CONSTANT PBMETAD PRINT DISTANCE WHOLEMOLECULES MATHEVAL BIASVALUE ANGLE | colvar generic function bias |
| 23.015 | MPCs aggregation | bio | opes_explore, dimerization, MPCs, self-assembly | Vikas Tiwari | COORDINATION UPPER_WALLS PRINT COM WHOLEMOLECULES DISTANCE OPES_METAD_EXPLORE LOWER_WALLS CUSTOM CENTER GROUP METAD | generic core bias opes vatom colvar function |
| 23.001 | Quantum phase diagram of water | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn-Løland Bore | ECV_UMBRELLAS_LINE INCLUDE ENVIRONMENTSIMILARITY UPPER_WALLS PRINT LOWER_WALLS RESTART OPES_EXPANDED | generic bias setup envsim opes |
| 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 | CONTACTMAP UPPER_WALLS PRINT WHOLEMOLECULES ENERGY LOWER_WALLS METAD | colvar generic bias |
| 22.045 | Binding mode and mechanism of enzymatic polyethylene terephthalate degradation | bio | metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation | Francesco Colizzi | ANGLE UPPER_WALLS PRINT COM WHOLEMOLECULES DISTANCE MOVINGRESTRAINT LOWER_WALLS METAD | vatom colvar generic bias |
| 22.033 | Reciprocal barrier restraint. Application to PROTAC passive permeability prediction | methods | PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR | Istvan Kolossvary | PRINT COM DISTANCE DRR UNITS FLUSH CUSTOM BIASVALUE METAD | drr generic bias setup vatom colvar function |
| 22.029 | Angiotensin-1-7_Metadynamics | bio | Metadynamics, Angiotensin-(1-7), peptide | L.-América Chi | COORDINATION GROUP UPPER_WALLS PRINT WHOLEMOLECULES FLUSH LOWER_WALLS GYRATION METAD | colvar generic core bias |
| 22.011 | Accelerating all-atom simulations and gaining mechanistic understanding of biophysical systems through State Predictive Information Bottleneck | methods | metadynamics, membrane permeation, protein folding | Shams Mehdi | CUSTOM ALPHABETA TORSION UPPER_WALLS COM PRINT DISTANCE WHOLEMOLECULES ZANGLES LOWER_WALLS XANGLES MATHEVAL COMBINE MOLINFO METAD YANGLES | generic bias multicolvar vatom colvar function |
| 22.009 | Glycosylation in calixarenes capsule | chemistry | Metadynamics, glycosylation, supramolecular catalysis | GiovanniMaria Piccini | DISTANCES COORDINATION GROUP ANGLE UPPER_WALLS FIT_TO_TEMPLATE PRINT WHOLEMOLECULES DISTANCE UNITS FLUSH LOWER_WALLS MATHEVAL COMBINE BRIDGE METAD RMSD | generic core bias setup multicolvar adjmat colvar function |
| 21.052 | On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets | materials | Ibuprofen, unbinding, WTmetaD | Matteo Salvalaglio | TORSION COMMITTOR PRINT COORDINATIONNUMBER DISTANCE CENTER ENDPLUMED METAD | generic bias symfunc vatom colvar |
| 21.042 | Peptoid-mediated Au nanocrystal growth | materials | parallel-bias metadynamics, peptoid, Au | Xin Qi | PBMETAD UPPER_WALLS COM PRINT DISTANCE MOLINFO GYRATION | vatom colvar generic bias |
| 21.039 | Deep learning the slow modes for rare events sampling | methods | collective variables, machine learning, slow modes, deep-tica, opes | Luigi Bonati | ENERGY COMBINE ENDPLUMED PRINT ECV_MULTITHERMAL WHOLEMOLECULES UNITS OPES_METAD LOAD GROUP VOLUME TORSION CONTACTMAP PYTORCH_MODEL Q6 FLUSH RMSD OPES_EXPANDED INCLUDE ENVIRONMENTSIMILARITY DISTANCE MOLINFO | generic core pytorch setup symfunc envsim opes colvar function |
| 21.022 | Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly | materials | parallel bias metadynamics, adsorption, peptide | Xin Qi | PBMETAD UPPER_WALLS COM PRINT DISTANCE ENERGY LOWER_WALLS MOLINFO GYRATION | vatom colvar generic bias |
| 20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Valerio Rizzi | COORDINATION GROUP PYTORCH_MODEL UPPER_WALLS FIT_TO_TEMPLATE PRINT WHOLEMOLECULES DISTANCE ENERGY OPES_METAD MATHEVAL FIXEDATOM CENTER ENDPLUMED ANGLE | generic core bias pytorch opes vatom colvar function |
| 20.024 | Gaussian Mixture Based Enhanced Sampling (GAMBES) | methods | enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias | Jayashrita Debnath | DISTANCES TORSION UPPER_WALLS PRINT DISTANCE ENERGY UNITS LOWER_WALLS COMBINE LOAD GROUP | generic core bias setup multicolvar colvar function |
| 20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Max Bonomi | COORDINATION ALPHABETA PBMETAD INCLUDE DIHCOR PRINT WHOLEMOLECULES MOLINFO GYRATION | generic colvar multicolvar bias |
| 20.016 | Predicting polymorphism in molecular crystals using orientational entropy | materials | metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy | Pablo Piaggi | VOLUME INCLUDE UPPER_WALLS PRINT CENTER LOAD GROUP METAD | generic core bias setup vatom colvar |
| 20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Pratyush Tiwary | TORSION UPPER_WALLS PRINT DISTANCE WHOLEMOLECULES COMBINE MOLINFO RESTART METAD RMSD | generic bias setup colvar function |
| 19.076 | Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones | bio | molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics | Salvatore Assenza | PRINT UNITS MOVINGRESTRAINT GYRATION ENDPLUMED | colvar generic bias setup |
| 19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Gareth Tribello | CELL UPPER_WALLS PRINT UNITS ENDPLUMED METAD FCCUBIC | generic bias setup symfunc colvar |
| 19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Paolo Raiteri | UPPER_WALLS PRINT DISTANCE FLUSH UNITS MATHEVAL RESTART METAD | generic bias setup colvar function |
| 19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Mattia Bernetti | ALPHARMSD PRINT WHOLEMOLECULES ENERGY GYRATION MOLINFO ENDPLUMED METAD | colvar generic secondarystructure bias |
| 19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Adriana Pietropaolo | CONSTANT TORSION PRINT WHOLEMOLECULES MATHEVAL BIASVALUE METAD | colvar generic function bias |
| 19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Carlo Camilloni | ENDPLUMED INCLUDE SAXS RESTRAINT STATS UPPER_WALLS PRINT WHOLEMOLECULES DISTANCE MOLINFO BIASVALUE CENTER GROUP RMSD | generic core bias isdb vatom colvar function |
| 25.022 | Imidazole Diffusion in SALEM-2 MOF | materials | OPES, Diffusion, Ring opening, MOFs, Machine Learning Potentials | Sudheesh Kumar Ethirajan | MOLINFO DISTANCES PROJECTION_ON_AXIS CENTER UNITS ENDPLUMED PRINT GROUP DISTANCE WHOLEMOLECULES OPES_METAD | vatom multicolvar setup opes generic colvar core |
| 25.015 | Assessment of Force Fields for Describing Conformational Polymorphic Crystals of ROY | materials | Molecular crystal, Force Field, Collective Variable | Pradip Si and Omar Valsson | DISTANCES DUMPMULTICOLVAR PRINT TORSIONS SMAC | multicolvar generic symfunc |
| 25.010 | Kinetic rates calculation with Ratchet&Pawl MD | methods | kinetics, ligand binding, ABMD, ratchet&pawl MD | Riccardo Capelli | FLUSH COM ABMD COMMITTOR PRINT GROUP DISTANCE WHOLEMOLECULES | vatom generic bias colvar core |
| 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 | PUCKERING TORSION MOLINFO RESTRAINT PRINT DISTANCE RESTART MOVINGRESTRAINT METAD | colvar setup generic bias |
| 24.031 | DeepLNE | methods | PATHCV, OPES, OneOPES | Thorben Fröhlking | MOLINFO COORDINATION COMBINE VOLUME OPES_EXPANDED ERMSD ECV_MULTITHERMAL ENERGY OPES_METAD_EXPLORE PRINT PYTORCH_MODEL RESTART | function setup opes generic pytorch colvar |
| 24.029 | Combination of OPES and OPES-Explore | methods | OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin | Dhiman Ray | FIXEDATOM ENERGY GROUP MATHEVAL POSITION METAD CONTACTMAP LOWER_WALLS ENDPLUMED UPPER_WALLS FIT_TO_TEMPLATE INCLUDE BIASVALUE RMSD DISTANCE COORDINATION PYTORCH_MODEL WHOLEMOLECULES MOLINFO COMBINE FLUSH CENTER UNITS PRINT CUSTOM OPES_METAD_EXPLORE OPES_METAD | vatom function setup opes generic bias pytorch colvar core |
| 23.046 | Lasso Peptides - HLDA CV | bio | metadynamics, protein folding, HLDA, harmonic | Gabriel da Hora | COMBINE UNITS PRINT DISTANCE WHOLEMOLECULES METAD | function setup generic bias colvar |
| 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 | INCLUDE BIASVALUE MOLINFO WRAPAROUND EMMIVOX PRINT GROUP DISTANCE UPPER_WALLS WHOLEMOLECULES | generic bias colvar isdb core |
| 23.039 | Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation | chemistry | metadynamics, ligand dissociation | Eric Beyerle | METAD MOLINFO RESTRAINT COMBINE FIXEDATOM CENTER PRINT DISTANCE UPPER_WALLS DUMPMASSCHARGE | vatom function generic bias colvar |
| 23.034 | Urea nucleation in water: do long-range forces matter? | materials | LMF theory, Metadynamics, Nucleation | Ziyue Zou | INCLUDE LOAD CENTER PRINT GROUP COORDINATIONNUMBER METAD | vatom symfunc setup generic bias core |
| 23.027 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, DFS, Q3, Pair Entropy | Aaron Finney | DUMPGRID CLUSTER_DISTRIBUTION LOCAL_AVERAGE LOAD RESTRAINT Q3 FIXEDATOM DFSCLUSTERING CONTACT_MATRIX UNITS PRINT GROUP DENSITY AROUND COORDINATIONNUMBER CLUSTER_NATOMS LOCAL_Q3 HISTOGRAM | vatom symfunc adjmat setup volumes generic bias gridtools clusters core |
| 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 | CONVERT_TO_FES DUMPGRID MOLINFO READ HISTOGRAM RMSD PRINT DISTANCE MATHEVAL REWEIGHT_METAD WHOLEMOLECULES METAD | function generic bias gridtools colvar |
| 23.012 | JAK2 2D meta-eABF PMF with statistical analysis | bio | 2D meta-eABF, path CV, PMF | Istvan Kolossvary | BIASVALUE LOWER_WALLS PATHMSD FLUSH DRR PRINT CUSTOM UPPER_WALLS METAD | function drr generic bias colvar |
| 22.038 | Enhanced Sampling Aided Design of Molecular Photoswitches | chemistry | reaction discovery, OPES explore, graph CV | Umberto Raucci | COORDINATION UNITS PYTORCH_MODEL PRINT CUSTOM OPES_METAD_EXPLORE | function setup opes pytorch generic colvar |
| 22.002 | GAMBES_SAMPL5_RATES | other | GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding | Jayashrita Debnath | FIT_TO_TEMPLATE LOAD COORDINATION FIXEDATOM FLUSH CENTER COMMITTOR ENDPLUMED ENERGY PRINT GROUP DISTANCE MATHEVAL PYTORCH_MODEL ANGLE UPPER_WALLS WHOLEMOLECULES | vatom function setup generic pytorch bias colvar core |
| 21.050 | N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity | methods | bio | Isabell Louise Grothaus | PRINT CENTER DISTANCE | colvar generic vatom |
| 21.046 | Ubiquitin Interacting Motifs, Duality Between Structured and Disordered Motifs | bio | wt metadynamics, ubiquitin, ataxin-3, short linear motifs, ubiquitin binding motif, moonlight functions, intrinsic disorder | Elena Papaleo | WHOLEMOLECULES GYRATION LOWER_WALLS ENDPLUMED PRINT GROUP UPPER_WALLS ALPHABETA METAD | multicolvar generic bias colvar core |
| 21.038 | Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics | materials | metadynamics, SGOOP, nucleation, urea | Ziyue Zou | INCLUDE LOAD COMBINE VOLUME CENTER PRINT ENERGY GROUP COORDINATIONNUMBER METAD | vatom symfunc function setup generic bias colvar core |
| 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 | DIHCOR GYRATION MOLINFO LOWER_WALLS RANDOM_EXCHANGES PARABETARMSD PRINT ANTIBETARMSD GROUP ALPHARMSD ENERGY COORDINATION UPPER_WALLS WHOLEMOLECULES METAD | multicolvar generic bias colvar secondarystructure core |
| 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 | INCLUDE GYRATION COM PBMETAD ENERGY PRINT DISTANCE COORDINATION TORSION ALPHABETA METAD | vatom multicolvar generic bias colvar |
| 21.029 | Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs | bio | metadynamics, small peptide, machine learning | Pratyush Tiwary | TORSION MOLINFO FLUSH PRINT ENERGY EXTERNAL RESTART | colvar setup generic bias |
| 21.028 | From Enhanced Sampling to Reaction Profiles | methods | collective variables, multi-state, machine learning, Deep-TDA | Enrico Trizio | FIXEDATOM GROUP MATHEVAL LOWER_WALLS ENDPLUMED UPPER_WALLS FIT_TO_TEMPLATE LOAD DISTANCES DISTANCE COORDINATION PYTORCH_MODEL TORSION WHOLEMOLECULES CENTER UNITS PRINT ANGLE OPES_METAD | vatom function setup multicolvar opes generic bias pytorch colvar core |
| 21.016 | MD SAXS GTPase associated center | bio | metadynamics, RNA, folding, SAXS | Giovanni Bussi | INCLUDE GYRATION MOLINFO LOWER_WALLS ERMSD PRINT CUSTOM GROUP SAXS UPPER_WALLS WHOLEMOLECULES METAD | function generic bias colvar isdb core |
| 21.015 | Coarse-grained metadynamics and umbrella sampling simulations to investigate interactions of carbohydrate-binding modules with chitin | bio | metadynamics, umbrella sampling, coarse-grained, MARTINI, chitin, carbohydrate-binding module | Gaston Courtade | RESTRAINT CENTER REWEIGHT_BIAS PRINT POSITION MATHEVAL COORDINATION RESTART WHOLEMOLECULES METAD | vatom function setup generic bias colvar |
| 21.010 | Step by Step Strecker Amino Acid Synthesis from Ab Initio Prebiotic Chemistry | chemistry | Strecker reaction, free energy landscape, ab initio molecular dynamics, glycine, prebiotic synthesis | Théo Magrino | generic | |
| 20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Faidon Brotzakis | DUMPGRID CONVERT_TO_FES WHOLEMOLECULES MOLINFO BIASVALUE READ DISTANCES EMMI RMSD PRINT GROUP HISTOGRAM | multicolvar generic bias gridtools colvar isdb core |
| 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 RESTRAINT PRINT STATS COORDINATION WHOLEMOLECULES | function colvar generic bias |
| 20.015 | Rational design of ASCT2 inhibitors using an integrated experimental-computational approach | bio | ASCT2 transporter, small-molecules, cryo-EM, metainference | Max Bonomi | LOAD BIASVALUE MOLINFO EMMIVOX PRINT GROUP DUMPATOMS WHOLEMOLECULES | setup generic bias isdb core |
| 20.005 | Muscarinic M2 receptor/ligand Frequency-Adaptive Metadynamics and QM/MM calculations | bio | Frequency-adaptive metadynamics, multiple-walkers metadynamics, well-tempered metadynamics, GPCR, receptor, Adiabatic Bias MD | Riccardo Capelli | READ ABMD HISTOGRAM METAD CONTACTMAP DUMPGRID LOWER_WALLS ENDPLUMED REWEIGHT_METAD UPPER_WALLS COM DISTANCE WHOLEMOLECULES CONVERT_TO_FES MOLINFO COMBINE FLUSH PRINT FUNCPATHMSD | vatom function generic bias gridtools colvar |
| 20.002 | Exploring conformational dynamics of the extracellular Venus flytrap domain of the GABAB receptor, a path-metadynamics study | bio | Metadynamics, path CVs | Riccardo Ocello | RESTART MOLINFO PATHMSD PRINT GROUP UPPER_WALLS WHOLEMOLECULES METAD | setup generic bias colvar core |
| 19.081 | Calculation of phase diagrams in the multithermal-multibaric ensemble | methods | VES, variationally enhanced sampling, multithermal-multibaric, energy, Wang Landau, RefCV, kernel, bcc, fcc, sodium, aluminum | Pablo Piaggi | READ VOLUME ENERGY MATHEVAL HISTOGRAM DUMPGRID LOWER_WALLS Q6 TD_WELLTEMPERED UPPER_WALLS OPT_DUMMY LOAD REWEIGHT_BIAS CELL BF_LEGENDRE REWEIGHT_TEMP_PRESS RESTART CONVERT_TO_FES VES_LINEAR_EXPANSION COMBINE PRINT OPT_AVERAGED_SGD TD_MULTITHERMAL_MULTIBARIC | symfunc function setup generic bias ves gridtools colvar |
| 19.045 | Adsorption free energy of Ca/CO3 ions on calcite steps in contact with water | materials | metadynamics, well-tempered, multiple walkers, LAMMPS | Marco De La Pierre | RESTART LOWER_WALLS FLUSH UNITS PRINT GROUP COORDINATION UPPER_WALLS POSITION METAD | setup generic bias colvar core |
| 19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | COMBINE FLUSH UNITS ENERGY PRINT DISTANCE UPPER_WALLS METAD | function setup generic bias colvar |
| 19.040 | Optimal Metric for Path Collective Variables | bio | metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path | Francesco Luigi Gervasio | ENDPLUMED PRINT MATHEVAL TORSION METAD | function colvar generic bias |
| 19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Carlo Camilloni | RESTART WHOLEMOLECULES BIASVALUE MOLINFO LOWER_WALLS FLUSH PBMETAD ENDPLUMED ANTIBETARMSD CS2BACKBONE GROUP PRINT UPPER_WALLS ALPHABETA | setup multicolvar generic bias isdb secondarystructure core |
| 19.035 | Dimerization of GPCRs from coarse-grained umbrella sampling | bio | Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization | Davide Provasi | RESTRAINT COM PRINT GROUP DISTANCE TORSION | vatom generic bias colvar core |
| 19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Silvio Pipolo | PIV LOWER_WALLS CELL PRINT UPPER_WALLS FUNCPATHMSD METAD | function generic bias piv colvar |
| 19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Elena Papaleo | ALPHABETA GYRATION MOLINFO LOWER_WALLS PRINT GROUP UPPER_WALLS WHOLEMOLECULES METAD | multicolvar generic bias colvar core |
| 19.023 | RECT | methods | metadynamics, replica exchange | Giovanni Bussi | GYRATION PRINT TORSION WHOLEMOLECULES METAD | colvar generic bias |
| 19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Glen Hocky | RESTRAINT COMBINE EDS PRINT DISTANCE TORSION | function eds generic bias colvar |
| 19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Matteo Salvalaglio | LOWER_WALLS CENTER COMMITTOR PRINT UPPER_WALLS DISTANCE TORSION METAD | colvar generic bias vatom |
| 19.003 | EMMI ClpP | bio | metainference, cryo-EM | Max Bonomi | BIASVALUE MOLINFO EMMI PRINT GROUP | isdb generic bias core |
| 25.020 | Revealing Water-Mediated Activation Mechanisms in the Beta 1-Adrenergic Receptor via OneOPES-Enhanced Free Energy Landscapes | bio | OneOPES, GPCR, ADRB1, activation, microswitches, conformational changes, allostery | Valerio Rizzi | PATHMSD RMSD LOWER_WALLS PRINT DISTANCES ENERGY OPES_METAD_EXPLORE ECV_MULTITHERMAL DISTANCE UPPER_WALLS GROUP OPES_EXPANDED CENTER COORDINATION CUSTOM GHOST | generic colvar core opes vatom function multicolvar bias |
| 25.012 | A Machine Learning-Driven, Probability-Based Approach to Enzyme Catalysis | bio | enzyme catalysis, transition state, structure-activity relationship, free energy surface, reaction mechanism, water, alpha-amylase, sugar, QM/MM MD, OPES, committor function, machine learning | Sudip Das | POSITION PRINT MATHEVAL ENERGY UNITS DISTANCE INCLUDE LOAD COORDINATION CELL COMBINE CUSTOM FLUSH OPES_METAD TORSION BIASVALUE | generic colvar opes setup function bias |
| 25.003 | Surrogate Model CV | methods | Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding | Sompriya Chatterjee | PYTORCH_MODEL TORSION PRINT MATHEVAL ENERGY COMMITTOR DISTANCE GROUP COMBINE OPES_METAD CUSTOM WHOLEMOLECULES MOLINFO ENDPLUMED | generic colvar core opes function pytorch |
| 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 | LOWER_WALLS PRINT COMMITTOR UNITS DISTANCE UPPER_WALLS GROUP RESTART COORDINATION CUSTOM OPES_METAD | generic colvar core setup opes function 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 | FIXEDATOM LOWER_WALLS ANGLE MATHEVAL OPES_METAD_EXPLORE PRINT TORSION DISTANCE FIT_TO_TEMPLATE GROUP UPPER_WALLS ENERGY ECV_MULTITHERMAL OPES_EXPANDED CENTER COORDINATION WHOLEMOLECULES ENDPLUMED | generic colvar core opes vatom function bias |
| 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 | COMMITTOR MATHEVAL UPPER_WALLS COMBINE PRINT OPES_METAD CUSTOM TORSION FIXEDATOM ANGLE METAD FIT_TO_TEMPLATE CONTACTMAP CENTER WHOLEMOLECULES ENDPLUMED RMSD DISTANCE GROUP COORDINATION MOLINFO | generic colvar core opes vatom function bias |
| 24.021 | Ab initio machine learning simulation of calcium carbonate from aqueous solutions to the solid state | chemistry | ion pairing, caco3, opes, proton transfer, crystallization | Pablo Piaggi | PRINT ENERGY DISTANCE UPPER_WALLS COORDINATION OPES_METAD | opes generic colvar bias |
| 24.008 | yCD Metadynamics | bio | volume-based MetaD, path CVs, infrequent MetaD, product release | James McCarty | MATHEVAL COM COMMITTOR UPPER_WALLS REWEIGHT_METAD READ PRINT INCLUDE FLUSH FIXEDATOM PATH METAD FIT_TO_TEMPLATE CONTACTMAP WHOLEMOLECULES ENDPLUMED DUMPGRID RMSD WRAPAROUND HISTOGRAM DISTANCE GROUP COORDINATION MOLINFO CONVERT_TO_FES | generic colvar core gridtools mapping vatom function bias |
| 23.040 | Supramolecular capsules assembly dynamics | chemistry | Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics | Riccardo Capelli | DISTANCES PRINT METAD COM UNITS DISTANCE GROUP CENTER WHOLEMOLECULES CUSTOM POSITION FLUSH | generic colvar core setup vatom function multicolvar bias |
| 23.035 | An Extended Metadynamics Protocol for Binding/Unbinding of Peptide Ligands to Class A G-Protein Coupled Receptors | bio | G protein coupled receptor, peptide ligands, metadynamics, multiple-walker | Timothy Clark | LOWER_WALLS PRINT METAD MATHEVAL CONSTANT DISTANCE UPPER_WALLS CENTER WHOLEMOLECULES BIASVALUE | generic colvar vatom function bias |
| 23.031 | Identifying small molecules binding sites in RNA conformational ensembles with SHAMAN | bio | RNA, metadynamics, probes, mixed-solvent MD, small molecules, binding sites | Max Bonomi | WRAPAROUND PRINT DISTANCES METAD UPPER_WALLS GROUP FIT_TO_TEMPLATE CENTER SHADOW WHOLEMOLECULES POSITION MOLINFO | generic colvar core vatom multicolvar bias isdb |
| 23.002 | Critical comparison of general-purpose collective variables for crystal nucleation | methods | metadynamics, umbrella sampling, commitor, entropy, PIV | Julien Lam | PRINT METAD ENERGY UNITS PAIRENTROPY UPPER_WALLS Q6 FUNCPATHMSD Q4 PIV VOLUME CUSTOM RESTRAINT LOCAL_AVERAGE | generic colvar piv setup bias symfunc function gridtools |
| 22.044 | Colloid Crystallisation Analyses | materials | Q4, Q6, Pair Entropy, DFS | Aaron Finney | MFILTER_LESS MFILTER_MORE PRINT DFSCLUSTERING Q6 Q4 GROUP CONTACT_MATRIX COORDINATIONNUMBER COMBINE CLUSTER_NATOMS LOCAL_Q4 LOCAL_Q6 LOCAL_AVERAGE | generic core adjmat symfunc function multicolvar clusters |
| 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 | PATHMSD PRINT METAD CUSTOM FLUSH BIASVALUE DRR | generic colvar drr function bias |
| 22.023 | Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy | bio | CryoEM, MEMMI,EMMI, Metadynamics, Metainference, IAPP, structural ensemble | Faidon Brotzakis | RMSD PRINT COM PBMETAD UPPER_WALLS GROUP EMMI RESTART COORDINATION WHOLEMOLECULES MOLINFO TORSION BIASVALUE | generic colvar core setup vatom bias isdb |
| 22.018 | Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations | bio | ligand binding, docking, EMMI, LAT1 | Max Bonomi | EMMIVOX PRINT GROUP LOAD WHOLEMOLECULES MOLINFO BIASVALUE | generic core setup bias isdb |
| 22.007 | Characterization of a natural variant of human NDP52 and its functional consequences on mitophagy | bio | metadynamics, well-tempered, protein-protein interactions, disordered proteins, mutations autophagy | Elena Papaleo | PRINT ANGLE ALPHABETA METAD DISTANCE UPPER_WALLS COORDINATION WHOLEMOLECULES ALPHARMSD FLUSH MOLINFO TORSION | generic colvar secondarystructure multicolvar bias |
| 22.006 | Peptide framework for screening the effects of amino acids on assembly | bio | metadynamics, peptides | Andrew White | DISTANCES HISTOGRAM METAD COM PRINT REWEIGHT_BIAS GROUP GYRATION COMBINE INCLUDE CONVERT_TO_FES DUMPGRID | generic colvar core bias vatom function 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 RMSD PRINT | generic colvar |
| 21.031 | Photo-switchable sulfonulureas in KATP channel | bio | metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels | Katarzyna Walczewska-Szewc | LOWER_WALLS PRINT METAD COM UNITS DISTANCE UPPER_WALLS WHOLEMOLECULES | generic colvar setup vatom bias |
| 21.027 | EGFR activating mutations mechanism | bio | metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA | Francesco Gervasio | LOWER_WALLS PRINT METAD ENERGY MATHEVAL DISTANCE UPPER_WALLS CONTACTMAP WHOLEMOLECULES ALPHARMSD INCLUDE MOLINFO | generic colvar secondarystructure function bias |
| 20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Adriana Pietropaolo | PRINT PBMETAD CENTER COORDINATION WHOLEMOLECULES | generic colvar vatom bias |
| 20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Vojtech Spiwok | TORSION PRINT METAD | generic colvar bias |
| 20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Matteo Salvalaglio | LOWER_WALLS PRINT METAD ENERGY MATHEVAL UPPER_WALLS VOLUME CELL | function generic colvar bias |
| 20.018 | Free energy barriers from biased molecular dynamics simulations | methods | kinetics, free energy barriers, chemical reactions, nucleation, metadynamics | Kristof Bal | PAIRENTROPY UPPER_WALLS REWEIGHT_BIAS DENSITY COORDINATIONNUMBER REWEIGHT_METAD COMBINE SPRINT LOWER_WALLS PRINT ENERGY Q6 VOLUME LOAD FLUSH METAD CENTER DUMPGRID HISTOGRAM UNITS DISTANCE CONTACT_MATRIX COORDINATION CONVERT_TO_FES LOCAL_AVERAGE | generic colvar sprint adjmat gridtools volumes setup vatom symfunc function bias |
| 20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Jim Pfaendtner | DISTANCES PRINT DISTANCE GROUP RESTART CENTER COORDINATION WHOLEMOLECULES | generic colvar core setup vatom multicolvar |
| 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 | DISTANCES PRINT METAD UNITS COORDINATION CUSTOM | generic colvar setup function multicolvar bias |
| 19.075 | PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python | other | Python, automatic differentiation | Toni Giorgino | TORSION PRINT ANGLE DUMPDERIVATIVES DISTANCE GROUP ENDPLUMED CENTER COMBINE CUSTOM RESTRAINT | generic colvar core vatom function bias |
| 19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Matteo Salvalaglio | PRINT DISTANCE GROUP CENTER INCLUDE ENDPLUMED | generic colvar vatom core |
| 19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Wei Chen | COM COMBINE POSITION RESTRAINT ANN | colvar annfunc vatom function bias |
| 19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Kim Jelfs | DISTANCES PRINT COM INPLANEDISTANCES RESTART MOVINGRESTRAINT FLUSH | generic setup vatom multicolvar bias |
| 19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Gareth Tribello | LOWER_WALLS PRINT METAD UNITS UPPER_WALLS FCCUBIC CELL ENDPLUMED AROUND | generic colvar volumes setup symfunc bias |
| 19.041 | Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces | bio | metadynamics, collective variables, conformational changes, multiple walkers, Well-Tempered MetaD, peptide, binding, phosphorylation, post-transitional motif, sio2, adsorption | Jim Pfaendtner | PRINT METAD ENERGY COM DISTANCE UPPER_WALLS | generic colvar vatom bias |
| 19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Vittorio Limongelli | FUNNEL RMSD LOWER_WALLS PRINT METAD COM DISTANCE UPPER_WALLS WHOLEMOLECULES FUNNEL_PS | generic colvar vatom funnel bias |
| 19.013 | RNA FF FITTING | methods | force field, RNA | Giovanni Bussi | MATHEVAL PUCKERING CONSTANT INCLUDE MOLINFO TORSION BIASVALUE | function generic colvar bias |
| 24.018 | A new route to the prebiotic synthesis of glycine via ab initio-based machine learning calculations | chemistry | prebiotic chemistry, glycine, Strecker synthesis, ab initio calculations, machine learning | Léon HUET | DISTANCE PRINT | colvar generic |
| 24.012 | Molecular simulations to investigate the impact of N6-methylation in RNA recognition | bio | metadynamics, alchemistry, RNA modification, RNA:protein interactions | Giovanni Bussi | COM GROUP UPPER_WALLS COMBINE BIASVALUE MOLINFO DISTANCE CENTER METAD COORDINATION DEBUG GHBFIX LOWER_WALLS PRINT | colvar generic vatom function core bias |
| 24.011 | Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble | methods | committor, machine learning | Peilin Kang | POSITION UPPER_WALLS BIASVALUE CUSTOM ENDPLUMED MOLINFO UNITS LOWER_WALLS LOAD DISTANCE RMSD TORSION CELL INCLUDE PRINT GROUP ENERGY MATHEVAL COORDINATION WHOLEMOLECULES | colvar generic setup function core bias |
| 23.033 | DNA G-quadruplex and G-hairpin folding with ST-metaD protocol | bio | DNA, G4, GQ, quadruplex, hairpin, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | ERMSD COMBINE BIASVALUE MOLINFO METAD COORDINATION GHBFIX WHOLEMOLECULES PRINT | generic bias colvar function |
| 23.022 | A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar | methods | collective variables, machine learning, toy model | Enrico Trizio | OPES_METAD POSITION UPPER_WALLS ENDPLUMED PYTORCH_MODEL BIASVALUE CUSTOM UNITS LOWER_WALLS PRINT | colvar generic setup function opes pytorch bias |
| 23.013 | Path meta-eABF simulation of large scale conformational change in STING protein | methods | meta-eABF, path CV, large scale conformational change, STING protein, reciprocal barrier restraint | Istvan Kolossvary | DRR TIME FLUSH PATHMSD UPPER_WALLS BIASVALUE CUSTOM UNITS METAD LOWER_WALLS PRINT | colvar generic setup function drr 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 UPPER_WALLS OPES_EXPANDED HISTOGRAM LOWER_WALLS ENVIRONMENTSIMILARITY ECV_UMBRELLAS_LINE RESTART PRINT | gridtools setup generic envsim opes bias |
| 22.039 | Driving and characterizing nucleation of urea and glycine polymorphs in water | bio | metadynamics, nucleation, amino acids, polymorphism | Eric Beyerle | LOAD Q6 COORDINATIONNUMBER GROUP PAIRENTROPY COMBINE Q4 MATHEVAL CENTER METAD INCLUDE PRINT | gridtools setup generic vatom function symfunc core bias |
| 22.036 | Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction | bio | Well-tempered MetaDynamics with Hamiltonian Replica Exchange | Miroslav Krepl | LOAD FLUSH GROUP UPPER_WALLS COMBINE BIASVALUE MOLINFO CUSTOM METAD COORDINATION GHBFIX PRINT | colvar generic setup function core bias |
| 22.025 | Bubble nucleation rate predictions in a Lennard-Jones fluid | materials | free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation | Kristof Bal | LOAD FLUSH ANN RESTRAINT COORDINATIONNUMBER DUMPGRID UPPER_WALLS MOVINGRESTRAINT VOLUME BIASVALUE HISTOGRAM CUSTOM UNITS REWEIGHT_BIAS CONVERT_TO_FES COMMITTOR PRINT | gridtools colvar generic setup function symfunc annfunc bias |
| 22.022 | Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir | bio | RMSD, protein-ligand interactions | Isabell Grothaus | RMSD PRINT | colvar generic |
| 22.016 | Homogeneous ice nucleation in an ab initio machine learning model of water | chemistry | ice, water, nucleation, seeding, environment similarity, interfacial free energy, interfaces | Pablo Piaggi | OPES_METAD DUMPGRID UPPER_WALLS ENERGY VOLUME HISTOGRAM AROUND ENVIRONMENTSIMILARITY CUSTOM RESTART PRINT | gridtools colvar setup generic envsim function volumes opes bias |
| 22.005 | Collective Variable for Metadynamics Derived from AlphaFold Output | bio | AlphaFold, protein folding, protein structure prediction, metadynamics, deep learning, free energy simulation, collective variable | Vojtech Spiwok | LOAD METAD WHOLEMOLECULES PRINT | bias generic setup |
| 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 UPPER_WALLS COMBINE DISTANCE METAD COORDINATION LOWER_WALLS PRINT | colvar generic function symfunc bias |
| 21.043 | Predicting the Conformational Variability of Oncogenic GTP-bound G12D Mutated KRas-4B Proteins at Cell Membranes | chemistry | well-tempered metadynamics, KRas-4B, anionic membrane, conformational variability | Huixia Lu | FIXEDATOM FIT_TO_TEMPLATE METAD TORSION PRINT | vatom colvar generic bias |
| 21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Kresten Lindorff-Larsen | FLUSH EEFSOLV GROUP PBMETAD METAINFERENCE BIASVALUE MOLINFO CENTER ALPHARMSD GYRATION SAXS WHOLEMOLECULES PRINT | colvar generic vatom secondarystructure isdb core bias |
| 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 | Q6 BF_LEGENDRE ECV_MULTITHERMAL_MULTIBARIC TD_UNIFORM UPPER_WALLS VES_LINEAR_EXPANSION ENERGY VOLUME OPT_AVERAGED_SGD OPES_EXPANDED MATHEVAL ENVIRONMENTSIMILARITY ECV_UMBRELLAS_LINE RESTART PRINT | colvar setup generic ves function envsim symfunc opes bias |
| 21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Tarsis Ferreira | WHOLEMOLECULES REWEIGHT_METAD GROUP DUMPGRID UPPER_WALLS PUCKERING ENERGY DISTANCE MOLINFO HISTOGRAM RANDOM_EXCHANGES METAD COORDINATION LOWER_WALLS INCLUDE PRINT | gridtools colvar generic core bias |
| 20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Carlo Camilloni | FLUSH ALPHABETA PBMETAD ENSEMBLE METAINFERENCE DISTANCE MOLINFO STATS CENTER GYRATION SAXS TORSION WHOLEMOLECULES PRINT | colvar generic multicolvar vatom function isdb bias |
| 20.006 | Class B GPCR activation mechanism | bio | metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | UPPER_WALLS COMBINE ENERGY DISTANCE MOLINFO RMSD MATHEVAL CENTER METAD LOWER_WALLS WHOLEMOLECULES PRINT | colvar generic vatom function bias |
| 19.073 | On the role of enthalpic and entropic contributions on the conformational free energy landscape of MIL-101(Cr) building units | materials | metadynamics, MOF, MIL101Cr, conformational | Matteo Salvalaglio | COORDINATIONNUMBER UPPER_WALLS ENDPLUMED DISTANCES ENERGY METAD GYRATION LOWER_WALLS PRINT | colvar generic multicolvar symfunc bias |
| 19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Mattia Bernetti | WHOLEMOLECULES PATHMSD UPPER_WALLS METAD LOWER_WALLS PRINT | bias colvar generic |
| 19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | GiovanniMaria Piccini | FLUSH UPPER_WALLS COMBINE ENERGY DISTANCE UNITS METAD LOWER_WALLS PRINT | colvar generic setup function bias |
| 19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | FLUSH UPPER_WALLS COMBINE DISTANCES DISTANCE UNITS METAD RESTART PRINT | colvar generic multicolvar setup function bias |
| 19.030 | Coarse-Grained MetaDynamics (CG-MetaD) | bio | Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy | Vittorio Limongelli | COM WHOLEMOLECULES UPPER_WALLS DISTANCE METAD LOWER_WALLS PRINT | vatom colvar generic bias |
| 19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Gabriele Cesare Sosso | Q6 DFSCLUSTERING FLUSH CONTACT_MATRIX ENDPLUMED CLUSTER_WITHSURFACE MFILTER_MORE OUTPUT_CLUSTER COMMITTOR LOCAL_Q6 CLUSTER_NATOMS | generic multicolvar symfunc adjmat clusters |
| 19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Jim Pfaendtner | EXTERNAL GROUP ENERGY METAD COORDINATION | colvar bias core |
| 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 | COORDINATION ANGLE DISTANCE PRINT COMBINE DISTANCES COM COORDINATIONNUMBER FIXEDATOM GROUP LOWER_WALLS UNITS METAD RESTRAINT FLUSH UPPER_WALLS | symfunc multicolvar setup generic bias function vatom colvar core |
| 25.013 | Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices | bio | umbrella sampling, temperature ramping | Alexander Berlaga | RESTRAINT PRINT DISTANCE GYRATION PYTORCH_MODEL | generic colvar pytorch bias |
| 25.000 | Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer | bio | metadynamics, pathCV | Sahithya Sridharan Iyer | MOLINFO COM WHOLEMOLECULES FUNCPATHGENERAL RESTART METAD GROUP DISTANCE PRINT UPPER_WALLS | generic vatom bias core colvar function setup |
| 24.030 | NMR guided simulation of dsRBD | bio | Metainference, NMR, protein dynamics | Debadutta Patra | MOLINFO WHOLEMOLECULES ALPHABETA STATS ENSEMBLE METAINFERENCE PRINT GROUP RDC DISTANCE FLUSH | generic multicolvar isdb core colvar function |
| 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 | FIT_TO_TEMPLATE FIXEDATOM COORDINATION CENTER WHOLEMOLECULES CUSTOM OPES_METAD RESTART PRINT GROUP DISTANCE LOWER_WALLS PYTORCH_MODEL TORSION PATH UPPER_WALLS | generic vatom pytorch opes bias mapping core colvar function setup |
| 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 LOAD METAD PRINT GROUP TORSION | generic bias core colvar setup |
| 24.017 | Absolute Binding Free Energies with OneOPES | methods | protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy | Francesco Gervasio | MOLINFO OPES_EXPANDED WHOLEMOLECULES CUSTOM PRINT METAD BIASVALUE LOWER_WALLS PROJECTION_ON_AXIS INCLUDE TORSION RMSD MATHEVAL GROUP UPPER_WALLS COORDINATION CONSTANT ENERGY RESTART CONTACTMAP OPES_METAD_EXPLORE COM ECV_MULTITHERMAL WRAPAROUND | generic vatom opes bias core colvar function setup |
| 24.001 | A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations | bio | OPES, OPES-Flooding, QM/MM, Kinetics, Enzyme Catalysis | Dhiman Ray | UNITS CUSTOM OPES_METAD PRINT DISTANCE COMBINE LOWER_WALLS TORSION COMMITTOR FLUSH UPPER_WALLS | generic opes bias colvar function setup |
| 23.045 | Minute-timescale simulations of G Protein Coupled Receptor A2A activation mechanism reveal a receptor pseudo-active state | bio | Path CVs Metadynamics, GPCRs activation transition | Vittorio Limongelli | MOLINFO PATHMSD METAD DISTANCE PRINT LOWER_WALLS INCLUDE FUNCPATHMSD UPPER_WALLS ALPHARMSD CONTACTMAP | generic secondarystructure bias colvar function |
| 23.044 | Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition | materials | metadynamics, interlocked molecules | Luigi Leanza | DUMPGRID COORDINATION READ METAD GROUP PRINT CONVERT_TO_FES HISTOGRAM COMMITTOR ENDPLUMED | generic bias core colvar gridtools |
| 23.032 | Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics | bio | metadynamics, tSNE, neural network, machine learning, trp-cage, folding | Vojtech Spiwok | MOLINFO FIT_TO_TEMPLATE ANN WHOLEMOLECULES POSITION COMBINE METAD PRINT ALPHARMSD | generic annfunc secondarystructure bias colvar function |
| 23.029 | An accurate and efficient SAXS/SANS implementation including solvation layer effects suitable for restrained Molecular Dynamics simulations | bio | SAXS, SANS, SAS, metainference, proteins, nucleic-acid | Federico Ballabio | MOLINFO CENTER RMSD STATS ENSEMBLE SAXS PRINT GROUP BIASVALUE DISTANCE WRAPAROUND UPPER_WALLS | generic vatom isdb bias core colvar function |
| 23.019 | Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors | bio | binding pathway, binding energy, sketch-map, drug development | Raitis Bobrovs | LANDMARK_SELECT_FPS COM WHOLEMOLECULES VSTACK PATHMSD VORONOI CUSTOM TRANSPOSE METAD PRINT DISTANCE DISSIMILARITIES COLLECT_FRAMES UPPER_WALLS SKETCHMAP SKETCHMAP_PROJECTION | vatom generic valtools landmarks dimred bias colvar matrixtools function |
| 23.018 | Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention | materials | metadynamics, surface binding, peptide adsorption | Kaylyn Torkelson | COM PBMETAD PRINT DISTANCE GYRATION UPPER_WALLS | vatom colvar generic bias |
| 23.011 | OneOPES, a combined enhanced sampling method to rule them all | bio | OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding | Valerio Rizzi | MOLINFO OPES_EXPANDED OPES_METAD_EXPLORE ENERGY ECV_MULTITHERMAL PRINT DISTANCE METAD TORSION ENDPLUMED | generic opes colvar bias |
| 23.008 | PBMetaD simulations of Histatin5 | bio | metadynamics, IDP, Rg, PPII | Francesco Pesce | MOLINFO WHOLEMOLECULES PBMETAD PRINT GROUP GYRATION TORSION | generic colvar core bias |
| 22.030 | Mixing physics across temperatures with generative artificial intelligence | methods | REMD, Generative AI, DDPM | Yihang Wang | TORSION PRINT WHOLEMOLECULES | colvar generic |
| 22.008 | Ab initio metadynamics determination of temperature-dependent free-energy landscape in ultrasmall silver clusters | materials | Well tempered metadynamics, ab-initio, ase | Daniel Sucerquia | COORDINATION COM UNITS METAD COMBINE COORDINATIONNUMBER LOWER_WALLS DISTANCE GYRATION FLUSH UPPER_WALLS | vatom generic bias symfunc colvar function setup |
| 22.004 | Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques | chemistry | reaction discovery, OPES, collective variables | Umberto Raucci | OPES_METAD_EXPLORE COORDINATION COM UNITS LOAD CUSTOM MATHEVAL OPES_METAD PRINT DISTANCE GROUP LOWER_WALLS PYTORCH_MODEL UPPER_WALLS | vatom generic pytorch opes bias core colvar function setup |
| 22.001 | Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials | methods | enhanced sampling, variationally enhanced sampling, ves, metadynamics, bias representation, wavelets, adam | Benjamin Pampel | PRINT DISTANCE METAD INCLUDE OPT_ADAM OPT_AVERAGED_SGD TD_UNIFORM UNITS BF_CUBIC_B_SPLINES UPPER_WALLS BF_GAUSSIANS TD_WELLTEMPERED COORDINATION ENERGY FLUSH BF_LEGENDRE BF_WAVELETS POSITION VES_LINEAR_EXPANSION VES_OUTPUT_BASISFUNCTIONS BF_CHEBYSHEV | generic ves bias colvar setup |
| 21.014 | how to determine statistically accurate conformational ensembles | bio | metadynamics, metainference, errors, cv, SAXS, ensemble determination | Cristina Paissoni | MOLINFO CENTER WHOLEMOLECULES ALPHABETA STATS ENSEMBLE SAXS ANTIBETARMSD METAD PRINT PBMETAD BIASVALUE GYRATION TORSION CONTACTMAP | generic vatom secondarystructure multicolvar isdb bias colvar function |
| 21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Tarak Karmakar | LOAD MATHEVAL OPES_METAD PRINT GROUP LOWER_WALLS PYTORCH_MODEL FLUSH UPPER_WALLS | generic pytorch opes bias core function setup |
| 21.004 | Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy | bio | machine learning, well-tempered metadynamics, path collective variable, potential of mean force, standard binding free energy calculations, host-guest, protein-ligand unbinding | Dorothea Gobbo | WHOLEMOLECULES PATHMSD RESTART PRINT METAD LOWER_WALLS UPPER_WALLS | generic colvar bias setup |
| 20.030 | Converging experimental and computational views of the knotting mechanism of the smallest knotted protein | bio | phi-values, transition state, knotted proteins | Cristina Paissoni | MOLINFO COORDINATION WHOLEMOLECULES STATS RESTRAINT COMBINE PRINT | generic colvar function bias |
| 20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Cristina Paissoni | MOLINFO CENTER WHOLEMOLECULES STATS RESTRAINT SAXS ENSEMBLE PRINT GROUP DISTANCE BIASVALUE INCLUDE | generic vatom isdb bias core colvar function |
| 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 | TORSION METAD PRINT DISTANCE | colvar generic bias |
| 20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Glen Hocky | FISST UNITS ENERGY RESTRAINT MATHEVAL PRINT GROUP DISTANCE BIASVALUE GYRATION | generic fisst bias core colvar function setup |
| 19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_OPTIMIZER_BIAS MAZE_LOSS POSITION UNITS PRINT MAZE_SIMULATED_ANNEALING | colvar maze generic setup |
| 19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Luigi Bonati | UNITS LOAD POSITION ENERGY PRINT Q6 TORSION ENDPLUMED ENVIRONMENTSIMILARITY | generic symfunc envsim colvar setup |
| 19.049 | Determining the sizes of solid/liquid clusters in MD trajectories of nucleation | methods | nucleation, metadynamics, clustering, Steinhardt order parameters | Gareth Tribello | DFSCLUSTERING CLUSTER_DISTRIBUTION ONES CONTACT_MATRIX LOCAL_Q6 MATRIX_VECTOR_PRODUCT MORE_THAN CUSTOM OUTPUT_CLUSTER CLUSTER_NATOMS CLUSTER_PROPERTIES PRINT COORDINATIONNUMBER METAD SMAC Q6 DISTANCES OUTER_PRODUCT | generic clusters multicolvar bias symfunc matrixtools adjmat function |
| 19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Davide Provasi | COM WHOLEMOLECULES RMSD PRINT DISTANCE METAD ENDPLUMED FUNCPATHMSD CONTACTMAP | vatom generic bias colvar function |
| 19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Pratyush Tiwary | COM WHOLEMOLECULES ALPHABETA RESTART COMBINE DISTANCE PRINT TORSION EXTERNAL COMMITTOR | vatom generic multicolvar bias colvar function setup |
| 19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Kresten Lindorff-Larsen | MOLINFO ALPHABETA PRINT METAD COMBINE COMMITTOR FLUSH | generic multicolvar function bias |
| 19.011 | Automatic Gradient Computation for Collective Variables | other | gradient, differentiation, curvature | Toni Giorgino | ENDPLUMED | generic |
| 25.023 | Molecular simulations of Tau-protein oligomers | bio | metadynamics, proteins, aggregation | Giovanni Bussi | CUSTOM CONTACTMAP PRINT RESTART RMSD RESTRAINT FLUSH METAD | generic setup colvar bias function |
| 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 | CUSTOM ECV_MULTITHERMAL PRINT COMBINE OPES_METAD_EXPLORE OPES_EXPANDED RMSD GROUP GHOST COORDINATION DISTANCE MOLINFO ENERGY CENTER | opes vatom generic colvar core function |
| 25.001 | RNA G-quadruplex folding with ST-metaD protocol | bio | RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | COMBINE ERMSD METAD WHOLEMOLECULES MOLINFO | bias generic colvar function |
| 24.036 | Leveraging cryptic ligand envelopes through enhanced molecular simulations | bio | HREX, conformational heterogeneity, drug discovery, ligand binding, plitidepsin, aplidin, ligand-target complexes, cryptic ligand envelope | Francesco Colizzi | HISTOGRAM ANGLE PRINT DUMPGRID GROUP TORSION COORDINATION WHOLEMOLECULES CONVERT_TO_FES DISTANCE | gridtools core colvar generic |
| 24.032 | DeepLNE++ | methods | PATHCV, OPES | Thorben Fröhlking | CUSTOM OPES_METAD PRINT COMBINE GROUP TORSION COORDINATION ENERGY DISTANCE LOAD | opes generic setup colvar core function |
| 24.028 | All-atom simulations of RNA-membrane interactions | bio | metadynamics, membrane, RNA | Giovanni Bussi | LOWER_WALLS POSITION PUCKERING PRINT COMBINE UPPER_WALLS GROUP MATHEVAL GHOST CENTER METAD DISTANCES WHOLEMOLECULES GYRATION MOLINFO DISTANCE SORT | vatom generic colvar bias multicolvar core function |
| 24.027 | Proline cis and trans subensembles of a disordered peptide | bio | intrinsically disordered proteins, proline cis trans isomerisation, metadynamics, collective variables | Alice Pettitt | DIHCOR ALPHARMSD GYRATION PBMETAD PRINT COMBINE FLUSH GROUP TORSION ANTIBETARMSD PARABETARMSD WHOLEMOLECULES INCLUDE COORDINATION MOLINFO ENDPLUMED DISTANCE | secondarystructure generic colvar bias multicolvar core function |
| 24.016 | Cryo-EM guided simulations of ribozyme | bio | metainference, cryo-EM | Giovanni Bussi | EMMIVOX PRINT ERMSD RESTRAINT GROUP WHOLEMOLECULES INCLUDE MOLINFO BIASVALUE | generic isdb colvar bias core |
| 24.002 | Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes | chemistry | metadynamics, ligand design, solvent extraction | Xiaoyu Wang | PRINT RESTART TORSION UNITS METAD | bias setup colvar generic |
| 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 | COORDINATIONNUMBER OPES_METAD PRINT UPPER_WALLS FLUSH GROUP ZDISTANCES UNITS FIXEDATOM DISTANCE | opes vatom generic symfunc setup colvar bias multicolvar core |
| 23.036 | Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? | bio | NaCl, nucleation, metadynamics | Ruiyu Wang | COORDINATIONNUMBER PRINT COMBINE VOLUME MATHEVAL METAD Q4 ENERGY Q6 | generic symfunc colvar bias function |
| 23.021 | Into the Dynamics of Rotaxanes at Atomistic Resolution | materials | metadynamics, rotaxanes, molecular shuttles, molecular machines | Luigi Leanza | CUSTOM PRINT UPPER_WALLS MATHEVAL TORSION METAD FIXEDATOM DISTANCE CENTER | vatom generic colvar bias function |
| 23.014 | Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 | bio | metadynamics, oligomerization, chemokine receptors, GPCR, membrane | Vittorio Limongelli | COM PRINT COMBINE UPPER_WALLS FLUSH TORSION METAD WHOLEMOLECULES DISTANCE | vatom generic colvar bias function |
| 23.007 | Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains | bio | metadynamics, peptoids, parallel-bias metadynamics | Jim Pfaendtner | PBMETAD PRINT COM RESTRAINT TORSION COORDINATION WHOLEMOLECULES INCLUDE GYRATION | vatom generic colvar bias |
| 22.042 | Metadynamics of NSP10 and variants | bio | metadynamics, NSP10, crystal structure, variants | Shozeb Haider | METAD TORSION PRINT | generic 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 | RMSD PRINT | colvar generic |
| 22.003 | Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling | methods | opes, metadynamics, reweighting, alanine, muller | Michele Invernizzi | CUSTOM OPES_METAD POSITION ECV_MULTITHERMAL LOWER_WALLS PBMETAD PRINT OPES_METAD_EXPLORE UPPER_WALLS OPES_EXPANDED TORSION ECV_UMBRELLAS_FILE METAD UNITS ENERGY ENDPLUMED BIASVALUE | opes generic setup colvar bias function |
| 21.051 | Automatic learning of hydrogen-bond fixes in an AMBER RNA force field | methods | force field, RNA | Giovanni Bussi | PRINT COMBINE ERMSD METAD COORDINATION WHOLEMOLECULES MOLINFO BIASVALUE | bias function 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 | CUSTOM PRINT COMBINE VOLUME METAD COORDINATION ENDPLUMED | bias generic colvar function |
| 21.020 | Reweighted Jarzynski sampling | methods | free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions | Kristof Bal | CUSTOM PRINT RESTRAINT MOVINGRESTRAINT METAD OPT_AVERAGED_SGD COMBINE ANN CONVERT_TO_FES VES_LINEAR_EXPANSION BIASVALUE TD_WELLTEMPERED COORDINATIONNUMBER UPPER_WALLS FLUSH DUMPGRID CONSTANT UNITS LOAD HISTOGRAM OPES_METAD REWEIGHT_METAD BF_CHEBYSHEV DISTANCE REWEIGHT_BIAS | opes generic symfunc setup annfunc colvar bias gridtools ves function |
| 21.019 | Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations | materials | Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen | Matteo Salvalaglio | COM PRINT TORSIONS MATHEVAL KDE DISTANCE | vatom generic colvar multicolvar gridtools function |
| 21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Adriana Pietropaolo | PBMETAD PRINT CONSTANT RESTART MATHEVAL TORSION WHOLEMOLECULES BIASVALUE | generic setup colvar bias function |
| 21.006 | OPES, On-the-fly Probability Enhanced Sampling Method | methods | opes, alanine dipeptide, well-tempered, multithermal, multiumbrella | Michele Invernizzi | OPES_METAD ECV_MULTITHERMAL ECV_UMBRELLAS_LINE PRINT OPES_EXPANDED TORSION ENERGY ENDPLUMED | opes colvar generic |
| 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 | PRINT STATS COORDINATION ENDPLUMED GYRATION METAINFERENCE DIHCOR ENSEMBLE PBMETAD COMBINE INCLUDE MOLINFO ALPHARMSD FLUSH GROUP ANTIBETARMSD PARABETARMSD WHOLEMOLECULES TORSION CS2BACKBONE | secondarystructure generic isdb colvar bias multicolvar core function |
| 19.080 | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | methods | ves, variationally enhanced sampling, vibrational excitation, chemical reactions | Kristof Bal | LOWER_WALLS HISTOGRAM ANGLE PRINT COMBINE EXTERNAL UPPER_WALLS FLUSH DUMPGRID BF_CHEBYSHEV TD_GRID UNITS COORDINATION OPT_AVERAGED_SGD CONVERT_TO_FES VES_LINEAR_EXPANSION DISTANCE TD_WELLTEMPERED | generic setup colvar bias gridtools ves function |
| 19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Giovanni Bussi | LOWER_WALLS RESTRAINT COORDINATION WHOLEMOLECULES ENDPLUMED DISTANCE | generic colvar bias |
| 19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Kim E. Jelfs | LOWER_WALLS COM PRINT UPPER_WALLS RESTART GROUP CENTER METAD DISTANCE | vatom generic setup colvar bias core |
| 19.059 | cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide | bio | bias-exchange metadynamics, cis-trans isomerization | Fabrizio Marinelli | PRINT TORSION RANDOM_EXCHANGES METAD INCLUDE | bias colvar generic |
| 19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Cristina Paissoni | SAXS ANGLE ENSEMBLE PBMETAD PRINT COMBINE GROUP MATHEVAL ALPHABETA CENTER STATS COORDINATION WHOLEMOLECULES INCLUDE MOLINFO ENDPLUMED BIASVALUE | vatom generic isdb colvar bias multicolvar core function |
| 19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Haochuan Chen | TORSION PRINT DRR | drr colvar generic |
| 19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Matteo Salvalaglio | CELL LOWER_WALLS PRINT COMBINE VOLUME UPPER_WALLS MATHEVAL TORSION METAD ENERGY ENDPLUMED | generic function colvar bias |
| 19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Matteo Salvalaglio | COORDINATIONNUMBER PRINT RESTART METAD DISTANCES ENDPLUMED GYRATION | generic symfunc setup colvar bias multicolvar |
| 19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Max Bonomi | PRINT EMMI GROUP WHOLEMOLECULES MOLINFO BIASVALUE | bias isdb core generic |
| 25.014 | Atomic resolution ensembles of intrinsically disordered and multi-domain proteins with Alphafold | bio | bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement | Vincent Schnapka | BAIES GROUP BIASVALUE PRINT | bias isdb generic core |
| 25.009 | Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water | chemistry | metadynamics, nitrate photolysis | Kam-Tung Chan | GROUP COORDINATION DISTANCE REWEIGHT_METAD RESTART METAD DUMPGRID UPPER_WALLS FLUSH CUSTOM READ HISTOGRAM PRINT | setup colvar core bias gridtools generic function |
| 25.002 | M3_PCV-ABMD | chemistry | Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor | Gian Marco Elisi | ABMD PATHMSD ENDPLUMED UPPER_WALLS UNITS PRINT | bias setup generic colvar |
| 24.034 | Umbrella sampling of ion in transporter SLC26A7 | bio | umbrella sampling, transporter, ions | Xiaoli Lu | POSITION UNITS RESTRAINT PRINT | setup bias generic colvar |
| 24.033 | Transient interactions between the fuzzy coat and the cross-b core of brain-derived Ab42 filaments | bio | CryoEM, MEMMI, Metadynamics, Metainference, Ab42 Fibrils, structural ensemble | Maria Milanesi | ALPHARMSD PBMETAD GROUP RMSD COM EMMI DUMPATOMS WHOLEMOLECULES COORDINATION DISTANCE BIASVALUE PARABETARMSD UPPER_WALLS DUMPMASSCHARGE CENTER MOLINFO PRINT | colvar core bias generic vatom secondarystructure isdb |
| 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 | ENERGY COMMITTOR DISTANCE BIASVALUE MATHEVAL RESTART METAD FLUSH RESTRAINT TORSION COORDINATIONNUMBER MOLINFO PRINT | setup generic colvar bias symfunc function |
| 23.037 | Estimating binding free energy of solid binding peptides without extensive sampling | bio | metadynamics, solid binding peptides | Xin Qi | PBMETAD COM LOWER_WALLS DISTANCE GYRATION UPPER_WALLS MOLINFO PRINT | bias generic vatom colvar |
| 23.030 | Data Driven Classification of Ligand Unbinding Pathways | bio | OPES Explore, OPES Flooding, Benzene T4 Lysozyme, Ligand unbinding, Pathway classification, Kinetics, Residence time | Dhiman Ray | LOWER_WALLS WHOLEMOLECULES POSITION ENDPLUMED UNITS TORSION CUSTOM ENERGY COM DISTANCE MATHEVAL GROUP WRAPAROUND COMMITTOR COORDINATION BIASVALUE CENTER PRINT OPES_METAD_EXPLORE FIT_TO_TEMPLATE FLUSH OPES_METAD UPPER_WALLS MOLINFO | setup colvar generic bias core vatom function opes |
| 23.026 | Machine Learning Nucleation Collective Variables with Graph Neural Networks | chemistry | Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks | Florian Dietrich | MFILTER_MORE COMBINE GROUP MOVINGRESTRAINT LOWER_WALLS METAD Q6 COORDINATIONNUMBER LOCAL_Q6 PRINT | generic core bias symfunc multicolvar function |
| 22.037 | Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site | chemistry | metadynamics, DNA, abasic | Mike Jones | DISTANCES METAD DISTANCE PRINT | bias multicolvar generic colvar |
| 22.035 | Deciphering the alphabet of disorder — Glu and Asp act differently on local but not global properties | bio | intrinsically disordered proteins, parallel bias metadynamics, protein | Kresten Lindorff-Larsen | PBMETAD WHOLEMOLECULES GYRATION TORSION MOLINFO | bias colvar generic |
| 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 | CELL LOWER_WALLS COMMITTOR DRMSD MATHEVAL METAD UPPER_WALLS CUSTOM PRINT | bias generic colvar function |
| 22.026 | Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification | materials | Peptoid, silica | Jim Pfaendtner | PBMETAD COM GYRATION DISTANCE UPPER_WALLS MOLINFO PRINT | bias generic vatom 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 | PATHMSD COM LOWER_WALLS WHOLEMOLECULES DISTANCE FUNNEL_PS METAD UPPER_WALLS FUNNEL PRINT | funnel generic colvar bias vatom |
| 22.000 | Amyloid precursor protein processing by human γ-secretase | bio | Bias Exchange Metadynamics, Helix unfolding, coupled binding | Xiaoli Lu | ALPHARMSD COORDINATION DISTANCE ANTIBETARMSD RANDOM_EXCHANGES METAD CONTACTMAP UNITS INCLUDE CENTER MOLINFO PRINT | setup generic colvar bias vatom secondarystructure |
| 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 METAD RANDOM_EXCHANGES ENDPLUMED INCLUDE TORSION PRINT | bias colvar generic |
| 21.032 | Metal-coupled folding mechanism to metallothionein | bio | parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination | Manuel-Peris Diaz | PBMETAD GROUP WHOLEMOLECULES COORDINATION UNITS | setup colvar generic bias core |
| 21.013 | Role of vibrational excitation in heterogeneous catalysis | chemistry | catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption | Kristof Bal | LOWER_WALLS UNITS LOAD TD_GRID HISTOGRAM COMBINE UWALLS DISTANCES DISTANCE REWEIGHT_METAD METAD REWEIGHT_BIAS COORDINATIONNUMBER CONVERT_TO_FES OPT_AVERAGED_SGD EXTERNAL COORDINATION VES_LINEAR_EXPANSION DUMPGRID RESTRAINT PRINT UPPER_WALLS FLUSH BF_CHEBYSHEV ANGLES | setup colvar generic bias gridtools symfunc multicolvar function ves |
| 21.000 | Uremic toxin time scale dynamics | bio | uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs) | Jim Pfaendtner | GROUP COM WHOLEMOLECULES DISTANCE PRINT | colvar vatom generic core |
| 20.012 | Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies | bio | metadynamics, well-tempered ensemble, ligand binding, binding affinity calculations, novel COLVAR, funnel restraints, Hamiltonian replica-exchange, PathCV, COMetPath, SWISH | Francesco Gervasio | GROUP COM LOWER_WALLS WHOLEMOLECULES DISTANCE BIASVALUE MATHEVAL FUNCPATHGENERAL METAD CONTACTMAP UPPER_WALLS LOAD INCLUDE CONSTANT PROJECTION_ON_AXIS MOLINFO PRINT | setup colvar generic bias core vatom 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 | OPT_AVERAGED_SGD OPT_DUMMY VES_LINEAR_EXPANSION RESTART MATHEVAL BF_LEGENDRE TD_WELLTEMPERED VOLUME ENVIRONMENTSIMILARITY UPPER_WALLS Q6 PRINT | setup envsim colvar bias symfunc generic function ves |
| 19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Valerio Rizzi | COMBINE GROUP DISTANCES RESTART METAD ENDPLUMED UNITS UPPER_WALLS FLUSH COORDINATIONNUMBER PRINT | setup generic core bias symfunc multicolvar function |
| 19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Matteo Salvalaglio | HISTOGRAM COMMITTOR EXTERNAL DISTANCE REWEIGHT_METAD BIASVALUE MATHEVAL METAD DUMPGRID REWEIGHT_BIAS TORSION READ CONVERT_TO_FES PRINT | colvar generic bias gridtools function |
| 19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Jakub Rydzewski | PATHMSD LOWER_WALLS RESTART METAD UPPER_WALLS UNITS PRINT | bias generic setup colvar |
| 19.056 | maze | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_OPTIMIZER_BIAS POSITION MAZE_LOSS UNITS MAZE_SIMULATED_ANNEALING PRINT | setup generic colvar maze |
| 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 | COMBINE GROUP ALPHABETA COM RMSD LOWER_WALLS WHOLEMOLECULES DISTANCES DISTANCE REWEIGHT_METAD BRIDGE METAD UPPER_WALLS FUNNEL TORSION MOLINFO PRINT | funnel colvar core bias generic multicolvar vatom function adjmat |
| 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 | WHOLEMOLECULES GROUP FIXEDATOM OPES_METAD_EXPLORE UPPER_WALLS COORDINATION ANGLE ENERGY FIT_TO_TEMPLATE PRINT CENTER MATHEVAL DISTANCE | bias function vatom opes generic colvar core |
| 25.011 | Chiral perovskite nucleation | chemistry | metadynamics, chiral perovskites, nucleation | Adriana Pietropaolo | MULTI_RMSD UNITS UPPER_WALLS RESTART LOWER_WALLS PBMETAD PRINT MATHEVAL DISTANCE | bias function setup generic colvar |
| 24.005 | Learning Markovian Dynamics with Spectral Maps | methods | spectral map, collective variables, machine learning | Jakub Rydzewski | BIASVALUE UNITS CUSTOM PRINT DISTANCE | bias function setup generic colvar |
| 23.028 | Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process | chemistry | Ammonia decomposition; Dynamics;OPES; Neural Network potential | Manyi Yang | GROUP FIXEDATOM UNITS DISTANCES UPPER_WALLS LOWER_WALLS COORDINATIONNUMBER OPES_METAD ZDISTANCES ENERGY CUSTOM PRINT FLUSH COM MATHEVAL DISTANCE COMMITTOR | bias function vatom setup symfunc opes generic multicolvar colvar core |
| 23.025 | Probing ion binding to G-quadruplexes and related events | chemistry | metadynamics, repulsive potential, nucleic acids, G-quadruplexes | Marcelo Poleto | WHOLEMOLECULES GROUP METAD WRAPAROUND UNITS DISTANCES LOWER_WALLS UPPER_WALLS RESTART DUMPATOMS FIT_TO_TEMPLATE POSITION PRINT FLUSH COM MATHEVAL DISTANCE | bias function setup vatom generic multicolvar colvar core |
| 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 | WHOLEMOLECULES BIASVALUE METAD UPPER_WALLS LOWER_WALLS CONSTANT PRINT MATHEVAL DISTANCE | function bias colvar 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 EXTRACV PRINT TORSION READ | bias colvar generic |
| 22.043 | Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES | bio | OPES, RNA, Tetraloop, Folding | Gül Zerze | WHOLEMOLECULES ECV_MULTITHERMAL CONTACTMAP OPES_EXPANDED ECV_UMBRELLAS_LINE ENERGY PRINT | opes colvar generic |
| 22.040 | From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure | bio | SARS-CoV-2, Spike, Omicron | Miłosz Wieczór | WHOLEMOLECULES METAD UPPER_WALLS LOWER_WALLS PRINT PCAVARS | bias generic mapping |
| 22.031 | Rare Event Kinetics from Adaptive Bias Enhanced Sampling | methods | OPES Flooding, Kinetics, Rate, OPES, Machine Learning | Dhiman Ray | WHOLEMOLECULES GROUP INCLUDE UNITS POSITION TORSION COMMITTOR RMSD BIASVALUE PYTORCH_MODEL DISTANCE ENDPLUMED ENERGY CONTACTMAP CUSTOM OPES_METAD MOLINFO COMBINE CONSTANT PRINT | pytorch bias function setup opes generic colvar core |
| 22.028 | N-glycan conformer distributions in atomistic simulation | bio | REST2, RECT, N-glycan, pucker | Isabell Grothaus | DUMPGRID METAD HISTOGRAM MOLINFO PRINT TORSION PUCKERING READ CONVERT_TO_FES | generic bias colvar gridtools |
| 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 | INCLUDE OPES_EXPANDED UPPER_WALLS LOWER_WALLS ECV_UMBRELLAS_LINE PRINT ENVIRONMENTSIMILARITY | opes bias generic envsim |
| 22.017 | Water regulates the residence time of Benzamidine in Trypsin | bio | ligand binding, water, opes, benzamidine trypsin, unbinding rates, machine learning, Deep-LDA, Deep-TICA | Narjes Ansari | WHOLEMOLECULES RMSD GROUP FIXEDATOM CUSTOM UPPER_WALLS COORDINATION LOWER_WALLS OPES_METAD PYTORCH_MODEL FIT_TO_TEMPLATE PRINT CENTER MATHEVAL DISTANCE COMMITTOR | pytorch bias function vatom opes generic colvar core |
| 22.015 | Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome | bio | photodynamics, bacteriophytochrome, variationally enhanced sampling | Jakub Rydzewski | BF_FOURIER PRINT TORSION OPT_AVERAGED_SGD VES_LINEAR_EXPANSION TD_UNIFORM | ves colvar generic |
| 22.012 | Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT | bio | contact maps, protein-protein interactions | Isabell-Louise Grothaus | CONTACTMAP CENTER DISTANCE PRINT | vatom colvar generic |
| 21.048 | Enhancing ligand exploration within a channel pore and fenestrations using metadynamics | bio | well-tempered metadynamics, protein-ligand enhanced sampling, sodium channel, Nav, small molecule drug | Elaine Tao | METAD UNITS CUSTOM UPPER_WALLS LOWER_WALLS PRINT TORSION COM DISTANCE | bias function setup vatom generic colvar |
| 21.047 | Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations | materials | pair entropy, metadynamics, ves, solids, crystallization | Pablo Piaggi | BF_LEGENDRE METAD LOAD PAIRENTROPY RESTART COMBINE ENERGY PRINT TD_WELLTEMPERED OPT_AVERAGED_SGD VOLUME VES_LINEAR_EXPANSION | bias ves gridtools function setup generic colvar |
| 21.044 | NaCl nucleation | chemistry | metadynamics, DFS clustering | Aaron Finney | CLUSTER_DISTRIBUTION GROUP METAD DUMPGRID FIXEDATOM INSPHERE COORDINATIONNUMBER LOCAL_Q6 COMBINE Q6 HISTOGRAM PRINT DFSCLUSTERING CONTACT_MATRIX CLUSTER_NATOMS MFILTER_MORE | clusters adjmat bias gridtools function vatom symfunc generic multicolvar volumes core |
| 21.033 | Multiple-path-metadynamics applied to DNA base-pairing transitions | bio | path-CV, metadynamics, multiple-walker, dna | Alberto Pérez-de-Alba-Ortíz | METAD INCLUDE UPPER_WALLS COMBINE CONSTANT PRINT MOVINGRESTRAINT RESTRAINT | function bias generic |
| 21.026 | Probing allosteric regulations with coevolution-driven molecular simulations | bio | metadynamics, coevolution, allostery, adenylate cyclase | Francesco Colizzi | WHOLEMOLECULES METAD UNITS UPPER_WALLS PRINT COM DISTANCE PATHMSD | bias setup vatom generic 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 METAD INCLUDE UNITS CUSTOM ENERGY CONSTANT PRINT TORSION DISTANCE | bias function setup generic colvar |
| 21.012 | NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition | bio | funnel metadynamics | Jim Pfaendtner | FUNNEL METAD UPPER_WALLS LOWER_WALLS PRINT COM FUNNEL_PS DISTANCE | funnel bias vatom generic colvar |
| 21.011 | CmuMD simulations of NaCl(aq) at graphite | chemistry | CmuMD, DFS clustering | Aaron Finney | CLUSTER_DISTRIBUTION MULTICOLVARDENS GROUP DUMPGRID FIXEDATOM DENSITY LOAD AROUND COORDINATIONNUMBER PRINT DFSCLUSTERING RESTRAINT CONTACT_MATRIX CLUSTER_NATOMS MFILTER_MORE | clusters adjmat bias gridtools vatom setup symfunc generic multicolvar volumes core |
| 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 | ERMSD RESTART MOLINFO PRINT ABMD TORSION CENTER DISTANCE | bias setup vatom 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 | METAD RESTART FIT_TO_TEMPLATE PRINT CENTER DISTANCE | bias setup vatom generic colvar |
| 20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Michele Invernizzi | WHOLEMOLECULES UNITS POSITION TORSION MATHEVAL ECV_MULTITHERMAL RMSD UPPER_WALLS ENVIRONMENTSIMILARITY VOLUME ENDPLUMED ECV_LINEAR ECV_MULTITHERMAL_MULTIBARIC OPES_EXPANDED ENERGY LOAD CUSTOM ECV_UMBRELLAS_LINE MOLINFO Q6 PRINT | bias function envsim setup opes symfunc generic colvar |
| 20.001 | Conformational stability and dynamics in solution and in crystals report similarly on unfolding and aggregation propensity of amyloidogenic proteins | bio | metainference, metadynamics, NMR, protein dynamics, b2m, protein crystals | Carlo Camilloni | WHOLEMOLECULES GROUP BIASVALUE PBMETAD LOWER_WALLS UPPER_WALLS ANTIBETARMSD ALPHABETA MOLINFO PRINT CS2BACKBONE FLUSH ENDPLUMED | isdb bias secondarystructure generic multicolvar core |
| 19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Valerio Rizzi | GROUP METAD UNITS RESTART COORDINATIONNUMBER COMBINE PRINT EXTERNAL FLUSH ENDPLUMED | bias function setup symfunc generic core |
| 19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Giovanni Bussi | WHOLEMOLECULES METAD MAXENT INCLUDE COORDINATION MOLINFO PRINT FLUSH TORSION SORT COM MATHEVAL DISTANCE | bias function vatom generic colvar |
| 19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | METAD UPPER_WALLS GYRATION MOLINFO ENERGY PRINT COM DISTANCE | vatom bias colvar generic |
| 19.050 | Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes | chemistry | metadynamics, membranes, Willard Chandler surface | Gareth Tribello | DUMPGRID METAD UPPER_WALLS RESTART HISTOGRAM DISTANCE_FROM_CONTOUR COMBINE PRINT READ CONVERT_TO_FES REWEIGHT_BIAS | contour bias function gridtools setup generic |
| 19.032 | Chemical reaction in solution using path collective variables based on coordination patterns | chemistry | chemical reactions, solutions, metadynamics, coordination patterns | Fabio Pietrucci | METAD PATH DISTANCES UPPER_WALLS RESTART PRINT FLUSH | bias mapping setup generic multicolvar |
| 19.009 | RNA tetraloops folding | bio | metadynamics, RNA, folding | Giovanni Bussi | WHOLEMOLECULES ERMSD RMSD METAD MOLINFO PRINT ENDPLUMED | bias colvar generic |
| 19.005 | Cmyc small molecule interaction | bio | metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP | Gabriella Heller | WHOLEMOLECULES GROUP INCLUDE PBMETAD COORDINATION GYRATION ALPHABETA MOLINFO METAINFERENCE PRINT CS2BACKBONE CENTER DISTANCE | isdb bias vatom generic multicolvar colvar core |
| 19.004 | MI Ubiquitin | bio | metainference, NMR | Max Bonomi | WHOLEMOLECULES GROUP RDC METAINFERENCE MOLINFO PRINT CS2BACKBONE | isdb core generic |
| 19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Giovanni Bussi | RANDOM_EXCHANGES ERMSD METAD INCLUDE DISTANCES UPPER_WALLS LOWER_WALLS MOLINFO COMBINE ANGLE PRINT FLUSH DISTANCE | bias function generic multicolvar colvar |
| 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 | BIASVALUE PRINT GROUP BAIES | bias isdb generic core |
| 25.008 | Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting | methods | metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting | Dhiman Ray | TORSION METAD RMSD WHOLEMOLECULES OPES_METAD ENERGY CUSTOM GROUP DISTANCE ENDPLUMED UPPER_WALLS PRINT PYTORCH_MODEL BIASVALUE UNITS POSITION LOWER_WALLS MOLINFO | bias function setup generic core opes colvar pytorch |
| 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 | TORSION WHOLEMOLECULES PBMETAD VOLUME ENERGY INCLUDE RESTART DISTANCE GYRATION PRINT DUMPATOMS READ UPDATE_IF MOLINFO CENTER | bias setup generic vatom colvar |
| 24.026 | Constant pH metadynamics of RNA oligomers | bio | metadynamics, pH, RNA | Giovanni Bussi | TORSION METAD PUCKERING RESTART PRINT MOLINFO | bias setup colvar generic |
| 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 | METAD FLUSH RMSD WHOLEMOLECULES DRR UPPER_WALLS PRINT PYTORCH_MODEL COORDINATION LOWER_WALLS MOLINFO | bias generic drr colvar pytorch |
| 24.010 | Oxytocin metadynamics simulation | bio | metadynamics, oxytocin, peptide | Jan Beránek | TORSION FLUSH WHOLEMOLECULES METAD RESTART PRINT | bias setup colvar generic |
| 24.003 | Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations | chemistry | steered molecular dynamics, foldamers, peptoids, bio-inspired | Kaylyn Torkelson | TORSION WHOLEMOLECULES INCLUDE ALPHABETA DISTANCE GYRATION PRINT COM MOVINGRESTRAINT COORDINATION | bias vatom generic multicolvar colvar |
| 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 | METAD RMSD WHOLEMOLECULES DISTANCE PRINT MATHEVAL MOLINFO | bias function colvar 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 setup generic |
| 23.023 | Rational design of novel biomimetic sequence-defined polymers for mineralization applications | methods | metadynamics, surface binding, biomimetic mineralization | Kaylyn Torkelson | PBMETAD UPPER_WALLS DISTANCE GYRATION PRINT COM COORDINATION | bias vatom colvar generic |
| 23.017 | How and When Does an Enzyme React? Unraveling α-Amylase Catalytic Activity with Enhanced Sampling Techniques | bio | enzymatic reaction discovery, reaction mechanism, catalysis, ligand-binding modes, water, alpha-amylase, sugar, QM/MM MD, OPES, OPES explore, graph CV, machine learning, Deep TDA CV, path CV | Sudip Das | TORSION PATH WHOLEMOLECULES OPES_METAD_EXPLORE OPES_METAD CUSTOM GROUP DISTANCE FIT_TO_TEMPLATE UNITS PRINT PYTORCH_MODEL UPPER_WALLS FIXEDATOM COORDINATION LOWER_WALLS CENTER | bias function setup generic mapping core opes vatom colvar pytorch |
| 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 FIT_TO_TEMPLATE FIXEDATOM COORDINATION ANGLE COMMITTOR CENTER OPES_METAD GROUP ENDPLUMED COMBINE RMSD WHOLEMOLECULES ENERGY UPPER_WALLS PYTORCH_MODEL CONTACTMAP INCLUDE DISTANCE PRINT MATHEVAL LOWER_WALLS MOLINFO | bias function generic core opes vatom colvar pytorch |
| 23.006 | Transcription factor unbinding | bio | metadynamics, DNA, conformational changes | Malin Lüking | METAD DUMPFORCES CONTACTMAP ALPHARMSD DISTANCE PRINT COM ANGLE MOLINFO | bias generic vatom secondarystructure colvar |
| 23.005 | A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs | bio | metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A | Timothy Clark | METAD RMSD WHOLEMOLECULES CONVERT_TO_FES DUMPGRID DISTANCE READ PRINT HISTOGRAM MATHEVAL REWEIGHT_METAD MOLINFO | bias function generic gridtools colvar |
| 22.041 | Skipping the Replica Exchange Ladder with Normalizing Flows | methods | OPES, alanine, normalizing flows, replica exchange | Michele Invernizzi | TORSION OPES_METAD ENERGY ECV_MULTITHERMAL OPES_EXPANDED ENDPLUMED UNITS PRINT POSITION | generic setup colvar opes |
| 22.024 | Conformational Entropy as a Potential Liability of Computationally Designed Antibodies | bio | metadynamics, conformational entropy, antibody, nanobody | Thomas Löhr | TORSION ANTIBETARMSD WHOLEMOLECULES PBMETAD ALPHARMSD ALPHABETA RESTART PRINT COM MOLINFO | bias setup vatom generic multicolvar secondarystructure colvar |
| 22.020 | Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix–Junction–Helix RNA | bio | RNA force field, Helix-Junction-Helix RNA, SAXS, Well tempered metadynamics | Weiwei He | TORSION METAD WHOLEMOLECULES GROUP DISTANCE PRINT COM | bias generic core vatom colvar |
| 22.013 | Ligand dissociation from PreQ1 riboswitch | bio | ligand, RNA, metadynamics, pRAVE | Yihang Wang | METAD RMSD WHOLEMOLECULES DISTANCE PRINT COORDINATIONNUMBER COM COMBINE MOLINFO COMMITTOR | bias function generic symfunc vatom colvar |
| 21.049 | Multiple-path-metadynamics and PathMaps | methods | path-CV, metadynamics, multiple-walker, multiple paths, pathmap | Alberto Pérez-de-Alba-Ortíz | TORSION METAD MOVINGRESTRAINT CONSTANT LOAD CUSTOM RESTRAINT UPPER_WALLS UNITS PRINT COMBINE LOWER_WALLS ENSEMBLE | bias setup function generic colvar |
| 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 | WHOLEMOLECULES RESTART GROUP UPPER_WALLS DISTANCE BIASVALUE PRINT COM MOLINFO EMMI | bias setup isdb generic core vatom colvar |
| 21.035 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, interface | Aaron Finney | LOAD RESTRAINT GROUP DISTANCE FIXEDATOM PRINT | bias setup generic core vatom colvar |
| 21.025 | Computational and biochemical analysis of type IV pilus dynamics and stability | bio | molecular dynamics, calcium binding, Type IV pilus | Yasaman Karami | UPPER_WALLS LOWER_WALLS PRINT DISTANCE | bias colvar generic |
| 21.018 | Localized Volume-based Metadynamics | bio | LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification | Riccardo Capelli | METAD FIXEDATOM COM COORDINATION MATHEVAL HISTOGRAM FLUSH GROUP ENDPLUMED READ CONVERT_TO_FES RMSD WHOLEMOLECULES UPPER_WALLS REWEIGHT_METAD DUMPGRID DISTANCE PRINT POSITION | bias function generic core gridtools vatom colvar |
| 21.017 | All-atom simulations of the Vav1 AD construct | bio | metadynamics, parallel-bias, well-tempered | Simone Orioli | METAD WHOLEMOLECULES PBMETAD ALPHARMSD CONTACTMAP ALPHABETA GROUP RESTART PRINT REWEIGHT_BIAS MOLINFO | bias setup generic core multicolvar secondarystructure colvar |
| 21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Kristof Bal | FLUSH METAD DUMPGRID LOAD REWEIGHT_METAD UPPER_WALLS UNITS COORDINATIONNUMBER PRINT MOVINGRESTRAINT CONVERT_TO_FES HISTOGRAM COMMITTOR | bias setup generic symfunc gridtools |
| 20.032 | Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil | materials | clustering, conformational isomers | Matteo Salvalaglio | TORSION ENDPLUMED PRINT | colvar generic |
| 20.026 | Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor | bio | Metadynamics, Umbrella sampling | Brandon Peters | METAD MULTI_RMSD DUMPGRID RESTRAINT REWEIGHT_METAD PRINT CONVERT_TO_FES HISTOGRAM | bias gridtools colvar generic |
| 20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Luigi Bonati | TORSION FLUSH LOAD OPES_METAD GROUP ENDPLUMED DISTANCE UPPER_WALLS PRINT PYTORCH_MODEL UNITS COM MATHEVAL LOWER_WALLS | bias setup function generic core opes vatom colvar pytorch |
| 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 | METAD CONVERT_TO_FES DUMPGRID REWEIGHT_METAD DISTANCE ENDPLUMED UPPER_WALLS PRINT COM READ COMBINE HISTOGRAM MATHEVAL LOWER_WALLS ABMD | bias function generic gridtools vatom colvar |
| 19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | METAD ENERGY DISTANCE UPPER_WALLS GYRATION PRINT COM MOLINFO | bias vatom colvar generic |
| 19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Sandro Bottaro | TORSION RMSD WHOLEMOLECULES METAD DISTANCE ERMSD PRINT MOLINFO | bias colvar generic |
| 19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Michele Invernizzi | TORSION METAD EXTERNAL OPES_METAD ENDPLUMED UNITS PRINT POSITION | bias setup generic opes colvar |
| 19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Jim Pfaendtner | METAD WHOLEMOLECULES ENERGY GYRATION PRINT | bias colvar generic |
| 19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Gareth Tribello | DUMPGRID GROUP FIND_CONTOUR_SURFACE UNITS FCCUBIC MULTICOLVARDENS MORE_THAN FOURIER_TRANSFORM CENTER | contour setup function symfunc core gridtools vatom fourier |
| 19.048 | Understanding Ligand Binding Selectivity in a Prototypical GPCR Family | bio | metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | METAD WHOLEMOLECULES CONSTANT DISTANCE UPPER_WALLS BIASVALUE PRINT COM MATHEVAL LOWER_WALLS | bias function generic vatom colvar |
| 19.025 | Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide | bio | metainference, NMR, protein dynamics, force-fields | Carlo Camilloni | TORSION FLUSH WHOLEMOLECULES STATS PBMETAD CS2BACKBONE JCOUPLING ENDPLUMED RDC GYRATION PRINT BIASVALUE METAINFERENCE ENSEMBLE MOLINFO | bias isdb function generic colvar |
| 19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Riccardo Capelli | METAD FLUSH WHOLEMOLECULES CONVERT_TO_FES DUMPGRID POSITION WRAPAROUND GROUP UPPER_WALLS FIT_TO_TEMPLATE ENDPLUMED PRINT COM READ COORDINATION MATHEVAL REWEIGHT_METAD HISTOGRAM | bias function generic core gridtools vatom colvar |
| 19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Carlo Camilloni | TORSION WHOLEMOLECULES STATS PBMETAD DHENERGY RESTRAINT ALPHABETA DIHCOR GROUP DISTANCE UPPER_WALLS RDC PRINT ENDPLUMED METAINFERENCE ENSEMBLE MOLINFO CENTER | bias function isdb generic vatom core multicolvar colvar |
| 19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Max Bonomi | GROUP BIASVALUE PRINT MOLINFO EMMI | bias isdb generic core |
| 19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Michele Invernizzi | TORSION METAD LOAD ENERGY RESTART ENDPLUMED UNITS PRINT VES_DELTA_F POSITION | bias ves setup generic colvar |