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 |
|---|---|---|---|---|---|---|
| 26.002 | A Transferable and Robust Computational Framework for Class A GPCR Activation Free Energies | bio | OneOPES, GPCR, ADRB1, activation, euclidean path, microswitches, conformational changes, allostery | Valerio Rizzi | PATHMSD OPES_EXPANDED ENERGY RMSD GROUP VOLUME UPPER_WALLS OPES_METAD_EXPLORE CUSTOM ECV_MULTITHERMAL LOWER_WALLS DISTANCE COORDINATION PRINT CENTER PATH | vatom core bias opes generic colvar mapping function |
| 26.001 | Molecular simulations Alx riboswitch | bio | RNA, riboswitch | Giovanni Bussi | MOVINGRESTRAINT MATHEVAL MOLINFO RESTRAINT DISTANCE ERMSD PRINT | bias colvar generic function |
| 25.014 | Atomic resolution ensembles of intrinsically disordered proteins with Alphafold | bio | bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement | Vincent Schnapka | GROUP BAIES BIASVALUE PRINT | bias isdb core generic |
| 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 | CENTER EMMI BIASVALUE DUMPATOMS ALPHARMSD RMSD MOLINFO GROUP PARABETARMSD UPPER_WALLS WHOLEMOLECULES PBMETAD DISTANCE COORDINATION PRINT COM DUMPMASSCHARGE | vatom isdb core bias generic secondarystructure colvar |
| 24.005 | Learning Markovian Dynamics with Spectral Maps | methods | spectral map, collective variables, machine learning | Jakub Rydzewski | BIASVALUE CUSTOM UNITS DISTANCE PRINT | bias setup generic colvar function |
| 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 | COMBINE TORSION UPPER_WALLS FLUSH CUSTOM COMMITTOR LOWER_WALLS UNITS DISTANCE PRINT OPES_METAD | bias setup generic opes colvar 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 | MATHEVAL MOLINFO OPES_METAD_EXPLORE CUSTOM COORDINATION WRAPAROUND COM POSITION BIASVALUE FIT_TO_TEMPLATE UPPER_WALLS WHOLEMOLECULES FLUSH UNITS PRINT OPES_METAD ENERGY COMMITTOR LOWER_WALLS DISTANCE CENTER ENDPLUMED TORSION GROUP | vatom core bias setup generic opes colvar function |
| 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 | ECV_UMBRELLAS_LINE OPES_EXPANDED HISTOGRAM RESTART UPPER_WALLS LOWER_WALLS ENVIRONMENTSIMILARITY PRINT DUMPGRID | envsim bias setup opes generic gridtools |
| 22.036 | Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction | bio | Well-tempered MetaDynamics with Hamiltonian Replica Exchange | Miroslav Krepl | COMBINE BIASVALUE MOLINFO GROUP UPPER_WALLS FLUSH CUSTOM GHBFIX LOAD METAD COORDINATION PRINT | core bias setup generic colvar function |
| 22.034 | Rationalising the difference in crystallisability of two Sulflowers using efficient in silico methods | materials | metadynamics, crystallizability, crystal structure prediction, sulflower, persulforated coronene | Matteo Salvalaglio | MATHEVAL UPPER_WALLS CELL CUSTOM COMMITTOR LOWER_WALLS METAD PRINT DRMSD | bias colvar generic function |
| 22.026 | Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification | materials | Peptoid, silica | Jim Pfaendtner | MOLINFO UPPER_WALLS PBMETAD DISTANCE PRINT GYRATION COM | bias colvar vatom generic |
| 22.011 | Accelerating all-atom simulations and gaining mechanistic understanding of biophysical systems through State Predictive Information Bottleneck | methods | metadynamics, membrane permeation, protein folding | Shams Mehdi | COMBINE MATHEVAL YANGLES MOLINFO TORSION UPPER_WALLS WHOLEMOLECULES CUSTOM ZANGLES LOWER_WALLS DISTANCE XANGLES METAD PRINT ALPHABETA COM | vatom multicolvar bias generic colvar function |
| 21.017 | All-atom simulations of the Vav1 AD construct | bio | metadynamics, parallel-bias, well-tempered | Simone Orioli | RESTART ALPHARMSD CONTACTMAP MOLINFO GROUP WHOLEMOLECULES PBMETAD REWEIGHT_BIAS METAD PRINT ALPHABETA | core multicolvar bias setup generic secondarystructure colvar |
| 21.014 | how to determine statistically accurate conformational ensembles | bio | metadynamics, metainference, errors, cv, SAXS, ensemble determination | Cristina Paissoni | BIASVALUE MOLINFO CONTACTMAP TORSION WHOLEMOLECULES PBMETAD ANTIBETARMSD METAD PRINT STATS ALPHABETA CENTER GYRATION SAXS ENSEMBLE | vatom isdb multicolvar bias generic secondarystructure colvar function |
| 21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Kristof Bal | HISTOGRAM MOVINGRESTRAINT REWEIGHT_METAD UPPER_WALLS FLUSH COMMITTOR COORDINATIONNUMBER METAD UNITS LOAD PRINT CONVERT_TO_FES DUMPGRID | bias setup generic symfunc gridtools |
| 20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Glen Hocky | BIASVALUE MATHEVAL ENERGY GROUP RESTRAINT FISST UNITS DISTANCE PRINT GYRATION | core fisst bias setup generic colvar function |
| 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 | ENDPLUMED ENERGY DISTANCES UPPER_WALLS COORDINATIONNUMBER LOWER_WALLS METAD PRINT GYRATION | multicolvar bias generic symfunc colvar |
| 19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Vittorio Limongelli | RMSD FUNNEL_PS UPPER_WALLS WHOLEMOLECULES FUNNEL METAD DISTANCE LOWER_WALLS PRINT COM | vatom funnel bias generic colvar |
| 19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Pratyush Tiwary | COMBINE RESTART EXTERNAL TORSION WHOLEMOLECULES COMMITTOR DISTANCE PRINT ALPHABETA COM | vatom multicolvar bias setup generic colvar function |
| 19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Gabriele Cesare Sosso | CONTACT_MATRIX ENDPLUMED CLUSTER_NATOMS Q6 FLUSH COMMITTOR DFSCLUSTERING OUTPUT_CLUSTER MFILTER_MORE LOCAL_Q6 CLUSTER_WITHSURFACE | multicolvar generic adjmat symfunc clusters |
| 19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Mattia Bernetti | ENDPLUMED MOLINFO ALPHARMSD ENERGY WHOLEMOLECULES METAD PRINT GYRATION | bias colvar secondarystructure generic |
| 19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Max Bonomi | EMMI BIASVALUE MOLINFO GROUP WHOLEMOLECULES PRINT | bias isdb core generic |
| 26.008 | Ensemble Dynamics | methods | State Exploration, Protein Folding, Drug Binding, Phase Transition | Florian M. Dietrich | POSITION BIASVALUE GROUP DISTANCE CELL CUSTOM LOAD OPES_METAD_EXPLORE TORSION PRINT UNITS | colvar opes bias function generic core setup |
| 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 COORDINATIONNUMBER OPES_METAD DISTANCE GROUP DISTANCES CUSTOM ZDISTANCES FIXEDATOM FLUSH PRINT UPPER_WALLS UNITS | colvar opes multicolvar symfunc bias vatom generic function core setup |
| 25.000 | Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer | bio | metadynamics, pathCV | Sahithya Sridharan Iyer | FUNCPATHGENERAL COM DISTANCE GROUP RESTART METAD WHOLEMOLECULES MOLINFO PRINT UPPER_WALLS | colvar bias vatom function generic core setup |
| 24.031 | DeepLNE | methods | PATHCV, OPES, OneOPES | Thorben Fröhlking | COMBINE PYTORCH_MODEL ENERGY MOLINFO RESTART ECV_MULTITHERMAL COORDINATION ERMSD VOLUME OPES_METAD_EXPLORE PRINT OPES_EXPANDED | colvar opes pytorch generic function setup |
| 24.017 | Absolute Binding Free Energies with OneOPES | methods | protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy | Francesco Gervasio | ENERGY RESTART METAD OPES_EXPANDED CONSTANT MATHEVAL BIASVALUE WHOLEMOLECULES TORSION UPPER_WALLS RMSD CUSTOM CONTACTMAP COORDINATION LOWER_WALLS PRINT COM GROUP PROJECTION_ON_AXIS WRAPAROUND INCLUDE ECV_MULTITHERMAL OPES_METAD_EXPLORE MOLINFO | colvar opes bias vatom generic function core setup |
| 24.010 | Oxytocin metadynamics simulation | bio | metadynamics, oxytocin, peptide | Jan Beránek | RESTART METAD WHOLEMOLECULES FLUSH TORSION PRINT | colvar setup generic bias |
| 24.009 | Weighted Shape Gaussian Mixture Models | bio | metadynamics, clustering | Glen Hocky | GROUP METAD TORSION PRINT UNITS | colvar bias generic core setup |
| 24.000 | Ammonia Decomposition on Non-stoichiometric Lithium Imide | chemistry | ammonia decomposition, non-stoichiometric lithium imide, machine learning interatomic potentials, enhanced sampling, heterogeneous catalysis | Francesco Mambretti | COORDINATIONNUMBER OPES_METAD DISTANCE GROUP ZDISTANCES FIXEDATOM FLUSH PRINT UPPER_WALLS UNITS | colvar opes multicolvar symfunc bias vatom generic core setup |
| 23.026 | Machine Learning Nucleation Collective Variables with Graph Neural Networks | chemistry | Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks | Florian Dietrich | MFILTER_MORE MOVINGRESTRAINT COORDINATIONNUMBER LOCAL_Q6 GROUP COMBINE METAD Q6 LOWER_WALLS PRINT | multicolvar symfunc bias function generic core |
| 23.024 | Permutationally Invariant Networks for Enhanced Sampling (PINES) | methods | collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent | Nicholas Herringer | PBMETAD PRINT LOAD | setup generic bias |
| 23.011 | OneOPES, a combined enhanced sampling method to rule them all | bio | OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding | Valerio Rizzi | DISTANCE ENERGY MOLINFO METAD ECV_MULTITHERMAL OPES_METAD_EXPLORE TORSION ENDPLUMED PRINT OPES_EXPANDED | colvar opes generic bias |
| 22.044 | Colloid Crystallisation Analyses | materials | Q4, Q6, Pair Entropy, DFS | Aaron Finney | MFILTER_MORE DFSCLUSTERING COORDINATIONNUMBER LOCAL_Q6 GROUP COMBINE MFILTER_LESS Q6 LOCAL_Q4 Q4 LOCAL_AVERAGE CONTACT_MATRIX PRINT CLUSTER_NATOMS | multicolvar adjmat symfunc clusters function generic core |
| 22.028 | N-glycan conformer distributions in atomistic simulation | bio | REST2, RECT, N-glycan, pucker | Isabell Grothaus | TORSION PRINT HISTOGRAM DUMPGRID CONVERT_TO_FES METAD READ MOLINFO PUCKERING | colvar bias generic gridtools |
| 22.024 | Conformational Entropy as a Potential Liability of Computationally Designed Antibodies | bio | metadynamics, conformational entropy, antibody, nanobody | Thomas Löhr | TORSION COM RESTART PBMETAD ALPHABETA ALPHARMSD WHOLEMOLECULES MOLINFO PRINT ANTIBETARMSD | colvar multicolvar secondarystructure bias vatom generic setup |
| 22.015 | Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome | bio | photodynamics, bacteriophytochrome, variationally enhanced sampling | Jakub Rydzewski | VES_LINEAR_EXPANSION OPT_AVERAGED_SGD TD_UNIFORM TORSION BF_FOURIER PRINT | colvar ves generic |
| 22.009 | Glycosylation in calixarenes capsule | chemistry | Metadynamics, glycosylation, supramolecular catalysis | GiovanniMaria Piccini | BRIDGE ANGLE RMSD DISTANCE GROUP COMBINE MATHEVAL DISTANCES METAD FIT_TO_TEMPLATE COORDINATION WHOLEMOLECULES FLUSH LOWER_WALLS PRINT UPPER_WALLS UNITS | colvar multicolvar adjmat bias function generic core setup |
| 22.006 | Peptide framework for screening the effects of amino acids on assembly | bio | metadynamics, peptides | Andrew White | GYRATION COM COMBINE GROUP HISTOGRAM DISTANCES INCLUDE METAD CONVERT_TO_FES DUMPGRID REWEIGHT_BIAS PRINT | colvar multicolvar bias vatom function gridtools core generic |
| 22.004 | Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques | chemistry | reaction discovery, OPES, collective variables | Umberto Raucci | OPES_METAD COM DISTANCE PYTORCH_MODEL MATHEVAL GROUP CUSTOM LOAD COORDINATION OPES_METAD_EXPLORE LOWER_WALLS PRINT UPPER_WALLS UNITS | colvar opes bias vatom function generic core setup pytorch |
| 21.051 | Automatic learning of hydrogen-bond fixes in an AMBER RNA force field | methods | force field, RNA | Giovanni Bussi | BIASVALUE COMBINE METAD COORDINATION WHOLEMOLECULES ERMSD MOLINFO PRINT | colvar generic function bias |
| 21.044 | NaCl nucleation | chemistry | metadynamics, DFS clustering | Aaron Finney | MFILTER_MORE CLUSTER_DISTRIBUTION DFSCLUSTERING COORDINATIONNUMBER LOCAL_Q6 GROUP COMBINE HISTOGRAM DUMPGRID METAD Q6 FIXEDATOM CONTACT_MATRIX PRINT CLUSTER_NATOMS INSPHERE | multicolvar adjmat volumes symfunc bias clusters vatom function gridtools core 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 CUSTOM METAD COORDINATION ENDPLUMED VOLUME PRINT | colvar generic function bias |
| 21.029 | Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs | bio | metadynamics, small peptide, machine learning | Pratyush Tiwary | ENERGY EXTERNAL MOLINFO RESTART FLUSH TORSION PRINT | colvar setup generic bias |
| 21.025 | Computational and biochemical analysis of type IV pilus dynamics and stability | bio | molecular dynamics, calcium binding, Type IV pilus | Yasaman Karami | LOWER_WALLS PRINT UPPER_WALLS DISTANCE | colvar generic bias |
| 21.013 | Role of vibrational excitation in heterogeneous catalysis | chemistry | catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption | Kristof Bal | DISTANCE EXTERNAL HISTOGRAM METAD ANGLES FLUSH RESTRAINT TD_GRID DUMPGRID REWEIGHT_BIAS UPPER_WALLS VES_LINEAR_EXPANSION OPT_AVERAGED_SGD LOAD BF_CHEBYSHEV REWEIGHT_METAD COORDINATION LOWER_WALLS PRINT UNITS COORDINATIONNUMBER COMBINE DISTANCES CONVERT_TO_FES UWALLS | colvar multicolvar symfunc bias generic gridtools function ves setup |
| 20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Adriana Pietropaolo | PBMETAD COORDINATION WHOLEMOLECULES CENTER PRINT | colvar vatom generic bias |
| 20.028 | Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane | bio | metadynamics, KRas-4B, anionic membrane | Huixia Lu | DISTANCE RESTART METAD FIT_TO_TEMPLATE CENTER PRINT | colvar bias vatom generic setup |
| 20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Valerio Rizzi | ANGLE OPES_METAD DISTANCE GROUP MATHEVAL PYTORCH_MODEL ENERGY FIT_TO_TEMPLATE FIXEDATOM CENTER WHOLEMOLECULES COORDINATION ENDPLUMED PRINT UPPER_WALLS | colvar opes bias vatom function generic core pytorch |
| 20.018 | Free energy barriers from biased molecular dynamics simulations | methods | kinetics, free energy barriers, chemical reactions, nucleation, metadynamics | Kristof Bal | DISTANCE ENERGY HISTOGRAM METAD FLUSH VOLUME SPRINT DUMPGRID CONTACT_MATRIX REWEIGHT_BIAS UPPER_WALLS LOAD REWEIGHT_METAD Q6 COORDINATION LOCAL_AVERAGE LOWER_WALLS PRINT PAIRENTROPY UNITS COORDINATIONNUMBER COMBINE CONVERT_TO_FES DENSITY CENTER | colvar sprint adjmat symfunc bias vatom generic gridtools function volumes setup |
| 20.016 | Predicting polymorphism in molecular crystals using orientational entropy | materials | metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy | Pablo Piaggi | GROUP INCLUDE METAD LOAD CENTER VOLUME PRINT UPPER_WALLS | colvar bias vatom generic core setup |
| 20.006 | Class B GPCR activation mechanism | bio | metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | RMSD DISTANCE ENERGY COMBINE MATHEVAL METAD WHOLEMOLECULES CENTER LOWER_WALLS MOLINFO PRINT UPPER_WALLS | colvar bias vatom generic function |
| 20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Luigi Bonati | OPES_METAD COM DISTANCE PYTORCH_MODEL MATHEVAL GROUP LOAD FLUSH ENDPLUMED LOWER_WALLS TORSION PRINT UPPER_WALLS UNITS | colvar opes bias vatom function generic core setup pytorch |
| 19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Jakub Rydzewski | POSITION MAZE_LOSS MAZE_OPTIMIZER_BIAS MAZE_SIMULATED_ANNEALING PRINT UNITS | colvar setup maze generic |
| 19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | GYRATION COM DISTANCE ENERGY METAD MOLINFO PRINT UPPER_WALLS | colvar vatom generic bias |
| 19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Gareth Tribello | FCCUBIC CELL METAD ENDPLUMED PRINT UPPER_WALLS UNITS | colvar symfunc bias generic setup |
| 19.046 | Optimal Collective from short simulations for Benzamidine-Trypsin ligand binding | bio | VAC-MetaD, optimised collective variables, binding free energy, unbinding rates, benzamidine trypsin, Structure Activity Relation | Faidon Brotzakis | BRIDGE RMSD FUNNEL COM DISTANCE GROUP COMBINE MOLINFO DISTANCES METAD ALPHABETA REWEIGHT_METAD WHOLEMOLECULES LOWER_WALLS TORSION PRINT UPPER_WALLS | colvar multicolvar adjmat funnel bias vatom function generic core |
| 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 | POSITION GROUP RESTART METAD COORDINATION FLUSH LOWER_WALLS PRINT UPPER_WALLS UNITS | colvar bias generic core setup |
| 19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Paolo Raiteri | DISTANCE MATHEVAL RESTART METAD FLUSH PRINT UPPER_WALLS UNITS | colvar bias generic function setup |
| 19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Matteo Salvalaglio | MATHEVAL ENERGY CELL COMBINE VOLUME METAD ENDPLUMED LOWER_WALLS TORSION PRINT UPPER_WALLS | colvar generic function bias |
| 19.003 | EMMI ClpP | bio | metainference, cryo-EM | Max Bonomi | EMMI BIASVALUE GROUP MOLINFO PRINT | core isdb generic bias |
| 19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Giovanni Bussi | ANGLE DISTANCE COMBINE RANDOM_EXCHANGES INCLUDE DISTANCES METAD FLUSH ERMSD LOWER_WALLS MOLINFO PRINT UPPER_WALLS | colvar multicolvar bias generic function |
| 25.029 | Energetic Constraints in the Enzymatic Depolymerization of Crystalline PET from enhanced molecular simulations | bio | HREX-Metadynamics, PETase, crystalline PET, amorphous PET, conformational ensembles, substrate binding, chain detachment | Ania Di Pede-Mattatelli and Francesco Colizzi | HISTOGRAM COM REWEIGHT_BIAS PRINT METAD WHOLEMOLECULES CONVERT_TO_FES MOLINFO LOWER_WALLS DISTANCE DUMPGRID UPPER_WALLS FIXEDATOM | bias colvar vatom generic gridtools |
| 25.013 | Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices | bio | umbrella sampling, temperature ramping | Alexander Berlaga | PRINT PYTORCH_MODEL GYRATION RESTRAINT DISTANCE | bias colvar pytorch generic |
| 25.008 | Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting | methods | metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting | Dhiman Ray | RMSD TORSION PRINT GROUP METAD UNITS PYTORCH_MODEL BIASVALUE WHOLEMOLECULES MOLINFO ENERGY POSITION CUSTOM LOWER_WALLS DISTANCE ENDPLUMED OPES_METAD UPPER_WALLS | core bias colvar pytorch generic function opes setup |
| 24.036 | Leveraging cryptic ligand envelopes through enhanced molecular simulations | bio | HREX, conformational heterogeneity, drug discovery, ligand binding, plitidepsin, aplidin, ligand-target complexes, cryptic ligand envelope | Francesco Colizzi | HISTOGRAM TORSION PRINT GROUP COORDINATION WHOLEMOLECULES CONVERT_TO_FES ANGLE DISTANCE DUMPGRID | core colvar generic gridtools |
| 24.011 | Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble | methods | committor, machine learning | Peilin Kang | PRINT COORDINATION CUSTOM LOAD GROUP UNITS LOWER_WALLS RMSD CELL BIASVALUE POSITION WHOLEMOLECULES DISTANCE ENDPLUMED UPPER_WALLS MATHEVAL TORSION INCLUDE MOLINFO ENERGY | core colvar bias generic function setup |
| 23.044 | Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition | materials | metadynamics, interlocked molecules | Luigi Leanza | COMMITTOR HISTOGRAM READ GROUP COORDINATION METAD PRINT CONVERT_TO_FES ENDPLUMED DUMPGRID | core bias colvar generic gridtools |
| 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 | MATHEVAL FLUSH SELECT_COMPONENTS PRINT METAD INCLUDE TRANSPOSE SUM | bias matrixtools generic function valtools |
| 23.037 | Estimating binding free energy of solid binding peptides without extensive sampling | bio | metadynamics, solid binding peptides | Xin Qi | COM PBMETAD PRINT GYRATION MOLINFO LOWER_WALLS DISTANCE UPPER_WALLS | colvar bias generic vatom |
| 23.033 | DNA G-quadruplex and G-hairpin folding with ST-metaD protocol | bio | DNA, G4, GQ, quadruplex, hairpin, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | PRINT COORDINATION METAD BIASVALUE WHOLEMOLECULES MOLINFO COMBINE ERMSD GHBFIX | bias function colvar generic |
| 23.027 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, DFS, Q3, Pair Entropy | Aaron Finney | LOCAL_Q3 AROUND HISTOGRAM DFSCLUSTERING LOCAL_AVERAGE GROUP UNITS DENSITY PRINT CONTACT_MATRIX RESTRAINT COORDINATIONNUMBER CLUSTER_DISTRIBUTION CLUSTER_NATOMS LOAD DUMPGRID Q3 FIXEDATOM | core bias vatom volumes generic gridtools adjmat clusters setup symfunc |
| 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 | PRINT COORDINATION ANGLE CUSTOM CONTACTMAP GROUP CENTER LOWER_WALLS FIT_TO_TEMPLATE RMSD COMMITTOR WHOLEMOLECULES DISTANCE ENDPLUMED UPPER_WALLS MATHEVAL INCLUDE PYTORCH_MODEL MOLINFO ENERGY COMBINE OPES_METAD FIXEDATOM | core colvar bias vatom pytorch generic function opes |
| 23.008 | PBMetaD simulations of Histatin5 | bio | metadynamics, IDP, Rg, PPII | Francesco Pesce | TORSION PBMETAD GROUP PRINT GYRATION WHOLEMOLECULES MOLINFO | bias colvar generic core |
| 23.007 | Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains | bio | metadynamics, peptoids, parallel-bias metadynamics | Jim Pfaendtner | COM TORSION PBMETAD PRINT COORDINATION INCLUDE GYRATION RESTRAINT WHOLEMOLECULES | bias colvar generic vatom |
| 22.040 | From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure | bio | SARS-CoV-2, Spike, Omicron | Miłosz Wieczór | PRINT METAD WHOLEMOLECULES PCAVARS LOWER_WALLS UPPER_WALLS | mapping bias generic |
| 22.035 | Deciphering the alphabet of disorder — Glu and Asp act differently on local but not global properties | bio | intrinsically disordered proteins, parallel bias metadynamics, protein | Kresten Lindorff-Larsen | TORSION PBMETAD GYRATION WHOLEMOLECULES MOLINFO | bias colvar generic |
| 22.025 | Bubble nucleation rate predictions in a Lennard-Jones fluid | materials | free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation | Kristof Bal | VOLUME HISTOGRAM FLUSH COMMITTOR REWEIGHT_BIAS PRINT UNITS BIASVALUE RESTRAINT CONVERT_TO_FES COORDINATIONNUMBER CUSTOM MOVINGRESTRAINT ANN LOAD DUMPGRID UPPER_WALLS | bias colvar annfunc generic gridtools function setup symfunc |
| 22.013 | Ligand dissociation from PreQ1 riboswitch | bio | ligand, RNA, metadynamics, pRAVE | Yihang Wang | RMSD COMMITTOR COM PRINT METAD WHOLEMOLECULES MOLINFO COORDINATIONNUMBER DISTANCE COMBINE | bias colvar vatom generic function symfunc |
| 21.043 | Predicting the Conformational Variability of Oncogenic GTP-bound G12D Mutated KRas-4B Proteins at Cell Membranes | chemistry | well-tempered metadynamics, KRas-4B, anionic membrane, conformational variability | Huixia Lu | TORSION PRINT METAD FIT_TO_TEMPLATE FIXEDATOM | bias colvar generic vatom |
| 21.039 | Deep learning the slow modes for rare events sampling | methods | collective variables, machine learning, slow modes, deep-tica, opes | Luigi Bonati | VOLUME PRINT ECV_MULTITHERMAL LOAD ENVIRONMENTSIMILARITY CONTACTMAP GROUP UNITS OPES_EXPANDED RMSD Q6 WHOLEMOLECULES DISTANCE ENDPLUMED FLUSH TORSION INCLUDE PYTORCH_MODEL ENERGY MOLINFO COMBINE OPES_METAD | core colvar pytorch generic function opes envsim setup symfunc |
| 21.028 | From Enhanced Sampling to Reaction Profiles | methods | collective variables, multi-state, machine learning, Deep-TDA | Enrico Trizio | PRINT COORDINATION ANGLE LOAD GROUP UNITS CENTER LOWER_WALLS FIT_TO_TEMPLATE WHOLEMOLECULES DISTANCE ENDPLUMED DISTANCES UPPER_WALLS MATHEVAL TORSION PYTORCH_MODEL OPES_METAD FIXEDATOM | core colvar bias vatom pytorch generic function opes multicolvar setup |
| 21.026 | Probing allosteric regulations with coevolution-driven molecular simulations | bio | metadynamics, coevolution, allostery, adenylate cyclase | Francesco Colizzi | COM PRINT UNITS METAD WHOLEMOLECULES DISTANCE UPPER_WALLS PATHMSD | colvar bias vatom generic setup |
| 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 | MATHEVAL RESTART PRINT COORDINATION REWEIGHT_BIAS METAD RESTRAINT WHOLEMOLECULES POSITION CENTER | bias colvar vatom generic function setup |
| 21.012 | NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition | bio | funnel metadynamics | Jim Pfaendtner | COM PRINT FUNNEL_PS METAD FUNNEL LOWER_WALLS DISTANCE UPPER_WALLS | colvar bias vatom funnel generic |
| 21.011 | CmuMD simulations of NaCl(aq) at graphite | chemistry | CmuMD, DFS clustering | Aaron Finney | AROUND DENSITY GROUP PRINT CONTACT_MATRIX RESTRAINT COORDINATIONNUMBER CLUSTER_DISTRIBUTION MULTICOLVARDENS CLUSTER_NATOMS LOAD MFILTER_MORE DUMPGRID DFSCLUSTERING FIXEDATOM | core bias vatom generic adjmat volumes gridtools multicolvar clusters setup symfunc |
| 21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Adriana Pietropaolo | MATHEVAL TORSION PBMETAD RESTART PRINT BIASVALUE WHOLEMOLECULES CONSTANT | colvar bias generic function setup |
| 20.027 | Allosteric Regulation of SARS-CoV-2 Protease. Towards Informed Structure-Based Drug Discovery | bio | SARS-CoV2, MPro, Covid-19, Molecular Dynamics, Metadynamics, Computer-Aided Drug Discovery | Khaled Abdel-Maksoud | PRINT METAD TORSION DISTANCE | colvar bias generic |
| 20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Pratyush Tiwary | RMSD TORSION RESTART PRINT METAD WHOLEMOLECULES MOLINFO DISTANCE COMBINE UPPER_WALLS | bias colvar generic function setup |
| 20.002 | Exploring conformational dynamics of the extracellular Venus flytrap domain of the GABAB receptor, a path-metadynamics study | bio | Metadynamics, path CVs | Riccardo Ocello | RESTART GROUP PRINT METAD WHOLEMOLECULES MOLINFO UPPER_WALLS PATHMSD | core colvar bias generic setup |
| 19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Matteo Salvalaglio | MATHEVAL COMMITTOR READ TORSION HISTOGRAM REWEIGHT_BIAS PRINT METAD BIASVALUE REWEIGHT_METAD CONVERT_TO_FES EXTERNAL DISTANCE DUMPGRID | bias colvar generic gridtools function |
| 19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Jim Pfaendtner | PRINT METAD GYRATION WHOLEMOLECULES ENERGY | colvar bias generic |
| 19.050 | Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes | chemistry | metadynamics, membranes, Willard Chandler surface | Gareth Tribello | HISTOGRAM READ REWEIGHT_BIAS PRINT RESTART METAD CONVERT_TO_FES DISTANCE_FROM_CONTOUR COMBINE DUMPGRID UPPER_WALLS | bias contour generic gridtools function setup |
| 19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | FLUSH PRINT UNITS METAD ENERGY DISTANCE COMBINE UPPER_WALLS | colvar bias generic function setup |
| 19.032 | Chemical reaction in solution using path collective variables based on coordination patterns | chemistry | chemical reactions, solutions, metadynamics, coordination patterns | Fabio Pietrucci | FLUSH PATH RESTART PRINT METAD DISTANCES UPPER_WALLS | bias generic mapping multicolvar setup |
| 19.023 | RECT | methods | metadynamics, replica exchange | Giovanni Bussi | TORSION PRINT METAD GYRATION WHOLEMOLECULES | bias colvar generic |
| 19.013 | RNA FF FITTING | methods | force field, RNA | Giovanni Bussi | MATHEVAL TORSION INCLUDE BIASVALUE PUCKERING MOLINFO CONSTANT | function bias colvar generic |
| 19.011 | Automatic Gradient Computation for Collective Variables | other | gradient, differentiation, curvature | Toni Giorgino | ENDPLUMED | generic |
| 19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Carlo Camilloni | PBMETAD TORSION DIHCOR GROUP RDC PRINT RESTRAINT WHOLEMOLECULES MOLINFO CENTER ENSEMBLE UPPER_WALLS DISTANCE ENDPLUMED ALPHABETA DHENERGY STATS METAINFERENCE | core colvar bias vatom generic function multicolvar isdb |
| 19.009 | RNA tetraloops folding | bio | metadynamics, RNA, folding | Giovanni Bussi | RMSD PRINT METAD WHOLEMOLECULES MOLINFO ENDPLUMED ERMSD | bias colvar generic |
| 26.005 | Cryptic pocket discovery in Alzheimer disease risk proteins BIN1, PICALM, and CD2AP via well-tempered metadynamics | methods | cryptic pockets, Alzheimer disease, BIN1, PICALM, CD2AP, well-tempered metadynamics, endocytosis, clathrin-mediated trafficking, virtual screening | Cagrı Ozkurt | PRINT METAD DISTANCE ANGLE WHOLEMOLECULES | bias colvar generic |
| 26.004 | Resolving the ambiguous binding site of quercetin at the calcineurin subunit junction using funnel metadynamics with deep learning collective variables | bio | metadynamics, funnel metadynamics, DeepTICA | Jason Loo | RMSD PRINT UPPER_WALLS FUNNEL METAD PYTORCH_MODEL COM GROUP FUNNEL_PS LOWER_WALLS ENERGY DISTANCE COORDINATION WHOLEMOLECULES WRAPAROUND MATHEVAL | bias generic colvar funnel function vatom core pytorch |
| 26.000 | OPES simulations of disordered proteins | bio | OPES, IDPs | Julian Streit | PRINT ECV_MULTITHERMAL RESTART ENERGY OPES_EXPANDED | opes colvar setup generic |
| 25.030 | Committor Regularization | methods | metadynamics, enhanced sampling, mlcvs, committor, machine learning | Florian Dietrich | MOVINGRESTRAINT PRINT METAD UNITS | bias setup generic |
| 25.026 | Deciphering the Molecular Mechanisms of Startle Disease - the Role of the Asn46Lys Mutation in the Glycine Receptor | bio | metadynamics, glycine receptors, funnel metadynamics | Jacob Adam Clark | PRINT UPPER_WALLS FUNNEL METAD COM FUNNEL_PS LOWER_WALLS | vatom bias funnel generic |
| 25.022 | Imidazole Diffusion in SALEM-2 MOF | materials | OPES, Diffusion, Ring opening, MOFs, Machine Learning Potentials | Sudheesh Kumar Ethirajan | PRINT DISTANCES OPES_METAD GROUP CENTER PROJECTION_ON_AXIS UNITS ENDPLUMED DISTANCE WHOLEMOLECULES MOLINFO | colvar multicolvar opes vatom core setup generic |
| 25.015 | Assessment of Force Fields for Describing Conformational Polymorphic Crystals of ROY | materials | Molecular crystal, Force Field, Collective Variable | Pradip Si and Omar Valsson | PRINT SMAC DISTANCES TORSIONS DUMPMULTICOLVAR | multicolvar symfunc 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 | TORSION GYRATION PRINT OPES_METAD DISTANCE CUSTOM ALPHARMSD COORDINATION WHOLEMOLECULES COMBINE MOLINFO | colvar function opes secondarystructure generic |
| 24.004 | Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables | materials | metadynamics, nucleation, machine learning | Ziyue Zou | PRINT RESTART METAD LOAD INCLUDE GROUP | core bias setup generic |
| 23.046 | Lasso Peptides - HLDA CV | bio | metadynamics, protein folding, HLDA, harmonic | Gabriel da Hora | PRINT METAD UNITS DISTANCE WHOLEMOLECULES COMBINE | bias colvar function setup generic |
| 23.015 | MPCs aggregation | bio | opes_explore, dimerization, MPCs, self-assembly | Vikas Tiwari | PRINT UPPER_WALLS METAD COM GROUP CENTER LOWER_WALLS CUSTOM OPES_METAD_EXPLORE DISTANCE COORDINATION WHOLEMOLECULES | bias colvar function opes vatom core generic |
| 23.006 | Transcription factor unbinding | bio | metadynamics, DNA, conformational changes | Malin Lüking | ALPHARMSD PRINT CONTACTMAP METAD COM DUMPFORCES DISTANCE ANGLE MOLINFO | bias colvar vatom secondarystructure generic |
| 22.045 | Binding mode and mechanism of enzymatic polyethylene terephthalate degradation | bio | metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation | Francesco Colizzi | PRINT UPPER_WALLS MOVINGRESTRAINT METAD COM LOWER_WALLS DISTANCE ANGLE WHOLEMOLECULES | vatom bias colvar generic |
| 22.043 | Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES | bio | OPES, RNA, Tetraloop, Folding | Gül Zerze | PRINT ECV_MULTITHERMAL CONTACTMAP ECV_UMBRELLAS_LINE ENERGY WHOLEMOLECULES OPES_EXPANDED | opes colvar generic |
| 22.041 | Skipping the Replica Exchange Ladder with Normalizing Flows | methods | OPES, alanine, normalizing flows, replica exchange | Michele Invernizzi | TORSION PRINT ECV_MULTITHERMAL OPES_METAD ENERGY UNITS ENDPLUMED POSITION OPES_EXPANDED | setup opes colvar generic |
| 22.038 | Enhanced Sampling Aided Design of Molecular Photoswitches | chemistry | reaction discovery, OPES explore, graph CV | Umberto Raucci | PRINT PYTORCH_MODEL UNITS CUSTOM OPES_METAD_EXPLORE COORDINATION | generic colvar function opes setup pytorch |
| 22.030 | Mixing physics across temperatures with generative artificial intelligence | methods | REMD, Generative AI, DDPM | Yihang Wang | TORSION PRINT WHOLEMOLECULES | colvar generic |
| 22.027 | Molecular Dynamics simulations of BANAL-236 RBD-hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, BANAL-236, receptor-binding domain | Max Bonomi | RMSD PRINT | colvar generic |
| 22.023 | Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy | bio | CryoEM, MEMMI,EMMI, Metadynamics, Metainference, IAPP, structural ensemble | Faidon Brotzakis | RMSD TORSION PRINT UPPER_WALLS RESTART COM BIASVALUE EMMI PBMETAD GROUP COORDINATION WHOLEMOLECULES MOLINFO | bias colvar vatom isdb core setup generic |
| 22.002 | GAMBES_SAMPL5_RATES | other | GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding | Jayashrita Debnath | PRINT UPPER_WALLS FIT_TO_TEMPLATE COMMITTOR LOAD PYTORCH_MODEL GROUP CENTER COORDINATION FLUSH ENERGY ENDPLUMED DISTANCE FIXEDATOM ANGLE WHOLEMOLECULES MATHEVAL | bias generic colvar function vatom core setup pytorch |
| 22.000 | Amyloid precursor protein processing by human γ-secretase | bio | Bias Exchange Metadynamics, Helix unfolding, coupled binding | Xiaoli Lu | ALPHARMSD PRINT CONTACTMAP METAD ANTIBETARMSD RANDOM_EXCHANGES CENTER UNITS INCLUDE DISTANCE COORDINATION MOLINFO | bias colvar vatom secondarystructure setup generic |
| 21.052 | On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets | materials | Ibuprofen, unbinding, WTmetaD | Matteo Salvalaglio | TORSION PRINT COMMITTOR METAD CENTER COORDINATIONNUMBER ENDPLUMED DISTANCE | bias colvar vatom symfunc generic |
| 21.047 | Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations | materials | pair entropy, metadynamics, ves, solids, crystallization | Pablo Piaggi | OPT_AVERAGED_SGD PRINT RESTART VOLUME METAD LOAD VES_LINEAR_EXPANSION PAIRENTROPY TD_WELLTEMPERED ENERGY COMBINE BF_LEGENDRE | bias colvar function ves gridtools setup generic |
| 21.046 | Ubiquitin Interacting Motifs, Duality Between Structured and Disordered Motifs | bio | wt metadynamics, ubiquitin, ataxin-3, short linear motifs, ubiquitin binding motif, moonlight functions, intrinsic disorder | Elena Papaleo | GYRATION PRINT UPPER_WALLS METAD LOWER_WALLS ALPHABETA ENDPLUMED GROUP WHOLEMOLECULES | bias colvar multicolvar core generic |
| 21.042 | Peptoid-mediated Au nanocrystal growth | materials | parallel-bias metadynamics, peptoid, Au | Xin Qi | GYRATION PRINT UPPER_WALLS COM PBMETAD DISTANCE MOLINFO | vatom bias colvar generic |
| 21.032 | Metal-coupled folding mechanism to metallothionein | bio | parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination | Manuel-Peris Diaz | PBMETAD UNITS GROUP COORDINATION WHOLEMOLECULES | bias colvar core setup generic |
| 21.027 | EGFR activating mutations mechanism | bio | metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA | Francesco Gervasio | ALPHARMSD PRINT UPPER_WALLS CONTACTMAP MATHEVAL METAD LOWER_WALLS ENERGY INCLUDE DISTANCE WHOLEMOLECULES MOLINFO | bias colvar function secondarystructure generic |
| 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 | ABMD TORSION PRINT RESTART ERMSD CENTER DISTANCE MOLINFO | bias colvar vatom setup generic |
| 20.015 | Rational design of ASCT2 inhibitors using an integrated experimental-computational approach | bio | ASCT2 transporter, small-molecules, cryo-EM, metainference | Max Bonomi | PRINT EMMIVOX LOAD BIASVALUE DUMPATOMS GROUP WHOLEMOLECULES MOLINFO | bias isdb core setup generic |
| 20.012 | Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies | bio | metadynamics, well-tempered ensemble, ligand binding, binding affinity calculations, novel COLVAR, funnel restraints, Hamiltonian replica-exchange, PathCV, COMetPath, SWISH | Francesco Gervasio | PRINT UPPER_WALLS CONTACTMAP METAD LOAD MOLINFO COM BIASVALUE GROUP PROJECTION_ON_AXIS LOWER_WALLS INCLUDE DISTANCE CONSTANT WHOLEMOLECULES FUNCPATHGENERAL MATHEVAL | bias colvar function vatom 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 | PRINT DISTANCES METAD CUSTOM UNITS COORDINATION | bias colvar function multicolvar setup generic |
| 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 | OPT_AVERAGED_SGD UPPER_WALLS TD_MULTITHERMAL_MULTIBARIC HISTOGRAM READ DUMPGRID BF_LEGENDRE COMBINE RESTART REWEIGHT_BIAS PRINT OPT_DUMMY LOAD CONVERT_TO_FES LOWER_WALLS CELL MATHEVAL Q6 VOLUME VES_LINEAR_EXPANSION TD_WELLTEMPERED ENERGY REWEIGHT_TEMP_PRESS | bias colvar function ves gridtools symfunc setup generic |
| 19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Luigi Bonati | TORSION Q6 PRINT ENVIRONMENTSIMILARITY LOAD ENERGY UNITS ENDPLUMED POSITION | envsim colvar symfunc setup generic |
| 19.048 | Understanding Ligand Binding Selectivity in a Prototypical GPCR Family | bio | metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | PRINT UPPER_WALLS METAD COM BIASVALUE LOWER_WALLS DISTANCE CONSTANT WHOLEMOLECULES MATHEVAL | bias colvar function vatom generic |
| 19.040 | Optimal Metric for Path Collective Variables | bio | metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path | Francesco Luigi Gervasio | TORSION PRINT METAD ENDPLUMED MATHEVAL | function bias colvar generic |
| 19.025 | Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide | bio | metainference, NMR, protein dynamics, force-fields | Carlo Camilloni | TORSION GYRATION PRINT RDC BIASVALUE JCOUPLING METAINFERENCE FLUSH PBMETAD STATS ENDPLUMED ENSEMBLE WHOLEMOLECULES CS2BACKBONE MOLINFO | bias colvar function isdb generic |
| 19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Haochuan Chen | DRR TORSION PRINT | drr colvar generic |
| 19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Matteo Salvalaglio | GYRATION PRINT RESTART DISTANCES METAD COORDINATIONNUMBER ENDPLUMED | bias colvar multicolvar symfunc setup generic |
| 25.027 | Enhanced-sampling MD simulations of a protein-peptide complex integrating SAXS and XL-MS experimental information | bio | steered MD, metadynamics, SAXS, XL-MS, ensemble reconstruction | Mattia Bernetti | GYRATION UPPER_WALLS PRINT METAD SAXS MOVINGRESTRAINT INCLUDE MOLINFO DISTANCE WHOLEMOLECULES CENTER GROUP | bias isdb colvar generic core vatom |
| 25.007 | Shaping the glycan landscape. Hidden relationships between linkage and ring distortion induced by carbohydrate-active enzmyes | bio | REST-RECT, REST2, glycan, enzyme, CAZyme, steered | Isabell Grothaus | PRINT METAD RESTART MOVINGRESTRAINT MOLINFO DISTANCE TORSION RESTRAINT PUCKERING | generic setup bias colvar |
| 25.006 | Characterizing the conformational ensemble of PROTAC degraders in solutions via atomistic simulations | methods | Enhanced sampling, Atomistic simulations, Conformational ensemble, PROTACs, Targeted Protein Degradation, Chamelonic molecules | Shikshya Bhusal, Omar Valsson | GYRATION READ PRINT PBMETAD UPDATE_IF RESTART INCLUDE MOLINFO DISTANCE VOLUME ENERGY DUMPATOMS TORSION WHOLEMOLECULES CENTER | bias colvar generic setup vatom |
| 24.030 | NMR guided simulation of dsRBD | bio | Metainference, NMR, protein dynamics | Debadutta Patra | ALPHABETA PRINT METAINFERENCE MOLINFO RDC ENSEMBLE DISTANCE STATS WHOLEMOLECULES GROUP FLUSH | isdb colvar generic multicolvar function core |
| 24.028 | All-atom simulations of RNA-membrane interactions | bio | metadynamics, membrane, RNA | Giovanni Bussi | GYRATION UPPER_WALLS SORT PRINT LOWER_WALLS METAD POSITION DISTANCES WHOLEMOLECULES COMBINE MATHEVAL GHOST MOLINFO DISTANCE CENTER GROUP PUCKERING | bias colvar generic multicolvar function core vatom |
| 24.026 | Constant pH metadynamics of RNA oligomers | bio | metadynamics, pH, RNA | Giovanni Bussi | PRINT METAD RESTART MOLINFO TORSION PUCKERING | generic setup bias 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 |
| 24.006 | Water vapor condensation | chemistry | metadynamics, homogeneous condensation, chemical potential | Shenghui Zhong | UPPER_WALLS CLUSTER_PROPERTIES CLUSTER_NATOMS PRINT DFSCLUSTERING METAD CONTACT_MATRIX UNITS COORDINATIONNUMBER | clusters bias adjmat generic setup symfunc |
| 24.002 | Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes | chemistry | metadynamics, ligand design, solvent extraction | Xiaoyu Wang | PRINT METAD RESTART TORSION UNITS | generic setup bias colvar |
| 23.038 | Determinants of Neutral Antagonism and Inverse Agonism in the β2-adrenergic receptor | bio | protein coupled receptor, beta-adrenergic, receptor activation, antagonism, inverse agonism, metadynamics | Timothy Clark | PRINT METAD RMSD MOLINFO DISTANCE WHOLEMOLECULES MATHEVAL | generic bias function colvar |
| 23.034 | Urea nucleation in water: do long-range forces matter? | materials | LMF theory, Metadynamics, Nucleation | Ziyue Zou | PRINT METAD LOAD INCLUDE CENTER COORDINATIONNUMBER GROUP | bias generic setup symfunc core vatom |
| 23.028 | Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process | chemistry | Ammonia decomposition; Dynamics;OPES; Neural Network potential | Manyi Yang | UPPER_WALLS LOWER_WALLS PRINT DISTANCES COMMITTOR ZDISTANCES OPES_METAD DISTANCE CUSTOM FLUSH ENERGY FIXEDATOM UNITS COM GROUP COORDINATIONNUMBER MATHEVAL | bias colvar generic multicolvar setup symfunc opes function core vatom |
| 23.025 | Probing ion binding to G-quadruplexes and related events | chemistry | metadynamics, repulsive potential, nucleic acids, G-quadruplexes | Marcelo Poleto | UPPER_WALLS COM PRINT DISTANCES POSITION METAD WHOLEMOLECULES RESTART DISTANCE WRAPAROUND FLUSH DUMPATOMS UNITS LOWER_WALLS GROUP FIT_TO_TEMPLATE MATHEVAL | bias colvar generic multicolvar setup function core vatom |
| 23.023 | Rational design of novel biomimetic sequence-defined polymers for mineralization applications | methods | metadynamics, surface binding, biomimetic mineralization | Kaylyn Torkelson | UPPER_WALLS GYRATION PRINT DISTANCE COORDINATION COM PBMETAD | generic vatom bias colvar |
| 23.018 | Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention | materials | metadynamics, surface binding, peptide adsorption | Kaylyn Torkelson | UPPER_WALLS GYRATION PRINT DISTANCE COM PBMETAD | generic vatom bias colvar |
| 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 | PATH UPPER_WALLS PYTORCH_MODEL PRINT WHOLEMOLECULES OPES_METAD UNITS OPES_METAD_EXPLORE DISTANCE CUSTOM TORSION FIXEDATOM COORDINATION LOWER_WALLS CENTER FIT_TO_TEMPLATE GROUP | bias colvar pytorch mapping generic setup opes function core vatom |
| 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 | UPPER_WALLS LOWER_WALLS PRINT CONSTANT METAD BIASVALUE DISTANCE WHOLEMOLECULES MATHEVAL | generic bias function colvar |
| 23.005 | A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs | bio | metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A | Timothy Clark | READ PRINT METAD RMSD HISTOGRAM MOLINFO DISTANCE REWEIGHT_METAD DUMPGRID CONVERT_TO_FES WHOLEMOLECULES MATHEVAL | gridtools bias colvar generic function |
| 23.002 | Critical comparison of general-purpose collective variables for crystal nucleation | methods | metadynamics, umbrella sampling, commitor, entropy, PIV | Julien Lam | Q6 UPPER_WALLS PRINT FUNCPATHMSD METAD PIV LOCAL_AVERAGE Q4 RESTRAINT CUSTOM VOLUME ENERGY UNITS PAIRENTROPY | gridtools bias generic colvar piv symfunc setup function |
| 23.000 | Atomistic simulations of RNA tetraloop folding via PTWTE-WTM | bio | parallel tempering, well-tempered metadynamics, well-tempered ensemble, RNA, Tetraloop, Folding | Gül Zerze | UPPER_WALLS PRINT METAD CONTACTMAP ENERGY WHOLEMOLECULES LOWER_WALLS | generic bias colvar |
| 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 | PRINT PATHMSD METAD BIASVALUE DRR CUSTOM FLUSH | drr bias colvar generic function |
| 22.029 | Angiotensin-1-7_Metadynamics | bio | Metadynamics, Angiotensin-(1-7), peptide | L.-América Chi | UPPER_WALLS GYRATION LOWER_WALLS PRINT METAD COORDINATION WHOLEMOLECULES GROUP FLUSH | generic bias core colvar |
| 22.020 | Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix–Junction–Helix RNA | bio | RNA force field, Helix-Junction-Helix RNA, SAXS, Well tempered metadynamics | Weiwei He | PRINT METAD WHOLEMOLECULES DISTANCE TORSION COM GROUP | bias colvar generic core vatom |
| 22.019 | Exploring aspartic protease inhibitor binding to design selective antimalarials | bio | ligand binding, loop opening, path CV, funnel metadynamics, drug development | Raitis Bobrovs | UPPER_WALLS PRINT PATHMSD METAD WHOLEMOLECULES FUNNEL_PS DISTANCE FUNNEL COM LOWER_WALLS | bias colvar funnel generic vatom |
| 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 | UPPER_WALLS PRINT RESTART HISTOGRAM OPES_METAD AROUND ENERGY CUSTOM VOLUME ENVIRONMENTSIMILARITY DUMPGRID | volumes gridtools bias envsim colvar generic setup opes function |
| 22.012 | Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT | bio | contact maps, protein-protein interactions | Isabell-Louise Grothaus | CENTER CONTACTMAP PRINT DISTANCE | generic colvar vatom |
| 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 | UPPER_WALLS GYRATION COM METAD COMBINE UNITS DISTANCE COORDINATION LOWER_WALLS COORDINATIONNUMBER FLUSH | bias generic colvar symfunc setup function vatom |
| 21.050 | N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity | methods | bio | Isabell Louise Grothaus | CENTER DISTANCE PRINT | generic colvar vatom |
| 21.038 | Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics | materials | metadynamics, SGOOP, nucleation, urea | Ziyue Zou | PRINT METAD COMBINE LOAD VOLUME ENERGY INCLUDE CENTER COORDINATIONNUMBER GROUP | bias colvar generic setup symfunc function core vatom |
| 20.024 | Gaussian Mixture Based Enhanced Sampling (GAMBES) | methods | enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias | Jayashrita Debnath | UPPER_WALLS PRINT DISTANCES COMBINE LOAD DISTANCE TORSION ENERGY UNITS LOWER_WALLS GROUP | bias colvar generic multicolvar setup function core |
| 20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Jim Pfaendtner | PRINT DISTANCES RESTART DISTANCE COORDINATION WHOLEMOLECULES CENTER GROUP | colvar generic multicolvar setup core vatom |
| 19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Valerio Rizzi | UPPER_WALLS PRINT DISTANCES METAD COMBINE RESTART COORDINATIONNUMBER UNITS GROUP ENDPLUMED FLUSH | bias generic multicolvar setup symfunc function core |
| 19.080 | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | methods | ves, variationally enhanced sampling, vibrational excitation, chemical reactions | Kristof Bal | UPPER_WALLS EXTERNAL PRINT CONVERT_TO_FES BF_CHEBYSHEV COMBINE TD_GRID HISTOGRAM TD_WELLTEMPERED UNITS VES_LINEAR_EXPANSION DUMPGRID DISTANCE ANGLE COORDINATION LOWER_WALLS FLUSH OPT_AVERAGED_SGD | ves gridtools bias colvar generic setup function |
| 19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | GYRATION UPPER_WALLS PRINT METAD MOLINFO DISTANCE ENERGY COM | generic vatom bias colvar |
| 19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Giovanni Bussi | DISTANCE RESTRAINT COORDINATION WHOLEMOLECULES ENDPLUMED LOWER_WALLS | generic bias colvar |
| 19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Elena Papaleo | ALPHABETA GYRATION UPPER_WALLS PRINT METAD WHOLEMOLECULES MOLINFO LOWER_WALLS GROUP | bias colvar generic multicolvar core |
| 19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Kresten Lindorff-Larsen | ALPHABETA PRINT METAD COMMITTOR COMBINE MOLINFO FLUSH | generic multicolvar bias function |
| 19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Adriana Pietropaolo | PRINT CONSTANT METAD BIASVALUE TORSION WHOLEMOLECULES MATHEVAL | generic bias function colvar |
| 25.024 | Sampling glycan-glycan interactions for B22 calculations | bio | B22, glycan, carbohydrates, distance, REST2, metadynamics, RECT, replica exchange | Isabell Louise Grothaus | COM POSITION COMBINE PRINT DISTANCE RESTRAINT METAD | bias function colvar generic vatom |
| 25.012 | A Machine Learning-Driven, Probability-Based Approach to Enzyme Catalysis | bio | enzyme catalysis, transition state, structure-activity relationship, free energy surface, reaction mechanism, water, alpha-amylase, sugar, QM/MM MD, OPES, committor function, machine learning | Sudip Das | COORDINATION POSITION CUSTOM BIASVALUE COMBINE LOAD OPES_METAD MATHEVAL FLUSH INCLUDE PRINT TORSION DISTANCE CELL ENERGY UNITS | bias function colvar opes generic setup |
| 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 | COM COORDINATION UPPER_WALLS COMBINE UNITS GROUP FLUSH COORDINATIONNUMBER DISTANCES PRINT DISTANCE ANGLE LOWER_WALLS RESTRAINT FIXEDATOM METAD | bias symfunc function colvar multicolvar generic setup core vatom |
| 24.021 | Ab initio machine learning simulation of calcium carbonate from aqueous solutions to the solid state | chemistry | ion pairing, caco3, opes, proton transfer, crystallization | Pablo Piaggi | COORDINATION UPPER_WALLS OPES_METAD PRINT DISTANCE ENERGY | bias opes generic colvar |
| 24.020 | Graph Neural Network-State Predictive Information Bottleneck (GNN-SPIB) approach for learning molecular thermodynamics and kinetics | bio | LJ7, alanine, well-tempered metadynamics, infrequent metadynamics, machine learning | Ziyue Zou, Dedi Wang, Pratyush Tiwary | GROUP LOAD PRINT TORSION COMMITTOR METAD | bias setup colvar generic core |
| 22.007 | Characterization of a natural variant of human NDP52 and its functional consequences on mitophagy | bio | metadynamics, well-tempered, protein-protein interactions, disordered proteins, mutations autophagy | Elena Papaleo | MOLINFO COORDINATION UPPER_WALLS ALPHABETA WHOLEMOLECULES ALPHARMSD FLUSH TORSION PRINT DISTANCE ANGLE METAD | bias colvar multicolvar secondarystructure generic |
| 22.005 | Collective Variable for Metadynamics Derived from AlphaFold Output | bio | AlphaFold, protein folding, protein structure prediction, metadynamics, deep learning, free energy simulation, collective variable | Vojtech Spiwok | WHOLEMOLECULES PRINT LOAD METAD | bias generic setup |
| 21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Tarak Karmakar | UPPER_WALLS GROUP LOAD MATHEVAL OPES_METAD FLUSH PRINT LOWER_WALLS PYTORCH_MODEL | bias pytorch function opes generic setup core |
| 20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Faidon Brotzakis | MOLINFO DUMPGRID WHOLEMOLECULES BIASVALUE GROUP RMSD READ CONVERT_TO_FES HISTOGRAM PRINT DISTANCES EMMI | gridtools bias colvar multicolvar isdb generic core |
| 20.032 | Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil | materials | clustering, conformational isomers | Matteo Salvalaglio | PRINT ENDPLUMED TORSION | generic colvar |
| 19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | GiovanniMaria Piccini | UPPER_WALLS COMBINE UNITS FLUSH PRINT DISTANCE ENERGY LOWER_WALLS METAD | bias setup function colvar generic |
| 19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | UPPER_WALLS COMBINE UNITS FLUSH DISTANCES PRINT DISTANCE RESTART METAD | bias setup function colvar multicolvar generic |
| 26.009 | Exploring the Conformational Landscape of HIV-1 TAR RNA by PT-WTE | bio | RNA, PT-WTE, HIV-1 TAR | Stefano Bosio | METAD GROUP WHOLEMOLECULES ENERGY MOLINFO PRINT | core colvar bias generic |
| 25.021 | All You Need Is Water. Converging Ligand Binding Simulations with Hydration Collective Variables | bio | OPES Explore, ligand binding, binding free energy, water, hydration CVs, SAMPL challenge, host-guest | Valerio Rizzi | GROUP WHOLEMOLECULES CENTER DISTANCE COORDINATION FIXEDATOM ENERGY OPES_METAD_EXPLORE ANGLE MATHEVAL UPPER_WALLS FIT_TO_TEMPLATE PRINT | opes core function bias generic colvar vatom |
| 25.020 | Revealing Water-Mediated Activation Mechanisms in the Beta 1-Adrenergic Receptor via OneOPES-Enhanced Free Energy Landscapes | bio | OneOPES, GPCR, ADRB1, activation, microswitches, conformational changes, allostery | Valerio Rizzi | ECV_MULTITHERMAL OPES_EXPANDED GROUP GHOST CENTER DISTANCE RMSD COORDINATION PATHMSD ENERGY CUSTOM OPES_METAD_EXPLORE UPPER_WALLS LOWER_WALLS DISTANCES PRINT | opes core function bias generic multicolvar colvar vatom |
| 25.010 | Kinetic rates calculation with Ratchet&Pawl MD | methods | kinetics, ligand binding, ABMD, ratchet&pawl MD | Riccardo Capelli | FLUSH GROUP WHOLEMOLECULES COMMITTOR DISTANCE COM ABMD PRINT | core bias generic colvar vatom |
| 25.003 | Surrogate Model CV | methods | Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding | Sompriya Chatterjee | GROUP WHOLEMOLECULES OPES_METAD PYTORCH_MODEL ENDPLUMED COMMITTOR DISTANCE ENERGY MATHEVAL CUSTOM MOLINFO COMBINE TORSION PRINT | pytorch opes core function generic colvar |
| 25.002 | M3_PCV-ABMD | chemistry | Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor | Gian Marco Elisi | ABMD ENDPLUMED PATHMSD UPPER_WALLS UNITS PRINT | colvar bias setup generic |
| 24.035 | Data efficient machine learning potentials for modeling catalytic reactivity via active learning and enhanced sampling | chemistry | opes, catalysis, ammonia, machine learning potentials | Luigi Bonati | GROUP OPES_METAD RESTART COMMITTOR COORDINATION DISTANCE CUSTOM LOWER_WALLS UPPER_WALLS UNITS PRINT | opes core function bias setup generic colvar |
| 24.034 | Umbrella sampling of ion in transporter SLC26A7 | bio | umbrella sampling, transporter, ions | Xiaoli Lu | RESTRAINT UNITS POSITION PRINT | colvar bias setup generic |
| 24.032 | DeepLNE++ | methods | PATHCV, OPES | Thorben Fröhlking | GROUP OPES_METAD DISTANCE COORDINATION ENERGY CUSTOM LOAD COMBINE TORSION PRINT | opes core function setup generic colvar |
| 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 | ECV_MULTITHERMAL OPES_EXPANDED GROUP DISTANCE COORDINATION ENERGY CUSTOM OPES_METAD_EXPLORE COMBINE RESTART TORSION PRINT | opes core function setup generic colvar |
| 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 | CENTER ENDPLUMED RMSD CUSTOM UPPER_WALLS TORSION METAD COMMITTOR FIXEDATOM FIT_TO_TEMPLATE OPES_METAD GROUP ANGLE COMBINE CONTACTMAP WHOLEMOLECULES DISTANCE COORDINATION MOLINFO MATHEVAL PRINT | opes core function bias generic colvar vatom |
| 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 | METAD CONTACTMAP DISTANCE ALPHARMSD PATHMSD INCLUDE MOLINFO FUNCPATHMSD UPPER_WALLS LOWER_WALLS PRINT | secondarystructure function bias generic colvar |
| 23.040 | Supramolecular capsules assembly dynamics | chemistry | Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics | Riccardo Capelli | FLUSH METAD GROUP WHOLEMOLECULES CENTER POSITION DISTANCE COM CUSTOM UNITS DISTANCES PRINT | core function bias setup generic multicolvar colvar vatom |
| 23.036 | Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? | bio | NaCl, nucleation, metadynamics | Ruiyu Wang | METAD Q4 Q6 VOLUME COMBINE ENERGY COORDINATIONNUMBER MATHEVAL PRINT | function bias generic symfunc colvar |
| 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 | METAD BIASVALUE WHOLEMOLECULES CENTER DISTANCE CONSTANT MATHEVAL UPPER_WALLS LOWER_WALLS PRINT | function bias generic colvar vatom |
| 23.020 | FEP simulations of ATOX1 homodimer | chemistry | parallel bias metadynamics, FEP, free-energy of metal ion dissociation | Adriana Pietropaolo | PBMETAD BIASVALUE WHOLEMOLECULES DISTANCE CONSTANT ANGLE MATHEVAL PRINT | colvar function bias generic |
| 23.014 | Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 | bio | metadynamics, oligomerization, chemokine receptors, GPCR, membrane | Vittorio Limongelli | METAD FLUSH WHOLEMOLECULES DISTANCE COM COMBINE UPPER_WALLS TORSION PRINT | function bias generic colvar vatom |
| 23.012 | JAK2 2D meta-eABF PMF with statistical analysis | bio | 2D meta-eABF, path CV, PMF | Istvan Kolossvary | METAD FLUSH BIASVALUE DRR PATHMSD CUSTOM UPPER_WALLS LOWER_WALLS PRINT | drr function bias generic colvar |
| 22.042 | Metadynamics of NSP10 and variants | bio | metadynamics, NSP10, crystal structure, variants | Shozeb Haider | METAD TORSION PRINT | colvar bias generic |
| 22.033 | Reciprocal barrier restraint. Application to PROTAC passive permeability prediction | methods | PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR | Istvan Kolossvary | METAD FLUSH BIASVALUE DISTANCE DRR COM CUSTOM UNITS PRINT | drr function bias setup generic colvar vatom |
| 21.049 | Multiple-path-metadynamics and PathMaps | methods | path-CV, metadynamics, multiple-walker, multiple paths, pathmap | Alberto Pérez-de-Alba-Ortíz | METAD RESTRAINT MOVINGRESTRAINT CONSTANT CUSTOM LOWER_WALLS ENSEMBLE LOAD COMBINE UPPER_WALLS UNITS TORSION PRINT | function bias setup generic colvar |
| 21.048 | Enhancing ligand exploration within a channel pore and fenestrations using metadynamics | bio | well-tempered metadynamics, protein-ligand enhanced sampling, sodium channel, Nav, small molecule drug | Elaine Tao | METAD DISTANCE UNITS COM CUSTOM UPPER_WALLS LOWER_WALLS TORSION PRINT | function bias setup generic colvar vatom |
| 21.031 | Photo-switchable sulfonulureas in KATP channel | bio | metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels | Katarzyna Walczewska-Szewc | METAD WHOLEMOLECULES DISTANCE UNITS COM UPPER_WALLS LOWER_WALLS PRINT | bias setup generic colvar vatom |
| 21.006 | OPES, On-the-fly Probability Enhanced Sampling Method | methods | opes, alanine dipeptide, well-tempered, multithermal, multiumbrella | Michele Invernizzi | ECV_MULTITHERMAL OPES_EXPANDED OPES_METAD ENDPLUMED ENERGY ECV_UMBRELLAS_LINE TORSION PRINT | opes colvar generic |
| 21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Tarsis Ferreira | METAD GROUP WHOLEMOLECULES HISTOGRAM DISTANCE COORDINATION RANDOM_EXCHANGES REWEIGHT_METAD ENERGY DUMPGRID INCLUDE PUCKERING MOLINFO UPPER_WALLS LOWER_WALLS PRINT | gridtools core bias generic colvar |
| 20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Vojtech Spiwok | METAD TORSION PRINT | colvar bias generic |
| 20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Michele Invernizzi | OPES_EXPANDED ENDPLUMED VOLUME RMSD ENVIRONMENTSIMILARITY ECV_LINEAR CUSTOM UPPER_WALLS UNITS TORSION ECV_MULTITHERMAL ECV_MULTITHERMAL_MULTIBARIC ENERGY ECV_UMBRELLAS_LINE POSITION Q6 LOAD WHOLEMOLECULES MOLINFO MATHEVAL PRINT | opes symfunc function envsim bias generic setup colvar |
| 20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Max Bonomi | PBMETAD WHOLEMOLECULES GYRATION ALPHABETA COORDINATION DIHCOR MOLINFO INCLUDE PRINT | multicolvar colvar bias 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 | CONVERT_TO_FES ENDPLUMED DUMPGRID ABMD UPPER_WALLS METAD COM READ COMBINE FUNCPATHMSD FLUSH CONTACTMAP WHOLEMOLECULES HISTOGRAM DISTANCE REWEIGHT_METAD MOLINFO LOWER_WALLS PRINT | gridtools function bias generic colvar vatom |
| 20.000 | Muscarinic M2 receptor-ligand funnel metadynamics | bio | multiple walker metadynamics, well-tempered metadynamics, funnel metadynamics, MC-HLDA, GPCR, receptor, Adiabatic Bias MD | Riccardo Capelli | METAD CONVERT_TO_FES UPPER_WALLS HISTOGRAM ENDPLUMED DISTANCE REWEIGHT_METAD COM MATHEVAL READ DUMPGRID COMBINE ABMD LOWER_WALLS PRINT | gridtools function bias generic colvar vatom |
| 19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Matteo Salvalaglio | GROUP CENTER ENDPLUMED DISTANCE INCLUDE PRINT | core colvar generic vatom |
| 19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Michele Invernizzi | METAD OPES_METAD POSITION ENDPLUMED EXTERNAL UNITS TORSION PRINT | opes bias setup generic colvar |
| 19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Gareth Tribello | METAD FCCUBIC CELL AROUND ENDPLUMED LOWER_WALLS UPPER_WALLS UNITS PRINT | bias setup generic symfunc volumes colvar |
| 19.049 | Determining the sizes of solid/liquid clusters in MD trajectories of nucleation | methods | nucleation, metadynamics, clustering, Steinhardt order parameters | Gareth Tribello | METAD OUTER_PRODUCT CLUSTER_DISTRIBUTION OUTPUT_CLUSTER Q6 DFSCLUSTERING LOCAL_Q6 MORE_THAN CUSTOM ONES CLUSTER_PROPERTIES COORDINATIONNUMBER CLUSTER_NATOMS SMAC CONTACT_MATRIX MATRIX_VECTOR_PRODUCT DISTANCES PRINT | matrixtools clusters function bias generic symfunc adjmat multicolvar |
| 19.030 | Coarse-Grained MetaDynamics (CG-MetaD) | bio | Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy | Vittorio Limongelli | METAD WHOLEMOLECULES DISTANCE COM UPPER_WALLS LOWER_WALLS PRINT | vatom colvar bias generic |
| 19.005 | Cmyc small molecule interaction | bio | metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP | Gabriella Heller | CS2BACKBONE PBMETAD GROUP WHOLEMOLECULES CENTER GYRATION ALPHABETA COORDINATION DISTANCE METAINFERENCE MOLINFO INCLUDE PRINT | core bias generic multicolvar isdb colvar vatom |
| 19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Max Bonomi | GROUP BIASVALUE EMMI MOLINFO PRINT | core isdb bias generic |
| 19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Michele Invernizzi | METAD POSITION ENDPLUMED RESTART ENERGY LOAD TORSION UNITS VES_DELTA_F PRINT | ves bias setup generic colvar |
| 26.007 | Metadynamics Simulations Reveal the Protonation-Dependent Conformational Landscape of GSK-3β Dual Inhibitors | chemistry | metadynamics, ligand unbinding, path CVs, funnel metadynamics | Gian Marco Elisi | COM LOWER_WALLS ENDPLUMED METAD FUNNEL COMBINE PATHMSD UNITS ANGLE FUNNEL_PS UPPER_WALLS MATHEVAL MOLINFO PRINT RMSD DISTANCE WHOLEMOLECULES | setup generic funnel vatom function bias colvar |
| 25.025 | Enhanced Sampling of Ligand Binding Coupled to RNA Conformational Dynamics | bio | OPES, OPES Flooding , Metadynamics, RNA, Ligand binding, Free Energy, Kinetics, Funnel | Revanth Elangovan and Dhiman Ray | WHOLEMOLECULES ENDPLUMED FUNNEL TORSION CENTER COMMITTOR DISTANCE METAD OPES_METAD FUNNEL_PS UPPER_WALLS MATHEVAL RMSD COM LOWER_WALLS COORDINATION GROUP CUSTOM WRAPAROUND PRINT | opes generic funnel vatom function bias colvar core |
| 25.009 | Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water | chemistry | metadynamics, nitrate photolysis | Kam-Tung Chan | DUMPGRID HISTOGRAM METAD FLUSH REWEIGHT_METAD COORDINATION READ GROUP CUSTOM UPPER_WALLS RESTART PRINT DISTANCE | setup generic gridtools function bias colvar core |
| 24.029 | Combination of OPES and OPES-Explore | methods | OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin | Dhiman Ray | FLUSH BIASVALUE ENERGY MOLINFO WHOLEMOLECULES PYTORCH_MODEL ENDPLUMED CENTER DISTANCE CONTACTMAP METAD OPES_METAD UPPER_WALLS POSITION FIT_TO_TEMPLATE MATHEVAL RMSD LOWER_WALLS COMBINE COORDINATION UNITS GROUP CUSTOM OPES_METAD_EXPLORE FIXEDATOM PRINT INCLUDE | setup opes generic pytorch vatom function bias colvar core |
| 24.024 | Host-Guest binding free energies à la carte, an automated OneOPES protocol | bio | OneOPES, ligand binding, binding free energy,SAMPL challenge, host-guest | Valerio Rizzi | LOWER_WALLS ENDPLUMED COORDINATION ECV_MULTITHERMAL TORSION GROUP CENTER ANGLE OPES_EXPANDED UPPER_WALLS OPES_METAD_EXPLORE FIT_TO_TEMPLATE MATHEVAL ENERGY FIXEDATOM PRINT DISTANCE WHOLEMOLECULES | opes generic vatom function bias colvar core |
| 24.014 | Learning Collective Variables with Synthetic Data Augmentation through Physics-inspired Geodesic Interpolation | methods | data augmentation, geodesic interpolation, collective variables, protein folding | Juno Nam | PYTORCH_MODEL LOWER_WALLS METAD FLUSH COORDINATION UPPER_WALLS DRR MOLINFO PRINT RMSD WHOLEMOLECULES | drr generic pytorch bias colvar |
| 24.003 | Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations | chemistry | steered molecular dynamics, foldamers, peptoids, bio-inspired | Kaylyn Torkelson | COM COORDINATION ALPHABETA TORSION GYRATION MOVINGRESTRAINT PRINT DISTANCE INCLUDE WHOLEMOLECULES | multicolvar generic vatom bias colvar |
| 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 | STATS BIASVALUE GROUP SAXS ENSEMBLE CENTER UPPER_WALLS MOLINFO WRAPAROUND PRINT RMSD DISTANCE | isdb generic vatom function bias colvar core |
| 23.021 | Into the Dynamics of Rotaxanes at Atomistic Resolution | materials | metadynamics, rotaxanes, molecular shuttles, molecular machines | Luigi Leanza | METAD TORSION CENTER CUSTOM UPPER_WALLS MATHEVAL FIXEDATOM PRINT DISTANCE | generic vatom function bias colvar |
| 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 |
| 22.021 | 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 | ENVIRONMENTSIMILARITY LOWER_WALLS ECV_UMBRELLAS_LINE UPPER_WALLS PRINT INCLUDE OPES_EXPANDED | bias envsim opes generic |
| 22.018 | Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations | bio | ligand binding, docking, EMMI, LAT1 | Max Bonomi | EMMIVOX GROUP BIASVALUE MOLINFO PRINT LOAD WHOLEMOLECULES | setup isdb generic bias core |
| 22.003 | Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling | methods | opes, metadynamics, reweighting, alanine, muller | Michele Invernizzi | LOWER_WALLS ENDPLUMED METAD ECV_MULTITHERMAL TORSION UNITS OPES_METAD BIASVALUE ECV_UMBRELLAS_FILE ENERGY OPES_METAD_EXPLORE CUSTOM UPPER_WALLS POSITION PRINT PBMETAD OPES_EXPANDED | setup opes generic function bias colvar |
| 22.001 | Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials | methods | enhanced sampling, variationally enhanced sampling, ves, metadynamics, bias representation, wavelets, adam | Benjamin Pampel | BF_WAVELETS FLUSH VES_LINEAR_EXPANSION ENERGY TD_UNIFORM BF_CUBIC_B_SPLINES TD_WELLTEMPERED OPT_AVERAGED_SGD BF_CHEBYSHEV VES_OUTPUT_BASISFUNCTIONS DISTANCE METAD UPPER_WALLS POSITION BF_GAUSSIANS BF_LEGENDRE OPT_ADAM COORDINATION UNITS PRINT INCLUDE | setup generic ves bias colvar |
| 21.034 | Efficient sampling of high-dimensional free energy landscapes using adaptive reinforced dynamics | bio | reinforced dynamics, bias-exchange metadynamics, parallel-bias metadynamics | Dongdong Wang | ENDPLUMED METAD PBMETAD RANDOM_EXCHANGES TORSION PRINT INCLUDE | generic bias colvar |
| 21.033 | Multiple-path-metadynamics applied to DNA base-pairing transitions | bio | path-CV, metadynamics, multiple-walker, dna | Alberto Pérez-de-Alba-Ortíz | CONSTANT METAD COMBINE MOVINGRESTRAINT UPPER_WALLS PRINT INCLUDE RESTRAINT | generic bias function |
| 21.020 | Reweighted Jarzynski sampling | methods | free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions | Kristof Bal | CONSTANT FLUSH VES_LINEAR_EXPANSION BIASVALUE TD_WELLTEMPERED REWEIGHT_BIAS MOVINGRESTRAINT REWEIGHT_METAD OPT_AVERAGED_SGD BF_CHEBYSHEV DISTANCE RESTRAINT HISTOGRAM METAD ANN OPES_METAD UPPER_WALLS DUMPGRID CONVERT_TO_FES COMBINE UNITS CUSTOM COORDINATIONNUMBER PRINT LOAD | setup annfunc opes generic ves gridtools function bias symfunc colvar |
| 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 | STATS COMBINE COORDINATION MOLINFO PRINT RESTRAINT WHOLEMOLECULES | generic bias colvar function |
| 20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Cristina Paissoni | STATS BIASVALUE GROUP CENTER SAXS ENSEMBLE MOLINFO PRINT DISTANCE INCLUDE RESTRAINT WHOLEMOLECULES | isdb generic vatom function bias colvar core |
| 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 | FLUSH ENSEMBLE MOLINFO METAINFERENCE WHOLEMOLECULES ENDPLUMED TORSION GYRATION DIHCOR CS2BACKBONE ANTIBETARMSD STATS PARABETARMSD PBMETAD COMBINE COORDINATION GROUP PRINT ALPHARMSD INCLUDE | multicolvar isdb generic secondarystructure function bias colvar core |
| 20.010 | Phase equilibrium of liquid water and hexagonal ice from enhanced sampling molecular dynamics simulations | materials | water, ice, TIP4P, crystallization, EnvironmentSimilarity, RefCV, kernel, VES, variationally enhanced sampling | Pablo Piaggi | ENVIRONMENTSIMILARITY OPT_AVERAGED_SGD VES_LINEAR_EXPANSION UPPER_WALLS MATHEVAL Q6 OPT_DUMMY RESTART VOLUME TD_WELLTEMPERED PRINT BF_LEGENDRE | setup generic envsim ves function bias symfunc colvar |
| 20.001 | Conformational stability and dynamics in solution and in crystals report similarly on unfolding and aggregation propensity of amyloidogenic proteins | bio | metainference, metadynamics, NMR, protein dynamics, b2m, protein crystals | Carlo Camilloni | LOWER_WALLS ENDPLUMED FLUSH ALPHABETA GROUP BIASVALUE ANTIBETARMSD UPPER_WALLS MOLINFO PRINT CS2BACKBONE PBMETAD WHOLEMOLECULES | multicolvar isdb generic secondarystructure bias core |
| 19.075 | PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python | other | Python, automatic differentiation | Toni Giorgino | ENDPLUMED DUMPDERIVATIVES COMBINE TORSION GROUP CENTER CUSTOM ANGLE PRINT DISTANCE RESTRAINT | generic vatom function bias colvar core |
| 19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Sandro Bottaro | ERMSD METAD TORSION MOLINFO PRINT RMSD DISTANCE WHOLEMOLECULES | bias colvar generic |
| 19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Jakub Rydzewski | LOWER_WALLS METAD PATHMSD UNITS UPPER_WALLS RESTART PRINT | bias setup colvar generic |
| 19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Kim E. Jelfs | COM LOWER_WALLS METAD GROUP CENTER UPPER_WALLS RESTART PRINT DISTANCE | setup generic vatom bias colvar core |
| 19.059 | cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide | bio | bias-exchange metadynamics, cis-trans isomerization | Fabrizio Marinelli | METAD RANDOM_EXCHANGES TORSION PRINT INCLUDE | bias generic colvar |
| 19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Riccardo Capelli | COM DUMPGRID HISTOGRAM METAD CONVERT_TO_FES FLUSH ENDPLUMED REWEIGHT_METAD COORDINATION GROUP READ UPPER_WALLS POSITION FIT_TO_TEMPLATE MATHEVAL WRAPAROUND PRINT WHOLEMOLECULES | generic vatom gridtools function bias colvar core |
| 19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Carlo Camilloni | STATS ENDPLUMED BIASVALUE GROUP CENTER SAXS UPPER_WALLS MOLINFO PRINT RMSD DISTANCE INCLUDE RESTRAINT WHOLEMOLECULES | isdb generic vatom function bias colvar core |
| 26.006 | Metadynamics simulations of buried phosphorylation sites and proline isomerisation | bio | metadynamics | Julian Streit | PRINT COORDINATION MOLINFO WHOLEMOLECULES METAD TORSION | generic colvar bias |
| 25.028 | Designing transferable transition state guided collective variable via interpretable machine learning model for enhanced sampling. A case study on polymer collapse transition | bio | metadynamics, polymer collapse transition, transferable CV,interpretable ML-model | Saikat Dhibar and Biman Jana | COMBINE PRINT DISTANCE COORDINATION WHOLEMOLECULES GYRATION GROUP CENTER METAD LOWER_WALLS MATHEVAL UPPER_WALLS | generic vatom colvar core function bias |
| 25.023 | Molecular simulations of Tau-protein oligomers | bio | metadynamics, proteins, aggregation | Giovanni Bussi | PRINT HISTOGRAM REWEIGHT_BIAS CONVERT_TO_FES CUSTOM RESTRAINT RESTART METAD RMSD FLUSH CONTACTMAP DUMPGRID | setup colvar gridtools generic function bias |
| 25.019 | The Arch from the Stones. Understanding Protein Folding Energy Landscapes via Bio-inspired Collective Variables | bio | protein folding, OPES, OneOPES, binding free energy | Valerio Rizzi | COMBINE PRINT COORDINATION DISTANCE GHOST ECV_MULTITHERMAL CUSTOM ENERGY OPES_EXPANDED MOLINFO GROUP CENTER OPES_METAD_EXPLORE RMSD | generic vatom colvar core opes function |
| 25.018 | Metainference simulation for dimerization of RNA binding protein | bio | Metainference, Metadynamics, SAXS, protein dimer | Debadutta Patra | PBMETAD PRINT DISTANCE UPPER_WALLS ENSEMBLE MOLINFO WHOLEMOLECULES CENTER TORSION GYRATION METAINFERENCE STATS FLUSH SAXS | vatom colvar isdb generic function bias |
| 25.017 | Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity | bio | EMMIVox, cryo-EM, allostery, decamer, filament, ensemble refinement, glutamine synthetase | Samuel Hoff | PRINT EMMIVOX BIASVALUE MOLINFO WHOLEMOLECULES GROUP | generic core isdb bias |
| 25.016 | Advancing in silico drug design with Bayesian refinement of AlphaFold models | bio | bAIes, AlphaFold, Bayesian refinement, virtual screening, docking, small-molecule, enrichment | Samiran Sen | BAIES GROUP PRINT BIASVALUE | generic core isdb bias |
| 25.001 | RNA G-quadruplex folding with ST-metaD protocol | bio | RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | COMBINE ERMSD MOLINFO WHOLEMOLECULES METAD | function generic colvar bias |
| 24.016 | Cryo-EM guided simulations of ribozyme | bio | metainference, cryo-EM | Giovanni Bussi | PRINT EMMIVOX ERMSD BIASVALUE RESTRAINT MOLINFO WHOLEMOLECULES GROUP INCLUDE | colvar isdb core generic bias |
| 24.013 | Estimating Free Energy Surfaces and their Convergence from multiple, independent static and history-dependent biased molecular-dynamics simulations with Mean Force Integration | methods | Mean Force Integration, Convergence, FES, Umbrella Sampling | Matteo Salvalaglio | COMMITTOR PRINT DISTANCE BIASVALUE RESTRAINT ENERGY RESTART MOLINFO COORDINATIONNUMBER METAD TORSION FLUSH MATHEVAL | setup colvar generic function symfunc bias |
| 24.012 | Molecular simulations to investigate the impact of N6-methylation in RNA recognition | bio | metadynamics, alchemistry, RNA modification, RNA:protein interactions | Giovanni Bussi | GHBFIX DEBUG COMBINE COM PRINT COORDINATION DISTANCE BIASVALUE MOLINFO CENTER GROUP METAD UPPER_WALLS LOWER_WALLS | vatom colvar core generic function bias |
| 24.008 | yCD Metadynamics | bio | volume-based MetaD, path CVs, infrequent MetaD, product release | James McCarty | FIT_TO_TEMPLATE PRINT CONVERT_TO_FES ENDPLUMED FLUSH CONTACTMAP COORDINATION DISTANCE HISTOGRAM WRAPAROUND PATH WHOLEMOLECULES GROUP INCLUDE MATHEVAL DUMPGRID COM MOLINFO UPPER_WALLS RMSD COMMITTOR READ FIXEDATOM METAD REWEIGHT_METAD | vatom colvar gridtools mapping core generic function bias |
| 24.007 | SWISH-X | bio | swish-x, SWISH-X, swish, expanded SWISH | Alberto Borsatto | PRINT OPES_EXPANDED ECV_MULTITHERMAL ENERGY MOLINFO WHOLEMOLECULES INCLUDE CONTACTMAP UPPER_WALLS | generic colvar opes bias |
| 23.039 | Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation | chemistry | metadynamics, ligand dissociation | Eric Beyerle | COMBINE PRINT DISTANCE FIXEDATOM RESTRAINT MOLINFO DUMPMASSCHARGE CENTER METAD UPPER_WALLS | generic vatom colvar function bias |
| 23.032 | Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics | bio | metadynamics, tSNE, neural network, machine learning, trp-cage, folding | Vojtech Spiwok | POSITION FIT_TO_TEMPLATE PRINT COMBINE ANN ALPHARMSD MOLINFO WHOLEMOLECULES METAD | colvar annfunc generic secondarystructure function bias |
| 23.013 | Path meta-eABF simulation of large scale conformational change in STING protein | methods | meta-eABF, path CV, large scale conformational change, STING protein, reciprocal barrier restraint | Istvan Kolossvary | PATHMSD PRINT UNITS DRR CUSTOM BIASVALUE METAD TIME LOWER_WALLS FLUSH UPPER_WALLS | setup colvar generic function drr bias |
| 23.001 | Quantum phase diagram of water | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn-Løland Bore | PRINT INCLUDE ECV_UMBRELLAS_LINE OPES_EXPANDED RESTART UPPER_WALLS LOWER_WALLS ENVIRONMENTSIMILARITY | envsim setup opes generic bias |
| 22.039 | Driving and characterizing nucleation of urea and glycine polymorphs in water | bio | metadynamics, nucleation, amino acids, polymorphism | Eric Beyerle | COMBINE PRINT Q4 Q6 LOAD PAIRENTROPY CENTER COORDINATIONNUMBER GROUP INCLUDE METAD MATHEVAL | generic setup vatom gridtools core function symfunc bias |
| 22.031 | Rare Event Kinetics from Adaptive Bias Enhanced Sampling | methods | OPES Flooding, Kinetics, Rate, OPES, Machine Learning | Dhiman Ray | PRINT ENDPLUMED CONTACTMAP COMBINE DISTANCE UNITS CUSTOM ENERGY PYTORCH_MODEL WHOLEMOLECULES GROUP INCLUDE MOLINFO RMSD COMMITTOR POSITION CONSTANT BIASVALUE OPES_METAD TORSION | setup colvar core opes generic function pytorch 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 | RMSD PRINT DISTANCE | generic colvar |
| 21.036 | Modelling the structure and interactions of intrinsically disordered peptides with multiple-replica, metadynamics-based sampling methods and force-field combinations | bio | Bias Exchange Metadynamics, PTWTE-metaD | Matteo Salvalaglio | PARABETARMSD PRINT COORDINATION ANTIBETARMSD ALPHARMSD RANDOM_EXCHANGES ENERGY MOLINFO WHOLEMOLECULES GROUP METAD UPPER_WALLS DIHCOR LOWER_WALLS GYRATION | colvar multicolvar core generic secondarystructure bias |
| 21.022 | Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly | materials | parallel bias metadynamics, adsorption, peptide | Xin Qi | PBMETAD COM PRINT DISTANCE ENERGY MOLINFO GYRATION UPPER_WALLS LOWER_WALLS | generic vatom colvar bias |
| 21.019 | Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations | materials | Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen | Matteo Salvalaglio | COM PRINT TORSIONS DISTANCE KDE MATHEVAL | vatom colvar multicolvar gridtools generic function |
| 21.018 | Localized Volume-based Metadynamics | bio | LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification | Riccardo Capelli | PRINT CONVERT_TO_FES ENDPLUMED FLUSH COORDINATION DISTANCE HISTOGRAM WHOLEMOLECULES GROUP MATHEVAL DUMPGRID COM UPPER_WALLS RMSD READ POSITION FIXEDATOM METAD REWEIGHT_METAD | vatom colvar gridtools core generic function bias |
| 21.016 | MD SAXS GTPase associated center | bio | metadynamics, RNA, folding, SAXS | Giovanni Bussi | PRINT ERMSD INCLUDE CUSTOM MOLINFO WHOLEMOLECULES GROUP GYRATION UPPER_WALLS METAD LOWER_WALLS SAXS | colvar isdb core generic function 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 PRINT DISTANCE GROUP WHOLEMOLECULES | generic core vatom colvar |
| 20.026 | Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor | bio | Metadynamics, Umbrella sampling | Brandon Peters | PRINT HISTOGRAM CONVERT_TO_FES MULTI_RMSD RESTRAINT REWEIGHT_METAD METAD DUMPGRID | generic bias colvar gridtools |
| 20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Matteo Salvalaglio | VOLUME PRINT ENERGY METAD CELL UPPER_WALLS LOWER_WALLS MATHEVAL | generic function colvar bias |
| 20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Carlo Camilloni | PBMETAD PRINT DISTANCE ENSEMBLE ALPHABETA MOLINFO WHOLEMOLECULES CENTER TORSION GYRATION METAINFERENCE STATS FLUSH SAXS | vatom colvar multicolvar isdb generic function bias |
| 19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Valerio Rizzi | COMBINE PRINT UNITS EXTERNAL RESTART ENDPLUMED GROUP METAD COORDINATIONNUMBER FLUSH | generic setup core function symfunc bias |
| 19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Mattia Bernetti | PATHMSD PRINT WHOLEMOLECULES METAD UPPER_WALLS LOWER_WALLS | generic colvar bias |
| 19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Kim Jelfs | COM PRINT DISTANCES MOVINGRESTRAINT INPLANEDISTANCES RESTART FLUSH | vatom setup multicolvar generic bias |
| 19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Gareth Tribello | MORE_THAN FIND_CONTOUR_SURFACE UNITS MULTICOLVARDENS CENTER GROUP FCCUBIC FOURIER_TRANSFORM DUMPGRID | vatom contour setup fourier gridtools core function symfunc |
| 19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Carlo Camilloni | PBMETAD PRINT CS2BACKBONE ALPHABETA MOLINFO RESTART BIASVALUE WHOLEMOLECULES GROUP ENDPLUMED ANTIBETARMSD LOWER_WALLS FLUSH UPPER_WALLS | setup multicolvar isdb core generic secondarystructure bias |
| 19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Silvio Pipolo | FUNCPATHMSD PRINT CELL PIV UPPER_WALLS METAD LOWER_WALLS | generic colvar piv function bias |
| 19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Jim Pfaendtner | COORDINATION ENERGY EXTERNAL GROUP METAD | core colvar bias |
| 19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Glen Hocky | COMBINE PRINT DISTANCE EDS RESTRAINT TORSION | generic colvar eds function bias |
| 19.004 | MI Ubiquitin | bio | metainference, NMR | Max Bonomi | PRINT CS2BACKBONE MOLINFO WHOLEMOLECULES GROUP METAINFERENCE RDC | generic core isdb |
| 25.011 | Chiral perovskite nucleation | chemistry | metadynamics, chiral perovskites, nucleation | Adriana Pietropaolo | MULTI_RMSD PRINT UNITS MATHEVAL RESTART DISTANCE UPPER_WALLS LOWER_WALLS PBMETAD | bias function generic setup colvar |
| 24.027 | Proline cis and trans subensembles of a disordered peptide | bio | intrinsically disordered proteins, proline cis trans isomerisation, metadynamics, collective variables | Alice Pettitt | GROUP WHOLEMOLECULES PARABETARMSD GYRATION ANTIBETARMSD MOLINFO PRINT ALPHARMSD PBMETAD COMBINE INCLUDE ENDPLUMED DISTANCE FLUSH COORDINATION TORSION DIHCOR | core secondarystructure bias function generic colvar multicolvar |
| 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 | CUSTOM FIXEDATOM GROUP PYTORCH_MODEL WHOLEMOLECULES OPES_METAD PRINT PATH RESTART FIT_TO_TEMPLATE CENTER DISTANCE UPPER_WALLS COORDINATION LOWER_WALLS TORSION | setup vatom core bias function mapping generic opes colvar pytorch |
| 23.041 | Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference | methods | EMMIVox, cryo-EM, single-structure refinement, ensemble refinement, Bayesian inference, B-factors, structural ensembles | Samuel Hoff | GROUP EMMIVOX WHOLEMOLECULES PRINT BIASVALUE INCLUDE DISTANCE WRAPAROUND UPPER_WALLS MOLINFO | isdb core bias 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 | GROUP WHOLEMOLECULES METAD PRINT DISTANCES FIT_TO_TEMPLATE CENTER WRAPAROUND POSITION UPPER_WALLS SHADOW MOLINFO | vatom isdb core bias generic multicolvar colvar |
| 23.022 | A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar | methods | collective variables, machine learning, toy model | Enrico Trizio | CUSTOM PYTORCH_MODEL OPES_METAD PRINT UNITS BIASVALUE ENDPLUMED POSITION UPPER_WALLS LOWER_WALLS | bias function generic setup opes colvar pytorch |
| 23.019 | Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors | bio | binding pathway, binding energy, sketch-map, drug development | Raitis Bobrovs | LANDMARK_SELECT_FPS CUSTOM WHOLEMOLECULES METAD PATHMSD SKETCHMAP VORONOI PRINT DISSIMILARITIES VSTACK COLLECT_FRAMES DISTANCE COM SKETCHMAP_PROJECTION UPPER_WALLS TRANSPOSE | vatom dimred valtools bias function generic matrixtools colvar landmarks |
| 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 | RMSD WHOLEMOLECULES METAD HISTOGRAM READ PRINT MATHEVAL REWEIGHT_METAD DUMPGRID DISTANCE CONVERT_TO_FES MOLINFO | bias function generic gridtools colvar |
| 23.003 | Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations | methods | metadynamics, alchemical variable, alchemical free energy calculations | Wei-Tse Hsu | METAD READ PRINT EXTRACV TORSION | 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 | METAD PRINT DISTANCE DISTANCES | multicolvar generic colvar bias |
| 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 | CUSTOM FIXEDATOM GROUP RMSD PYTORCH_MODEL WHOLEMOLECULES OPES_METAD PRINT MATHEVAL FIT_TO_TEMPLATE CENTER DISTANCE UPPER_WALLS COORDINATION LOWER_WALLS COMMITTOR | vatom core bias function generic colvar opes pytorch |
| 21.040 | A structural ensemble of a tau-microtubule complex reveals regulatory tau phosphorylation and acetylation mechanisms | bio | EMMI, CryoEM, tau-microtubules, post-translational modifications, chemical mutagenesis, structural ensemble, Metainference | Faidon Brotzakis | GROUP WHOLEMOLECULES EMMI PRINT BIASVALUE RESTART DISTANCE COM UPPER_WALLS MOLINFO | vatom isdb core bias generic setup colvar |
| 21.035 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, interface | Aaron Finney | FIXEDATOM GROUP PRINT DISTANCE LOAD RESTRAINT | vatom core bias generic setup colvar |
| 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 | ENERGY METAD GYRATION PRINT PBMETAD INCLUDE DISTANCE COM COORDINATION TORSION ALPHABETA | vatom bias generic multicolvar 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 | CUSTOM ENERGY METAD CONSTANT PRINT UNITS BIASVALUE INCLUDE DISTANCE TORSION REWEIGHT_METAD | setup bias function generic 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 | |
| 21.004 | Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy | bio | machine learning, well-tempered metadynamics, path collective variable, potential of mean force, standard binding free energy calculations, host-guest, protein-ligand unbinding | Dorothea Gobbo | WHOLEMOLECULES METAD PATHMSD PRINT RESTART UPPER_WALLS LOWER_WALLS | bias setup colvar generic |
| 21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Kresten Lindorff-Larsen | GROUP WHOLEMOLECULES GYRATION MOLINFO PRINT ALPHARMSD BIASVALUE EEFSOLV CENTER SAXS METAINFERENCE FLUSH PBMETAD | vatom isdb core secondarystructure bias generic 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 | ENVIRONMENTSIMILARITY ENERGY TD_UNIFORM PRINT ECV_MULTITHERMAL_MULTIBARIC OPES_EXPANDED MATHEVAL VES_LINEAR_EXPANSION Q6 RESTART VOLUME BF_LEGENDRE UPPER_WALLS ECV_UMBRELLAS_LINE OPT_AVERAGED_SGD | setup symfunc envsim ves bias function generic opes colvar |
| 20.021 | Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins. | bio | phi-values, restrained MD, transition-state, protein folding, disordered proteins, protein evolution | Cristina Paissoni | WHOLEMOLECULES PRINT STATS COORDINATION RESTRAINT MOLINFO | bias function colvar 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 PRINT UNITS ENDPLUMED MOVINGRESTRAINT | setup generic bias colvar |
| 19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Giovanni Bussi | WHOLEMOLECULES METAD PRINT MATHEVAL SORT INCLUDE DISTANCE COM MAXENT COORDINATION TORSION FLUSH MOLINFO | vatom bias function generic colvar |
| 19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Wei Chen | ANN POSITION COM RESTRAINT COMBINE | vatom bias function annfunc colvar |
| 19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Cristina Paissoni | GROUP WHOLEMOLECULES MOLINFO PRINT MATHEVAL PBMETAD COMBINE INCLUDE ANGLE CENTER BIASVALUE ENSEMBLE ENDPLUMED SAXS STATS COORDINATION ALPHABETA | vatom isdb core bias function generic colvar multicolvar |
| 19.056 | maze | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_LOSS PRINT MAZE_OPTIMIZER_BIAS UNITS POSITION MAZE_SIMULATED_ANNEALING | setup maze colvar 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 | ENERGY METAD PRINT DISTANCE COM UPPER_WALLS | bias vatom generic colvar |
| 19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Davide Provasi | CONTACTMAP RMSD WHOLEMOLECULES METAD PRINT ENDPLUMED DISTANCE FUNCPATHMSD COM | vatom bias function generic colvar |
| 19.035 | Dimerization of GPCRs from coarse-grained umbrella sampling | bio | Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization | Davide Provasi | GROUP PRINT DISTANCE COM TORSION RESTRAINT | vatom core bias generic colvar |
| 19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Matteo Salvalaglio | METAD PRINT DISTANCE CENTER UPPER_WALLS LOWER_WALLS TORSION COMMITTOR | vatom generic colvar bias |