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 |
|---|---|---|---|---|---|---|
| 25.004 | Machine Learning-Driven Molecular Dynamics Unveil a Bulk Phase Transformation Driving Ammonia Synthesis on Barium Hydride | chemistry | OPES, OPES flooding, Catalysis, Ammonia Synthesis | Axel Tosello Gardini | COMMITTOR OPES_METAD DISTANCES ZDISTANCES MEAN UNITS FIXEDATOM GROUP CUSTOM MATRIX_VECTOR_PRODUCT COORDINATIONNUMBER FLUSH DISTANCE CONTACT_MATRIX PRINT UPPER_WALLS ONES SUM | core bias vatom function colvar matrixtools symfunc setup multicolvar generic adjmat opes |
| 24.034 | Umbrella sampling of ion in transporter SLC26A7 | bio | umbrella sampling, transporter, ions | Xiaoli Lu | PRINT POSITION RESTRAINT UNITS | bias colvar generic setup |
| 24.002 | Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes | chemistry | metadynamics, ligand design, solvent extraction | Xiaoyu Wang | RESTART METAD UNITS PRINT TORSION | bias colvar generic setup |
| 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 | OPES_METAD_EXPLORE COORDINATION GROUP FIT_TO_TEMPLATE FIXEDATOM CONSTANT UNITS CUSTOM DISTANCE PYTORCH_MODEL UPPER_WALLS OPES_METAD LOWEST PRINT SUM EUCLIDEAN_DISTANCE LOWER_WALLS WHOLEMOLECULES COMBINE CENTER PDB2CONSTANT TORSION PATH | core bias refdist vatom function colvar pytorch setup generic mapping opes |
| 23.014 | Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 | bio | metadynamics, oligomerization, chemokine receptors, GPCR, membrane | Vittorio Limongelli | METAD COM FLUSH DISTANCE WHOLEMOLECULES PRINT COMBINE UPPER_WALLS TORSION | bias vatom function colvar generic |
| 23.008 | PBMetaD simulations of Histatin5 | bio | metadynamics, IDP, Rg, PPII | Francesco Pesce | GROUP GYRATION WHOLEMOLECULES PRINT PBMETAD MOLINFO TORSION | core bias colvar generic |
| 23.001 | Quantum phase diagram of water | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn-Løland Bore | RESTART LOWER_WALLS ENVIRONMENTSIMILARITY ECV_UMBRELLAS_LINE MORE_THAN MEAN ONES GROUP CUSTOM MATRIX_VECTOR_PRODUCT PRINT UPPER_WALLS OPES_EXPANDED INCLUDE SUM DISTANCE_MATRIX | core bias function envsim matrixtools setup generic adjmat opes |
| 22.040 | From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure | bio | SARS-CoV-2, Spike, Omicron | Miłosz Wieczór | RMSD LOWER_WALLS CONSTANT SELECT_COMPONENTS METAD CUSTOM MATRIX_VECTOR_PRODUCT BIASVALUE WHOLEMOLECULES PCAVARS PRINT UPPER_WALLS COMBINE SUM | bias function colvar valtools matrixtools generic mapping |
| 22.034 | Rationalising the difference in crystallisability of two Sulflowers using efficient in silico methods | materials | metadynamics, crystallizability, crystal structure prediction, sulflower, persulforated coronene | Matteo Salvalaglio | COMMITTOR LOWER_WALLS MATHEVAL CONSTANT METAD CUSTOM DISTANCE PRINT UPPER_WALLS DRMSD CELL SUM | function bias colvar generic |
| 22.028 | N-glycan conformer distributions in atomistic simulation | bio | REST2, RECT, N-glycan, pucker | Isabell Grothaus | METAD DUMPGRID PUCKERING PRINT CONVERT_TO_FES HISTOGRAM READ MOLINFO TORSION | bias colvar generic gridtools |
| 22.009 | Glycosylation in calixarenes capsule | chemistry | Metadynamics, glycosylation, supramolecular catalysis | GiovanniMaria Piccini | COORDINATION BRIDGE ANGLE MEAN GROUP FIT_TO_TEMPLATE RMSD UNITS BRIDGE_MATRIX FLUSH DISTANCE UPPER_WALLS MATHEVAL DISTANCES PRINT LOWER_WALLS METAD WHOLEMOLECULES COMBINE SUM | core bias function colvar setup multicolvar generic adjmat |
| 22.003 | Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling | methods | opes, metadynamics, reweighting, alanine, muller | Michele Invernizzi | OPES_METAD_EXPLORE OPES_METAD LOWER_WALLS METAD UNITS ECV_MULTITHERMAL CUSTOM BIASVALUE PRINT ENERGY PBMETAD POSITION UPPER_WALLS OPES_EXPANDED ENDPLUMED TORSION ECV_UMBRELLAS_FILE | bias function colvar setup generic opes |
| 21.050 | N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity | methods | bio | Isabell Louise Grothaus | PRINT CENTER DISTANCE | colvar generic vatom |
| 21.019 | Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations | materials | Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen | Matteo Salvalaglio | MATHEVAL COM TORSIONS DISTANCE KDE PRINT | vatom function colvar gridtools multicolvar generic |
| 21.016 | MD SAXS GTPase associated center | bio | metadynamics, RNA, folding, SAXS | Giovanni Bussi | LOWER_WALLS SAXS METAD ERMSD GROUP GYRATION CUSTOM WHOLEMOLECULES PRINT UPPER_WALLS MOLINFO INCLUDE | core bias isdb function colvar generic |
| 21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Tarak Karmakar | OPES_METAD MATHEVAL LOWER_WALLS GROUP FLUSH LOAD PYTORCH_MODEL PRINT UPPER_WALLS | core bias function pytorch setup generic opes |
| 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 | RESTART LOWER_WALLS METAD WHOLEMOLECULES PRINT UPPER_WALLS PATHMSD | bias colvar generic setup |
| 20.032 | Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil | materials | clustering, conformational isomers | Matteo Salvalaglio | PRINT TORSION ENDPLUMED | colvar generic |
| 20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Matteo Salvalaglio | LOWER_WALLS MATHEVAL METAD ENERGY UPPER_WALLS PRINT CELL VOLUME | function bias colvar generic |
| 20.013 | Improving accuracy of biased Alchemistic simulations | methods | flying Gaussian method, Alchemistic simulations, thermodynamic integration, reweighting | Vojtech Spiwok | PRINT METAD TORSION | bias colvar generic |
| 20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Luigi Bonati | OPES_METAD MATHEVAL LOWER_WALLS UNITS COM GROUP FLUSH DISTANCE PYTORCH_MODEL LOAD PRINT UPPER_WALLS ENDPLUMED TORSION | core bias vatom function colvar pytorch setup generic opes |
| 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 | RESTART Q6 LOAD DUMPGRID CONVERT_TO_FES HISTOGRAM REWEIGHT_TEMP_PRESS CELL VES_LINEAR_EXPANSION ENERGY UPPER_WALLS VOLUME MATHEVAL BF_LEGENDRE TD_MULTITHERMAL_MULTIBARIC OPT_AVERAGED_SGD PRINT OPT_DUMMY LOWER_WALLS TD_WELLTEMPERED COMBINE READ REWEIGHT_BIAS | bias function colvar ves symfunc gridtools setup generic |
| 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 COORDINATION ANGLE UNITS TD_WELLTEMPERED BF_CHEBYSHEV TD_GRID FLUSH DISTANCE EXTERNAL OPT_AVERAGED_SGD PRINT UPPER_WALLS COMBINE HISTOGRAM CONVERT_TO_FES DUMPGRID VES_LINEAR_EXPANSION | bias function colvar ves gridtools setup generic |
| 19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Luigi Bonati | ENVIRONMENTSIMILARITY UNITS Q6 LOAD PRINT POSITION ENERGY ENDPLUMED TORSION | envsim colvar symfunc setup generic |
| 19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | RESTART DISTANCES UNITS METAD FLUSH DISTANCE PRINT UPPER_WALLS COMBINE | bias function colvar setup multicolvar generic |
| 19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Silvio Pipolo | LOWER_WALLS METAD PRINT PIV UPPER_WALLS CELL FUNCPATHMSD | bias function colvar piv generic |
| 19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Mattia Bernetti | LESS_THAN METAD SECONDARY_STRUCTURE_RMSD GYRATION WHOLEMOLECULES ENERGY PRINT MOLINFO ALPHARMSD ENDPLUMED SUM | bias function colvar secondarystructure generic |
| 19.011 | Automatic Gradient Computation for Collective Variables | other | gradient, differentiation, curvature | Toni Giorgino | ENDPLUMED | generic |
| 19.009 | RNA tetraloops folding | bio | metadynamics, RNA, folding | Giovanni Bussi | RMSD METAD ERMSD WHOLEMOLECULES PRINT MOLINFO ENDPLUMED | bias colvar generic |
| 19.008 | anncolvar | methods | neural network, dimensionality reduction | Vojtech Spiwok | LESS_THAN MATHEVAL METAD SECONDARY_STRUCTURE_RMSD WHOLEMOLECULES POSITION COMBINE PRINT ALPHARMSD FIT_TO_TEMPLATE MOLINFO SUM | bias function colvar secondarystructure generic |
| 19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Max Bonomi | GROUP BIASVALUE WHOLEMOLECULES PRINT EMMI MOLINFO | core bias generic isdb |
| 19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Giovanni Bussi | RANDOM_EXCHANGES LOWER_WALLS ANGLE DISTANCES METAD ERMSD FLUSH DISTANCE LOWEST PRINT COMBINE UPPER_WALLS MOLINFO INCLUDE | bias function colvar multicolvar generic |
| 25.000 | Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer | bio | metadynamics, pathCV | Sahithya Sridharan Iyer | PRINT GROUP UPPER_WALLS METAD RESTART FUNCPATHGENERAL MOLINFO COM WHOLEMOLECULES DISTANCE | function generic vatom bias core colvar setup |
| 24.031 | DeepLNE | methods | PATHCV, OPES, OneOPES | Thorben Fröhlking | PRINT VOLUME COMBINE COORDINATION ENERGY RESTART PYTORCH_MODEL MOLINFO OPES_EXPANDED ECV_MULTITHERMAL ERMSD OPES_METAD_EXPLORE | function generic pytorch opes colvar setup |
| 24.006 | Water vapor condensation | chemistry | metadynamics, homogeneous condensation, chemical potential | Shenghui Zhong | SUM PRINT CLUSTER_PROPERTIES GROUP LESS_THAN METAD CONTACT_MATRIX COORDINATIONNUMBER DFSCLUSTERING UNITS MATRIX_VECTOR_PRODUCT MEAN ONES CLUSTER_NATOMS UPPER_WALLS | function setup generic clusters adjmat symfunc core matrixtools bias |
| 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 | CONTACTMAP SUM PRINT INCLUDE LESS_THAN PATHMSD LOWER_WALLS UPPER_WALLS METAD MOLINFO ALPHARMSD SECONDARY_STRUCTURE_RMSD FUNCPATHMSD DISTANCE | function generic secondarystructure colvar bias |
| 23.043 | Modeling the ferroelectric phase transition in barium titanate with DFT accuracy and converged sampling | materials | Barium Titanate, ferroelectric phase transition, Machine Learning, polarization order parameters | Lorenzo Gigli | TRANSPOSE SUM PRINT INCLUDE FLUSH METAD MATHEVAL SELECT_COMPONENTS | valtools function generic matrixtools 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 | PRINT COMBINE COORDINATION METAD GHBFIX MOLINFO BIASVALUE ERMSD WHOLEMOLECULES | generic function colvar bias |
| 23.025 | Probing ion binding to G-quadruplexes and related events | chemistry | metadynamics, repulsive potential, nucleic acids, G-quadruplexes | Marcelo Poleto | PRINT POSITION FIT_TO_TEMPLATE GROUP WRAPAROUND LOWEST LOWER_WALLS UPPER_WALLS METAD DUMPATOMS DISTANCES FLUSH UNITS RESTART COM MATHEVAL WHOLEMOLECULES DISTANCE | function setup generic multicolvar vatom core colvar bias |
| 22.045 | Binding mode and mechanism of enzymatic polyethylene terephthalate degradation | bio | metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation | Francesco Colizzi | MOVINGRESTRAINT PRINT LOWER_WALLS METAD COM WHOLEMOLECULES ANGLE UPPER_WALLS DISTANCE | generic colvar vatom bias |
| 22.043 | Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES | bio | OPES, RNA, Tetraloop, Folding | Gül Zerze | CONTACTMAP PRINT ENERGY ECV_UMBRELLAS_LINE OPES_EXPANDED ECV_MULTITHERMAL WHOLEMOLECULES | generic colvar opes |
| 22.041 | Skipping the Replica Exchange Ladder with Normalizing Flows | methods | OPES, alanine, normalizing flows, replica exchange | Michele Invernizzi | PRINT POSITION ENERGY UNITS TORSION OPES_EXPANDED OPES_METAD ECV_MULTITHERMAL ENDPLUMED | generic colvar setup opes |
| 22.038 | Enhanced Sampling Aided Design of Molecular Photoswitches | chemistry | reaction discovery, OPES explore, graph CV | Umberto Raucci | PRINT PYTORCH_MODEL UNITS CUSTOM COORDINATION OPES_METAD_EXPLORE | function generic pytorch opes colvar setup |
| 22.027 | Molecular Dynamics simulations of BANAL-236 RBD-hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, BANAL-236, receptor-binding domain | Max Bonomi | PRINT RMSD | generic colvar |
| 22.002 | GAMBES_SAMPL5_RATES | other | GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding | Jayashrita Debnath | FIXEDATOM PRINT GROUP COMMITTOR FLUSH ENERGY UPPER_WALLS PYTORCH_MODEL ENDPLUMED CENTER LOAD MATHEVAL WHOLEMOLECULES ANGLE COORDINATION FIT_TO_TEMPLATE DISTANCE | function setup generic vatom pytorch core colvar bias |
| 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 | SUM PRINT GROUP LOWER_WALLS COMBINE GYRATION UPPER_WALLS METAD ALPHABETA TORSION CONSTANT CUSTOM ENDPLUMED WHOLEMOLECULES | function generic multicolvar core colvar bias |
| 21.044 | NaCl nucleation | chemistry | metadynamics, DFS clustering | Aaron Finney | SUM GROUP HISTOGRAM METAD MORE_THAN MEAN CUSTOM FIXEDATOM PRINT Q6 CLUSTER_DISTRIBUTION CONTACT_MATRIX COORDINATIONNUMBER DFSCLUSTERING DUMPGRID MFILTER_MORE COMBINE LOCAL_Q6 INSPHERE MATRIX_VECTOR_PRODUCT ONES CLUSTER_NATOMS | function generic multicolvar vatom clusters adjmat volumes symfunc core gridtools matrixtools bias |
| 21.037 | Molecular Dynamics simulations of RBD/hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain | Max Bonomi | PRINT RMSD DISTANCE | generic colvar |
| 21.024 | Property map collective variable as a useful tool for force field correction | chemistry | molecular mechanics | Vojtech Spiwok | PRINT PROPERTYMAP METAD TORSION BIASVALUE WHOLEMOLECULES | generic colvar bias |
| 21.021 | ATLAS | methods | Machine Learning, Metadynamics | Federico Giberti | PRINT GROUP DUMPATOMS GYRATION METAD CONTACT_MATRIX COORDINATIONNUMBER UNITS TORSION MATHEVAL MATRIX_VECTOR_PRODUCT ONES MEAN WHOLEMOLECULES COORDINATION BIASVALUE DISTANCE | function setup generic adjmat symfunc core matrixtools colvar bias |
| 21.007 | Sampling enhancement by metadynamics driven by machine learning and de novo protein modelling | bio | metadynamics, machine learning, protein folding | Vojtech Spiwok | SUM POSITION FIT_TO_TEMPLATE COMBINE LESS_THAN MOLINFO ALPHARMSD MATHEVAL SECONDARY_STRUCTURE_RMSD WHOLEMOLECULES | generic function colvar secondarystructure |
| 20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Jim Pfaendtner | SUM PRINT GROUP RESTART DISTANCES CENTER CUSTOM COORDINATION WHOLEMOLECULES DISTANCE | function generic multicolvar vatom core colvar setup |
| 20.006 | Class B GPCR activation mechanism | bio | metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | PRINT RMSD COMBINE LOWER_WALLS ENERGY UPPER_WALLS METAD MOLINFO CENTER MATHEVAL WHOLEMOLECULES DISTANCE | function generic vatom colvar bias |
| 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 | SUM GROUP LESS_THAN ALPHABETA UPPER_WALLS TORSION CONSTANT CUSTOM PRINT ENDPLUMED WHOLEMOLECULES CS2BACKBONE ANTIBETARMSD COMBINE LOWER_WALLS FLUSH MOLINFO SECONDARY_STRUCTURE_RMSD PBMETAD BIASVALUE | function generic multicolvar secondarystructure core isdb colvar bias |
| 20.000 | Muscarinic M2 receptor-ligand funnel metadynamics | bio | multiple walker metadynamics, well-tempered metadynamics, funnel metadynamics, MC-HLDA, GPCR, receptor, Adiabatic Bias MD | Riccardo Capelli | PRINT COMBINE LOWER_WALLS REWEIGHT_METAD METAD READ HISTOGRAM CONVERT_TO_FES COM MATHEVAL DUMPGRID ENDPLUMED UPPER_WALLS DISTANCE ABMD | function generic vatom gridtools colvar bias |
| 19.078 | Iterative unbiasing of quasi-equilibrium sampling | methods | metadynamics, reweighting | Federico Giberti | PRINT GROUP DUMPATOMS METAD REWEIGHT_BIAS CONTACT_MATRIX COORDINATIONNUMBER UNITS ONES MATHEVAL MATRIX_VECTOR_PRODUCT COLLECT_FRAMES MEAN BIASVALUE DISTANCE | function setup generic adjmat symfunc landmarks core matrixtools colvar bias |
| 19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Giovanni Bussi | PRINT INCLUDE FLUSH METAD TORSION MOLINFO COM MATHEVAL MAXENT SORT COORDINATION WHOLEMOLECULES DISTANCE | function generic vatom colvar bias |
| 19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Matteo Salvalaglio | PRINT COMMITTOR REWEIGHT_METAD METAD READ REWEIGHT_BIAS TORSION CONVERT_TO_FES MATHEVAL DUMPGRID EXTERNAL BIASVALUE DISTANCE HISTOGRAM | function generic gridtools colvar bias |
| 19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Sandro Bottaro | PRINT RMSD METAD TORSION MOLINFO ERMSD WHOLEMOLECULES DISTANCE | generic colvar bias |
| 19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Jim Pfaendtner | PRINT ENERGY GYRATION METAD WHOLEMOLECULES | generic colvar bias |
| 19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Kim E. Jelfs | PRINT GROUP LOWER_WALLS METAD RESTART CENTER COM UPPER_WALLS DISTANCE | generic vatom bias core colvar setup |
| 19.050 | Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes | chemistry | metadynamics, membranes, Willard Chandler surface | Gareth Tribello | PRINT COMBINE READ REWEIGHT_BIAS METAD RESTART CONVERT_TO_FES DUMPGRID DISTANCE_FROM_CONTOUR UPPER_WALLS HISTOGRAM | function setup generic contour gridtools bias |
| 19.044 | Multithermal-multibaric simulations using VES | methods | ves, Wang Landau, multicanonical, water, density anomaly | Pablo Piaggi | VES_LINEAR_EXPANSION REWEIGHT_TEMP_PRESS OPT_DUMMY HISTOGRAM VOLUME OPT_AVERAGED_SGD ENERGY ACCUMULATE AVERAGE CONVERT_TO_FES CUSTOM BF_LEGENDRE PRINT TD_MULTITHERMAL_MULTIBARIC REWEIGHT_BIAS DUMPGRID COMBINE READ RESTART | function setup generic ves gridtools colvar bias |
| 19.035 | Dimerization of GPCRs from coarse-grained umbrella sampling | bio | Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization | Davide Provasi | PRINT GROUP RESTRAINT TORSION COM DISTANCE | generic vatom core colvar bias |
| 19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Gabriele Cesare Sosso | COMMITTOR FLUSH Q6 CONTACT_MATRIX DFSCLUSTERING LOCAL_Q6 ENDPLUMED CLUSTER_WITHSURFACE CLUSTER_NATOMS OUTPUT_CLUSTER MFILTER_MORE | generic multicolvar adjmat clusters symfunc |
| 19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Jim Pfaendtner | GROUP ENERGY METAD EXTERNAL COORDINATION | colvar bias core |
| 19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Matteo Salvalaglio | PRINT LOWER_WALLS COMMITTOR METAD TORSION CENTER UPPER_WALLS DISTANCE | generic vatom colvar bias |
| 19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Carlo Camilloni | SUM GROUP ALPHABETA CENTER DIHCOR UPPER_WALLS DISTANCE DHENERGY METAINFERENCE TORSION CONSTANT CUSTOM ENSEMBLE PRINT DIHEDRAL_CORRELATION ENDPLUMED WHOLEMOLECULES STATS RDC COMBINE RESTRAINT MOLINFO PBMETAD | function generic multicolvar vatom core isdb colvar bias |
| 19.006 | Flying Gaussian proof | methods | flying Gaussians, alanine dipeptide | Vojtech Spiwok | PRINT METAD TORSION | generic colvar bias |
| 19.004 | MI Ubiquitin | bio | metainference, NMR | Max Bonomi | RDC PRINT METAINFERENCE GROUP MOLINFO WHOLEMOLECULES CS2BACKBONE | isdb generic core |
| 19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Max Bonomi | PRINT GROUP MOLINFO BIASVALUE EMMI | isdb generic bias core |
| 19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Michele Invernizzi | PRINT POSITION ENERGY METAD RESTART UNITS TORSION LOAD VES_DELTA_F ENDPLUMED | setup generic ves colvar bias |
| 24.036 | Leveraging cryptic ligand envelopes through enhanced molecular simulations | bio | HREX, conformational heterogeneity, drug discovery, ligand binding, plitidepsin, aplidin, ligand-target complexes, cryptic ligand envelope | Francesco Colizzi | CONVERT_TO_FES DUMPGRID DISTANCE WHOLEMOLECULES GROUP ANGLE PRINT TORSION HISTOGRAM COORDINATION | generic gridtools core colvar |
| 24.011 | Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble | methods | committor, machine learning | Peilin Kang | WHOLEMOLECULES PRINT UNITS UPPER_WALLS COORDINATION CELL GROUP MATHEVAL ENERGY DISTANCE TORSION LOWER_WALLS INCLUDE BIASVALUE ENDPLUMED MOLINFO CUSTOM LOAD RMSD POSITION | core function bias generic colvar setup |
| 24.003 | Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations | chemistry | steered molecular dynamics, foldamers, peptoids, bio-inspired | Kaylyn Torkelson | WHOLEMOLECULES DISTANCE PRINT TORSION GYRATION COM ALPHABETA COORDINATION MOVINGRESTRAINT INCLUDE | vatom bias generic colvar multicolvar |
| 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 | BIASVALUE MOLINFO GROUP WHOLEMOLECULES DISTANCE PRINT EMMIVOX WRAPAROUND UPPER_WALLS INCLUDE | isdb colvar bias generic core |
| 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 | BIASVALUE CENTER MOLINFO GROUP DISTANCE SAXS STATS PRINT ENSEMBLE RMSD WRAPAROUND UPPER_WALLS | colvar isdb function vatom generic core bias |
| 23.023 | Rational design of novel biomimetic sequence-defined polymers for mineralization applications | methods | metadynamics, surface binding, biomimetic mineralization | Kaylyn Torkelson | DISTANCE PRINT GYRATION UPPER_WALLS COM COORDINATION PBMETAD | generic vatom colvar bias |
| 23.006 | Transcription factor unbinding | bio | metadynamics, DNA, conformational changes | Malin Lüking | MOLINFO LESS_THAN DISTANCE ANGLE SECONDARY_STRUCTURE_RMSD PRINT METAD CONTACTMAP COM SUM ALPHARMSD DUMPFORCES | vatom function secondarystructure bias generic colvar |
| 23.002 | Critical comparison of general-purpose collective variables for crystal nucleation | methods | metadynamics, umbrella sampling, commitor, entropy, PIV | Julien Lam | CUSTOM Q6 PRINT ENERGY PAIRENTROPY FUNCPATHMSD METAD VOLUME UNITS LOCAL_AVERAGE Q4 PIV UPPER_WALLS RESTRAINT | piv symfunc gridtools function bias generic colvar setup |
| 22.039 | Driving and characterizing nucleation of urea and glycine polymorphs in water | bio | metadynamics, nucleation, amino acids, polymorphism | Eric Beyerle | PRINT MATRIX_VECTOR_PRODUCT MEAN GROUP COMBINE MATHEVAL CONTACT_MATRIX PAIRENTROPY METAD Q4 SUM CENTER Q6 MORE_THAN SPHERICAL_HARMONIC COORDINATIONNUMBER ONES INCLUDE CUSTOM LOAD | vatom matrixtools gridtools symfunc adjmat function bias generic core setup |
| 22.030 | Mixing physics across temperatures with generative artificial intelligence | methods | REMD, Generative AI, DDPM | Yihang Wang | PRINT TORSION WHOLEMOLECULES | generic colvar |
| 22.023 | Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy | bio | CryoEM, MEMMI,EMMI, Metadynamics, Metainference, IAPP, structural ensemble | Faidon Brotzakis | BIASVALUE MOLINFO WHOLEMOLECULES GROUP PRINT TORSION COORDINATION EMMI RESTART COM RMSD UPPER_WALLS PBMETAD | vatom isdb colvar bias generic core setup |
| 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 | CENTER GROUP WHOLEMOLECULES MATHEVAL DISTANCE CUSTOM COMMITTOR PRINT UPPER_WALLS FIXEDATOM LOWER_WALLS RMSD OPES_METAD COORDINATION FIT_TO_TEMPLATE PYTORCH_MODEL | opes colvar function pytorch vatom generic core bias |
| 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 | CENTER CONTACTMAP PRINT DISTANCE | generic colvar vatom |
| 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 | WHOLEMOLECULES PRINT UPPER_WALLS MEAN XANGLES COMBINE MATHEVAL METAD YANGLES COM SUM DISTANCE TORSION LOWER_WALLS ZANGLES MOLINFO CUSTOM CONSTANT ALPHABETA | function vatom generic colvar bias multicolvar |
| 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 UNITS OPT_AVERAGED_SGD UPPER_WALLS COORDINATION BF_GAUSSIANS TD_UNIFORM ENERGY TD_WELLTEMPERED METAD BF_CUBIC_B_SPLINES BF_WAVELETS BF_CHEBYSHEV DISTANCE VES_OUTPUT_BASISFUNCTIONS FLUSH OPT_ADAM INCLUDE VES_LINEAR_EXPANSION POSITION BF_LEGENDRE | ves bias generic colvar setup |
| 21.051 | Automatic learning of hydrogen-bond fixes in an AMBER RNA force field | methods | force field, RNA | Giovanni Bussi | BIASVALUE MOLINFO COMBINE WHOLEMOLECULES PRINT ERMSD METAD COORDINATION | generic function colvar bias |
| 21.039 | Deep learning the slow modes for rare events sampling | methods | collective variables, machine learning, slow modes, deep-tica, opes | Luigi Bonati | WHOLEMOLECULES PRINT UNITS MATRIX_VECTOR_PRODUCT DISTANCE_MATRIX ECV_MULTITHERMAL ENVIRONMENTSIMILARITY PYTORCH_MODEL MEAN GROUP COMBINE CONTACT_MATRIX ENERGY VOLUME SUM DISTANCE Q6 TORSION MORE_THAN SPHERICAL_HARMONIC OPES_METAD ONES FLUSH ENDPLUMED OPES_EXPANDED MOLINFO INCLUDE CUSTOM LOAD CONTACTMAP RMSD | opes envsim matrixtools symfunc colvar adjmat function pytorch generic core setup |
| 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 | ENDPLUMED PRINT TORSION METAD RANDOM_EXCHANGES PBMETAD INCLUDE | generic colvar bias |
| 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 PRINT LOWER_WALLS DISTANCE | generic colvar bias |
| 21.020 | Reweighted Jarzynski sampling | methods | free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions | Kristof Bal | CONVERT_TO_FES DUMPGRID PRINT UNITS MATRIX_VECTOR_PRODUCT OPT_AVERAGED_SGD UPPER_WALLS MEAN GROUP COMBINE CONTACT_MATRIX METAD TD_WELLTEMPERED ANN SUM RESTRAINT REWEIGHT_METAD BF_CHEBYSHEV DISTANCE MORE_THAN REWEIGHT_BIAS COORDINATIONNUMBER HISTOGRAM OPES_METAD ONES MOVINGRESTRAINT FLUSH BIASVALUE CUSTOM LOAD VES_LINEAR_EXPANSION CONSTANT | ves annfunc opes matrixtools gridtools symfunc colvar function adjmat bias generic core setup |
| 21.018 | Localized Volume-based Metadynamics | bio | LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification | Riccardo Capelli | CONVERT_TO_FES DUMPGRID WHOLEMOLECULES PRINT COORDINATION UPPER_WALLS READ GROUP MATHEVAL METAD FIXEDATOM COM REWEIGHT_METAD DISTANCE HISTOGRAM FLUSH ENDPLUMED RMSD POSITION | vatom gridtools colvar function bias generic 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 | CENTER MOLINFO DISTANCE ABMD PRINT TORSION ERMSD RESTART | vatom bias generic colvar setup |
| 20.026 | Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor | bio | Metadynamics, Umbrella sampling | Brandon Peters | CONVERT_TO_FES DUMPGRID WHOLEMOLECULES COMBINE CUSTOM CONSTANT PRINT MULTI_RMSD METAD RESTRAINT HISTOGRAM CONCATENATE RMSD_VECTOR POSITION REWEIGHT_METAD | gridtools function bias valtools generic colvar |
| 20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Glen Hocky | BIASVALUE GROUP DISTANCE MATHEVAL PRINT ENERGY GYRATION FISST UNITS RESTRAINT | fisst colvar function bias generic core setup |
| 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 | BIASVALUE MOLINFO FUNCPATHGENERAL GROUP WHOLEMOLECULES LOAD DISTANCE MATHEVAL CONSTANT PRINT METAD CONTACTMAP COM LOWER_WALLS UPPER_WALLS PROJECTION_ON_AXIS INCLUDE | vatom colvar function bias generic core setup |
| 20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Pratyush Tiwary | MOLINFO WHOLEMOLECULES DISTANCE COMBINE PRINT TORSION METAD RESTART RMSD UPPER_WALLS | function bias generic colvar setup |
| 20.002 | Exploring conformational dynamics of the extracellular Venus flytrap domain of the GABAB receptor, a path-metadynamics study | bio | Metadynamics, path CVs | Riccardo Ocello | MOLINFO WHOLEMOLECULES GROUP PRINT METAD PATHMSD RESTART UPPER_WALLS | colvar bias generic core setup |
| 19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Michele Invernizzi | ENDPLUMED EXTERNAL PRINT TORSION METAD UNITS OPES_METAD POSITION | opes bias generic colvar setup |
| 19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Kim Jelfs | CUSTOM DISTANCE ANGLE PRINT INPLANEDISTANCES RESTART COM SUM DISTANCES MOVINGRESTRAINT FLUSH | function vatom generic colvar setup bias multicolvar |
| 19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | COMBINE DISTANCE PRINT ENERGY METAD UNITS UPPER_WALLS FLUSH | function bias generic colvar setup |
| 19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Vittorio Limongelli | WHOLEMOLECULES FUNNEL_PS DISTANCE PRINT METAD FUNNEL COM RMSD LOWER_WALLS UPPER_WALLS | funnel vatom generic colvar bias |
| 19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Davide Provasi | ENDPLUMED WHOLEMOLECULES DISTANCE PRINT FUNCPATHMSD METAD CONTACTMAP COM RMSD | function vatom generic colvar bias |
| 19.013 | RNA FF FITTING | methods | force field, RNA | Giovanni Bussi | BIASVALUE MOLINFO MATHEVAL PUCKERING CONSTANT TORSION INCLUDE | generic function colvar bias |
| 19.005 | Cmyc small molecule interaction | bio | metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP | Gabriella Heller | CENTER MOLINFO METAINFERENCE GROUP WHOLEMOLECULES DISTANCE PRINT GYRATION ALPHABETA COORDINATION CS2BACKBONE PBMETAD INCLUDE | colvar isdb vatom generic core bias multicolvar |
| 25.003 | Surrogate Model CV | methods | Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding | Sompriya Chatterjee | DISTANCE OPES_METAD MOLINFO ENDPLUMED PYTORCH_MODEL GROUP COMBINE TORSION PRINT CUSTOM MATHEVAL COMMITTOR WHOLEMOLECULES ENERGY | core colvar pytorch generic function opes |
| 24.021 | Ab initio machine learning simulation of calcium carbonate from aqueous solutions to the solid state | chemistry | ion pairing, caco3, opes, proton transfer, crystallization | Pablo Piaggi | DISTANCE OPES_METAD PRINT UPPER_WALLS COORDINATION ENERGY | bias colvar opes generic |
| 24.004 | Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables | materials | metadynamics, nucleation, machine learning | Ziyue Zou | GROUP METAD PRINT RESTART LOAD INCLUDE | setup bias core 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 | DISTANCE OPES_METAD SUM COORDINATIONNUMBER FLUSH CONTACT_MATRIX GROUP FIXEDATOM ZDISTANCES PRINT CUSTOM UPPER_WALLS ONES MEAN UNITS MATRIX_VECTOR_PRODUCT | setup multicolvar colvar core symfunc matrixtools adjmat generic vatom bias function opes |
| 23.034 | Urea nucleation in water: do long-range forces matter? | materials | LMF theory, Metadynamics, Nucleation | Ziyue Zou | SUM COORDINATIONNUMBER MATRIX_VECTOR_PRODUCT GROUP CONTACT_MATRIX MORE_THAN METAD CENTER PRINT CUSTOM ONES MEAN LOAD INCLUDE | setup core generic symfunc adjmat matrixtools vatom bias function |
| 23.032 | Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics | bio | metadynamics, tSNE, neural network, machine learning, trp-cage, folding | Vojtech Spiwok | ALPHARMSD MOLINFO SUM FIT_TO_TEMPLATE LESS_THAN COMBINE METAD PRINT SECONDARY_STRUCTURE_RMSD WHOLEMOLECULES ANN POSITION | colvar annfunc secondarystructure generic bias function |
| 23.026 | Machine Learning Nucleation Collective Variables with Graph Neural Networks | chemistry | Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks | Florian Dietrich | LOWER_WALLS COORDINATIONNUMBER GROUP COMBINE METAD PRINT Q6 LOCAL_Q6 MOVINGRESTRAINT MFILTER_MORE | multicolvar core symfunc generic bias function |
| 23.012 | JAK2 2D meta-eABF PMF with statistical analysis | bio | 2D meta-eABF, path CV, PMF | Istvan Kolossvary | LOWER_WALLS PATHMSD METAD PRINT CUSTOM BIASVALUE UPPER_WALLS DRR FLUSH | colvar drr generic bias function |
| 23.011 | OneOPES, a combined enhanced sampling method to rule them all | bio | OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding | Valerio Rizzi | DISTANCE MOLINFO OPES_METAD_EXPLORE ENDPLUMED METAD TORSION PRINT OPES_EXPANDED ECV_MULTITHERMAL ENERGY | bias colvar opes generic |
| 23.010 | An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G‑Protein-Coupled Receptor Ligands | bio | GPCR, binding free energy, free energy surface | Timothy Clark | DISTANCE LOWER_WALLS CONSTANT METAD PRINT UPPER_WALLS MATHEVAL BIASVALUE WHOLEMOLECULES | function bias colvar generic |
| 23.004 | Melting curves of ice polymorphs in the vicinity of the liquid-liquid critical point | chemistry | water, liquid-liquid transition, second critical point, ice, polymorphs, melting curves, environment similarity, opes, density-functional theory, scan, machine learning potential | Pablo Piaggi | SUM LOWER_WALLS HISTOGRAM GROUP MORE_THAN PRINT ECV_UMBRELLAS_LINE CUSTOM OPES_EXPANDED UPPER_WALLS ONES RESTART DISTANCE_MATRIX DUMPGRID ENVIRONMENTSIMILARITY MATRIX_VECTOR_PRODUCT | setup core matrixtools adjmat gridtools generic envsim bias function opes |
| 22.035 | Deciphering the alphabet of disorder — Glu and Asp act differently on local but not global properties | bio | intrinsically disordered proteins, parallel bias metadynamics, protein | Kresten Lindorff-Larsen | MOLINFO GYRATION TORSION PBMETAD WHOLEMOLECULES | bias colvar generic |
| 22.032 | Reciprocal barrier restraint. Application to path-meta-eABF | methods | restraint, upper wall, lower wall, path colvar, meta-eABF, metadynamics, DRR, protein conformational transition, PROTAC | Istvan Kolossvary | PATHMSD METAD PRINT CUSTOM BIASVALUE DRR FLUSH | colvar drr generic bias function |
| 22.024 | Conformational Entropy as a Potential Liability of Computationally Designed Antibodies | bio | metadynamics, conformational entropy, antibody, nanobody | Thomas Löhr | ALPHABETA ALPHARMSD MOLINFO SUM ANTIBETARMSD CONSTANT LESS_THAN COMBINE TORSION SECONDARY_STRUCTURE_RMSD PRINT CUSTOM COM RESTART PBMETAD WHOLEMOLECULES | setup multicolvar colvar secondarystructure generic vatom bias function |
| 22.018 | Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations | bio | ligand binding, docking, EMMI, LAT1 | Max Bonomi | MOLINFO GROUP PRINT BIASVALUE EMMIVOX LOAD WHOLEMOLECULES | setup core isdb generic bias |
| 21.040 | A structural ensemble of a tau-microtubule complex reveals regulatory tau phosphorylation and acetylation mechanisms | bio | EMMI, CryoEM, tau-microtubules, post-translational modifications, chemical mutagenesis, structural ensemble, Metainference | Faidon Brotzakis | DISTANCE MOLINFO EMMI GROUP COM PRINT UPPER_WALLS BIASVALUE RESTART WHOLEMOLECULES | setup core colvar isdb generic vatom bias |
| 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 | ANTIBETARMSD MOLINFO LOWER_WALLS PRINT COORDINATION DIHCOR GYRATION LESS_THAN METAD UPPER_WALLS WHOLEMOLECULES RANDOM_EXCHANGES GROUP SECONDARY_STRUCTURE_RMSD DIHEDRAL_CORRELATION PARABETARMSD ENERGY ALPHARMSD SUM LOWEST | multicolvar colvar core secondarystructure generic bias function |
| 21.017 | All-atom simulations of the Vav1 AD construct | bio | metadynamics, parallel-bias, well-tempered | Simone Orioli | ALPHABETA ALPHARMSD MOLINFO SUM CONSTANT GROUP LESS_THAN REWEIGHT_BIAS COMBINE METAD TORSION SECONDARY_STRUCTURE_RMSD PRINT CUSTOM RESTART PBMETAD WHOLEMOLECULES CONTACTMAP | setup multicolvar core colvar secondarystructure generic bias function |
| 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 REWEIGHT_BIAS METAD CENTER PRINT MATHEVAL RESTART WHOLEMOLECULES COORDINATION POSITION | setup colvar generic vatom bias function |
| 21.013 | Role of vibrational excitation in heterogeneous catalysis | chemistry | catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption | Kristof Bal | DISTANCE LOWER_WALLS COORD_ANGLES CONTACT_MATRIX OPT_AVERAGED_SGD COMBINE PRINT VES_LINEAR_EXPANSION COORDINATION EXTERNAL DISTANCES TD_GRID METAD CUSTOM UPPER_WALLS UWALLS FLUSH MATRIX_VECTOR_PRODUCT RESTRAINT HISTOGRAM COORDINATIONNUMBER GROUP BF_CHEBYSHEV MEAN LOAD UNITS ANGLES REWEIGHT_BIAS REWEIGHT_METAD CONVERT_TO_FES ONES DUMPGRID | setup ves multicolvar colvar core symfunc matrixtools adjmat gridtools generic bias function |
| 20.024 | Gaussian Mixture Based Enhanced Sampling (GAMBES) | methods | enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias | Jayashrita Debnath | DISTANCE DISTANCES LOWER_WALLS GROUP COMBINE TORSION PRINT ENERGY UPPER_WALLS LOAD UNITS | setup multicolvar colvar core generic bias function |
| 20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Vojtech Spiwok | METAD TORSION PRINT | bias colvar generic |
| 20.021 | Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins. | bio | phi-values, restrained MD, transition-state, protein folding, disordered proteins, protein evolution | Cristina Paissoni | RESTRAINT MOLINFO PRINT STATS WHOLEMOLECULES COORDINATION | bias function colvar generic |
| 19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Matteo Salvalaglio | DISTANCE ENDPLUMED GROUP CENTER PRINT INCLUDE | vatom colvar core generic |
| 19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_OPTIMIZER_BIAS PRINT UNITS MAZE_LOSS POSITION MAZE_SIMULATED_ANNEALING | maze setup colvar generic |
| 19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Cristina Paissoni | ALPHABETA MOLINFO ENDPLUMED ANGLE GROUP COMBINE CENTER PRINT MATHEVAL BIASVALUE SAXS ENSEMBLE STATS PBMETAD WHOLEMOLECULES COORDINATION INCLUDE | multicolvar colvar core isdb generic vatom bias function |
| 19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Glen Hocky | DISTANCE RESTRAINT COMBINE TORSION PRINT EDS | colvar generic eds bias function |
| 19.003 | EMMI ClpP | bio | metainference, cryo-EM | Max Bonomi | MOLINFO EMMI GROUP PRINT BIASVALUE | bias core isdb generic |
| 25.001 | RNA G-quadruplex folding with ST-metaD protocol | bio | RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | WHOLEMOLECULES MOLINFO METAD COMBINE ERMSD | function generic bias colvar |
| 24.035 | Data efficient machine learning potentials for modeling catalytic reactivity via active learning and enhanced sampling | chemistry | opes, catalysis, ammonia, machine learning potentials | Luigi Bonati | UPPER_WALLS LOWER_WALLS DISTANCE GROUP CUSTOM PRINT COMMITTOR OPES_METAD COORDINATION UNITS RESTART | function colvar bias core setup generic opes |
| 24.029 | Combination of OPES and OPES-Explore | methods | OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin | Dhiman Ray | LOWER_WALLS BIASVALUE RMSD OPES_METAD_EXPLORE ENERGY FIXEDATOM PYTORCH_MODEL MOLINFO UPPER_WALLS CENTER PRINT COMBINE COORDINATION UNITS CONTACTMAP WHOLEMOLECULES DISTANCE FLUSH GROUP CUSTOM OPES_METAD POSITION METAD FIT_TO_TEMPLATE INCLUDE MATHEVAL ENDPLUMED | pytorch function vatom colvar bias core setup generic opes |
| 24.028 | All-atom simulations of RNA-membrane interactions | bio | metadynamics, membrane, RNA | Giovanni Bussi | WHOLEMOLECULES MOLINFO UPPER_WALLS CENTER DISTANCE POSITION GROUP METAD PRINT COMBINE SORT LOWEST MATHEVAL GHOST DISTANCES | function vatom colvar multicolvar bias core generic |
| 24.020 | Graph Neural Network-State Predictive Information Bottleneck (GNN-SPIB) approach for learning molecular thermodynamics and kinetics | bio | LJ7, alanine, well-tempered metadynamics, infrequent metadynamics, machine learning | Ziyue Zou, Dedi Wang, Pratyush Tiwary | TORSION METAD GROUP PRINT COMMITTOR LOAD | colvar bias core setup generic |
| 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 | WHOLEMOLECULES TORSION MOLINFO LESS_THAN GYRATION DISTANCE SUM SECONDARY_STRUCTURE_RMSD CUSTOM PRINT OPES_METAD COMBINE ALPHARMSD COORDINATION | secondarystructure colvar generic function opes |
| 24.010 | Oxytocin metadynamics simulation | bio | metadynamics, oxytocin, peptide | Jan Beránek | WHOLEMOLECULES TORSION FLUSH METAD PRINT RESTART | setup generic bias colvar |
| 23.046 | Lasso Peptides - HLDA CV | bio | metadynamics, protein folding, HLDA, harmonic | Gabriel da Hora | WHOLEMOLECULES DISTANCE METAD PRINT COMBINE UNITS | colvar generic bias setup function |
| 23.039 | Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation | chemistry | metadynamics, ligand dissociation | Eric Beyerle | UPPER_WALLS MOLINFO CENTER DISTANCE RESTRAINT METAD PRINT COMBINE DUMPMASSCHARGE FIXEDATOM | vatom colvar generic bias function |
| 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 BIASVALUE OPES_METAD_EXPLORE ENERGY WRAPAROUND TORSION MOLINFO UPPER_WALLS CENTER PRINT COORDINATION UNITS WHOLEMOLECULES COM DISTANCE FLUSH GROUP CUSTOM COMMITTOR OPES_METAD POSITION FIT_TO_TEMPLATE MATHEVAL ENDPLUMED | function vatom colvar bias core setup generic opes |
| 23.020 | FEP simulations of ATOX1 homodimer | chemistry | parallel bias metadynamics, FEP, free-energy of metal ion dissociation | Adriana Pietropaolo | WHOLEMOLECULES DISTANCE PBMETAD BIASVALUE CONSTANT PRINT ANGLE MATHEVAL | function generic bias colvar |
| 23.013 | Path meta-eABF simulation of large scale conformational change in STING protein | methods | meta-eABF, path CV, large scale conformational change, STING protein, reciprocal barrier restraint | Istvan Kolossvary | PATHMSD UPPER_WALLS LOWER_WALLS TIME METAD FLUSH CUSTOM BIASVALUE PRINT DRR UNITS | drr colvar generic bias setup function |
| 22.033 | Reciprocal barrier restraint. Application to PROTAC passive permeability prediction | methods | PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR | Istvan Kolossvary | COM DISTANCE FLUSH METAD CUSTOM BIASVALUE PRINT DRR UNITS | drr vatom colvar generic bias setup function |
| 22.031 | Rare Event Kinetics from Adaptive Bias Enhanced Sampling | methods | OPES Flooding, Kinetics, Rate, OPES, Machine Learning | Dhiman Ray | BIASVALUE RMSD ENERGY PYTORCH_MODEL TORSION MOLINFO PRINT COMBINE UNITS CONTACTMAP WHOLEMOLECULES DISTANCE GROUP CUSTOM CONSTANT COMMITTOR OPES_METAD POSITION INCLUDE ENDPLUMED | pytorch colvar generic bias core setup function opes |
| 22.022 | Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir | bio | RMSD, protein-ligand interactions | Isabell Grothaus | PRINT RMSD | generic colvar |
| 22.019 | Exploring aspartic protease inhibitor binding to design selective antimalarials | bio | ligand binding, loop opening, path CV, funnel metadynamics, drug development | Raitis Bobrovs | WHOLEMOLECULES PATHMSD UPPER_WALLS COM LOWER_WALLS DISTANCE METAD PRINT FUNNEL_PS FUNNEL | vatom colvar bias generic funnel |
| 22.014 | Quasi Liquid Layer Order Parameters | materials | Quasi-Liquid Layer, Steinhardt Order Parameter, Entropy Fingerprint | Jihong Shi | Q6 DUMPMULTICOLVAR LOCAL_AVERAGE Q4 Q3 HISTOGRAM LOCAL_Q3 LOCAL_Q4 LOCAL_Q6 PAIRENTROPIES UNITS DUMPGRID ENDPLUMED LOAD | symfunc multicolvar setup generic gridtools |
| 21.049 | Multiple-path-metadynamics and PathMaps | methods | path-CV, metadynamics, multiple-walker, multiple paths, pathmap | Alberto Pérez-de-Alba-Ortíz | TORSION UPPER_WALLS RESTRAINT LOWER_WALLS MOVINGRESTRAINT METAD CUSTOM PRINT CONSTANT COMBINE UNITS ENSEMBLE LOAD | function colvar bias setup generic |
| 21.029 | Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs | bio | metadynamics, small peptide, machine learning | Pratyush Tiwary | EXTERNAL TORSION MOLINFO FLUSH PRINT RESTART ENERGY | 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 | |
| 21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Kristof Bal | MEAN MORE_THAN HISTOGRAM LOAD UPPER_WALLS PRINT ONES UNITS MATRIX_VECTOR_PRODUCT SUM FLUSH GROUP COMMITTOR DUMPGRID REWEIGHT_METAD CONVERT_TO_FES MOVINGRESTRAINT CONTACT_MATRIX METAD COORDINATIONNUMBER | function adjmat symfunc matrixtools bias core setup generic gridtools |
| 20.027 | Allosteric Regulation of SARS-CoV-2 Protease. Towards Informed Structure-Based Drug Discovery | bio | SARS-CoV2, MPro, Covid-19, Molecular Dynamics, Metadynamics, Computer-Aided Drug Discovery | Khaled Abdel-Maksoud | TORSION PRINT METAD DISTANCE | generic bias colvar |
| 20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Valerio Rizzi | WHOLEMOLECULES UPPER_WALLS CENTER DISTANCE GROUP PRINT FIT_TO_TEMPLATE OPES_METAD COORDINATION ANGLE ENERGY MATHEVAL ENDPLUMED FIXEDATOM PYTORCH_MODEL | function pytorch vatom colvar bias core generic opes |
| 20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Max Bonomi | WHOLEMOLECULES TORSION MOLINFO GYRATION DIHCOR PBMETAD SUM CUSTOM PRINT CONSTANT ALPHABETA COMBINE COORDINATION DIHEDRAL_CORRELATION INCLUDE | colvar multicolvar generic bias function |
| 20.015 | Rational design of ASCT2 inhibitors using an integrated experimental-computational approach | bio | ASCT2 transporter, small-molecules, cryo-EM, metainference | Max Bonomi | WHOLEMOLECULES DUMPATOMS MOLINFO EMMIVOX GROUP BIASVALUE PRINT LOAD | isdb bias core setup generic |
| 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 | DISTANCE SUM METAD CUSTOM PRINT COORDINATION UNITS DISTANCES | function colvar multicolvar bias setup generic |
| 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 | LOWER_WALLS HISTOGRAM READ MOLINFO UPPER_WALLS PRINT COMBINE ABMD CONTACTMAP WHOLEMOLECULES COM DISTANCE FLUSH DUMPGRID REWEIGHT_METAD CONVERT_TO_FES METAD ENDPLUMED FUNCPATHMSD | vatom colvar generic bias function gridtools |
| 19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Valerio Rizzi | MEAN UPPER_WALLS DISTANCE SUM FLUSH CONTACT_MATRIX GROUP CUSTOM METAD PRINT ONES COMBINE COORDINATIONNUMBER UNITS RESTART ENDPLUMED MATRIX_VECTOR_PRODUCT DISTANCES | function adjmat symfunc colvar matrixtools multicolvar bias core setup generic |
| 19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Valerio Rizzi | EXTERNAL MEAN SUM FLUSH CONTACT_MATRIX GROUP CUSTOM METAD PRINT ONES COMBINE COORDINATIONNUMBER UNITS RESTART ENDPLUMED MATRIX_VECTOR_PRODUCT | function adjmat symfunc matrixtools bias core setup generic |
| 19.076 | Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones | bio | molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics | Salvatore Assenza | GYRATION MOVINGRESTRAINT PRINT UNITS ENDPLUMED | setup generic bias colvar |
| 19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Wei Chen | RESTRAINT COM POSITION COMBINE ANN | vatom colvar annfunc bias function |
| 19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Mattia Bernetti | WHOLEMOLECULES PATHMSD UPPER_WALLS LOWER_WALLS METAD PRINT | generic bias colvar |
| 19.046 | Optimal Collective from short simulations for Benzamidine-Trypsin ligand binding | bio | VAC-MetaD, optimised collective variables, binding free energy, unbinding rates, benzamidine trypsin, Structure Activity Relation | Faidon Brotzakis | WHOLEMOLECULES TORSION MOLINFO COM UPPER_WALLS LOWER_WALLS DISTANCE GROUP METAD PRINT ALPHABETA FUNNEL RMSD COMBINE BRIDGE REWEIGHT_METAD DISTANCES | function adjmat vatom colvar multicolvar bias core generic funnel |
| 19.045 | Adsorption free energy of Ca/CO3 ions on calcite steps in contact with water | materials | metadynamics, well-tempered, multiple walkers, LAMMPS | Marco De La Pierre | UPPER_WALLS LOWER_WALLS POSITION FLUSH GROUP METAD PRINT COORDINATION UNITS RESTART | colvar bias core setup generic |
| 19.041 | Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces | bio | metadynamics, collective variables, conformational changes, multiple walkers, Well-Tempered MetaD, peptide, binding, phosphorylation, post-transitional motif, sio2, adsorption | Jim Pfaendtner | UPPER_WALLS COM DISTANCE METAD PRINT ENERGY | generic vatom bias colvar |
| 19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Haochuan Chen | TORSION PRINT DRR | drr generic colvar |
| 19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Kresten Lindorff-Larsen | TORSION MOLINFO SUM FLUSH METAD CUSTOM PRINT CONSTANT ALPHABETA COMMITTOR COMBINE | colvar multicolvar generic bias function |
| 24.033 | Transient interactions between the fuzzy coat and the cross-b core of brain-derived Ab42 filaments | bio | CryoEM, MEMMI, Metadynamics, Metainference, Ab42 Fibrils, structural ensemble | Maria Milanesi | COM PARABETARMSD GROUP DISTANCE DUMPMASSCHARGE CENTER WHOLEMOLECULES EMMI SECONDARY_STRUCTURE_RMSD RMSD SUM LOWEST ALPHARMSD BIASVALUE UPPER_WALLS LESS_THAN MOLINFO COORDINATION PRINT PBMETAD DUMPATOMS | core function bias secondarystructure colvar vatom generic isdb |
| 24.032 | DeepLNE++ | methods | PATHCV, OPES | Thorben Fröhlking | GROUP DISTANCE COMBINE COORDINATION ENERGY OPES_METAD LOAD TORSION PRINT CUSTOM | function generic colvar core setup opes |
| 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 | GROUP ENDPLUMED OPES_METAD_EXPLORE ECV_MULTITHERMAL DISTANCE COORDINATION ENERGY TORSION ANGLE CENTER FIT_TO_TEMPLATE MATHEVAL PRINT WHOLEMOLECULES LOWER_WALLS FIXEDATOM OPES_EXPANDED UPPER_WALLS | core function bias colvar vatom generic opes |
| 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 | GROUP OPES_METAD_EXPLORE ECV_MULTITHERMAL DISTANCE COMBINE COORDINATION ENERGY RESTART TORSION PRINT OPES_EXPANDED CUSTOM | function generic colvar core setup opes |
| 24.017 | Absolute Binding Free Energies with OneOPES | methods | protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy | Francesco Gervasio | COM GROUP CONTACTMAP PROJECTION_ON_AXIS WHOLEMOLECULES INCLUDE OPES_METAD_EXPLORE ENERGY METAD RMSD LOWER_WALLS OPES_EXPANDED RESTART MATHEVAL BIASVALUE UPPER_WALLS MOLINFO WRAPAROUND COORDINATION ECV_MULTITHERMAL TORSION PRINT CUSTOM CONSTANT | core function bias colvar vatom generic setup opes |
| 24.014 | Learning Collective Variables with Synthetic Data Augmentation through Physics-inspired Geodesic Interpolation | methods | data augmentation, geodesic interpolation, collective variables, protein folding | Juno Nam | MOLINFO COORDINATION PYTORCH_MODEL METAD DRR FLUSH RMSD PRINT WHOLEMOLECULES LOWER_WALLS UPPER_WALLS | bias drr colvar pytorch generic |
| 24.013 | Estimating Free Energy Surfaces and their Convergence from multiple, independent static and history-dependent biased molecular-dynamics simulations with Mean Force Integration | methods | Mean Force Integration, Convergence, FES, Umbrella Sampling | Matteo Salvalaglio | MOLINFO DISTANCE RESTRAINT ENERGY COORDINATIONNUMBER METAD TORSION RESTART FLUSH MATHEVAL PRINT BIASVALUE COMMITTOR | function bias symfunc colvar generic setup |
| 24.007 | SWISH-X | bio | swish-x, SWISH-X, swish, expanded SWISH | Alberto Borsatto | INCLUDE MOLINFO ECV_MULTITHERMAL CONTACTMAP ENERGY PRINT WHOLEMOLECULES OPES_EXPANDED UPPER_WALLS | generic colvar bias opes |
| 24.005 | Learning Markovian Dynamics with Spectral Maps | methods | spectral map, collective variables, machine learning | Jakub Rydzewski | DISTANCE UNITS PRINT BIASVALUE CUSTOM | function bias colvar generic setup |
| 24.001 | A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations | bio | OPES, OPES-Flooding, QM/MM, Kinetics, Enzyme Catalysis | Dhiman Ray | DISTANCE COMBINE OPES_METAD UNITS FLUSH TORSION PRINT LOWER_WALLS COMMITTOR CUSTOM UPPER_WALLS | function bias colvar generic setup opes |
| 23.019 | Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors | bio | binding pathway, binding energy, sketch-map, drug development | Raitis Bobrovs | COM DISTANCE PATHMSD COLLECT_FRAMES WHOLEMOLECULES PROJECT_POINTS SKETCHMAP_PROJECTION METAD PDB2CONSTANT TRANSPOSE SUM DISSIMILARITIES VSTACK LANDMARK_SELECT_FPS SKETCHMAP UPPER_WALLS VORONOI MORE_THAN EUCLIDEAN_DISTANCE PRINT CUSTOM CONSTANT | refdist dimred matrixtools function valtools bias colvar vatom generic landmarks |
| 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 | GROUP DISTANCE CONTACTMAP CENTER WHOLEMOLECULES ENDPLUMED COMMITTOR INCLUDE ENERGY COMBINE ANGLE RMSD LOWER_WALLS OPES_METAD FIT_TO_TEMPLATE MATHEVAL UPPER_WALLS MOLINFO COORDINATION PYTORCH_MODEL PRINT FIXEDATOM CUSTOM | core function bias colvar vatom pytorch generic opes |
| 22.044 | Colloid Crystallisation Analyses | materials | Q4, Q6, Pair Entropy, DFS | Aaron Finney | GROUP LOCAL_Q4 MFILTER_LESS COORDINATIONNUMBER COMBINE LOCAL_Q6 MFILTER_MORE Q6 Q4 CONTACT_MATRIX PRINT CLUSTER_NATOMS LOCAL_AVERAGE DFSCLUSTERING | adjmat multicolvar function clusters symfunc generic core |
| 22.042 | Metadynamics of NSP10 and variants | bio | metadynamics, NSP10, crystal structure, variants | Shozeb Haider | TORSION PRINT METAD | generic colvar bias |
| 22.037 | Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site | chemistry | metadynamics, DNA, abasic | Mike Jones | GROUP DISTANCE METAD DISTANCES CENTER PRINT MEAN | multicolvar function bias generic colvar vatom core |
| 22.025 | Bubble nucleation rate predictions in a Lennard-Jones fluid | materials | free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation | Kristof Bal | GROUP RESTRAINT REWEIGHT_BIAS VOLUME ONES COMMITTOR MOVINGRESTRAINT MATRIX_VECTOR_PRODUCT DUMPGRID HISTOGRAM ANN CONTACT_MATRIX SUM COORDINATIONNUMBER LOAD FLUSH BIASVALUE UPPER_WALLS LESS_THAN CONVERT_TO_FES UNITS PRINT MEAN CUSTOM | adjmat core gridtools matrixtools annfunc function bias symfunc colvar generic setup |
| 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 | GROUP INCLUDE MATRIX_VECTOR_PRODUCT ENVIRONMENTSIMILARITY MORE_THAN SUM DISTANCE_MATRIX MEAN OPES_EXPANDED ONES PRINT LOWER_WALLS ECV_UMBRELLAS_LINE CUSTOM UPPER_WALLS | adjmat core matrixtools function bias envsim generic opes |
| 22.015 | Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome | bio | photodynamics, bacteriophytochrome, variationally enhanced sampling | Jakub Rydzewski | VES_LINEAR_EXPANSION BF_FOURIER OPT_AVERAGED_SGD PRINT TORSION TD_UNIFORM | ves generic colvar |
| 22.013 | Ligand dissociation from PreQ1 riboswitch | bio | ligand, RNA, metadynamics, pRAVE | Yihang Wang | COM GROUP MOLINFO DISTANCE COMBINE COORDINATIONNUMBER MATRIX_VECTOR_PRODUCT METAD SUM CONTACT_MATRIX RMSD PRINT WHOLEMOLECULES MEAN COMMITTOR CUSTOM ONES | adjmat core matrixtools function bias symfunc colvar vatom generic |
| 21.052 | On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets | materials | Ibuprofen, unbinding, WTmetaD | Matteo Salvalaglio | GROUP ENDPLUMED DISTANCE COORDINATIONNUMBER MATRIX_VECTOR_PRODUCT METAD CONTACT_MATRIX CENTER TORSION PRINT MEAN COMMITTOR ONES | adjmat core matrixtools function bias symfunc colvar vatom generic |
| 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 | GROUP DISTANCE COMBINE COORDINATION COORDINATIONNUMBER MATRIX_VECTOR_PRODUCT METAD MEAN CONTACT_MATRIX ONES PRINT LOWER_WALLS UPPER_WALLS | adjmat matrixtools function bias symfunc generic colvar core |
| 21.042 | Peptoid-mediated Au nanocrystal growth | materials | parallel-bias metadynamics, peptoid, Au | Xin Qi | COM MOLINFO DISTANCE GYRATION PRINT PBMETAD UPPER_WALLS | generic colvar vatom bias |
| 21.032 | Metal-coupled folding mechanism to metallothionein | bio | parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination | Manuel-Peris Diaz | GROUP COORDINATION PBMETAD UNITS WHOLEMOLECULES | core bias colvar generic setup |
| 21.031 | Photo-switchable sulfonulureas in KATP channel | bio | metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels | Katarzyna Walczewska-Szewc | COM DISTANCE METAD UNITS PRINT WHOLEMOLECULES LOWER_WALLS UPPER_WALLS | bias colvar vatom generic setup |
| 21.030 | Thermodynamic Basis for Stabilization of Helical Peptoids by Chiral Sidechains | bio | parallel bias parallel tempered metadynamics in WTE, synthetic foldamers, self-assembly, peptoid secondary structure | Jim Pfaendtner | COM INCLUDE DISTANCE COMBINE COORDINATION ENERGY GYRATION METAD SUM ALPHABETA TORSION PRINT PBMETAD CUSTOM CONSTANT | function multicolvar bias colvar vatom generic |
| 21.022 | Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly | materials | parallel bias metadynamics, adsorption, peptide | Xin Qi | COM MOLINFO DISTANCE ENERGY GYRATION PRINT PBMETAD LOWER_WALLS UPPER_WALLS | generic colvar vatom bias |
| 21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Adriana Pietropaolo | MATHEVAL PBMETAD RESTART TORSION PRINT WHOLEMOLECULES BIASVALUE CONSTANT | function bias colvar generic 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 COMBINE RESTRAINT PRINT WHOLEMOLECULES STATS | generic colvar function bias |
| 20.018 | Free energy barriers from biased molecular dynamics simulations | methods | kinetics, free energy barriers, chemical reactions, nucleation, metadynamics | Kristof Bal | DISTANCE REWEIGHT_METAD REWEIGHT_BIAS CENTER LOCAL_AVERAGE VOLUME PAIRENTROPY COMBINE DUMPGRID ENERGY METAD HISTOGRAM CONTACT_MATRIX LOWER_WALLS COORDINATIONNUMBER LOAD Q6 FLUSH UPPER_WALLS DENSITY COORDINATION CONVERT_TO_FES UNITS PRINT SPRINT | adjmat sprint gridtools function bias symfunc volumes colvar vatom generic setup |
| 19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Gareth Tribello | GROUP ACCUMULATE MULTICOLVARDENS CENTER ONES MATRIX_VECTOR_PRODUCT DUMPGRID FCCUBIC_FUNC CONTACT_MATRIX DISTANCES FCCUBIC SUM CHARGE FOURIER_TRANSFORM MORE_THAN POSITION UNITS KDE MASS ARGS2VATOM FIND_CONTOUR_SURFACE CUSTOM | adjmat fourier core gridtools matrixtools multicolvar function contour symfunc colvar vatom generic setup |
| 19.047 | Close Structure | methods | metadynamics, RMSD, path collective variables, property map | Vojtech Spiwok | PROPERTYMAP PRINT WHOLEMOLECULES METAD | generic colvar bias |
| 19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Paolo Raiteri | DISTANCE METAD UNITS RESTART FLUSH MATHEVAL PRINT UPPER_WALLS | function bias colvar generic setup |
| 19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Adriana Pietropaolo | MATHEVAL METAD TORSION PRINT WHOLEMOLECULES BIASVALUE CONSTANT | generic function colvar bias |
| 19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Riccardo Capelli | COM GROUP ENDPLUMED WRAPAROUND COORDINATION DUMPGRID METAD REWEIGHT_METAD POSITION HISTOGRAM CONVERT_TO_FES FLUSH FIT_TO_TEMPLATE MATHEVAL PRINT WHOLEMOLECULES READ UPPER_WALLS | core gridtools function bias colvar vatom generic |
| 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 | COMBINE LOWER_WALLS COORDINATION LOWEST CONSTANT SUM RESTART PDB2CONSTANT OPES_METAD PATH FIXEDATOM GROUP DISTANCE CUSTOM TORSION WHOLEMOLECULES CENTER PYTORCH_MODEL UPPER_WALLS EUCLIDEAN_DISTANCE FIT_TO_TEMPLATE | vatom generic refdist mapping opes core function colvar pytorch bias setup |
| 24.012 | Molecular simulations to investigate the impact of N6-methylation in RNA recognition | bio | metadynamics, alchemistry, RNA modification, RNA:protein interactions | Giovanni Bussi | COMBINE LOWER_WALLS BIASVALUE CENTER COORDINATION MOLINFO COM GHBFIX UPPER_WALLS DEBUG PRINT METAD GROUP DISTANCE | vatom generic core function colvar bias |
| 23.044 | Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition | materials | metadynamics, interlocked molecules | Luigi Leanza | DUMPGRID CONVERT_TO_FES COORDINATION HISTOGRAM READ PRINT ENDPLUMED METAD GROUP COMMITTOR | generic core colvar bias gridtools |
| 23.040 | Supramolecular capsules assembly dynamics | chemistry | Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics | Riccardo Capelli | METAD POSITION LESS_THAN CUSTOM BETWEEN WHOLEMOLECULES CENTER FLUSH UNITS PRINT DISTANCES COM SUM GROUP DISTANCE | vatom generic multicolvar core colvar function bias setup |
| 23.038 | Determinants of Neutral Antagonism and Inverse Agonism in the β2-adrenergic receptor | bio | protein coupled receptor, beta-adrenergic, receptor activation, antagonism, inverse agonism, metadynamics | Timothy Clark | WHOLEMOLECULES RMSD MATHEVAL MOLINFO PRINT METAD DISTANCE | bias colvar function generic |
| 23.036 | Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? | bio | NaCl, nucleation, metadynamics | Ruiyu Wang | COMBINE METAD Q4 MORE_THAN VOLUME ONES MEAN COORDINATIONNUMBER CUSTOM MATRIX_VECTOR_PRODUCT CONTACT_MATRIX Q6 ENERGY SPHERICAL_HARMONIC MATHEVAL PRINT SUM GROUP | generic core adjmat function colvar matrixtools bias symfunc |
| 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 BIASVALUE WHOLEMOLECULES CENTER CONSTANT MATHEVAL PRINT UPPER_WALLS METAD DISTANCE | vatom generic function colvar bias |
| 23.028 | Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process | chemistry | Ammonia decomposition; Dynamics;OPES; Neural Network potential | Manyi Yang | LOWER_WALLS COORDINATIONNUMBER CONTACT_MATRIX FLUSH PRINT ONES MEAN ENERGY DISTANCES SUM OPES_METAD MATRIX_VECTOR_PRODUCT MATHEVAL ZDISTANCES FIXEDATOM GROUP DISTANCE CUSTOM UNITS COM UPPER_WALLS LESS_THAN COMMITTOR | vatom generic multicolvar opes core adjmat function colvar matrixtools bias symfunc setup |
| 23.022 | A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar | methods | collective variables, machine learning, toy model | Enrico Trizio | LOWER_WALLS POSITION OPES_METAD BIASVALUE CUSTOM UNITS PRINT UPPER_WALLS PYTORCH_MODEL ENDPLUMED | generic opes colvar function pytorch bias setup |
| 23.021 | Into the Dynamics of Rotaxanes at Atomistic Resolution | materials | metadynamics, rotaxanes, molecular shuttles, molecular machines | Luigi Leanza | CUSTOM TORSION CENTER MATHEVAL PRINT UPPER_WALLS FIXEDATOM METAD DISTANCE | vatom generic function colvar bias |
| 23.016 | Activation/deactivation free-energy profiles for the β2-adrenergic receptor: Ligand modes of action | bio | G protein coupled receptor, beta-adrenergic, receptor activation, partial agonism, metadynamics | Timothy Clark | REWEIGHT_METAD DUMPGRID WHOLEMOLECULES HISTOGRAM RMSD MATHEVAL MOLINFO PRINT READ METAD DISTANCE CONVERT_TO_FES | generic function colvar bias gridtools |
| 22.029 | Angiotensin-1-7_Metadynamics | bio | Metadynamics, Angiotensin-(1-7), peptide | L.-América Chi | LOWER_WALLS WHOLEMOLECULES COORDINATION FLUSH PRINT UPPER_WALLS GYRATION METAD GROUP | bias core 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 | COMBINE LOWER_WALLS COORDINATIONNUMBER ONES MEAN CUSTOM MATRIX_VECTOR_PRODUCT COORDINATION FLUSH UNITS CONTACT_MATRIX UPPER_WALLS COM GYRATION METAD GROUP DISTANCE | vatom generic core adjmat function colvar matrixtools bias symfunc setup |
| 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 | COMBINE METAD LESS_THAN SECONDARY_STRUCTURE_RMSD CUSTOM ANGLE TORSION WHOLEMOLECULES COORDINATION FLUSH CONSTANT ALPHABETA MOLINFO UPPER_WALLS PRINT SUM DISTANCE ALPHARMSD | generic multicolvar secondarystructure function colvar bias |
| 22.006 | Peptide framework for screening the effects of amino acids on assembly | bio | metadynamics, peptides | Andrew White | COMBINE DISTANCE DUMPGRID MEAN HISTOGRAM INCLUDE DISTANCES COM PRINT GYRATION METAD GROUP REWEIGHT_BIAS CONVERT_TO_FES | vatom generic multicolvar core function colvar bias gridtools |
| 22.004 | Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques | chemistry | reaction discovery, OPES, collective variables | Umberto Raucci | LOWER_WALLS OPES_METAD LOAD CUSTOM COORDINATION UNITS MATHEVAL PYTORCH_MODEL COM UPPER_WALLS OPES_METAD_EXPLORE PRINT GROUP DISTANCE | vatom generic opes core function colvar pytorch bias setup |
| 21.047 | Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations | materials | pair entropy, metadynamics, ves, solids, crystallization | Pablo Piaggi | COMBINE METAD VOLUME LOAD TD_WELLTEMPERED OPT_AVERAGED_SGD PAIRENTROPY VES_LINEAR_EXPANSION ENERGY PRINT RESTART BF_LEGENDRE | ves generic function colvar bias gridtools setup |
| 21.043 | Predicting the Conformational Variability of Oncogenic GTP-bound G12D Mutated KRas-4B Proteins at Cell Membranes | chemistry | well-tempered metadynamics, KRas-4B, anionic membrane, conformational variability | Huixia Lu | TORSION PRINT FIXEDATOM METAD FIT_TO_TEMPLATE | bias colvar vatom 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 | COMBINE VOLUME CUSTOM COORDINATION PRINT ENDPLUMED METAD | bias function colvar generic |
| 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 LESS_THAN SECONDARY_STRUCTURE_RMSD WHOLEMOLECULES SUM INCLUDE MATHEVAL MOLINFO CONTACTMAP UPPER_WALLS ENERGY PRINT METAD DISTANCE ALPHARMSD | generic secondarystructure function colvar bias |
| 21.026 | Probing allosteric regulations with coevolution-driven molecular simulations | bio | metadynamics, coevolution, allostery, adenylate cyclase | Francesco Colizzi | PATHMSD WHOLEMOLECULES UNITS PRINT COM UPPER_WALLS METAD DISTANCE | vatom generic colvar bias setup |
| 21.014 | how to determine statistically accurate conformational ensembles | bio | metadynamics, metainference, errors, cv, SAXS, ensemble determination | Cristina Paissoni | COMBINE ANTIBETARMSD PRINT ENSEMBLE CONSTANT CONTACTMAP STATS GYRATION SUM SECONDARY_STRUCTURE_RMSD BIASVALUE METAD CUSTOM TORSION WHOLEMOLECULES CENTER PBMETAD ALPHABETA MOLINFO SAXS LESS_THAN | vatom generic multicolvar secondarystructure function colvar isdb bias |
| 21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Tarsis Ferreira | LOWER_WALLS REWEIGHT_METAD PUCKERING DUMPGRID WHOLEMOLECULES COORDINATION HISTOGRAM ENERGY INCLUDE PRINT UPPER_WALLS MOLINFO RANDOM_EXCHANGES METAD GROUP DISTANCE | generic core colvar bias gridtools |
| 20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Faidon Brotzakis | BIASVALUE DUMPGRID WHOLEMOLECULES HISTOGRAM RMSD READ PRINT MOLINFO DISTANCES EMMI GROUP CONVERT_TO_FES | generic multicolvar core colvar isdb bias gridtools |
| 20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Adriana Pietropaolo | WHOLEMOLECULES COORDINATION CENTER PBMETAD PRINT | bias colvar vatom generic |
| 20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Cristina Paissoni | BIASVALUE WHOLEMOLECULES CENTER ENSEMBLE INCLUDE MOLINFO PRINT SAXS STATS RESTRAINT GROUP DISTANCE | vatom generic core function isdb colvar bias |
| 20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Carlo Camilloni | COMBINE METAINFERENCE CUSTOM TORSION WHOLEMOLECULES CENTER ENSEMBLE CONSTANT ALPHABETA MOLINFO SAXS STATS GYRATION PBMETAD FLUSH SUM PRINT DISTANCE | vatom generic multicolvar function colvar isdb bias |
| 19.075 | PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python | other | Python, automatic differentiation | Toni Giorgino | COMBINE DISTANCE CUSTOM ANGLE TORSION CENTER PRINT RESTRAINT ENDPLUMED GROUP DUMPDERIVATIVES | vatom generic core function colvar bias |
| 19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Jakub Rydzewski | LOWER_WALLS PATHMSD RESTART UNITS PRINT UPPER_WALLS METAD | bias colvar generic setup |
| 19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | GiovanniMaria Piccini | COMBINE LOWER_WALLS FLUSH UNITS ENERGY PRINT UPPER_WALLS METAD DISTANCE | generic function colvar bias setup |
| 19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Gareth Tribello | METAD MORE_THAN CELL ONES MEAN CUSTOM FCCUBIC_FUNC MATRIX_VECTOR_PRODUCT CONTACT_MATRIX FCCUBIC UNITS PRINT UPPER_WALLS ENDPLUMED SUM GROUP | generic core adjmat function colvar matrixtools bias symfunc setup |
| 19.048 | Understanding Ligand Binding Selectivity in a Prototypical GPCR Family | bio | metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | LOWER_WALLS BIASVALUE WHOLEMOLECULES CONSTANT MATHEVAL PRINT COM UPPER_WALLS METAD DISTANCE | vatom generic function colvar bias |
| 19.040 | Optimal Metric for Path Collective Variables | bio | metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path | Francesco Luigi Gervasio | TORSION MATHEVAL PRINT ENDPLUMED METAD | bias colvar function 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 FLUSH DISTANCES UPPER_WALLS PRINT RESTART | generic multicolvar mapping bias setup |
| 19.025 | Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide | bio | metainference, NMR, protein dynamics, force-fields | Carlo Camilloni | METAINFERENCE RDC BIASVALUE CS2BACKBONE TORSION WHOLEMOLECULES FLUSH ENSEMBLE PBMETAD MOLINFO PRINT STATS GYRATION ENDPLUMED JCOUPLING | generic isdb function colvar bias |
| 19.023 | RECT | methods | metadynamics, replica exchange | Giovanni Bussi | TORSION WHOLEMOLECULES PRINT GYRATION METAD | bias colvar generic |
| 19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Matteo Salvalaglio | COMBINE LOWER_WALLS VOLUME CELL TORSION ENERGY MATHEVAL PRINT UPPER_WALLS ENDPLUMED METAD | bias function colvar generic |
| 25.006 | Characterizing the conformational ensemble of PROTAC degraders in solutions via atomistic simulations | methods | Enhanced sampling, Atomistic simulations, Conformational ensemble, PROTACs, Targeted Protein Degradation, Chamelonic molecules | Shikshya Bhusal, Omar Valsson | READ CENTER INCLUDE GYRATION ENERGY PBMETAD RESTART TORSION VOLUME PRINT DISTANCE | bias setup generic vatom colvar |
| 25.002 | M3_PCV-ABMD | chemistry | Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor | Gian Marco Elisi | ABMD PATHMSD UPPER_WALLS UNITS ENDPLUMED PRINT | bias colvar setup generic |
| 24.027 | Proline cis and trans subensembles of a disordered peptide | bio | intrinsically disordered proteins, proline cis trans isomerisation, metadynamics, collective variables | Alice Pettitt | WHOLEMOLECULES ENDPLUMED FLUSH INCLUDE MOLINFO GYRATION COORDINATION PARABETARMSD ANTIBETARMSD PBMETAD DIHCOR TORSION GROUP PRINT COMBINE DISTANCE ALPHARMSD | bias multicolvar core generic secondarystructure function colvar |
| 24.026 | Constant pH metadynamics of RNA oligomers | bio | metadynamics, pH, RNA | Giovanni Bussi | MOLINFO PUCKERING RESTART TORSION METAD PRINT | setup bias generic colvar |
| 24.018 | A new route to the prebiotic synthesis of glycine via ab initio-based machine learning calculations | chemistry | prebiotic chemistry, glycine, Strecker synthesis, ab initio calculations, machine learning | Léon HUET | PRINT DISTANCE | generic colvar |
| 24.009 | Weighted Shape Gaussian Mixture Models | bio | metadynamics, clustering | Glen Hocky | GROUP UNITS TORSION METAD PRINT | bias setup core generic colvar |
| 23.031 | Identifying small molecules binding sites in RNA conformational ensembles with SHAMAN | bio | RNA, metadynamics, probes, mixed-solvent MD, small molecules, binding sites | Max Bonomi | WHOLEMOLECULES METAD SHADOW UPPER_WALLS CENTER CUSTOM POSITION MOLINFO WRAPAROUND DISTANCES FIT_TO_TEMPLATE GROUP PRINT DISTANCE SUM | isdb bias multicolvar core generic vatom function colvar |
| 23.027 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, DFS, Q3, Pair Entropy | Aaron Finney | DENSITY CONTACT_MATRIX UNITS FIXEDATOM DFSCLUSTERING LOAD AROUND CLUSTER_NATOMS RESTRAINT LOCAL_Q3 LOCAL_AVERAGE Q3 DUMPGRID HISTOGRAM COORDINATIONNUMBER GROUP PRINT CLUSTER_DISTRIBUTION | clusters gridtools bias symfunc setup core volumes generic vatom adjmat |
| 23.024 | Permutationally Invariant Networks for Enhanced Sampling (PINES) | methods | collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent | Nicholas Herringer | PBMETAD LOAD PRINT | bias generic setup |
| 23.018 | Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention | materials | metadynamics, surface binding, peptide adsorption | Kaylyn Torkelson | UPPER_WALLS GYRATION COM PBMETAD PRINT DISTANCE | bias colvar vatom generic |
| 23.015 | MPCs aggregation | bio | opes_explore, dimerization, MPCs, self-assembly | Vikas Tiwari | WHOLEMOLECULES METAD UPPER_WALLS CENTER CUSTOM LOWER_WALLS OPES_METAD_EXPLORE COORDINATION COM GROUP PRINT DISTANCE | opes bias core generic vatom function colvar |
| 23.007 | Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains | bio | metadynamics, peptoids, parallel-bias metadynamics | Jim Pfaendtner | WHOLEMOLECULES INCLUDE GYRATION COORDINATION COM RESTRAINT PBMETAD TORSION PRINT | vatom bias generic colvar |
| 22.026 | Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification | materials | Peptoid, silica | Jim Pfaendtner | UPPER_WALLS MOLINFO GYRATION COM PBMETAD PRINT DISTANCE | bias generic colvar vatom |
| 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 | WHOLEMOLECULES METAD COM TORSION GROUP PRINT DISTANCE | bias core generic vatom colvar |
| 22.000 | Amyloid precursor protein processing by human γ-secretase | bio | Bias Exchange Metadynamics, Helix unfolding, coupled binding | Xiaoli Lu | SUM UNITS CENTER INCLUDE MOLINFO COORDINATION ANTIBETARMSD RANDOM_EXCHANGES CONTACTMAP METAD PRINT LESS_THAN SECONDARY_STRUCTURE_RMSD DISTANCE ALPHARMSD | bias setup generic vatom secondarystructure function 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 | CONSTANT UNITS CUSTOM INCLUDE ENERGY REWEIGHT_METAD TORSION BIASVALUE METAD PRINT DISTANCE | bias setup generic function colvar |
| 21.012 | NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition | bio | funnel metadynamics | Jim Pfaendtner | FUNNEL UPPER_WALLS LOWER_WALLS COM FUNNEL_PS METAD PRINT DISTANCE | bias generic vatom funnel colvar |
| 21.011 | CmuMD simulations of NaCl(aq) at graphite | chemistry | CmuMD, DFS clustering | Aaron Finney | DENSITY CONTACT_MATRIX FIXEDATOM DFSCLUSTERING LOAD AROUND MFILTER_MORE CLUSTER_NATOMS RESTRAINT DUMPGRID MULTICOLVARDENS COORDINATIONNUMBER GROUP PRINT CLUSTER_DISTRIBUTION | clusters gridtools bias multicolvar symfunc setup core volumes generic vatom adjmat |
| 21.006 | OPES, On-the-fly Probability Enhanced Sampling Method | methods | opes, alanine dipeptide, well-tempered, multithermal, multiumbrella | Michele Invernizzi | ENDPLUMED ECV_MULTITHERMAL ENERGY ECV_UMBRELLAS_LINE TORSION OPES_EXPANDED PRINT OPES_METAD | generic opes colvar |
| 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 | OPT_AVERAGED_SGD MEAN CONTACT_MATRIX UPPER_WALLS ENERGY MATRIX_VECTOR_PRODUCT MORE_THAN ECV_MULTITHERMAL_MULTIBARIC ECV_UMBRELLAS_LINE RESTART ENVIRONMENTSIMILARITY COMBINE Q6 VES_LINEAR_EXPANSION CUSTOM ONES SPHERICAL_HARMONIC OPES_EXPANDED BF_LEGENDRE MATHEVAL TD_UNIFORM VOLUME GROUP PRINT DISTANCE_MATRIX SUM | envsim opes bias symfunc matrixtools ves colvar setup core generic function adjmat |
| 20.028 | Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane | bio | metadynamics, KRas-4B, anionic membrane | Huixia Lu | CENTER FIT_TO_TEMPLATE RESTART METAD PRINT DISTANCE | bias setup generic vatom colvar |
| 20.016 | Predicting polymorphism in molecular crystals using orientational entropy | materials | metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy | Pablo Piaggi | METAD UPPER_WALLS CENTER LOAD INCLUDE VOLUME GROUP PRINT | bias setup core generic vatom colvar |
| 20.014 | amyloid beta small molecule interaction | bio | intrinsically disordered proteins, disordered proteins, IDPs, fuzzy binding, small molecule, drugs, entropy, binding, Alzheimer’s disease, amyloid beta | Gabriella Heller | INCLUDE MOLINFO ANTIBETARMSD PBMETAD ENDPLUMED ENSEMBLE ALPHARMSD CS2BACKBONE PARABETARMSD DIHCOR METAINFERENCE TORSION COMBINE COORDINATION WHOLEMOLECULES FLUSH STATS GYRATION GROUP PRINT | isdb bias multicolvar core generic secondarystructure function colvar |
| 20.010 | Phase equilibrium of liquid water and hexagonal ice from enhanced sampling molecular dynamics simulations | materials | water, ice, TIP4P, crystallization, EnvironmentSimilarity, RefCV, kernel, VES, variationally enhanced sampling | Pablo Piaggi | OPT_AVERAGED_SGD MEAN CONTACT_MATRIX UPPER_WALLS MATRIX_VECTOR_PRODUCT OPT_DUMMY MORE_THAN RESTART ENVIRONMENTSIMILARITY COMBINE Q6 VES_LINEAR_EXPANSION CUSTOM ONES SPHERICAL_HARMONIC TD_WELLTEMPERED BF_LEGENDRE MATHEVAL VOLUME GROUP PRINT DISTANCE_MATRIX SUM | envsim bias symfunc matrixtools ves setup colvar core generic function adjmat |
| 20.003 | Enhanced sampling of transition states | methods | Variationally Enhanced Sampling, Target distribution, Transition state, Enhanced Sampling, Nucleation, chemical reaction | Jayashrita Debnath | OPT_AVERAGED_SGD UNITS VES_LINEAR_EXPANSION LOAD POSITION ENERGY PRINT BF_LEGENDRE | setup colvar ves generic |
| 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 | METAD MORE_THAN SUM CONTACT_MATRIX MEAN UPPER_WALLS ENDPLUMED LOWER_WALLS GYRATION DISTANCES ENERGY ONES COORDINATIONNUMBER MATRIX_VECTOR_PRODUCT GROUP PRINT DISTANCE LOWEST | bias multicolvar symfunc colvar matrixtools core generic function adjmat |
| 19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | UPPER_WALLS MOLINFO GYRATION ENERGY COM METAD PRINT DISTANCE | bias generic colvar vatom |
| 19.056 | maze | methods | maze, ligand unbinding | Jakub Rydzewski | UNITS POSITION MAZE_LOSS MAZE_OPTIMIZER_BIAS PRINT MAZE_SIMULATED_ANNEALING | colvar setup maze generic |
| 19.055 | Flying Gaussian method | methods | flying Gaussians, alanine dipeptide, peptide bond, Met-enkephalin | Vojtech Spiwok | MATHEVAL TORSION METAD PRINT COMBINE DISTANCE | bias function colvar generic |
| 19.049 | Determining the sizes of solid/liquid clusters in MD trajectories of nucleation | methods | nucleation, metadynamics, clustering, Steinhardt order parameters | Gareth Tribello | METAD MORE_THAN CLUSTER_PROPERTIES CONTACT_MATRIX DFSCLUSTERING CUSTOM CLUSTER_DISTRIBUTION LOCAL_Q6 CLUSTER_NATOMS DISTANCES ONES OUTER_PRODUCT MATRIX_VECTOR_PRODUCT COORDINATIONNUMBER SMAC OUTPUT_CLUSTER PRINT Q6 | clusters bias symfunc multicolvar matrixtools generic function adjmat |
| 19.030 | Coarse-Grained MetaDynamics (CG-MetaD) | bio | Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy | Vittorio Limongelli | WHOLEMOLECULES UPPER_WALLS LOWER_WALLS COM METAD PRINT DISTANCE | bias colvar generic vatom |
| 19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Elena Papaleo | WHOLEMOLECULES METAD UPPER_WALLS CONSTANT CUSTOM LOWER_WALLS MOLINFO GYRATION TORSION GROUP PRINT COMBINE ALPHABETA SUM | bias multicolvar core generic function colvar |
| 19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Pratyush Tiwary | WHOLEMOLECULES ALPHABETA COMMITTOR CONSTANT CUSTOM COM TORSION EXTERNAL RESTART PRINT COMBINE DISTANCE SUM | bias multicolvar setup generic vatom function colvar |
| 19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Matteo Salvalaglio | METAD MORE_THAN CONTACT_MATRIX MEAN ENDPLUMED GYRATION DISTANCES LOWEST ONES COORDINATIONNUMBER RESTART MATRIX_VECTOR_PRODUCT GROUP PRINT DISTANCE SUM | bias multicolvar symfunc colvar setup matrixtools core generic function adjmat |
| 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 | MOVINGRESTRAINT DISTANCE METAD RESTRAINT MOLINFO TORSION RESTART PRINT PUCKERING | colvar bias setup generic |
| 24.030 | NMR guided simulation of dsRBD | bio | Metainference, NMR, protein dynamics | Debadutta Patra | FLUSH CONSTANT SUM COMBINE ENSEMBLE DISTANCE GROUP WHOLEMOLECULES METAINFERENCE MOLINFO CUSTOM RDC STATS TORSION ALPHABETA PRINT | colvar multicolvar generic function core isdb |
| 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 | GROUP UPPER_WALLS TORSION OPES_METAD MATHEVAL FIT_TO_TEMPLATE DISTANCE COMMITTOR ANGLE FIXEDATOM COMBINE WHOLEMOLECULES METAD CONTACTMAP CENTER PRINT ENDPLUMED RMSD COORDINATION MOLINFO CUSTOM | colvar generic core opes function vatom bias |
| 24.016 | Cryo-EM guided simulations of ribozyme | bio | metainference, cryo-EM | Giovanni Bussi | BIASVALUE GROUP WHOLEMOLECULES MOLINFO EMMIVOX RESTRAINT ERMSD PRINT INCLUDE | colvar generic core isdb bias |
| 24.015 | nanocluster QM/MM | chemistry | nanocluster, QM/MM, pathCV, OPES, reaction modelling | Vikas Tiwari | FLUSH DISTANCE COMMITTOR UPPER_WALLS RESTRAINT UNITS LOWER_WALLS CENTER PRINT OPES_METAD | colvar setup generic opes vatom bias |
| 24.008 | yCD Metadynamics | bio | volume-based MetaD, path CVs, infrequent MetaD, product release | James McCarty | GROUP UPPER_WALLS INCLUDE MATHEVAL DUMPGRID FIT_TO_TEMPLATE DISTANCE COMMITTOR READ FIXEDATOM CONVERT_TO_FES COMBINE PATH WHOLEMOLECULES REWEIGHT_METAD METAD CONTACTMAP WRAPAROUND PRINT ENDPLUMED RMSD FLUSH COM MOLINFO COORDINATION HISTOGRAM GPATH | colvar generic core function gridtools mapping vatom bias |
| 23.037 | Estimating binding free energy of solid binding peptides without extensive sampling | bio | metadynamics, solid binding peptides | Xin Qi | COM DISTANCE GYRATION UPPER_WALLS MOLINFO LOWER_WALLS PRINT PBMETAD | vatom colvar bias generic |
| 23.005 | A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs | bio | metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A | Timothy Clark | RMSD DISTANCE WHOLEMOLECULES REWEIGHT_METAD METAD MOLINFO READ HISTOGRAM CONVERT_TO_FES PRINT MATHEVAL DUMPGRID | colvar generic function gridtools bias |
| 23.003 | Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations | methods | metadynamics, alchemical variable, alchemical free energy calculations | Wei-Tse Hsu | EXTRACV METAD PUT READ TORSION PRINT | core colvar bias generic |
| 23.000 | Atomistic simulations of RNA tetraloop folding via PTWTE-WTM | bio | parallel tempering, well-tempered metadynamics, well-tempered ensemble, RNA, Tetraloop, Folding | Gül Zerze | WHOLEMOLECULES UPPER_WALLS METAD LOWER_WALLS ENERGY CONTACTMAP PRINT | colvar bias generic |
| 22.036 | Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction | bio | Well-tempered MetaDynamics with Hamiltonian Replica Exchange | Miroslav Krepl | FLUSH GHBFIX COMBINE BIASVALUE LOAD GROUP UPPER_WALLS METAD MOLINFO COORDINATION CUSTOM PRINT | colvar setup generic function core bias |
| 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 | DISTANCE_MATRIX SUM MORE_THAN GROUP ONES UPPER_WALLS ENERGY MATRIX_VECTOR_PRODUCT CUSTOM PRINT AROUND RESTART HISTOGRAM VOLUME ENVIRONMENTSIMILARITY OPES_METAD MEAN DUMPGRID | volumes colvar setup matrixtools generic function core envsim opes adjmat gridtools 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 | WHOLEMOLECULES METAD LOAD PRINT | bias setup 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 | COM DISTANCE UPPER_WALLS METAD LOWER_WALLS UNITS CUSTOM TORSION PRINT | colvar setup generic function vatom bias |
| 21.038 | Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics | materials | metadynamics, SGOOP, nucleation, urea | Ziyue Zou | COMBINE VOLUME LOAD COORDINATIONNUMBER GROUP ONES METAD ENERGY MATRIX_VECTOR_PRODUCT CONTACT_MATRIX CENTER PRINT INCLUDE MEAN | colvar setup symfunc matrixtools generic function core adjmat vatom bias |
| 21.035 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, interface | Aaron Finney | LOAD DISTANCE GROUP RESTRAINT FIXEDATOM PRINT | colvar setup generic core vatom bias |
| 21.033 | Multiple-path-metadynamics applied to DNA base-pairing transitions | bio | path-CV, metadynamics, multiple-walker, dna | Alberto Pérez-de-Alba-Ortíz | CONSTANT COMBINE MOVINGRESTRAINT UPPER_WALLS METAD RESTRAINT PRINT INCLUDE | function bias generic |
| 21.028 | From Enhanced Sampling to Reaction Profiles | methods | collective variables, multi-state, machine learning, Deep-TDA | Enrico Trizio | GROUP UPPER_WALLS TORSION OPES_METAD MATHEVAL LOAD FIT_TO_TEMPLATE DISTANCE LOWER_WALLS ANGLE FIXEDATOM WHOLEMOLECULES UNITS PYTORCH_MODEL CENTER PRINT ENDPLUMED DISTANCES COORDINATION | colvar setup pytorch multicolvar generic core opes function vatom bias |
| 21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Kresten Lindorff-Larsen | FLUSH BIASVALUE SAXS GROUP WHOLEMOLECULES METAINFERENCE MOLINFO PBMETAD CENTER EEFSOLV ALPHARMSD PRINT GYRATION | colvar generic core secondarystructure isdb vatom bias |
| 21.000 | Uremic toxin time scale dynamics | bio | uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs) | Jim Pfaendtner | COM DISTANCE GROUP WHOLEMOLECULES PRINT | vatom colvar core generic |
| 20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Michele Invernizzi | ECV_MULTITHERMAL_MULTIBARIC GROUP ONES UPPER_WALLS CONTACT_MATRIX TORSION ECV_UMBRELLAS_LINE ENVIRONMENTSIMILARITY SPHERICAL_HARMONIC MATHEVAL MORE_THAN LOAD Q6 ENERGY VOLUME MEAN DISTANCE_MATRIX ECV_MULTITHERMAL COMBINE WHOLEMOLECULES UNITS PRINT ENDPLUMED RMSD SUM OPES_EXPANDED ECV_LINEAR MOLINFO MATRIX_VECTOR_PRODUCT CUSTOM POSITION | colvar symfunc setup matrixtools generic core opes envsim function adjmat bias |
| 19.079 | Impact of Glutamate Carboxylation in the Adsorption of the alpha-1 Domain of Osteocalcin to Hydroxyapatite and Titania | bio | metadynamics, peptide adsorption, parallel tempering, well-tempered ensemble | Sarah Alamdari | COM DISTANCE GROUP UPPER_WALLS METAD MOLINFO ENERGY PRINT GYRATION | colvar generic core vatom bias |
| 19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | COM DISTANCE UPPER_WALLS METAD MOLINFO ENERGY PRINT GYRATION | vatom colvar bias generic |
| 19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Giovanni Bussi | DISTANCE WHOLEMOLECULES RESTRAINT COORDINATION LOWER_WALLS ENDPLUMED | colvar bias generic |
| 19.059 | cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide | bio | bias-exchange metadynamics, cis-trans isomerization | Fabrizio Marinelli | METAD TORSION PRINT INCLUDE RANDOM_EXCHANGES | colvar bias generic |
| 19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Gareth Tribello | CELL GROUP ONES UPPER_WALLS CONTACT_MATRIX LESS_THAN MORE_THAN LOWER_WALLS AROUND MEAN METAD UNITS PRINT ENDPLUMED FCCUBIC_FUNC SUM MATRIX_VECTOR_PRODUCT CUSTOM FCCUBIC | volumes colvar setup symfunc matrixtools generic core function adjmat bias |
| 19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Carlo Camilloni | CONSTANT GROUP UPPER_WALLS TORSION ALPHABETA LESS_THAN BIASVALUE LOWER_WALLS RESTART SECONDARY_STRUCTURE_RMSD COMBINE WHOLEMOLECULES PRINT PBMETAD ENDPLUMED FLUSH SUM ANTIBETARMSD MOLINFO CUSTOM CS2BACKBONE | colvar setup multicolvar generic core function secondarystructure isdb bias |
| 19.027 | Multithermal-multibaric simulations using VES | methods | ves, Wang Landau, multicanonical, liquid sodium, density anomaly | Pablo Piaggi | ACCUMULATE VES_LINEAR_EXPANSION DUMPGRID OPT_AVERAGED_SGD ENERGY READ RESTART TD_MULTICANONICAL CONVERT_TO_FES AVERAGE COMBINE BF_LEGENDRE UNITS OPT_DUMMY PRINT REWEIGHT_BIAS REWEIGHT_TEMP_PRESS CUSTOM HISTOGRAM | colvar setup generic function gridtools ves bias |
| 19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Carlo Camilloni | RMSD BIASVALUE SAXS DISTANCE GROUP WHOLEMOLECULES UPPER_WALLS MOLINFO RESTRAINT CENTER STATS PRINT INCLUDE ENDPLUMED | colvar generic core function isdb vatom bias |
| 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 | RESTRAINT GROUP COMBINE PRINT DISTANCE CONTACT_MATRIX FIXEDATOM UNITS LOWER_WALLS CUSTOM FLUSH SUM COM UPPER_WALLS COORDINATIONNUMBER MATRIX_VECTOR_PRODUCT MEAN LOWEST ONES METAD ANGLE COORDINATION DISTANCES | generic colvar setup core multicolvar vatom function adjmat bias matrixtools symfunc |