Browse the eggs in PLUMED-NEST
PLUMED-NEST provides all the data needed to reproduce the results of a PLUMED-enhanced molecular dynamics simulation or analysis contained in a published paper. Furthermore, PLUMED-NEST monitors the compatibility of the provided PLUMED input files with the current and development versions of the code and integrates links from these files to the PLUMED manual.
Here is the list of projects already deposited in PLUMED-NEST, while a complete bibliography can be found here.
| plumID | Name | Category | Keywords | Contributor | Actions | Modules |
|---|---|---|---|---|---|---|
| 25.005 | Mechanism of Nanocluster Formation from Machine-Learned Potential-based Simulations | chemistry | WT-metadynamics, metal nanoclusters, nucleation, neural network potential, deepMD | Vikas Tiwari, Tarak Karmakar | RESTRAINT ANGLE PRINT UPPER_WALLS COORDINATIONNUMBER UNITS COM DISTANCE GROUP FLUSH COORDINATION METAD DISTANCES LOWER_WALLS COMBINE FIXEDATOM | symfunc colvar setup vatom multicolvar function generic core 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 | PRINT GROUP BIASVALUE BAIES | core generic bias isdb |
| 25.014 | Atomic resolution ensembles of intrinsically disordered and multi-domain proteins with Alphafold | bio | bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement | Vincent Schnapka | PRINT GROUP BIASVALUE BAIES | core generic bias isdb |
| 25.013 | Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices | bio | umbrella sampling, temperature ramping | Alexander Berlaga | PYTORCH_MODEL RESTRAINT PRINT GYRATION DISTANCE | pytorch colvar generic bias |
| 25.010 | Kinetic rates calculation with Ratchet&Pawl MD | methods | kinetics, ligand binding, ABMD, ratchet&pawl MD | Riccardo Capelli | FLUSH PRINT GROUP WHOLEMOLECULES COM DISTANCE COMMITTOR ABMD | vatom colvar generic core bias |
| 25.002 | M3_PCV-ABMD | chemistry | Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor | Gian Marco Elisi | ENDPLUMED UPPER_WALLS PRINT PATHMSD UNITS ABMD | colvar generic bias setup |
| 25.001 | RNA G-quadruplex folding with ST-metaD protocol | bio | RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | METAD WHOLEMOLECULES MOLINFO ERMSD COMBINE | function colvar generic bias |
| 24.034 | Umbrella sampling of ion in transporter SLC26A7 | bio | umbrella sampling, transporter, ions | Xiaoli Lu | RESTRAINT POSITION PRINT UNITS | colvar generic bias setup |
| 24.027 | Proline cis and trans subensembles of a disordered peptide | bio | intrinsically disordered proteins, proline cis trans isomerisation, metadynamics, collective variables | Alice Pettitt | PBMETAD ENDPLUMED FLUSH TORSION PARABETARMSD PRINT GROUP COORDINATION WHOLEMOLECULES DIHCOR MOLINFO GYRATION DISTANCE INCLUDE ANTIBETARMSD ALPHARMSD COMBINE | function secondarystructure multicolvar colvar generic core bias |
| 24.024 | Host-Guest binding free energies à la carte, an automated OneOPES protocol | bio | OneOPES, ligand binding, binding free energy,SAMPL challenge, host-guest | Valerio Rizzi | ECV_MULTITHERMAL ENERGY ENDPLUMED ANGLE UPPER_WALLS TORSION CENTER PRINT GROUP OPES_METAD_EXPLORE FIT_TO_TEMPLATE MATHEVAL COORDINATION WHOLEMOLECULES FIXEDATOM DISTANCE LOWER_WALLS OPES_EXPANDED | function vatom opes colvar generic core bias |
| 23.038 | Determinants of Neutral Antagonism and Inverse Agonism in the β2-adrenergic receptor | bio | protein coupled receptor, beta-adrenergic, receptor activation, antagonism, inverse agonism, metadynamics | Timothy Clark | METAD PRINT MATHEVAL WHOLEMOLECULES MOLINFO DISTANCE RMSD | function colvar generic bias |
| 23.027 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, DFS, Q3, Pair Entropy | Aaron Finney | LOCAL_Q3 DENSITY DFSCLUSTERING AROUND HISTOGRAM PRINT GROUP RESTRAINT LOAD UNITS FIXEDATOM DUMPGRID Q3 COORDINATIONNUMBER CLUSTER_NATOMS CONTACT_MATRIX LOCAL_AVERAGE CLUSTER_DISTRIBUTION | adjmat vatom volumes generic setup bias clusters core symfunc gridtools |
| 23.025 | Probing ion binding to G-quadruplexes and related events | chemistry | metadynamics, repulsive potential, nucleic acids, G-quadruplexes | Marcelo Poleto | WRAPAROUND METAD UPPER_WALLS FLUSH POSITION GROUP PRINT FIT_TO_TEMPLATE UNITS MATHEVAL WHOLEMOLECULES DISTANCES DISTANCE RESTART LOWER_WALLS DUMPATOMS COM | function vatom multicolvar colvar generic setup core bias |
| 23.024 | Permutationally Invariant Networks for Enhanced Sampling (PINES) | methods | collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent | Nicholas Herringer | PRINT PBMETAD LOAD | generic bias setup |
| 23.017 | How and When Does an Enzyme React? Unraveling α-Amylase Catalytic Activity with Enhanced Sampling Techniques | bio | enzymatic reaction discovery, reaction mechanism, catalysis, ligand-binding modes, water, alpha-amylase, sugar, QM/MM MD, OPES, OPES explore, graph CV, machine learning, Deep TDA CV, path CV | Sudip Das | OPES_METAD UPPER_WALLS PYTORCH_MODEL TORSION CENTER PRINT CUSTOM OPES_METAD_EXPLORE GROUP UNITS COORDINATION FIT_TO_TEMPLATE WHOLEMOLECULES FIXEDATOM DISTANCE LOWER_WALLS PATH | function mapping vatom opes colvar generic setup pytorch core bias |
| 23.014 | Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 | bio | metadynamics, oligomerization, chemokine receptors, GPCR, membrane | Vittorio Limongelli | METAD UPPER_WALLS FLUSH TORSION PRINT WHOLEMOLECULES DISTANCE COM COMBINE | function vatom colvar generic bias |
| 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 | METAD UPPER_WALLS CONSTANT PRINT MATHEVAL WHOLEMOLECULES BIASVALUE DISTANCE LOWER_WALLS | function colvar generic bias |
| 22.044 | Colloid Crystallisation Analyses | materials | Q4, Q6, Pair Entropy, DFS | Aaron Finney | DFSCLUSTERING MFILTER_LESS MFILTER_MORE LOCAL_Q4 GROUP PRINT Q6 Q4 LOCAL_Q6 COORDINATIONNUMBER CLUSTER_NATOMS CONTACT_MATRIX COMBINE LOCAL_AVERAGE | adjmat function multicolvar generic clusters core symfunc |
| 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 | PBMETAD UPPER_WALLS TORSION PRINT GROUP EMMI COORDINATION WHOLEMOLECULES BIASVALUE MOLINFO RMSD RESTART COM | vatom isdb colvar generic setup core bias |
| 22.012 | Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT | bio | contact maps, protein-protein interactions | Isabell-Louise Grothaus | PRINT CONTACTMAP DISTANCE CENTER | colvar generic vatom |
| 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 | OPT_AVERAGED_SGD ENERGY BF_CHEBYSHEV DISTANCE BF_GAUSSIANS BF_WAVELETS BF_LEGENDRE TD_WELLTEMPERED TD_UNIFORM METAD VES_OUTPUT_BASISFUNCTIONS BF_CUBIC_B_SPLINES COORDINATION VES_LINEAR_EXPANSION UPPER_WALLS FLUSH OPT_ADAM PRINT POSITION UNITS INCLUDE | ves colvar generic setup bias |
| 21.043 | Predicting the Conformational Variability of Oncogenic GTP-bound G12D Mutated KRas-4B Proteins at Cell Membranes | chemistry | well-tempered metadynamics, KRas-4B, anionic membrane, conformational variability | Huixia Lu | METAD TORSION PRINT FIT_TO_TEMPLATE FIXEDATOM | colvar generic bias vatom |
| 21.031 | Photo-switchable sulfonulureas in KATP channel | bio | metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels | Katarzyna Walczewska-Szewc | METAD UPPER_WALLS PRINT UNITS WHOLEMOLECULES DISTANCE LOWER_WALLS COM | vatom colvar generic setup bias |
| 21.028 | From Enhanced Sampling to Reaction Profiles | methods | collective variables, multi-state, machine learning, Deep-TDA | Enrico Trizio | ENDPLUMED ANGLE TORSION FIT_TO_TEMPLATE MATHEVAL DISTANCES FIXEDATOM DISTANCE OPES_METAD CENTER COORDINATION LOAD UPPER_WALLS PYTORCH_MODEL PRINT GROUP UNITS WHOLEMOLECULES LOWER_WALLS | function vatom opes multicolvar colvar generic setup pytorch core bias |
| 21.026 | Probing allosteric regulations with coevolution-driven molecular simulations | bio | metadynamics, coevolution, allostery, adenylate cyclase | Francesco Colizzi | METAD UPPER_WALLS PRINT PATHMSD UNITS WHOLEMOLECULES DISTANCE COM | vatom colvar generic setup bias |
| 21.023 | Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling | methods | enhanced sampling, collective variables, machine learning | Jakub Rydzewski | METAD ENERGY CONSTANT TORSION PRINT CUSTOM UNITS BIASVALUE REWEIGHT_METAD DISTANCE INCLUDE | function colvar generic setup bias |
| 21.022 | Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly | materials | parallel bias metadynamics, adsorption, peptide | Xin Qi | ENERGY PBMETAD UPPER_WALLS PRINT MOLINFO GYRATION DISTANCE LOWER_WALLS COM | colvar generic bias vatom |
| 21.019 | Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations | materials | Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen | Matteo Salvalaglio | KDE PRINT MATHEVAL DISTANCE TORSIONS COM | function vatom multicolvar colvar generic gridtools |
| 21.016 | MD SAXS GTPase associated center | bio | metadynamics, RNA, folding, SAXS | Giovanni Bussi | SAXS METAD UPPER_WALLS CUSTOM GROUP PRINT WHOLEMOLECULES INCLUDE MOLINFO GYRATION LOWER_WALLS ERMSD | function isdb colvar generic core bias |
| 21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Adriana Pietropaolo | PBMETAD CONSTANT TORSION PRINT MATHEVAL WHOLEMOLECULES BIASVALUE RESTART | function colvar generic setup bias |
| 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 | RESTRAINT PRINT COORDINATION WHOLEMOLECULES MOLINFO STATS COMBINE | function colvar generic bias |
| 20.018 | Free energy barriers from biased molecular dynamics simulations | methods | kinetics, free energy barriers, chemical reactions, nucleation, metadynamics | Kristof Bal | DENSITY ENERGY Q6 DISTANCE CONTACT_MATRIX REWEIGHT_BIAS LOCAL_AVERAGE PAIRENTROPY CONVERT_TO_FES COMBINE METAD SPRINT CENTER COORDINATION LOAD UPPER_WALLS FLUSH HISTOGRAM PRINT VOLUME UNITS REWEIGHT_METAD DUMPGRID LOWER_WALLS COORDINATIONNUMBER | adjmat function vatom sprint volumes colvar generic setup symfunc bias gridtools |
| 20.013 | Improving accuracy of biased Alchemistic simulations | methods | flying Gaussian method, Alchemistic simulations, thermodynamic integration, reweighting | Vojtech Spiwok | PRINT METAD TORSION | colvar generic bias |
| 20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Jim Pfaendtner | CENTER PRINT GROUP COORDINATION WHOLEMOLECULES DISTANCES DISTANCE RESTART | vatom multicolvar colvar generic setup core |
| 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 ENDPLUMED UPPER_WALLS HISTOGRAM PRINT MATHEVAL READ REWEIGHT_METAD DUMPGRID DISTANCE LOWER_WALLS COM CONVERT_TO_FES COMBINE ABMD | function vatom colvar generic bias gridtools |
| 19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Kim Jelfs | MOVINGRESTRAINT FLUSH PRINT INPLANEDISTANCES DISTANCES RESTART COM | vatom multicolvar generic setup bias |
| 19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Silvio Pipolo | METAD UPPER_WALLS PRINT FUNCPATHMSD PIV LOWER_WALLS CELL | function piv colvar generic bias |
| 19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Elena Papaleo | METAD UPPER_WALLS PRINT GROUP WHOLEMOLECULES MOLINFO GYRATION LOWER_WALLS ALPHABETA | multicolvar colvar generic core bias |
| 19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Riccardo Capelli | WRAPAROUND METAD ENDPLUMED UPPER_WALLS FLUSH HISTOGRAM POSITION GROUP PRINT FIT_TO_TEMPLATE MATHEVAL COORDINATION WHOLEMOLECULES READ REWEIGHT_METAD DUMPGRID COM CONVERT_TO_FES | function vatom colvar generic core bias gridtools |
| 19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Max Bonomi | PRINT EMMI GROUP WHOLEMOLECULES BIASVALUE MOLINFO | core generic bias isdb |
| 19.005 | Cmyc small molecule interaction | bio | metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP | Gabriella Heller | CS2BACKBONE PBMETAD CENTER PRINT GROUP METAINFERENCE COORDINATION WHOLEMOLECULES MOLINFO GYRATION DISTANCE INCLUDE ALPHABETA | vatom multicolvar isdb colvar generic core bias |
| 25.009 | Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water | chemistry | metadynamics, nitrate photolysis | Kam-Tung Chan | RESTART DUMPGRID REWEIGHT_METAD UPPER_WALLS DISTANCE METAD GROUP CUSTOM PRINT HISTOGRAM FLUSH COORDINATION READ | core colvar gridtools setup bias generic function |
| 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 | ZDISTANCES COMMITTOR UPPER_WALLS DISTANCE UNITS FIXEDATOM GROUP CUSTOM PRINT FLUSH COORDINATIONNUMBER OPES_METAD DISTANCES | core colvar setup opes vatom bias generic function multicolvar symfunc |
| 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 | DUMPGRID TORSION DISTANCE GROUP PRINT HISTOGRAM COORDINATION CONVERT_TO_FES ANGLE WHOLEMOLECULES | generic core colvar gridtools |
| 24.020 | Graph Neural Network-State Predictive Information Bottleneck (GNN-SPIB) approach for learning molecular thermodynamics and kinetics | bio | LJ7, alanine, well-tempered metadynamics, infrequent metadynamics, machine learning | Ziyue Zou, Dedi Wang, Pratyush Tiwary | COMMITTOR TORSION METAD GROUP PRINT LOAD | core colvar setup bias generic |
| 24.012 | Molecular simulations to investigate the impact of N6-methylation in RNA recognition | bio | metadynamics, alchemistry, RNA modification, RNA:protein interactions | Giovanni Bussi | DEBUG UPPER_WALLS COM CENTER DISTANCE GHBFIX METAD GROUP BIASVALUE COMBINE PRINT COORDINATION MOLINFO LOWER_WALLS | core colvar vatom bias generic function |
| 24.004 | Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables | materials | metadynamics, nucleation, machine learning | Ziyue Zou | RESTART METAD GROUP PRINT INCLUDE LOAD | generic core bias 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 | ZDISTANCES UPPER_WALLS DISTANCE UNITS FIXEDATOM GROUP PRINT FLUSH COORDINATIONNUMBER OPES_METAD | core colvar setup opes vatom bias generic multicolvar symfunc |
| 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 | UPPER_WALLS DISTANCE EMMIVOX GROUP BIASVALUE WRAPAROUND PRINT INCLUDE MOLINFO WHOLEMOLECULES | core colvar isdb bias generic |
| 23.029 | An accurate and efficient SAXS/SANS implementation including solvation layer effects suitable for restrained Molecular Dynamics simulations | bio | SAXS, SANS, SAS, metainference, proteins, nucleic-acid | Federico Ballabio | UPPER_WALLS CENTER DISTANCE SAXS ENSEMBLE BIASVALUE GROUP WRAPAROUND PRINT MOLINFO STATS RMSD | core colvar isdb vatom bias generic function |
| 23.015 | MPCs aggregation | bio | opes_explore, dimerization, MPCs, self-assembly | Vikas Tiwari | UPPER_WALLS CENTER DISTANCE COM METAD GROUP CUSTOM PRINT COORDINATION LOWER_WALLS OPES_METAD_EXPLORE WHOLEMOLECULES | core colvar opes vatom bias generic function |
| 22.037 | Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site | chemistry | metadynamics, DNA, abasic | Mike Jones | PRINT DISTANCES DISTANCE METAD | generic bias colvar multicolvar |
| 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 | UPPER_WALLS COMMITTOR METAD CUSTOM PRINT MATHEVAL DRMSD LOWER_WALLS CELL | generic function colvar bias |
| 22.015 | Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome | bio | photodynamics, bacteriophytochrome, variationally enhanced sampling | Jakub Rydzewski | TORSION OPT_AVERAGED_SGD TD_UNIFORM PRINT VES_LINEAR_EXPANSION BF_FOURIER | ves generic colvar |
| 21.046 | Ubiquitin Interacting Motifs, Duality Between Structured and Disordered Motifs | bio | wt metadynamics, ubiquitin, ataxin-3, short linear motifs, ubiquitin binding motif, moonlight functions, intrinsic disorder | Elena Papaleo | UPPER_WALLS METAD GROUP PRINT ENDPLUMED GYRATION ALPHABETA LOWER_WALLS WHOLEMOLECULES | core colvar bias generic multicolvar |
| 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 | RESTART UPPER_WALLS COM DISTANCE GROUP BIASVALUE PRINT EMMI MOLINFO WHOLEMOLECULES | core colvar setup isdb vatom bias generic |
| 21.027 | EGFR activating mutations mechanism | bio | metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA | Francesco Gervasio | UPPER_WALLS DISTANCE METAD CONTACTMAP ALPHARMSD PRINT INCLUDE MATHEVAL MOLINFO ENERGY LOWER_WALLS WHOLEMOLECULES | secondarystructure colvar bias generic function |
| 21.007 | Sampling enhancement by metadynamics driven by machine learning and de novo protein modelling | bio | metadynamics, machine learning, protein folding | Vojtech Spiwok | ALPHARMSD COMBINE MATHEVAL FIT_TO_TEMPLATE MOLINFO POSITION WHOLEMOLECULES | generic function secondarystructure colvar |
| 20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Carlo Camilloni | CENTER DISTANCE TORSION PBMETAD SAXS ENSEMBLE METAINFERENCE ALPHABETA PRINT FLUSH GYRATION MOLINFO STATS WHOLEMOLECULES | colvar isdb vatom bias generic function multicolvar |
| 20.006 | Class B GPCR activation mechanism | bio | metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | UPPER_WALLS CENTER DISTANCE METAD COMBINE PRINT MATHEVAL ENERGY MOLINFO LOWER_WALLS RMSD WHOLEMOLECULES | colvar vatom bias generic function |
| 19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Wei Chen | RESTRAINT COM COMBINE ANN POSITION | colvar vatom bias annfunc function |
| 19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Kim E. Jelfs | RESTART UPPER_WALLS CENTER COM DISTANCE METAD GROUP PRINT LOWER_WALLS | core colvar setup vatom bias generic |
| 19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | UPPER_WALLS DISTANCE METAD UNITS COMBINE PRINT FLUSH ENERGY | colvar setup bias generic function |
| 19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Michele Invernizzi | RESTART TORSION METAD UNITS PRINT ENDPLUMED VES_DELTA_F ENERGY LOAD POSITION | colvar setup bias generic ves |
| 25.000 | Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer | bio | metadynamics, pathCV | Sahithya Sridharan Iyer | METAD UPPER_WALLS COM MOLINFO RESTART PRINT WHOLEMOLECULES DISTANCE GROUP FUNCPATHGENERAL | bias colvar core setup generic function vatom |
| 24.028 | All-atom simulations of RNA-membrane interactions | bio | metadynamics, membrane, RNA | Giovanni Bussi | GYRATION DISTANCES GHOST METAD COMBINE UPPER_WALLS LOWER_WALLS MATHEVAL MOLINFO SORT PUCKERING PRINT WHOLEMOLECULES DISTANCE GROUP POSITION CENTER | bias colvar multicolvar core function generic vatom |
| 24.014 | Learning Collective Variables with Synthetic Data Augmentation through Physics-inspired Geodesic Interpolation | methods | data augmentation, geodesic interpolation, collective variables, protein folding | Juno Nam | METAD UPPER_WALLS COORDINATION LOWER_WALLS DRR FLUSH MOLINFO PRINT WHOLEMOLECULES PYTORCH_MODEL RMSD | bias drr colvar pytorch generic |
| 23.019 | Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors | bio | binding pathway, binding energy, sketch-map, drug development | Raitis Bobrovs | METAD DISTANCE TRANSPOSE UPPER_WALLS CUSTOM COM COLLECT_FRAMES VSTACK VORONOI SKETCHMAP PRINT WHOLEMOLECULES DISSIMILARITIES PATHMSD SKETCHMAP_PROJECTION LANDMARK_SELECT_FPS | bias colvar valtools function matrixtools generic dimred vatom landmarks |
| 23.004 | Melting curves of ice polymorphs in the vicinity of the liquid-liquid critical point | chemistry | water, liquid-liquid transition, second critical point, ice, polymorphs, melting curves, environment similarity, opes, density-functional theory, scan, machine learning potential | Pablo Piaggi | DUMPGRID UPPER_WALLS ENVIRONMENTSIMILARITY HISTOGRAM ECV_UMBRELLAS_LINE OPES_EXPANDED LOWER_WALLS RESTART PRINT | bias gridtools setup generic envsim opes |
| 22.024 | Conformational Entropy as a Potential Liability of Computationally Designed Antibodies | bio | metadynamics, conformational entropy, antibody, nanobody | Thomas Löhr | PBMETAD ALPHABETA ANTIBETARMSD COM MOLINFO RESTART PRINT WHOLEMOLECULES ALPHARMSD TORSION | bias colvar multicolvar setup generic vatom secondarystructure |
| 22.013 | Ligand dissociation from PreQ1 riboswitch | bio | ligand, RNA, metadynamics, pRAVE | Yihang Wang | COMMITTOR METAD DISTANCE COORDINATIONNUMBER COMBINE COM MOLINFO PRINT WHOLEMOLECULES RMSD | bias colvar function generic symfunc vatom |
| 21.037 | Molecular Dynamics simulations of RBD/hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain | Max Bonomi | PRINT DISTANCE RMSD | generic colvar |
| 21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Tarsis Ferreira | METAD RANDOM_EXCHANGES REWEIGHT_METAD DUMPGRID UPPER_WALLS COORDINATION HISTOGRAM LOWER_WALLS ENERGY MOLINFO PUCKERING PRINT INCLUDE DISTANCE GROUP WHOLEMOLECULES | bias colvar core gridtools generic |
| 20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Vojtech Spiwok | PRINT METAD TORSION | bias generic colvar |
| 20.003 | Enhanced sampling of transition states | methods | Variationally Enhanced Sampling, Target distribution, Transition state, Enhanced Sampling, Nucleation, chemical reaction | Jayashrita Debnath | LOAD OPT_AVERAGED_SGD UNITS ENERGY VES_LINEAR_EXPANSION BF_LEGENDRE PRINT POSITION | ves setup colvar generic |
| 19.055 | Flying Gaussian method | methods | flying Gaussians, alanine dipeptide, peptide bond, Met-enkephalin | Vojtech Spiwok | METAD COMBINE MATHEVAL PRINT DISTANCE TORSION | bias function colvar generic |
| 19.049 | Determining the sizes of solid/liquid clusters in MD trajectories of nucleation | methods | nucleation, metadynamics, clustering, Steinhardt order parameters | Gareth Tribello | DISTANCES METAD COORDINATIONNUMBER Q6 MATRIX_VECTOR_PRODUCT OUTER_PRODUCT ONES CUSTOM DFSCLUSTERING CONTACT_MATRIX CLUSTER_DISTRIBUTION MORE_THAN OUTPUT_CLUSTER CLUSTER_NATOMS CLUSTER_PROPERTIES SMAC PRINT LOCAL_Q6 | bias clusters multicolvar adjmat generic matrixtools symfunc function |
| 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 | DISTANCES ALPHABETA METAD REWEIGHT_METAD COMBINE UPPER_WALLS RMSD COM LOWER_WALLS BRIDGE MOLINFO PRINT WHOLEMOLECULES DISTANCE GROUP TORSION FUNNEL | bias colvar multicolvar adjmat core function generic vatom funnel |
| 19.044 | Multithermal-multibaric simulations using VES | methods | ves, Wang Landau, multicanonical, water, density anomaly | Pablo Piaggi | DUMPGRID CONVERT_TO_FES COMBINE HISTOGRAM AVERAGE REWEIGHT_BIAS BF_LEGENDRE OPT_AVERAGED_SGD READ TD_MULTITHERMAL_MULTIBARIC ENERGY REWEIGHT_TEMP_PRESS VOLUME PRINT RESTART VES_LINEAR_EXPANSION OPT_DUMMY | bias colvar gridtools ves setup function generic |
| 19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | DISTANCES METAD COMBINE UPPER_WALLS UNITS FLUSH RESTART PRINT DISTANCE | bias colvar multicolvar setup function generic |
| 19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Pratyush Tiwary | COMMITTOR ALPHABETA COMBINE EXTERNAL COM RESTART PRINT WHOLEMOLECULES DISTANCE TORSION | bias colvar multicolvar setup function generic vatom |
| 19.004 | MI Ubiquitin | bio | metainference, NMR | Max Bonomi | METAINFERENCE RDC MOLINFO CS2BACKBONE PRINT WHOLEMOLECULES GROUP | isdb generic core |
| 25.008 | Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting | methods | metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting | Dhiman Ray | DISTANCE ENDPLUMED PRINT METAD CUSTOM RMSD PYTORCH_MODEL LOWER_WALLS OPES_METAD ENERGY WHOLEMOLECULES MOLINFO GROUP TORSION UNITS UPPER_WALLS POSITION BIASVALUE | opes core bias colvar generic setup function pytorch |
| 24.011 | Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble | methods | committor, machine learning | Peilin Kang | COORDINATION ENDPLUMED CUSTOM GROUP ENERGY UNITS TORSION BIASVALUE PRINT LOWER_WALLS CELL UPPER_WALLS RMSD LOAD INCLUDE MOLINFO POSITION DISTANCE MATHEVAL WHOLEMOLECULES | core bias colvar generic setup function |
| 24.007 | SWISH-X | bio | swish-x, SWISH-X, swish, expanded SWISH | Alberto Borsatto | PRINT ECV_MULTITHERMAL INCLUDE CONTACTMAP WHOLEMOLECULES ENERGY MOLINFO UPPER_WALLS OPES_EXPANDED | bias colvar opes generic |
| 24.001 | A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations | bio | OPES, OPES-Flooding, QM/MM, Kinetics, Enzyme Catalysis | Dhiman Ray | DISTANCE PRINT CUSTOM COMBINE COMMITTOR LOWER_WALLS OPES_METAD UNITS UPPER_WALLS TORSION FLUSH | opes bias colvar generic setup function |
| 23.031 | Identifying small molecules binding sites in RNA conformational ensembles with SHAMAN | bio | RNA, metadynamics, probes, mixed-solvent MD, small molecules, binding sites | Max Bonomi | METAD PRINT DISTANCES SHADOW GROUP WHOLEMOLECULES WRAPAROUND MOLINFO UPPER_WALLS FIT_TO_TEMPLATE CENTER POSITION | multicolvar core bias colvar generic isdb vatom |
| 23.007 | Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains | bio | metadynamics, peptoids, parallel-bias metadynamics | Jim Pfaendtner | GYRATION COORDINATION PBMETAD PRINT RESTRAINT INCLUDE COM WHOLEMOLECULES TORSION | vatom bias colvar generic |
| 23.006 | Transcription factor unbinding | bio | metadynamics, DNA, conformational changes | Malin Lüking | DISTANCE METAD PRINT COM CONTACTMAP DUMPFORCES ALPHARMSD MOLINFO ANGLE | bias colvar generic secondarystructure vatom |
| 23.003 | Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations | methods | metadynamics, alchemical variable, alchemical free energy calculations | Wei-Tse Hsu | METAD PRINT READ TORSION EXTRACV | bias colvar generic |
| 23.002 | Critical comparison of general-purpose collective variables for crystal nucleation | methods | metadynamics, umbrella sampling, commitor, entropy, PIV | Julien Lam | METAD PRINT CUSTOM RESTRAINT LOCAL_AVERAGE Q4 VOLUME ENERGY PIV Q6 UNITS UPPER_WALLS FUNCPATHMSD PAIRENTROPY | gridtools symfunc bias colvar generic piv setup function |
| 22.030 | Mixing physics across temperatures with generative artificial intelligence | methods | REMD, Generative AI, DDPM | Yihang Wang | WHOLEMOLECULES PRINT TORSION | colvar generic |
| 21.041 | Nucleating a Different Coordination in a Crystal under Pressure. A Study of the B1−B2 Transition in NaCl by Metadynamics | methods | metadynamics, structural phase transitions, pressure-induced phase transition, martensitic transitions | Matej Badin | METAD COORDINATION PRINT CUSTOM COMBINE ENDPLUMED VOLUME | function bias colvar generic |
| 21.035 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, interface | Aaron Finney | DISTANCE PRINT RESTRAINT LOAD GROUP FIXEDATOM | core bias colvar generic setup vatom |
| 21.034 | Efficient sampling of high-dimensional free energy landscapes using adaptive reinforced dynamics | bio | reinforced dynamics, bias-exchange metadynamics, parallel-bias metadynamics | Dongdong Wang | METAD ENDPLUMED PRINT PBMETAD INCLUDE RANDOM_EXCHANGES TORSION | bias colvar generic |
| 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 | DISTANCE COORDINATION ALPHABETA GYRATION METAD PBMETAD PRINT INCLUDE COM ENERGY TORSION | multicolvar bias colvar generic vatom |
| 21.024 | Property map collective variable as a useful tool for force field correction | chemistry | molecular mechanics | Vojtech Spiwok | METAD PRINT WHOLEMOLECULES PROPERTYMAP TORSION BIASVALUE | bias colvar generic |
| 21.020 | Reweighted Jarzynski sampling | methods | free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions | Kristof Bal | CUSTOM CONVERT_TO_FES ANN UNITS CONSTANT FLUSH BIASVALUE PRINT COMBINE REWEIGHT_BIAS TD_WELLTEMPERED UPPER_WALLS RESTRAINT LOAD MOVINGRESTRAINT VES_LINEAR_EXPANSION DUMPGRID COORDINATIONNUMBER HISTOGRAM BF_CHEBYSHEV DISTANCE METAD OPES_METAD OPT_AVERAGED_SGD REWEIGHT_METAD | opes gridtools bias symfunc colvar generic setup ves function annfunc |
| 21.017 | All-atom simulations of the Vav1 AD construct | bio | metadynamics, parallel-bias, well-tempered | Simone Orioli | METAD PBMETAD ALPHABETA PRINT RESTART REWEIGHT_BIAS CONTACTMAP GROUP WHOLEMOLECULES ALPHARMSD MOLINFO | multicolvar core bias colvar generic setup secondarystructure |
| 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 | ECV_UMBRELLAS_LINE PRINT RESTART BF_LEGENDRE VES_LINEAR_EXPANSION MATHEVAL VOLUME ENERGY OPT_AVERAGED_SGD Q6 TD_UNIFORM ECV_MULTITHERMAL_MULTIBARIC UPPER_WALLS ENVIRONMENTSIMILARITY OPES_EXPANDED | opes symfunc bias colvar generic envsim setup ves function |
| 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 | DISTANCE PRINT RESTART MOLINFO TORSION CENTER ERMSD ABMD | bias colvar generic setup vatom |
| 20.027 | Allosteric Regulation of SARS-CoV-2 Protease. Towards Informed Structure-Based Drug Discovery | bio | SARS-CoV2, MPro, Covid-19, Molecular Dynamics, Metadynamics, Computer-Aided Drug Discovery | Khaled Abdel-Maksoud | METAD PRINT TORSION DISTANCE | bias colvar generic |
| 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 | METAD PRINT RESTART GROUP WHOLEMOLECULES PATHMSD MOLINFO UPPER_WALLS | core bias colvar generic setup |
| 19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Valerio Rizzi | METAD ENDPLUMED PRINT COMBINE RESTART EXTERNAL GROUP COORDINATIONNUMBER UNITS FLUSH | core bias symfunc generic setup function |
| 19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | DISTANCE GYRATION PRINT METAD COM ENERGY MOLINFO UPPER_WALLS | vatom bias colvar generic |
| 19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Sandro Bottaro | DISTANCE METAD PRINT RMSD WHOLEMOLECULES MOLINFO TORSION ERMSD | bias colvar generic |
| 19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Jakub Rydzewski | METAD PRINT RESTART LOWER_WALLS PATHMSD UNITS UPPER_WALLS | setup bias colvar generic |
| 19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | GiovanniMaria Piccini | DISTANCE METAD PRINT COMBINE LOWER_WALLS ENERGY UNITS UPPER_WALLS FLUSH | bias colvar generic setup function |
| 19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Gabriele Cesare Sosso | ENDPLUMED CLUSTER_NATOMS CONTACT_MATRIX COMMITTOR Q6 DFSCLUSTERING CLUSTER_WITHSURFACE MFILTER_MORE FLUSH LOCAL_Q6 OUTPUT_CLUSTER | multicolvar symfunc generic clusters adjmat |
| 19.025 | Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide | bio | metainference, NMR, protein dynamics, force-fields | Carlo Camilloni | GYRATION PBMETAD PRINT METAINFERENCE CS2BACKBONE STATS ENDPLUMED JCOUPLING WHOLEMOLECULES ENSEMBLE RDC MOLINFO TORSION FLUSH BIASVALUE | bias colvar generic isdb function |
| 19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Adriana Pietropaolo | METAD PRINT MATHEVAL WHOLEMOLECULES TORSION CONSTANT BIASVALUE | function bias colvar generic |
| 19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Matteo Salvalaglio | METAD ENDPLUMED PRINT GYRATION RESTART DISTANCES COORDINATIONNUMBER | multicolvar bias symfunc colvar generic setup |
| 19.011 | Automatic Gradient Computation for Collective Variables | other | gradient, differentiation, curvature | Toni Giorgino | ENDPLUMED | generic |
| 19.003 | EMMI ClpP | bio | metainference, cryo-EM | Max Bonomi | PRINT EMMI GROUP MOLINFO BIASVALUE | isdb core bias generic |
| 19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Giovanni Bussi | DISTANCE METAD PRINT COMBINE INCLUDE DISTANCES RANDOM_EXCHANGES LOWER_WALLS MOLINFO UPPER_WALLS ANGLE ERMSD FLUSH | multicolvar bias colvar generic function |
| 25.011 | Chiral perovskite nucleation | chemistry | metadynamics, chiral perovskites, nucleation | Adriana Pietropaolo | LOWER_WALLS UNITS DISTANCE PBMETAD MULTI_RMSD RESTART MATHEVAL UPPER_WALLS PRINT | setup bias colvar function generic |
| 25.007 | Shaping the glycan landscape. Hidden relationships between linkage and ring distortion induced by carbohydrate-active enzmyes | bio | REST-RECT, REST2, glycan, enzyme, CAZyme, steered | Isabell Grothaus | METAD TORSION DISTANCE MOVINGRESTRAINT MOLINFO PUCKERING RESTRAINT RESTART PRINT | colvar generic setup bias |
| 24.029 | Combination of OPES and OPES-Explore | methods | OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin | Dhiman Ray | INCLUDE GROUP UPPER_WALLS POSITION CONTACTMAP OPES_METAD CENTER CUSTOM FIXEDATOM ENDPLUMED PRINT METAD DISTANCE COMBINE MOLINFO MATHEVAL RMSD BIASVALUE FIT_TO_TEMPLATE LOWER_WALLS UNITS COORDINATION FLUSH ENERGY WHOLEMOLECULES PYTORCH_MODEL OPES_METAD_EXPLORE | setup opes bias colvar function generic core pytorch vatom |
| 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 | TORSION DISTANCE COMBINE OPES_METAD_EXPLORE COORDINATION OPES_EXPANDED RESTART ENERGY CUSTOM ECV_MULTITHERMAL GROUP PRINT | setup opes colvar function generic core |
| 24.018 | A new route to the prebiotic synthesis of glycine via ab initio-based machine learning calculations | chemistry | prebiotic chemistry, glycine, Strecker synthesis, ab initio calculations, machine learning | Léon HUET | DISTANCE PRINT | colvar generic |
| 24.016 | Cryo-EM guided simulations of ribozyme | bio | metainference, cryo-EM | Giovanni Bussi | EMMIVOX ERMSD MOLINFO RESTRAINT WHOLEMOLECULES INCLUDE GROUP BIASVALUE PRINT | bias colvar isdb generic core |
| 24.002 | Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes | chemistry | metadynamics, ligand design, solvent extraction | Xiaoyu Wang | METAD TORSION UNITS RESTART PRINT | colvar generic setup bias |
| 23.040 | Supramolecular capsules assembly dynamics | chemistry | Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics | Riccardo Capelli | METAD UNITS DISTANCE POSITION CENTER DISTANCES FLUSH COM WHOLEMOLECULES CUSTOM GROUP PRINT | setup bias colvar multicolvar function generic core vatom |
| 23.039 | Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation | chemistry | metadynamics, ligand dissociation | Eric Beyerle | METAD DISTANCE COMBINE MOLINFO CENTER RESTRAINT FIXEDATOM UPPER_WALLS DUMPMASSCHARGE PRINT | bias colvar function generic vatom |
| 23.037 | Estimating binding free energy of solid binding peptides without extensive sampling | bio | metadynamics, solid binding peptides | Xin Qi | LOWER_WALLS GYRATION DISTANCE MOLINFO PBMETAD COM UPPER_WALLS PRINT | colvar generic bias vatom |
| 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 | GROUP UPPER_WALLS POSITION CENTER COMMITTOR OPES_METAD WRAPAROUND CUSTOM ENDPLUMED PRINT TORSION DISTANCE MOLINFO MATHEVAL COM BIASVALUE FIT_TO_TEMPLATE LOWER_WALLS UNITS COORDINATION FLUSH ENERGY WHOLEMOLECULES OPES_METAD_EXPLORE | setup opes bias colvar function generic core vatom |
| 23.020 | FEP simulations of ATOX1 homodimer | chemistry | parallel bias metadynamics, FEP, free-energy of metal ion dissociation | Adriana Pietropaolo | DISTANCE CONSTANT PBMETAD ANGLE MATHEVAL WHOLEMOLECULES BIASVALUE PRINT | colvar generic function bias |
| 23.018 | Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention | materials | metadynamics, surface binding, peptide adsorption | Kaylyn Torkelson | GYRATION DISTANCE PBMETAD COM UPPER_WALLS PRINT | colvar generic bias vatom |
| 22.045 | Binding mode and mechanism of enzymatic polyethylene terephthalate degradation | bio | metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation | Francesco Colizzi | METAD LOWER_WALLS DISTANCE MOVINGRESTRAINT ANGLE WHOLEMOLECULES COM UPPER_WALLS PRINT | colvar generic bias vatom |
| 22.043 | Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES | bio | OPES, RNA, Tetraloop, Folding | Gül Zerze | ECV_UMBRELLAS_LINE CONTACTMAP OPES_EXPANDED ENERGY WHOLEMOLECULES ECV_MULTITHERMAL PRINT | colvar generic opes |
| 22.042 | Metadynamics of NSP10 and variants | bio | metadynamics, NSP10, crystal structure, variants | Shozeb Haider | METAD TORSION PRINT | colvar generic bias |
| 22.031 | Rare Event Kinetics from Adaptive Bias Enhanced Sampling | methods | OPES Flooding, Kinetics, Rate, OPES, Machine Learning | Dhiman Ray | INCLUDE GROUP CONSTANT POSITION CONTACTMAP OPES_METAD COMMITTOR CUSTOM ENDPLUMED PRINT TORSION DISTANCE COMBINE MOLINFO RMSD BIASVALUE UNITS ENERGY WHOLEMOLECULES PYTORCH_MODEL | setup opes bias colvar function generic core pytorch |
| 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 |
| 22.025 | Bubble nucleation rate predictions in a Lennard-Jones fluid | materials | free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation | Kristof Bal | UNITS MOVINGRESTRAINT COORDINATIONNUMBER DUMPGRID LOAD ANN REWEIGHT_BIAS COMMITTOR FLUSH RESTRAINT VOLUME CUSTOM BIASVALUE PRINT CONVERT_TO_FES UPPER_WALLS HISTOGRAM | setup symfunc bias colvar function generic annfunc gridtools |
| 22.020 | Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix–Junction–Helix RNA | bio | RNA force field, Helix-Junction-Helix RNA, SAXS, Well tempered metadynamics | Weiwei He | METAD TORSION DISTANCE WHOLEMOLECULES COM GROUP PRINT | bias colvar generic core vatom |
| 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 | LOWER_WALLS DISTANCE CENTER COORDINATION OPES_METAD CUSTOM COMMITTOR MATHEVAL RMSD WHOLEMOLECULES GROUP FIXEDATOM PYTORCH_MODEL UPPER_WALLS FIT_TO_TEMPLATE PRINT | opes bias colvar function generic core pytorch vatom |
| 22.006 | Peptide framework for screening the effects of amino acids on assembly | bio | metadynamics, peptides | Andrew White | GYRATION METAD COMBINE DUMPGRID REWEIGHT_BIAS DISTANCES INCLUDE CONVERT_TO_FES COM PRINT GROUP HISTOGRAM | bias core colvar multicolvar function generic gridtools vatom |
| 22.002 | GAMBES_SAMPL5_RATES | other | GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding | Jayashrita Debnath | DISTANCE LOAD PYTORCH_MODEL COORDINATION CENTER FLUSH COMMITTOR ANGLE MATHEVAL ENERGY WHOLEMOLECULES GROUP FIXEDATOM ENDPLUMED UPPER_WALLS FIT_TO_TEMPLATE PRINT | setup bias core colvar function generic pytorch vatom |
| 21.047 | Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations | materials | pair entropy, metadynamics, ves, solids, crystallization | Pablo Piaggi | METAD COMBINE PAIRENTROPY OPT_AVERAGED_SGD LOAD BF_LEGENDRE VES_LINEAR_EXPANSION RESTART ENERGY VOLUME TD_WELLTEMPERED PRINT | setup ves bias colvar function generic gridtools |
| 21.042 | Peptoid-mediated Au nanocrystal growth | materials | parallel-bias metadynamics, peptoid, Au | Xin Qi | GYRATION DISTANCE MOLINFO PBMETAD COM UPPER_WALLS PRINT | colvar generic bias vatom |
| 21.021 | ATLAS | methods | Machine Learning, Metadynamics | Federico Giberti | METAD TORSION UNITS DISTANCE COORDINATIONNUMBER GYRATION COORDINATION MATHEVAL DUMPATOMS WHOLEMOLECULES GROUP BIASVALUE PRINT | setup symfunc bias colvar function generic core |
| 21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Kresten Lindorff-Larsen | GYRATION MOLINFO EEFSOLV CENTER PBMETAD METAINFERENCE FLUSH ALPHARMSD SAXS WHOLEMOLECULES GROUP BIASVALUE PRINT | bias colvar isdb generic secondarystructure core vatom |
| 21.000 | Uremic toxin time scale dynamics | bio | uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs) | Jim Pfaendtner | DISTANCE COM WHOLEMOLECULES GROUP PRINT | colvar generic core vatom |
| 20.024 | Gaussian Mixture Based Enhanced Sampling (GAMBES) | methods | enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias | Jayashrita Debnath | LOWER_WALLS TORSION UNITS DISTANCE COMBINE LOAD DISTANCES ENERGY GROUP UPPER_WALLS PRINT | setup bias colvar multicolvar function generic core |
| 20.021 | Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins. | bio | phi-values, restrained MD, transition-state, protein folding, disordered proteins, protein evolution | Cristina Paissoni | STATS MOLINFO COORDINATION RESTRAINT WHOLEMOLECULES PRINT | colvar generic function bias |
| 20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Glen Hocky | GYRATION UNITS DISTANCE FISST RESTRAINT ENERGY MATHEVAL GROUP BIASVALUE PRINT | setup bias colvar function fisst generic core |
| 19.075 | PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python | other | Python, automatic differentiation | Toni Giorgino | TORSION DISTANCE COMBINE DUMPDERIVATIVES CENTER RESTRAINT ANGLE CUSTOM ENDPLUMED GROUP PRINT | bias colvar function generic core vatom |
| 19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Jim Pfaendtner | GYRATION METAD ENERGY WHOLEMOLECULES PRINT | colvar generic bias |
| 19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Gareth Tribello | METAD UNITS ENDPLUMED CELL UPPER_WALLS FCCUBIC PRINT | setup symfunc bias colvar generic |
| 19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Vittorio Limongelli | METAD LOWER_WALLS DISTANCE FUNNEL_PS RMSD WHOLEMOLECULES COM UPPER_WALLS FUNNEL PRINT | bias colvar funnel generic vatom |
| 19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Glen Hocky | TORSION DISTANCE COMBINE RESTRAINT EDS PRINT | bias colvar function generic eds |
| 19.013 | RNA FF FITTING | methods | force field, RNA | Giovanni Bussi | TORSION CONSTANT MOLINFO PUCKERING MATHEVAL INCLUDE BIASVALUE | colvar generic function bias |
| 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 | DISTANCE PATH UPPER_WALLS COORDINATION LOWER_WALLS CUSTOM TORSION FIXEDATOM FIT_TO_TEMPLATE WHOLEMOLECULES OPES_METAD PRINT RESTART CENTER GROUP PYTORCH_MODEL | vatom generic pytorch colvar core function setup mapping opes bias |
| 24.021 | Ab initio machine learning simulation of calcium carbonate from aqueous solutions to the solid state | chemistry | ion pairing, caco3, opes, proton transfer, crystallization | Pablo Piaggi | UPPER_WALLS COORDINATION ENERGY PRINT OPES_METAD DISTANCE | colvar generic opes bias |
| 24.006 | Water vapor condensation | chemistry | metadynamics, homogeneous condensation, chemical potential | Shenghui Zhong | UPPER_WALLS CLUSTER_PROPERTIES CONTACT_MATRIX UNITS PRINT COORDINATIONNUMBER DFSCLUSTERING CLUSTER_NATOMS METAD | generic clusters symfunc bias setup adjmat |
| 24.003 | Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations | chemistry | steered molecular dynamics, foldamers, peptoids, bio-inspired | Kaylyn Torkelson | GYRATION COORDINATION MOVINGRESTRAINT TORSION WHOLEMOLECULES PRINT ALPHABETA COM INCLUDE DISTANCE | vatom generic colvar multicolvar bias |
| 23.046 | Lasso Peptides - HLDA CV | bio | metadynamics, protein folding, HLDA, harmonic | Gabriel da Hora | METAD WHOLEMOLECULES PRINT DISTANCE COMBINE UNITS | generic colvar function setup bias |
| 23.045 | Minute-timescale simulations of G Protein Coupled Receptor A2A activation mechanism reveal a receptor pseudo-active state | bio | Path CVs Metadynamics, GPCRs activation transition | Vittorio Limongelli | UPPER_WALLS LOWER_WALLS PATHMSD FUNCPATHMSD ALPHARMSD CONTACTMAP MOLINFO PRINT INCLUDE DISTANCE METAD | generic colvar secondarystructure function bias |
| 23.026 | Machine Learning Nucleation Collective Variables with Graph Neural Networks | chemistry | Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks | Florian Dietrich | LOWER_WALLS LOCAL_Q6 Q6 MFILTER_MORE MOVINGRESTRAINT PRINT COORDINATIONNUMBER GROUP COMBINE METAD | generic symfunc core function multicolvar bias |
| 23.016 | Activation/deactivation free-energy profiles for the β2-adrenergic receptor: Ligand modes of action | bio | G protein coupled receptor, beta-adrenergic, receptor activation, partial agonism, metadynamics | Timothy Clark | RMSD MATHEVAL READ REWEIGHT_METAD WHOLEMOLECULES HISTOGRAM PRINT MOLINFO DUMPGRID CONVERT_TO_FES DISTANCE METAD | generic colvar function gridtools bias |
| 22.041 | Skipping the Replica Exchange Ladder with Normalizing Flows | methods | OPES, alanine, normalizing flows, replica exchange | Michele Invernizzi | ENERGY TORSION ECV_MULTITHERMAL OPES_EXPANDED PRINT OPES_METAD POSITION ENDPLUMED UNITS | colvar opes setup generic |
| 22.040 | From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure | bio | SARS-CoV-2, Spike, Omicron | Miłosz Wieczór | PCAVARS UPPER_WALLS LOWER_WALLS WHOLEMOLECULES PRINT METAD | mapping generic bias |
| 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 LOWER_WALLS PATHMSD WHOLEMOLECULES FUNNEL_PS FUNNEL PRINT COM DISTANCE METAD | vatom generic colvar funnel bias |
| 22.018 | Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations | bio | ligand binding, docking, EMMI, LAT1 | Max Bonomi | EMMIVOX BIASVALUE LOAD WHOLEMOLECULES PRINT MOLINFO GROUP | generic isdb core setup bias |
| 22.008 | Ab initio metadynamics determination of temperature-dependent free-energy landscape in ultrasmall silver clusters | materials | Well tempered metadynamics, ab-initio, ase | Daniel Sucerquia | FLUSH GYRATION UPPER_WALLS COORDINATION LOWER_WALLS UNITS COORDINATIONNUMBER COM DISTANCE COMBINE METAD | vatom generic colvar symfunc function setup bias |
| 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 | FLUSH UPPER_WALLS COORDINATION TORSION ANGLE WHOLEMOLECULES ALPHARMSD PRINT ALPHABETA MOLINFO DISTANCE METAD | generic colvar secondarystructure multicolvar bias |
| 22.005 | Collective Variable for Metadynamics Derived from AlphaFold Output | bio | AlphaFold, protein folding, protein structure prediction, metadynamics, deep learning, free energy simulation, collective variable | Vojtech Spiwok | WHOLEMOLECULES LOAD PRINT METAD | setup generic bias |
| 22.004 | Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques | chemistry | reaction discovery, OPES, collective variables | Umberto Raucci | PYTORCH_MODEL UPPER_WALLS OPES_METAD_EXPLORE COORDINATION LOWER_WALLS MATHEVAL LOAD CUSTOM PRINT OPES_METAD COM GROUP DISTANCE UNITS | vatom generic pytorch colvar core function setup opes bias |
| 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 | UPPER_WALLS LOWER_WALLS CUSTOM TORSION UNITS PRINT COM DISTANCE METAD | vatom generic colvar function setup bias |
| 21.045 | QM/MM metadynamics of thiol-disulfide exchange between methylthiolate and dimethyldisulfide in water with an imposed external electrostatic potential (ESP) | chemistry | metadynamics, QM/MM, electrostatic potential, thiol-disulfide exchange | Denis Maag | UPPER_WALLS COORDINATION LOWER_WALLS PRINT COORDINATIONNUMBER DISTANCE COMBINE METAD | generic colvar symfunc function bias |
| 21.036 | Modelling the structure and interactions of intrinsically disordered peptides with multiple-replica, metadynamics-based sampling methods and force-field combinations | bio | Bias Exchange Metadynamics, PTWTE-metaD | Matteo Salvalaglio | GYRATION UPPER_WALLS COORDINATION RANDOM_EXCHANGES LOWER_WALLS DIHCOR ENERGY PARABETARMSD WHOLEMOLECULES ALPHARMSD PRINT MOLINFO ANTIBETARMSD GROUP METAD | generic colvar secondarystructure core multicolvar bias |
| 21.033 | Multiple-path-metadynamics applied to DNA base-pairing transitions | bio | path-CV, metadynamics, multiple-walker, dna | Alberto Pérez-de-Alba-Ortíz | CONSTANT UPPER_WALLS MOVINGRESTRAINT RESTRAINT PRINT INCLUDE COMBINE METAD | generic function bias |
| 21.018 | Localized Volume-based Metadynamics | bio | LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification | Riccardo Capelli | UPPER_WALLS MATHEVAL WHOLEMOLECULES HISTOGRAM POSITION PRINT ENDPLUMED CONVERT_TO_FES FLUSH RMSD REWEIGHT_METAD GROUP COORDINATION COM DUMPGRID READ FIXEDATOM DISTANCE METAD | vatom generic colvar core function gridtools bias |
| 21.014 | how to determine statistically accurate conformational ensembles | bio | metadynamics, metainference, errors, cv, SAXS, ensemble determination | Cristina Paissoni | GYRATION BIASVALUE STATS TORSION SAXS WHOLEMOLECULES CONTACTMAP MOLINFO ALPHABETA ANTIBETARMSD PRINT ENSEMBLE CENTER METAD PBMETAD | vatom generic isdb colvar secondarystructure function multicolvar bias |
| 21.013 | Role of vibrational excitation in heterogeneous catalysis | chemistry | catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption | Kristof Bal | TD_GRID UPPER_WALLS HISTOGRAM PRINT UNITS CONVERT_TO_FES EXTERNAL FLUSH LOWER_WALLS REWEIGHT_METAD RESTRAINT UWALLS COMBINE COORDINATION DUMPGRID REWEIGHT_BIAS LOAD DISTANCES VES_LINEAR_EXPANSION ANGLES BF_CHEBYSHEV COORDINATIONNUMBER OPT_AVERAGED_SGD DISTANCE METAD | generic colvar ves symfunc multicolvar gridtools function setup bias |
| 20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Adriana Pietropaolo | COORDINATION WHOLEMOLECULES PRINT CENTER PBMETAD | vatom colvar generic bias |
| 20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Cristina Paissoni | BIASVALUE STATS RESTRAINT SAXS WHOLEMOLECULES PRINT MOLINFO ENSEMBLE GROUP INCLUDE CENTER DISTANCE | vatom generic isdb colvar core function bias |
| 20.026 | Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor | bio | Metadynamics, Umbrella sampling | Brandon Peters | METAD MULTI_RMSD REWEIGHT_METAD RESTRAINT HISTOGRAM PRINT CONVERT_TO_FES DUMPGRID | colvar generic bias gridtools |
| 20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Max Bonomi | GYRATION DIHCOR COORDINATION WHOLEMOLECULES PRINT MOLINFO ALPHABETA INCLUDE PBMETAD | multicolvar colvar generic bias |
| 19.080 | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | methods | ves, variationally enhanced sampling, vibrational excitation, chemical reactions | Kristof Bal | EXTERNAL FLUSH DISTANCE UPPER_WALLS TD_GRID COORDINATION LOWER_WALLS VES_LINEAR_EXPANSION DUMPGRID ANGLE TD_WELLTEMPERED HISTOGRAM PRINT OPT_AVERAGED_SGD CONVERT_TO_FES BF_CHEBYSHEV COMBINE UNITS | generic colvar ves gridtools function setup bias |
| 19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Giovanni Bussi | COORDINATION LOWER_WALLS RESTRAINT WHOLEMOLECULES DISTANCE ENDPLUMED | colvar generic bias |
| 19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Matteo Salvalaglio | DISTANCE PRINT GROUP INCLUDE CENTER ENDPLUMED | vatom colvar generic core |
| 19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Michele Invernizzi | EXTERNAL TORSION UNITS PRINT OPES_METAD POSITION ENDPLUMED METAD | generic colvar setup opes bias |
| 19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | GYRATION UPPER_WALLS ENERGY PRINT MOLINFO COM DISTANCE METAD | vatom colvar generic bias |
| 19.059 | cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide | bio | bias-exchange metadynamics, cis-trans isomerization | Fabrizio Marinelli | RANDOM_EXCHANGES TORSION PRINT INCLUDE METAD | colvar generic bias |
| 19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Gareth Tribello | FOURIER_TRANSFORM FCCUBIC MORE_THAN UNITS GROUP CENTER MULTICOLVARDENS FIND_CONTOUR_SURFACE DUMPGRID | vatom fourier symfunc core function gridtools setup contour |
| 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 | FLUSH UPPER_WALLS COORDINATION LOWER_WALLS UNITS POSITION PRINT RESTART GROUP METAD | generic colvar core setup bias |
| 19.040 | Optimal Metric for Path Collective Variables | bio | metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path | Francesco Luigi Gervasio | MATHEVAL TORSION PRINT ENDPLUMED METAD | bias colvar generic function |
| 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 UPPER_WALLS DISTANCES PRINT RESTART METAD | generic setup mapping multicolvar bias |
| 19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Jim Pfaendtner | EXTERNAL COORDINATION ENERGY GROUP METAD | colvar core bias |
| 19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Haochuan Chen | DRR PRINT TORSION | drr colvar generic |
| 19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Max Bonomi | BIASVALUE EMMI PRINT MOLINFO GROUP | core generic isdb bias |
| 25.012 | A Machine Learning-Driven, Probability-Based Approach to Enzyme Catalysis | bio | enzyme catalysis, transition state, structure-activity relationship, free energy surface, reaction mechanism, water, alpha-amylase, sugar, QM/MM MD, OPES, committor function, machine learning | Sudip Das | INCLUDE ENERGY FLUSH MATHEVAL LOAD DISTANCE BIASVALUE PRINT TORSION UNITS COMBINE OPES_METAD CUSTOM CELL POSITION COORDINATION | colvar setup generic bias opes function |
| 24.033 | Transient interactions between the fuzzy coat and the cross-b core of brain-derived Ab42 filaments | bio | CryoEM, MEMMI, Metadynamics, Metainference, Ab42 Fibrils, structural ensemble | Maria Milanesi | COM EMMI DUMPMASSCHARGE RMSD CENTER ALPHARMSD UPPER_WALLS MOLINFO WHOLEMOLECULES DISTANCE PARABETARMSD PBMETAD BIASVALUE PRINT DUMPATOMS GROUP COORDINATION | colvar vatom secondarystructure isdb generic bias core |
| 24.030 | NMR guided simulation of dsRBD | bio | Metainference, NMR, protein dynamics | Debadutta Patra | FLUSH MOLINFO WHOLEMOLECULES DISTANCE ALPHABETA PRINT RDC METAINFERENCE ENSEMBLE GROUP STATS | colvar isdb generic core multicolvar function |
| 24.010 | Oxytocin metadynamics simulation | bio | metadynamics, oxytocin, peptide | Jan Beránek | METAD FLUSH WHOLEMOLECULES PRINT RESTART TORSION | colvar bias setup generic |
| 24.009 | Weighted Shape Gaussian Mixture Models | bio | metadynamics, clustering | Glen Hocky | METAD PRINT UNITS TORSION GROUP | colvar setup bias generic core |
| 24.008 | yCD Metadynamics | bio | volume-based MetaD, path CVs, infrequent MetaD, product release | James McCarty | MATHEVAL DISTANCE FIXEDATOM FIT_TO_TEMPLATE PATH WRAPAROUND READ COMMITTOR COM COORDINATION METAD RMSD DUMPGRID PRINT CONTACTMAP CONVERT_TO_FES GROUP ENDPLUMED INCLUDE HISTOGRAM UPPER_WALLS FLUSH WHOLEMOLECULES MOLINFO REWEIGHT_METAD | colvar vatom gridtools mapping generic bias core function |
| 23.044 | Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition | materials | metadynamics, interlocked molecules | Luigi Leanza | ENDPLUMED METAD CONVERT_TO_FES HISTOGRAM DUMPGRID PRINT READ COORDINATION GROUP COMMITTOR | colvar gridtools generic bias core |
| 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 CENTER UPPER_WALLS MATHEVAL WHOLEMOLECULES DISTANCE BIASVALUE PRINT CONSTANT LOWER_WALLS | colvar vatom bias generic function |
| 23.028 | Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process | chemistry | Ammonia decomposition; Dynamics;OPES; Neural Network potential | Manyi Yang | COM LOWER_WALLS ENERGY FLUSH MATHEVAL UPPER_WALLS DISTANCE COORDINATIONNUMBER PRINT ZDISTANCES UNITS FIXEDATOM OPES_METAD CUSTOM DISTANCES GROUP COMMITTOR | colvar vatom setup bias generic symfunc core opes multicolvar function |
| 23.022 | A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar | methods | collective variables, machine learning, toy model | Enrico Trizio | UPPER_WALLS PYTORCH_MODEL BIASVALUE PRINT UNITS LOWER_WALLS CUSTOM OPES_METAD POSITION ENDPLUMED | colvar opes setup bias generic pytorch function |
| 23.001 | Quantum phase diagram of water | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn-Løland Bore | INCLUDE ECV_UMBRELLAS_LINE UPPER_WALLS PRINT RESTART LOWER_WALLS ENVIRONMENTSIMILARITY OPES_EXPANDED | setup envsim generic bias opes |
| 22.039 | Driving and characterizing nucleation of urea and glycine polymorphs in water | bio | metadynamics, nucleation, amino acids, polymorphism | Eric Beyerle | METAD INCLUDE CENTER MATHEVAL Q4 LOAD COORDINATIONNUMBER Q6 PRINT COMBINE GROUP PAIRENTROPY | vatom gridtools setup bias symfunc generic core function |
| 22.038 | Enhanced Sampling Aided Design of Molecular Photoswitches | chemistry | reaction discovery, OPES explore, graph CV | Umberto Raucci | PYTORCH_MODEL PRINT UNITS OPES_METAD_EXPLORE CUSTOM COORDINATION | colvar opes setup generic pytorch function |
| 22.035 | Deciphering the alphabet of disorder — Glu and Asp act differently on local but not global properties | bio | intrinsically disordered proteins, parallel bias metadynamics, protein | Kresten Lindorff-Larsen | MOLINFO WHOLEMOLECULES GYRATION PBMETAD TORSION | colvar generic bias |
| 22.033 | Reciprocal barrier restraint. Application to PROTAC passive permeability prediction | methods | PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR | Istvan Kolossvary | COM METAD DRR FLUSH DISTANCE BIASVALUE PRINT UNITS CUSTOM | colvar vatom setup bias generic drr function |
| 22.022 | Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir | bio | RMSD, protein-ligand interactions | Isabell Grothaus | PRINT RMSD | colvar generic |
| 22.011 | Accelerating all-atom simulations and gaining mechanistic understanding of biophysical systems through State Predictive Information Bottleneck | methods | metadynamics, membrane permeation, protein folding | Shams Mehdi | COM YANGLES METAD UPPER_WALLS MATHEVAL WHOLEMOLECULES MOLINFO DISTANCE ZANGLES PRINT COMBINE LOWER_WALLS CUSTOM TORSION XANGLES ALPHABETA | colvar vatom bias generic multicolvar function |
| 21.050 | N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity | methods | bio | Isabell Louise Grothaus | PRINT CENTER DISTANCE | colvar generic vatom |
| 21.044 | NaCl nucleation | chemistry | metadynamics, DFS clustering | Aaron Finney | METAD LOCAL_Q6 HISTOGRAM MFILTER_MORE CONTACT_MATRIX DUMPGRID CLUSTER_NATOMS COORDINATIONNUMBER PRINT Q6 DFSCLUSTERING COMBINE FIXEDATOM CLUSTER_DISTRIBUTION INSPHERE GROUP | vatom gridtools clusters bias symfunc generic adjmat volumes core multicolvar function |
| 21.039 | Deep learning the slow modes for rare events sampling | methods | collective variables, machine learning, slow modes, deep-tica, opes | Luigi Bonati | ENERGY DISTANCE TORSION OPES_EXPANDED COMBINE OPES_METAD RMSD PYTORCH_MODEL LOAD PRINT CONTACTMAP ENVIRONMENTSIMILARITY GROUP ENDPLUMED VOLUME INCLUDE FLUSH WHOLEMOLECULES MOLINFO ECV_MULTITHERMAL Q6 UNITS | colvar opes setup envsim generic symfunc core pytorch function |
| 21.038 | Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics | materials | metadynamics, SGOOP, nucleation, urea | Ziyue Zou | VOLUME METAD INCLUDE CENTER ENERGY LOAD PRINT COORDINATIONNUMBER COMBINE GROUP | colvar vatom setup bias generic symfunc core function |
| 21.032 | Metal-coupled folding mechanism to metallothionein | bio | parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination | Manuel-Peris Diaz | WHOLEMOLECULES PBMETAD UNITS GROUP COORDINATION | colvar setup generic bias core |
| 21.029 | Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs | bio | metadynamics, small peptide, machine learning | Pratyush Tiwary | EXTERNAL ENERGY FLUSH MOLINFO PRINT RESTART TORSION | colvar bias setup generic |
| 21.010 | Step by Step Strecker Amino Acid Synthesis from Ab Initio Prebiotic Chemistry | chemistry | Strecker reaction, free energy landscape, ab initio molecular dynamics, glycine, prebiotic synthesis | Théo Magrino | generic | |
| 20.032 | Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil | materials | clustering, conformational isomers | Matteo Salvalaglio | PRINT TORSION ENDPLUMED | colvar generic |
| 20.016 | Predicting polymorphism in molecular crystals using orientational entropy | materials | metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy | Pablo Piaggi | VOLUME METAD INCLUDE CENTER UPPER_WALLS LOAD PRINT GROUP | colvar vatom setup bias generic core |
| 19.081 | Calculation of phase diagrams in the multithermal-multibaric ensemble | methods | VES, variationally enhanced sampling, multithermal-multibaric, energy, Wang Landau, RefCV, kernel, bcc, fcc, sodium, aluminum | Pablo Piaggi | ENERGY MATHEVAL RESTART CELL READ COMBINE OPT_DUMMY BF_LEGENDRE LOAD DUMPGRID TD_WELLTEMPERED PRINT REWEIGHT_TEMP_PRESS CONVERT_TO_FES VOLUME HISTOGRAM UPPER_WALLS OPT_AVERAGED_SGD Q6 VES_LINEAR_EXPANSION TD_MULTITHERMAL_MULTIBARIC LOWER_WALLS REWEIGHT_BIAS | colvar gridtools setup generic bias symfunc ves function |
| 19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Giovanni Bussi | COM METAD INCLUDE FLUSH MATHEVAL WHOLEMOLECULES MOLINFO DISTANCE PRINT SORT MAXENT TORSION COORDINATION | colvar vatom bias generic function |
| 19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Matteo Salvalaglio | EXTERNAL METAD HISTOGRAM MATHEVAL DUMPGRID DISTANCE BIASVALUE PRINT READ REWEIGHT_METAD CONVERT_TO_FES REWEIGHT_BIAS TORSION COMMITTOR | colvar gridtools bias generic function |
| 19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Cristina Paissoni | ANGLE ENDPLUMED INCLUDE CENTER MATHEVAL WHOLEMOLECULES MOLINFO ALPHABETA PBMETAD BIASVALUE PRINT COMBINE COORDINATION SAXS ENSEMBLE GROUP STATS | colvar vatom isdb generic bias core multicolvar function |
| 19.056 | maze | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_OPTIMIZER_BIAS PRINT UNITS MAZE_SIMULATED_ANNEALING POSITION MAZE_LOSS | colvar maze generic setup |
| 19.047 | Close Structure | methods | metadynamics, RMSD, path collective variables, property map | Vojtech Spiwok | PRINT PROPERTYMAP METAD WHOLEMOLECULES | colvar generic bias |
| 19.041 | Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces | bio | metadynamics, collective variables, conformational changes, multiple walkers, Well-Tempered MetaD, peptide, binding, phosphorylation, post-transitional motif, sio2, adsorption | Jim Pfaendtner | COM METAD ENERGY UPPER_WALLS DISTANCE PRINT | colvar vatom bias generic |
| 19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Carlo Camilloni | ANTIBETARMSD CS2BACKBONE UPPER_WALLS FLUSH WHOLEMOLECULES MOLINFO PBMETAD BIASVALUE PRINT ALPHABETA RESTART LOWER_WALLS GROUP ENDPLUMED | secondarystructure setup isdb bias generic core multicolvar |
| 19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Davide Provasi | COM METAD RMSD WHOLEMOLECULES DISTANCE PRINT CONTACTMAP FUNCPATHMSD ENDPLUMED | colvar vatom bias generic function |
| 19.030 | Coarse-Grained MetaDynamics (CG-MetaD) | bio | Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy | Vittorio Limongelli | COM METAD UPPER_WALLS WHOLEMOLECULES DISTANCE PRINT LOWER_WALLS | colvar vatom bias generic |
| 19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Matteo Salvalaglio | CELL VOLUME METAD ENERGY UPPER_WALLS MATHEVAL PRINT COMBINE LOWER_WALLS TORSION ENDPLUMED | colvar bias generic function |
| 19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Carlo Camilloni | ENDPLUMED INCLUDE RMSD CENTER UPPER_WALLS WHOLEMOLECULES MOLINFO DISTANCE BIASVALUE PRINT RESTRAINT SAXS GROUP STATS | colvar vatom isdb generic bias core function |
| 19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Carlo Camilloni | ENDPLUMED DIHCOR CENTER UPPER_WALLS WHOLEMOLECULES MOLINFO DISTANCE ALPHABETA DHENERGY PBMETAD PRINT RDC RESTRAINT METAINFERENCE TORSION ENSEMBLE GROUP STATS | colvar vatom isdb generic bias core multicolvar function |
| 19.009 | RNA tetraloops folding | bio | metadynamics, RNA, folding | Giovanni Bussi | METAD RMSD ERMSD WHOLEMOLECULES MOLINFO PRINT ENDPLUMED | colvar bias generic |
| 19.008 | anncolvar | methods | neural network, dimensionality reduction | Vojtech Spiwok | METAD ALPHARMSD MATHEVAL WHOLEMOLECULES MOLINFO PRINT COMBINE FIT_TO_TEMPLATE POSITION | colvar secondarystructure bias generic function |
| 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 | SMAC TORSIONS PRINT DISTANCES DUMPMULTICOLVAR | generic multicolvar symfunc |
| 24.032 | DeepLNE++ | methods | PATHCV, OPES | Thorben Fröhlking | DISTANCE ENERGY CUSTOM COORDINATION OPES_METAD PRINT LOAD COMBINE TORSION GROUP | setup function generic opes colvar core |
| 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 | DISTANCE ALPHARMSD CUSTOM GYRATION COORDINATION OPES_METAD PRINT TORSION COMBINE MOLINFO WHOLEMOLECULES | function generic opes colvar secondarystructure |
| 24.017 | Absolute Binding Free Energies with OneOPES | methods | protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy | Francesco Gervasio | PRINT MATHEVAL TORSION RESTART UPPER_WALLS GROUP WHOLEMOLECULES COM LOWER_WALLS MOLINFO RMSD INCLUDE OPES_EXPANDED CONSTANT COORDINATION WRAPAROUND ENERGY METAD OPES_METAD_EXPLORE BIASVALUE CUSTOM CONTACTMAP PROJECTION_ON_AXIS ECV_MULTITHERMAL | setup bias vatom function generic opes colvar core |
| 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 | DISTANCE ENERGY METAD COORDINATIONNUMBER RESTRAINT BIASVALUE COMMITTOR PRINT MATHEVAL TORSION RESTART FLUSH MOLINFO | setup bias function generic symfunc colvar |
| 24.005 | Learning Markovian Dynamics with Spectral Maps | methods | spectral map, collective variables, machine learning | Jakub Rydzewski | DISTANCE BIASVALUE CUSTOM UNITS PRINT | setup bias function generic colvar |
| 23.043 | Modeling the ferroelectric phase transition in barium titanate with DFT accuracy and converged sampling | materials | Barium Titanate, ferroelectric phase transition, Machine Learning, polarization order parameters | Lorenzo Gigli | INCLUDE METAD PRINT SUM MATHEVAL FLUSH SELECT_COMPONENTS TRANSPOSE | bias function generic matrixtools valtools |
| 23.036 | Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? | bio | NaCl, nucleation, metadynamics | Ruiyu Wang | Q4 Q6 ENERGY VOLUME COORDINATIONNUMBER METAD PRINT MATHEVAL COMBINE | bias function generic symfunc colvar |
| 23.034 | Urea nucleation in water: do long-range forces matter? | materials | LMF theory, Metadynamics, Nucleation | Ziyue Zou | INCLUDE METAD COORDINATIONNUMBER CENTER PRINT LOAD GROUP | vatom bias setup generic symfunc core |
| 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 | METAD GHBFIX BIASVALUE ERMSD COORDINATION PRINT COMBINE MOLINFO WHOLEMOLECULES | colvar bias generic function |
| 23.021 | Into the Dynamics of Rotaxanes at Atomistic Resolution | materials | metadynamics, rotaxanes, molecular shuttles, molecular machines | Luigi Leanza | DISTANCE METAD CUSTOM CENTER FIXEDATOM PRINT MATHEVAL TORSION UPPER_WALLS | vatom bias function generic colvar |
| 23.013 | Path meta-eABF simulation of large scale conformational change in STING protein | methods | meta-eABF, path CV, large scale conformational change, STING protein, reciprocal barrier restraint | Istvan Kolossvary | DRR METAD BIASVALUE CUSTOM UNITS TIME PRINT LOWER_WALLS UPPER_WALLS PATHMSD FLUSH | setup bias function generic colvar drr |
| 23.012 | JAK2 2D meta-eABF PMF with statistical analysis | bio | 2D meta-eABF, path CV, PMF | Istvan Kolossvary | DRR METAD BIASVALUE CUSTOM PRINT LOWER_WALLS UPPER_WALLS PATHMSD FLUSH | bias function generic colvar drr |
| 23.008 | PBMetaD simulations of Histatin5 | bio | metadynamics, IDP, Rg, PPII | Francesco Pesce | PBMETAD GYRATION PRINT TORSION GROUP MOLINFO WHOLEMOLECULES | colvar bias generic core |
| 23.000 | Atomistic simulations of RNA tetraloop folding via PTWTE-WTM | bio | parallel tempering, well-tempered metadynamics, well-tempered ensemble, RNA, Tetraloop, Folding | Gül Zerze | ENERGY METAD PRINT LOWER_WALLS CONTACTMAP UPPER_WALLS WHOLEMOLECULES | colvar bias generic |
| 22.029 | Angiotensin-1-7_Metadynamics | bio | Metadynamics, Angiotensin-(1-7), peptide | L.-América Chi | METAD GYRATION COORDINATION PRINT LOWER_WALLS UPPER_WALLS GROUP FLUSH WHOLEMOLECULES | colvar bias generic core |
| 22.028 | N-glycan conformer distributions in atomistic simulation | bio | REST2, RECT, N-glycan, pucker | Isabell Grothaus | CONVERT_TO_FES HISTOGRAM PUCKERING METAD READ DUMPGRID PRINT TORSION MOLINFO | colvar gridtools bias generic |
| 22.026 | Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification | materials | Peptoid, silica | Jim Pfaendtner | DISTANCE PBMETAD COM GYRATION PRINT UPPER_WALLS MOLINFO | colvar vatom bias generic |
| 22.003 | Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling | methods | opes, metadynamics, reweighting, alanine, muller | Michele Invernizzi | PBMETAD ENERGY ECV_UMBRELLAS_FILE METAD OPES_METAD_EXPLORE POSITION BIASVALUE CUSTOM OPES_EXPANDED UNITS OPES_METAD PRINT TORSION ENDPLUMED LOWER_WALLS ECV_MULTITHERMAL UPPER_WALLS | setup bias function generic opes colvar |
| 21.051 | Automatic learning of hydrogen-bond fixes in an AMBER RNA force field | methods | force field, RNA | Giovanni Bussi | METAD BIASVALUE ERMSD COORDINATION PRINT COMBINE MOLINFO WHOLEMOLECULES | colvar bias generic function |
| 21.025 | Computational and biochemical analysis of type IV pilus dynamics and stability | bio | molecular dynamics, calcium binding, Type IV pilus | Yasaman Karami | UPPER_WALLS DISTANCE PRINT LOWER_WALLS | colvar bias generic |
| 21.012 | NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition | bio | funnel metadynamics | Jim Pfaendtner | DISTANCE METAD COM PRINT LOWER_WALLS FUNNEL FUNNEL_PS UPPER_WALLS | funnel vatom bias generic colvar |
| 21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Kristof Bal | REWEIGHT_METAD CONVERT_TO_FES HISTOGRAM METAD COORDINATIONNUMBER MOVINGRESTRAINT COMMITTOR UNITS DUMPGRID PRINT LOAD UPPER_WALLS FLUSH | setup bias generic gridtools symfunc |
| 21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Tarak Karmakar | PYTORCH_MODEL OPES_METAD MATHEVAL LOWER_WALLS LOAD UPPER_WALLS GROUP PRINT FLUSH | setup bias function generic opes pytorch core |
| 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 | METAD PRINT LOWER_WALLS RESTART UPPER_WALLS PATHMSD WHOLEMOLECULES | generic setup bias colvar |
| 20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Matteo Salvalaglio | ENERGY METAD VOLUME CELL PRINT MATHEVAL LOWER_WALLS UPPER_WALLS | colvar bias generic function |
| 20.015 | Rational design of ASCT2 inhibitors using an integrated experimental-computational approach | bio | ASCT2 transporter, small-molecules, cryo-EM, metainference | Max Bonomi | EMMIVOX DUMPATOMS BIASVALUE PRINT LOAD GROUP MOLINFO WHOLEMOLECULES | isdb setup bias generic 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 | PBMETAD ALPHARMSD ANTIBETARMSD DIHCOR PRINT TORSION GROUP FLUSH WHOLEMOLECULES METAINFERENCE GYRATION CS2BACKBONE PARABETARMSD ENSEMBLE MOLINFO INCLUDE STATS COORDINATION COMBINE ENDPLUMED | isdb bias function generic colvar multicolvar secondarystructure core |
| 20.012 | Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies | bio | metadynamics, well-tempered ensemble, ligand binding, binding affinity calculations, novel COLVAR, funnel restraints, Hamiltonian replica-exchange, PathCV, COMetPath, SWISH | Francesco Gervasio | DISTANCE INCLUDE METAD FUNCPATHGENERAL COM BIASVALUE CONSTANT CONTACTMAP PRINT MATHEVAL LOAD LOWER_WALLS UPPER_WALLS GROUP PROJECTION_ON_AXIS MOLINFO WHOLEMOLECULES | vatom bias setup function generic 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 | OPT_DUMMY ENVIRONMENTSIMILARITY Q6 VOLUME BF_LEGENDRE VES_LINEAR_EXPANSION OPT_AVERAGED_SGD PRINT MATHEVAL RESTART UPPER_WALLS TD_WELLTEMPERED | setup bias function ves generic symfunc colvar envsim |
| 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 | METAD CUSTOM UNITS COORDINATION PRINT DISTANCES | setup bias function generic colvar multicolvar |
| 20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Pratyush Tiwary | RMSD DISTANCE METAD PRINT RESTART TORSION COMBINE UPPER_WALLS MOLINFO WHOLEMOLECULES | setup bias function generic colvar |
| 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 | DUMPGRID PRINT UPPER_WALLS FLUSH WHOLEMOLECULES FUNCPATHMSD DISTANCE COM ABMD LOWER_WALLS MOLINFO REWEIGHT_METAD CONVERT_TO_FES HISTOGRAM READ COMBINE ENDPLUMED METAD CONTACTMAP | vatom bias function generic gridtools colvar |
| 19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Valerio Rizzi | COMBINE METAD COORDINATIONNUMBER UNITS RESTART PRINT DISTANCES ENDPLUMED UPPER_WALLS GROUP FLUSH | setup bias function generic symfunc multicolvar core |
| 19.079 | Impact of Glutamate Carboxylation in the Adsorption of the alpha-1 Domain of Osteocalcin to Hydroxyapatite and Titania | bio | metadynamics, peptide adsorption, parallel tempering, well-tempered ensemble | Sarah Alamdari | DISTANCE ENERGY METAD COM GYRATION PRINT UPPER_WALLS GROUP MOLINFO | vatom bias generic colvar core |
| 19.078 | Iterative unbiasing of quasi-equilibrium sampling | methods | metadynamics, reweighting | Federico Giberti | DISTANCE DUMPATOMS METAD COORDINATIONNUMBER BIASVALUE UNITS PRINT MATHEVAL COLLECT_FRAMES REWEIGHT_BIAS | setup bias function generic symfunc landmarks colvar |
| 19.076 | Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones | bio | molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics | Salvatore Assenza | MOVINGRESTRAINT GYRATION UNITS PRINT ENDPLUMED | colvar setup bias generic |
| 19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_LOSS MAZE_OPTIMIZER_BIAS UNITS PRINT MAZE_SIMULATED_ANNEALING POSITION | generic setup colvar maze |
| 19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Gareth Tribello | METAD UNITS FCCUBIC CELL AROUND PRINT LOWER_WALLS ENDPLUMED UPPER_WALLS | volumes setup bias generic symfunc colvar |
| 19.050 | Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes | chemistry | metadynamics, membranes, Willard Chandler surface | Gareth Tribello | CONVERT_TO_FES HISTOGRAM COMBINE METAD DISTANCE_FROM_CONTOUR READ DUMPGRID PRINT RESTART UPPER_WALLS REWEIGHT_BIAS | setup bias contour function generic gridtools |
| 19.035 | Dimerization of GPCRs from coarse-grained umbrella sampling | bio | Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization | Davide Provasi | DISTANCE COM RESTRAINT PRINT TORSION GROUP | vatom bias generic colvar core |
| 19.027 | Multithermal-multibaric simulations using VES | methods | ves, Wang Landau, multicanonical, liquid sodium, density anomaly | Pablo Piaggi | CONVERT_TO_FES HISTOGRAM OPT_DUMMY ENERGY REWEIGHT_TEMP_PRESS AVERAGE BF_LEGENDRE READ VES_LINEAR_EXPANSION UNITS OPT_AVERAGED_SGD DUMPGRID PRINT RESTART COMBINE TD_MULTICANONICAL REWEIGHT_BIAS | setup bias function ves generic gridtools colvar |
| 19.023 | RECT | methods | metadynamics, replica exchange | Giovanni Bussi | METAD GYRATION PRINT TORSION WHOLEMOLECULES | colvar bias generic |
| 19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Kresten Lindorff-Larsen | METAD ALPHABETA COMMITTOR PRINT COMBINE FLUSH MOLINFO | generic bias function multicolvar |
| 19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Matteo Salvalaglio | DISTANCE METAD CENTER COMMITTOR PRINT LOWER_WALLS TORSION UPPER_WALLS | colvar vatom bias generic |
| 25.006 | Characterizing the conformational ensemble of PROTAC degraders in solutions via atomistic simulations | methods | Enhanced sampling, Atomistic simulations, Conformational ensemble, PROTACs, Targeted Protein Degradation, Chamelonic molecules | Shikshya Bhusal, Omar Valsson | CENTER PRINT READ VOLUME TORSION GYRATION ENERGY PBMETAD DISTANCE RESTART INCLUDE | bias setup vatom colvar generic |
| 25.003 | Surrogate Model CV | methods | Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding | Sompriya Chatterjee | MOLINFO COMMITTOR MATHEVAL WHOLEMOLECULES PRINT CUSTOM PYTORCH_MODEL OPES_METAD ENERGY GROUP COMBINE ENDPLUMED DISTANCE TORSION | function colvar pytorch generic core opes |
| 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 | COORDINATION UPPER_WALLS PRINT LOWER_WALLS CUSTOM OPES_METAD UNITS GROUP COMMITTOR DISTANCE RESTART | function bias setup colvar generic core opes |
| 24.031 | DeepLNE | methods | PATHCV, OPES, OneOPES | Thorben Fröhlking | MOLINFO COMBINE COORDINATION PRINT OPES_EXPANDED VOLUME ECV_MULTITHERMAL PYTORCH_MODEL ENERGY OPES_METAD_EXPLORE ERMSD RESTART | function setup colvar pytorch generic opes |
| 24.026 | Constant pH metadynamics of RNA oligomers | bio | metadynamics, pH, RNA | Giovanni Bussi | MOLINFO PUCKERING METAD PRINT RESTART TORSION | setup colvar generic bias |
| 24.022 | Integrating Path Sampling with Enhanced Sampling for Rare-event Kinetics | methods | OPES Flooding, Weighted Ensemble, Metadynamics, Kinetics, Infrequent Metadynamics, Integrated Sampling | Dhiman Ray | MATHEVAL METAD GROUP DISTANCE PRINT RMSD ANGLE MOLINFO COORDINATION CENTER FIT_TO_TEMPLATE CUSTOM COMMITTOR TORSION WHOLEMOLECULES UPPER_WALLS CONTACTMAP OPES_METAD COMBINE ENDPLUMED FIXEDATOM | function bias colvar vatom generic core opes |
| 23.032 | Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics | bio | metadynamics, tSNE, neural network, machine learning, trp-cage, folding | Vojtech Spiwok | MOLINFO ALPHARMSD WHOLEMOLECULES METAD PRINT FIT_TO_TEMPLATE POSITION ANN COMBINE | function bias colvar generic secondarystructure annfunc |
| 23.023 | Rational design of novel biomimetic sequence-defined polymers for mineralization applications | methods | metadynamics, surface binding, biomimetic mineralization | Kaylyn Torkelson | COORDINATION UPPER_WALLS PRINT GYRATION PBMETAD DISTANCE COM | vatom colvar generic bias |
| 23.011 | OneOPES, a combined enhanced sampling method to rule them all | bio | OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding | Valerio Rizzi | MOLINFO METAD PRINT OPES_EXPANDED ECV_MULTITHERMAL ENERGY OPES_METAD_EXPLORE ENDPLUMED DISTANCE TORSION | colvar generic bias opes |
| 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 | MATHEVAL LOWER_WALLS GROUP DISTANCE PRINT RMSD ANGLE ENERGY MOLINFO COORDINATION CENTER FIT_TO_TEMPLATE CUSTOM PYTORCH_MODEL COMMITTOR INCLUDE WHOLEMOLECULES UPPER_WALLS CONTACTMAP OPES_METAD COMBINE ENDPLUMED FIXEDATOM | function bias colvar vatom generic pytorch core opes |
| 23.005 | A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs | bio | metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A | Timothy Clark | MOLINFO DUMPGRID MATHEVAL WHOLEMOLECULES METAD HISTOGRAM PRINT READ RMSD DISTANCE REWEIGHT_METAD CONVERT_TO_FES | gridtools function bias colvar generic |
| 22.036 | Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction | bio | Well-tempered MetaDynamics with Hamiltonian Replica Exchange | Miroslav Krepl | MOLINFO METAD UPPER_WALLS COORDINATION PRINT FLUSH CUSTOM LOAD GROUP COMBINE GHBFIX BIASVALUE | function bias setup colvar generic core |
| 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 | METAD DRR PRINT CUSTOM PATHMSD FLUSH BIASVALUE | function bias drr colvar generic |
| 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 | UPPER_WALLS PRINT ECV_UMBRELLAS_LINE LOWER_WALLS OPES_EXPANDED ENVIRONMENTSIMILARITY INCLUDE | generic bias opes envsim |
| 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 | DUMPGRID UPPER_WALLS HISTOGRAM PRINT AROUND VOLUME CUSTOM OPES_METAD ENERGY ENVIRONMENTSIMILARITY RESTART | gridtools function bias setup colvar generic opes volumes envsim |
| 22.009 | Glycosylation in calixarenes capsule | chemistry | Metadynamics, glycosylation, supramolecular catalysis | GiovanniMaria Piccini | MATHEVAL WHOLEMOLECULES COMBINE METAD UPPER_WALLS COORDINATION BRIDGE PRINT FIT_TO_TEMPLATE LOWER_WALLS RMSD ANGLE DISTANCES UNITS GROUP FLUSH DISTANCE | function bias setup colvar adjmat generic core multicolvar |
| 22.000 | Amyloid precursor protein processing by human γ-secretase | bio | Bias Exchange Metadynamics, Helix unfolding, coupled binding | Xiaoli Lu | MOLINFO ALPHARMSD RANDOM_EXCHANGES ANTIBETARMSD METAD COORDINATION CENTER PRINT CONTACTMAP UNITS DISTANCE INCLUDE | bias setup colvar vatom generic secondarystructure |
| 21.052 | On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets | materials | Ibuprofen, unbinding, WTmetaD | Matteo Salvalaglio | COMMITTOR METAD CENTER PRINT COORDINATIONNUMBER ENDPLUMED DISTANCE TORSION | bias symfunc vatom colvar generic |
| 21.049 | Multiple-path-metadynamics and PathMaps | methods | path-CV, metadynamics, multiple-walker, multiple paths, pathmap | Alberto Pérez-de-Alba-Ortíz | METAD UPPER_WALLS ENSEMBLE PRINT LOWER_WALLS MOVINGRESTRAINT RESTRAINT CUSTOM UNITS LOAD CONSTANT COMBINE TORSION | function bias setup colvar generic |
| 21.015 | Coarse-grained metadynamics and umbrella sampling simulations to investigate interactions of carbohydrate-binding modules with chitin | bio | metadynamics, umbrella sampling, coarse-grained, MARTINI, chitin, carbohydrate-binding module | Gaston Courtade | MATHEVAL WHOLEMOLECULES REWEIGHT_BIAS METAD COORDINATION CENTER PRINT RESTRAINT POSITION RESTART | function bias setup vatom colvar generic |
| 21.011 | CmuMD simulations of NaCl(aq) at graphite | chemistry | CmuMD, DFS clustering | Aaron Finney | DUMPGRID CLUSTER_DISTRIBUTION CONTACT_MATRIX DENSITY PRINT COORDINATIONNUMBER AROUND CLUSTER_NATOMS RESTRAINT MFILTER_MORE MULTICOLVARDENS LOAD GROUP FIXEDATOM DFSCLUSTERING | gridtools bias symfunc setup adjmat vatom generic core clusters volumes multicolvar |
| 21.006 | OPES, On-the-fly Probability Enhanced Sampling Method | methods | opes, alanine dipeptide, well-tempered, multithermal, multiumbrella | Michele Invernizzi | PRINT ECV_UMBRELLAS_LINE ENDPLUMED ECV_MULTITHERMAL OPES_METAD ENERGY OPES_EXPANDED TORSION | colvar generic opes |
| 20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Faidon Brotzakis | DUMPGRID MOLINFO WHOLEMOLECULES HISTOGRAM PRINT READ RMSD DISTANCES EMMI GROUP BIASVALUE CONVERT_TO_FES | gridtools isdb bias colvar generic core multicolvar |
| 20.028 | Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane | bio | metadynamics, KRas-4B, anionic membrane | Huixia Lu | METAD CENTER PRINT FIT_TO_TEMPLATE DISTANCE RESTART | bias setup vatom colvar generic |
| 20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Valerio Rizzi | MATHEVAL WHOLEMOLECULES UPPER_WALLS CENTER COORDINATION PRINT FIT_TO_TEMPLATE ANGLE PYTORCH_MODEL OPES_METAD ENERGY GROUP ENDPLUMED FIXEDATOM DISTANCE | function bias vatom colvar generic pytorch core opes |
| 20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Michele Invernizzi | MATHEVAL ECV_LINEAR OPES_EXPANDED ECV_MULTITHERMAL_MULTIBARIC PRINT VOLUME RMSD LOAD ENERGY MOLINFO ECV_UMBRELLAS_LINE CUSTOM UNITS Q6 POSITION TORSION WHOLEMOLECULES UPPER_WALLS ECV_MULTITHERMAL ENDPLUMED ENVIRONMENTSIMILARITY | function bias symfunc setup colvar generic opes envsim |
| 20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Luigi Bonati | MATHEVAL UPPER_WALLS PRINT LOWER_WALLS PYTORCH_MODEL OPES_METAD UNITS LOAD GROUP FLUSH ENDPLUMED DISTANCE COM TORSION | function bias setup colvar pytorch generic vatom core opes |
| 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 | MOLINFO WHOLEMOLECULES ANTIBETARMSD UPPER_WALLS PRINT LOWER_WALLS CS2BACKBONE GROUP FLUSH ENDPLUMED PBMETAD BIASVALUE ALPHABETA | bias isdb generic secondarystructure core multicolvar |
| 19.073 | On the role of enthalpic and entropic contributions on the conformational free energy landscape of MIL-101(Cr) building units | materials | metadynamics, MOF, MIL101Cr, conformational | Matteo Salvalaglio | METAD UPPER_WALLS PRINT COORDINATIONNUMBER LOWER_WALLS DISTANCES ENERGY ENDPLUMED GYRATION | bias symfunc colvar generic multicolvar |
| 19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Mattia Bernetti | WHOLEMOLECULES METAD UPPER_WALLS PRINT LOWER_WALLS PATHMSD | colvar generic bias |
| 19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Luigi Bonati | PRINT UNITS LOAD ENERGY Q6 POSITION ENDPLUMED ENVIRONMENTSIMILARITY TORSION | symfunc setup colvar generic envsim |
| 19.048 | Understanding Ligand Binding Selectivity in a Prototypical GPCR Family | bio | metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | MATHEVAL WHOLEMOLECULES METAD UPPER_WALLS PRINT LOWER_WALLS CONSTANT DISTANCE BIASVALUE COM | function bias vatom colvar generic |
| 19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Paolo Raiteri | MATHEVAL METAD UPPER_WALLS PRINT UNITS FLUSH DISTANCE RESTART | function bias setup colvar generic |
| 19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Mattia Bernetti | MOLINFO ALPHARMSD WHOLEMOLECULES METAD PRINT ENERGY ENDPLUMED GYRATION | secondarystructure colvar generic bias |
| 19.006 | Flying Gaussian proof | methods | flying Gaussians, alanine dipeptide | Vojtech Spiwok | PRINT TORSION METAD | colvar generic bias |