Browse the 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 |
|---|---|---|---|---|---|---|
| 24.016 | Cryo-EM guided simulations of ribozyme | bio | metainference, cryo-EM | Bussi G. | PRINT EMMIVOX RESTRAINT WHOLEMOLECULES MOLINFO BIASVALUE GROUP INCLUDE ERMSD | colvar generic bias core isdb |
| 24.006 | Water vapor condensation | chemistry | metadynamics, homogeneous condensation, chemical potential | Zhong S. | PRINT SUM MEAN COORDINATIONNUMBER METAD LESS_THAN CLUSTER_NATOMS GROUP UPPER_WALLS DFSCLUSTERING CLUSTER_PROPERTIES CONTACT_MATRIX ONES UNITS MATRIX_VECTOR_PRODUCT | symfunc clusters adjmat function matrixtools setup generic bias core |
| 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 | Gigli L. | PRINT METAD TRANSPOSE MATHEVAL FLUSH INCLUDE SUM SELECT_COMPONENTS | valtools function matrixtools generic bias |
| 23.032 | Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics | bio | metadynamics, tSNE, neural network, machine learning, trp-cage, folding | Spiwok V. | PRINT WHOLEMOLECULES COMBINE METAD POSITION FIT_TO_TEMPLATE MOLINFO LESS_THAN ANN SUM SECONDARY_STRUCTURE_RMSD ALPHARMSD | annfunc secondarystructure function colvar generic bias |
| 23.022 | A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar | methods | collective variables, machine learning, toy model | Trizio E. | PRINT CUSTOM ENDPLUMED POSITION OPES_METAD BIASVALUE LOWER_WALLS PYTORCH_MODEL UPPER_WALLS UNITS | opes pytorch function colvar setup generic bias |
| 23.012 | JAK2 2D meta-eABF PMF with statistical analysis | bio | 2D meta-eABF, path CV, PMF | Kolossvary I. | PRINT CUSTOM METAD BIASVALUE LOWER_WALLS PATHMSD FLUSH UPPER_WALLS DRR | function colvar drr generic bias |
| 23.002 | Critical comparison of general-purpose collective variables for crystal nucleation | methods | metadynamics, umbrella sampling, commitor, entropy, PIV | Lam J. | PRINT RESTRAINT CUSTOM METAD VOLUME LOCAL_AVERAGE PAIRENTROPY Q4 Q6 ENERGY UPPER_WALLS PIV FUNCPATHMSD UNITS | piv symfunc gridtools function colvar setup generic bias |
| 22.038 | Enhanced Sampling Aided Design of Molecular Photoswitches | chemistry | reaction discovery, OPES explore, graph CV | Raucci U. | PRINT CUSTOM COORDINATION PYTORCH_MODEL OPES_METAD_EXPLORE UNITS | opes pytorch function colvar setup generic |
| 22.028 | N-glycan conformer distributions in atomistic simulation | bio | REST2, RECT, N-glycan, pucker | Grothaus I. | PUCKERING PRINT METAD MOLINFO READ CONVERT_TO_FES HISTOGRAM TORSION DUMPGRID | generic bias colvar gridtools |
| 22.018 | Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations | bio | ligand binding, docking, EMMI, LAT1 | Bonomi M. | PRINT EMMIVOX WHOLEMOLECULES MOLINFO BIASVALUE GROUP LOAD | setup generic bias core isdb |
| 22.007 | Characterization of a natural variant of human NDP52 and its functional consequences on mitophagy | bio | metadynamics, well-tempered, protein-protein interactions, disordered proteins, mutations autophagy | Papaleo E. | PRINT ANGLE ALPHABETA WHOLEMOLECULES COMBINE CUSTOM METAD MOLINFO DISTANCE CONSTANT COORDINATION LESS_THAN FLUSH TORSION UPPER_WALLS SUM SECONDARY_STRUCTURE_RMSD ALPHARMSD | secondarystructure function colvar multicolvar generic bias |
| 21.050 | N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity | methods | bio | Grothaus I. | PRINT DISTANCE CENTER | generic colvar vatom |
| 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 | Brotzakis F. | PRINT WHOLEMOLECULES MOLINFO DISTANCE BIASVALUE GROUP EMMI COM UPPER_WALLS RESTART | vatom colvar setup generic bias core isdb |
| 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 | Pfaendtner J. | PRINT ALPHABETA GYRATION CUSTOM COMBINE METAD DISTANCE CONSTANT COORDINATION INCLUDE COM TORSION ENERGY SUM PBMETAD | vatom function colvar multicolvar generic bias |
| 21.020 | Reweighted Jarzynski sampling | methods | free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions | Bal K. | MEAN OPT_AVERAGED_SGD CONSTANT CONVERT_TO_FES KDE UPPER_WALLS REWEIGHT_METAD COMBINE METAD OPES_METAD DISTANCE REWEIGHT_BIAS HISTOGRAM DUMPGRID UNITS MATRIX_VECTOR_PRODUCT CUSTOM BIASVALUE ACCUMULATE MORE_THAN VES_LINEAR_EXPANSION ANN MOVINGRESTRAINT SUM PRINT RESTRAINT COORDINATIONNUMBER FLUSH GROUP LOAD TD_WELLTEMPERED BF_CHEBYSHEV CONTACT_MATRIX ONES | opes ves symfunc annfunc bias adjmat function colvar matrixtools setup generic gridtools core |
| 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 | Magrino T. | generic | |
| 21.000 | Uremic toxin time scale dynamics | bio | uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs) | Pfaendtner J. | PRINT WHOLEMOLECULES DISTANCE GROUP COM | generic colvar core vatom |
| 20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Rizzi V. | PRINT ANGLE WHOLEMOLECULES ENDPLUMED FIXEDATOM FIT_TO_TEMPLATE DISTANCE MATHEVAL OPES_METAD COORDINATION GROUP PYTORCH_MODEL ENERGY UPPER_WALLS CENTER | opes vatom pytorch function colvar generic bias core |
| 20.015 | Rational design of ASCT2 inhibitors using an integrated experimental-computational approach | bio | ASCT2 transporter, small-molecules, cryo-EM, metainference | Bonomi M. | PRINT EMMIVOX WHOLEMOLECULES MOLINFO BIASVALUE GROUP LOAD DUMPATOMS | setup generic bias core isdb |
| 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 | Capelli R. | LOWER_WALLS CONVERT_TO_FES UPPER_WALLS REWEIGHT_METAD ENDPLUMED METAD COMBINE DISTANCE ABMD READ HISTOGRAM DUMPGRID CUSTOM MOLINFO ACCUMULATE ONES PRINT WHOLEMOLECULES FLUSH CONTACTMAP COM KDE FUNCPATHMSD | vatom gridtools function colvar generic bias |
| 19.079 | Impact of Glutamate Carboxylation in the Adsorption of the alpha-1 Domain of Osteocalcin to Hydroxyapatite and Titania | bio | metadynamics, peptide adsorption, parallel tempering, well-tempered ensemble | Alamdari S. | PRINT GYRATION METAD MOLINFO DISTANCE GROUP COM ENERGY UPPER_WALLS | vatom colvar generic bias core |
| 19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Salvalaglio M. | PRINT DISTANCES GYRATION ENDPLUMED DISTANCE GROUP INCLUDE DUMPMULTICOLVAR CENTER | vatom colvar multicolvar generic core |
| 19.059 | cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide | bio | bias-exchange metadynamics, cis-trans isomerization | Marinelli F. | PRINT METAD RANDOM_EXCHANGES INCLUDE TORSION | generic bias colvar |
| 19.049 | Determining the sizes of solid/liquid clusters in MD trajectories of nucleation | methods | nucleation, metadynamics, clustering, Steinhardt order parameters | Tribello G. | MEAN SMAC DISTANCES METAD LOCAL_Q6 CLUSTER_NATOMS Q6 DFSCLUSTERING MATRIX_VECTOR_PRODUCT CUSTOM OUTPUT_CLUSTER MORE_THAN SUM CLUSTER_DISTRIBUTION PRINT COORDINATIONNUMBER OUTER_PRODUCT GROUP CLUSTER_WEIGHTS CLUSTER_PROPERTIES CONTACT_MATRIX ONES | symfunc clusters adjmat function multicolvar matrixtools generic bias core |
| 19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Limongelli V. | FUNNEL_PS PRINT WHOLEMOLECULES FUNNEL RMSD METAD DISTANCE LOWER_WALLS COM UPPER_WALLS | vatom colvar funnel generic bias |
| 19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Papaleo E. | PRINT ALPHABETA WHOLEMOLECULES GYRATION COMBINE CUSTOM MOLINFO METAD LOWER_WALLS CONSTANT GROUP TORSION UPPER_WALLS SUM | function colvar multicolvar generic bias core |
| 19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Lindorff-Larsen K. | PRINT ALPHABETA COMBINE CUSTOM METAD MOLINFO CONSTANT FLUSH TORSION COMMITTOR SUM | function colvar multicolvar generic bias |
| 19.009 | RNA tetraloops folding | bio | metadynamics, RNA, folding | Bussi G. | PRINT WHOLEMOLECULES ENDPLUMED METAD RMSD MOLINFO ERMSD | generic bias colvar |
| 24.015 | nanocluster QM/MM | chemistry | nanocluster, QM/MM, pathCV, OPES, reaction modelling | Tiwari V. | UPPER_WALLS LOWER_WALLS RESTRAINT CENTER COMMITTOR DISTANCE UNITS PRINT OPES_METAD FLUSH | colvar generic opes bias vatom setup |
| 24.005 | Learning Markovian Dynamics with Spectral Maps | methods | spectral map, collective variables, machine learning | Rydzewski J. | BIASVALUE CUSTOM DISTANCE UNITS PRINT | colvar generic bias setup function |
| 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 | Hoff S. | BIASVALUE UPPER_WALLS INCLUDE MOLINFO WHOLEMOLECULES WRAPAROUND DISTANCE GROUP PRINT EMMIVOX | colvar generic core isdb bias |
| 23.031 | Identifying small molecules binding sites in RNA conformational ensembles with SHAMAN | bio | RNA, metadynamics, probes, mixed-solvent MD, small molecules, binding sites | Bonomi M. | SHADOW UPPER_WALLS POSITION METAD DISTANCES CUSTOM CENTER MOLINFO WHOLEMOLECULES WRAPAROUND DISTANCE GROUP SUM PRINT FIT_TO_TEMPLATE | colvar generic core isdb bias vatom multicolvar function |
| 23.021 | Into the Dynamics of Rotaxanes at Atomistic Resolution | materials | metadynamics, rotaxanes, molecular shuttles, molecular machines | Leanza L. | UPPER_WALLS TORSION METAD MATHEVAL CUSTOM CENTER DISTANCE PRINT FIXEDATOM | colvar generic bias vatom function |
| 23.011 | OneOPES, a combined enhanced sampling method to rule them all | bio | OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding | Rizzi V. | TORSION METAD ECV_MULTITHERMAL ENDPLUMED OPES_EXPANDED MOLINFO OPES_METAD_EXPLORE ENERGY DISTANCE PRINT | generic colvar opes bias |
| 23.001 | Quantum phase diagram of water | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Bore S. | UPPER_WALLS ECV_UMBRELLAS_LINE MORE_THAN LOWER_WALLS ONES CUSTOM OPES_EXPANDED RESTART ENVIRONMENTSIMILARITY MATRIX_VECTOR_PRODUCT DISTANCE_MATRIX GROUP SUM MEAN PRINT INCLUDE | envsim matrixtools generic opes adjmat core bias setup function |
| 22.037 | Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site | chemistry | metadynamics, DNA, abasic | Jones M. | DISTANCES METAD CENTER DISTANCE MEAN PRINT GROUP | colvar generic core bias vatom multicolvar function |
| 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 | Bonomi M. | RMSD PRINT | generic colvar |
| 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 | Ansari N. | RMSD UPPER_WALLS LOWER_WALLS MATHEVAL PYTORCH_MODEL OPES_METAD CENTER COORDINATION CUSTOM WHOLEMOLECULES DISTANCE COMMITTOR GROUP PRINT FIT_TO_TEMPLATE FIXEDATOM | colvar generic opes core pytorch bias vatom function |
| 22.006 | Peptide framework for screening the effects of amino acids on assembly | bio | metadynamics, peptides | White A. | ONES DISTANCE METAD CUSTOM COM COMBINE REWEIGHT_BIAS CONVERT_TO_FES DISTANCES DUMPGRID CENTER KDE MEAN HISTOGRAM GYRATION ACCUMULATE SUM GROUP PRINT INCLUDE | colvar gridtools generic core bias vatom multicolvar function |
| 21.049 | Multiple-path-metadynamics and PathMaps | methods | path-CV, metadynamics, multiple-walker, multiple paths, pathmap | Pérez-de-Alba-Ortíz A. | CONSTANT UPPER_WALLS TORSION METAD LOWER_WALLS MOVINGRESTRAINT ENSEMBLE CUSTOM RESTRAINT LOAD UNITS PRINT COMBINE | colvar generic bias setup function |
| 21.039 | Deep learning the slow modes for rare events sampling | methods | collective variables, machine learning, slow modes, deep-tica, opes | Bonati L. | ECV_MULTITHERMAL ENDPLUMED MOLINFO WHOLEMOLECULES MATRIX_VECTOR_PRODUCT ONES DISTANCE PYTORCH_MODEL CUSTOM OPES_EXPANDED DISTANCE_MATRIX LOAD UNITS ENVIRONMENTSIMILARITY COMBINE MORE_THAN TORSION SPHERICAL_HARMONIC MEAN VOLUME Q6 RMSD CONTACT_MATRIX CONTACTMAP SUM ENERGY GROUP PRINT OPES_METAD INCLUDE FLUSH | envsim colvar symfunc matrixtools generic opes adjmat core pytorch setup function |
| 21.029 | Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs | bio | metadynamics, small peptide, machine learning | Tiwary P. | EXTERNAL TORSION MOLINFO RESTART ENERGY PRINT FLUSH | setup generic bias colvar |
| 21.019 | Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations | materials | Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen | Salvalaglio M. | TORSIONS MATHEVAL COM DISTANCE KDE PRINT | colvar gridtools generic vatom multicolvar function |
| 21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Bal K. | UPPER_WALLS MATRIX_VECTOR_PRODUCT ONES COORDINATIONNUMBER METAD LOAD UNITS CONVERT_TO_FES MORE_THAN DUMPGRID MEAN HISTOGRAM REWEIGHT_METAD MOVINGRESTRAINT CONTACT_MATRIX SUM COMMITTOR GROUP PRINT FLUSH | symfunc matrixtools gridtools generic adjmat core bias setup 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 | Bottaro S. | TORSION CENTER MOLINFO RESTART DISTANCE ERMSD PRINT ABMD | colvar generic bias vatom setup |
| 20.024 | Gaussian Mixture Based Enhanced Sampling (GAMBES) | methods | enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias | Debnath J. | UPPER_WALLS TORSION DISTANCES LOWER_WALLS HIGHEST CUSTOM CENTER SUM DISTANCE ENERGY LOAD UNITS PRINT GROUP COMBINE | colvar generic core bias vatom setup multicolvar function |
| 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 | Heller G. | ENDPLUMED ALPHARMSD MOLINFO WHOLEMOLECULES ENSEMBLE METAINFERENCE COMBINE TORSION ANTIBETARMSD DIHCOR PARABETARMSD COORDINATION STATS PBMETAD GYRATION CS2BACKBONE GROUP PRINT INCLUDE FLUSH | colvar generic secondarystructure core isdb bias multicolvar function |
| 20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Bonati L. | UPPER_WALLS TORSION ENDPLUMED GROUP LOWER_WALLS MATHEVAL PYTORCH_MODEL COM LOAD DISTANCE UNITS PRINT OPES_METAD FLUSH | colvar generic opes core bias pytorch vatom setup function |
| 19.078 | Iterative unbiasing of quasi-equilibrium sampling | methods | metadynamics, reweighting | Giberti F. | BIASVALUE COORDINATIONNUMBER METAD COLLECT_FRAMES MATHEVAL CONTACT_MATRIX DUMPATOMS MATRIX_VECTOR_PRODUCT ONES DISTANCE UNITS MEAN PRINT GROUP REWEIGHT_BIAS | colvar symfunc matrixtools generic adjmat landmarks core bias setup function |
| 19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Invernizzi M. | EXTERNAL POSITION TORSION METAD ENDPLUMED UNITS PRINT OPES_METAD | colvar generic opes bias setup |
| 19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Jelfs K. | PRINT DISTANCES ANGLE INPLANEDISTANCES MOVINGRESTRAINT CUSTOM CENTER SUM RESTART DISTANCE COM GROUP FLUSH | colvar generic core bias vatom setup multicolvar function |
| 19.048 | Understanding Ligand Binding Selectivity in a Prototypical GPCR Family | bio | metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding | Gervasio F. | BIASVALUE PRINT UPPER_WALLS METAD LOWER_WALLS MATHEVAL WHOLEMOLECULES DISTANCE COM CONSTANT | colvar generic bias vatom function |
| 19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Camilloni C. | UPPER_WALLS ENDPLUMED MOLINFO WHOLEMOLECULES CONSTANT BIASVALUE CUSTOM ALPHABETA COMBINE TORSION ANTIBETARMSD SECONDARY_STRUCTURE_RMSD LOWER_WALLS PBMETAD LESS_THAN RESTART SUM CS2BACKBONE GROUP PRINT FLUSH | colvar generic secondarystructure core isdb bias setup multicolvar function |
| 19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Tiwary P. | CONSTANT EXTERNAL PRINT TORSION CUSTOM RESTART WHOLEMOLECULES SUM COMMITTOR DISTANCE ALPHABETA COM COMBINE | colvar generic bias vatom setup multicolvar function |
| 19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Pietropaolo A. | BIASVALUE TORSION METAD MATHEVAL WHOLEMOLECULES PRINT CONSTANT | generic bias colvar function |
| 19.008 | anncolvar | methods | neural network, dimensionality reduction | Spiwok V. | POSITION METAD ALPHARMSD LESS_THAN MATHEVAL MOLINFO WHOLEMOLECULES SUM PRINT FIT_TO_TEMPLATE COMBINE SECONDARY_STRUCTURE_RMSD | colvar generic secondarystructure bias function |
| 24.014 | Learning Collective Variables with Synthetic Data Augmentation through Physics-inspired Geodesic Interpolation | methods | data augmentation, geodesic interpolation, collective variables, protein folding | Nam J. | METAD WHOLEMOLECULES FLUSH PYTORCH_MODEL LOWER_WALLS PRINT DRR COORDINATION MOLINFO RMSD UPPER_WALLS | drr generic colvar bias pytorch |
| 24.004 | Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables | materials | metadynamics, nucleation, machine learning | Zou Z. | METAD GROUP INCLUDE COM PRINT RESTART LOAD CENTER | vatom generic setup core bias |
| 23.040 | Supramolecular capsules assembly dynamics | chemistry | Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics | Capelli R. | UNITS BETWEEN DISTANCE LESS_THAN METAD WHOLEMOLECULES GROUP FLUSH DISTANCES SUM COM PRINT CUSTOM POSITION CENTER | vatom generic colvar setup core multicolvar function bias |
| 23.030 | Data Driven Classification of Ligand Unbinding Pathways | bio | OPES Explore, OPES Flooding, Benzene T4 Lysozyme, Ligand unbinding, Pathway classification, Kinetics, Residence time | Ray D. | DISTANCE ENDPLUMED CUSTOM UNITS PRINT BIASVALUE ENERGY MOLINFO OPES_METAD MATHEVAL FLUSH LOWER_WALLS COM COORDINATION COMMITTOR TORSION UPPER_WALLS OPES_METAD_EXPLORE WHOLEMOLECULES GROUP WRAPAROUND FIT_TO_TEMPLATE POSITION CENTER | vatom generic opes colvar setup core function bias |
| 23.020 | FEP simulations of ATOX1 homodimer | chemistry | parallel bias metadynamics, FEP, free-energy of metal ion dissociation | Pietropaolo A. | PBMETAD DISTANCE WHOLEMOLECULES PRINT BIASVALUE ANGLE MATHEVAL CONSTANT | bias colvar function generic |
| 23.010 | An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G‑Protein-Coupled Receptor Ligands | bio | GPCR, binding free energy, free energy surface | Clark T. | DISTANCE METAD WHOLEMOLECULES LOWER_WALLS PRINT BIASVALUE MATHEVAL CONSTANT UPPER_WALLS | bias colvar function generic |
| 23.000 | Atomistic simulations of RNA tetraloop folding via PTWTE-WTM | bio | parallel tempering, well-tempered metadynamics, well-tempered ensemble, RNA, Tetraloop, Folding | Zerze G. | METAD WHOLEMOLECULES LOWER_WALLS PRINT ENERGY CONTACTMAP UPPER_WALLS | bias colvar generic |
| 22.036 | Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction | bio | Well-tempered MetaDynamics with Hamiltonian Replica Exchange | Krepl M. | GHBFIX METAD FLUSH GROUP PRINT BIASVALUE CUSTOM COORDINATION MOLINFO LOAD COMBINE UPPER_WALLS | generic colvar setup core function bias |
| 22.026 | Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification | materials | Peptoid, silica | Pfaendtner J. | GYRATION PBMETAD DISTANCE COM PRINT MOLINFO UPPER_WALLS | bias colvar vatom generic |
| 22.016 | Homogeneous ice nucleation in an ab initio machine learning model of water | chemistry | ice, water, nucleation, seeding, environment similarity, interfacial free energy, interfaces | Piaggi P. | DUMPGRID MORE_THAN CUSTOM MEAN DISTANCE_MATRIX SUM PRINT ENERGY ENVIRONMENTSIMILARITY OPES_METAD VOLUME RESTART HISTOGRAM UPPER_WALLS GROUP AROUND ONES ACCUMULATE MATRIX_VECTOR_PRODUCT KDE | generic opes volumes gridtools colvar setup adjmat core function matrixtools bias envsim |
| 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 | Spiwok V. | LOAD METAD PRINT WHOLEMOLECULES | bias setup generic |
| 21.048 | Enhancing ligand exploration within a channel pore and fenestrations using metadynamics | bio | well-tempered metadynamics, protein-ligand enhanced sampling, sodium channel, Nav, small molecule drug | Tao E. | UNITS DISTANCE METAD LOWER_WALLS COM UPPER_WALLS PRINT CUSTOM TORSION | vatom generic colvar setup function bias |
| 21.038 | Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics | materials | metadynamics, SGOOP, nucleation, urea | Zou Z. | CONTACT_MATRIX METAD GROUP INCLUDE VOLUME MATRIX_VECTOR_PRODUCT PRINT ENERGY CENTER MEAN ONES LOAD COMBINE COORDINATIONNUMBER | vatom generic colvar setup adjmat core function matrixtools bias symfunc |
| 21.028 | From Enhanced Sampling to Reaction Profiles | methods | collective variables, multi-state, machine learning, Deep-TDA | Trizio E. | DISTANCE ENDPLUMED LOAD UNITS FIXEDATOM DISTANCES PRINT CENTER ANGLE OPES_METAD LOWER_WALLS COORDINATION TORSION UPPER_WALLS WHOLEMOLECULES GROUP PYTORCH_MODEL FIT_TO_TEMPLATE MATHEVAL | vatom generic opes colvar setup multicolvar core function bias pytorch |
| 21.018 | Localized Volume-based Metadynamics | bio | LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification | Capelli R. | DISTANCE DUMPGRID ENDPLUMED CUSTOM CONVERT_TO_FES REWEIGHT_METAD FIXEDATOM PRINT RMSD FLUSH COM COORDINATION HISTOGRAM READ UPPER_WALLS METAD WHOLEMOLECULES GROUP POSITION ONES ACCUMULATE MATHEVAL KDE | vatom generic gridtools colvar core function bias |
| 21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Pietropaolo A. | PBMETAD WHOLEMOLECULES PRINT BIASVALUE RESTART MATHEVAL CONSTANT TORSION | generic colvar setup function bias |
| 20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Brotzakis F. | WHOLEMOLECULES DUMPGRID GROUP DISTANCES PRINT BIASVALUE RMSD CUSTOM EMMI CONVERT_TO_FES MOLINFO ONES ACCUMULATE HISTOGRAM READ KDE | generic gridtools colvar multicolvar core isdb function bias |
| 20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Spiwok V. | METAD PRINT TORSION | bias colvar generic |
| 20.013 | Improving accuracy of biased Alchemistic simulations | methods | flying Gaussian method, Alchemistic simulations, thermodynamic integration, reweighting | Spiwok V. | METAD PRINT TORSION | bias colvar generic |
| 20.003 | Enhanced sampling of transition states | methods | Variationally Enhanced Sampling, Target distribution, Transition state, Enhanced Sampling, Nucleation, chemical reaction | Debnath J. | UNITS VES_LINEAR_EXPANSION OPT_AVERAGED_SGD PRINT ENERGY BF_LEGENDRE POSITION LOAD | colvar setup generic ves |
| 19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Pfaendtner J. | GYRATION DISTANCE METAD COM PRINT ENERGY MOLINFO UPPER_WALLS | bias colvar vatom generic |
| 19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Rydzewski J. | UNITS METAD PATHMSD LOWER_WALLS PRINT RESTART UPPER_WALLS | bias colvar setup generic |
| 19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Paissoni C. | MATHEVAL PBMETAD SAXS WHOLEMOLECULES GROUP INCLUDE ENDPLUMED PRINT BIASVALUE COMBINE COORDINATION MOLINFO ANGLE STATS ENSEMBLE CENTER ALPHABETA | vatom generic colvar core multicolvar isdb function bias |
| 19.047 | Close Structure | methods | metadynamics, RMSD, path collective variables, property map | Spiwok V. | PROPERTYMAP METAD PRINT WHOLEMOLECULES | bias colvar generic |
| 19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Raiteri P. | UNITS DISTANCE METAD FLUSH PRINT RESTART MATHEVAL UPPER_WALLS | generic colvar setup function bias |
| 19.027 | Multithermal-multibaric simulations using VES | methods | ves, Wang Landau, multicanonical, liquid sodium, density anomaly | Piaggi P. | DUMPGRID CUSTOM AVERAGE CONVERT_TO_FES COMBINE REWEIGHT_TEMP_PRESS UNITS VES_LINEAR_EXPANSION PRINT ENERGY TD_MULTICANONICAL OPT_AVERAGED_SGD OPT_DUMMY RESTART HISTOGRAM READ REWEIGHT_BIAS BF_LEGENDRE ONES ACCUMULATE KDE | generic gridtools colvar setup function bias ves |
| 19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Capelli R. | DUMPGRID ENDPLUMED CUSTOM CONVERT_TO_FES REWEIGHT_METAD PRINT FLUSH COM COORDINATION HISTOGRAM READ UPPER_WALLS METAD WHOLEMOLECULES GROUP WRAPAROUND FIT_TO_TEMPLATE POSITION ONES ACCUMULATE MATHEVAL KDE | vatom generic gridtools colvar core function bias |
| 19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Bonomi M. | WHOLEMOLECULES GROUP PRINT BIASVALUE MOLINFO EMMI | isdb bias core generic |
| 24.013 | Estimating Free Energy Surfaces and their Convergence from multiple, independent static and history-dependent biased molecular-dynamics simulations with Mean Force Integration | methods | Mean Force Integration, Convergence, FES, Umbrella Sampling | Salvalaglio M. | FLUSH MATHEVAL MOLINFO DISTANCE COORDINATIONNUMBER TORSION ENERGY RESTRAINT BIASVALUE METAD PRINT RESTART COMMITTOR | function symfunc generic bias colvar setup |
| 24.003 | Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations | chemistry | steered molecular dynamics, foldamers, peptoids, bio-inspired | Torkelson K. | ALPHABETA MOVINGRESTRAINT INCLUDE DISTANCE COM TORSION PRINT COORDINATION GYRATION WHOLEMOLECULES | vatom multicolvar generic bias colvar |
| 23.039 | Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation | chemistry | metadynamics, ligand dissociation | Beyerle E. | FIXEDATOM MOLINFO DISTANCE DUMPMASSCHARGE CENTER COMBINE UPPER_WALLS RESTRAINT METAD PRINT | function vatom generic bias colvar |
| 23.029 | An accurate and efficient SAXS/SANS implementation including solvation layer effects suitable for restrained Molecular Dynamics simulations | bio | SAXS, SANS, SAS, metainference, proteins, nucleic-acid | Ballabio F. | SAXS GROUP MOLINFO DISTANCE CENTER UPPER_WALLS WRAPAROUND RMSD BIASVALUE STATS PRINT ENSEMBLE | bias function vatom isdb generic core colvar |
| 23.019 | Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors | bio | binding pathway, binding energy, sketch-map, drug development | Bobrovs R. | CUSTOM DISSIMILARITIES LANDMARK_SELECT_FPS DISTANCE TRANSPOSE PATHMSD SKETCHMAP COM VSTACK UPPER_WALLS SKETCHMAP_PROJECTION METAD PRINT COLLECT_FRAMES VORONOI WHOLEMOLECULES | valtools function landmarks vatom matrixtools generic bias colvar dimred |
| 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 | Ray D. | CENTER ENDPLUMED LOWER_WALLS COMMITTOR WHOLEMOLECULES OPES_METAD MOLINFO CONTACTMAP FIT_TO_TEMPLATE UPPER_WALLS FIXEDATOM MATHEVAL INCLUDE PYTORCH_MODEL COORDINATION GROUP DISTANCE COMBINE ENERGY RMSD PRINT ANGLE CUSTOM | function vatom core generic opes pytorch bias colvar |
| 22.045 | Binding mode and mechanism of enzymatic polyethylene terephthalate degradation | bio | metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation | Colizzi F. | MOVINGRESTRAINT DISTANCE PRINT COM UPPER_WALLS METAD LOWER_WALLS ANGLE WHOLEMOLECULES | generic colvar vatom bias |
| 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 | Lindorff-Larsen K. | MOLINFO PBMETAD TORSION GYRATION WHOLEMOLECULES | generic colvar bias |
| 22.025 | Bubble nucleation rate predictions in a Lennard-Jones fluid | materials | free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation | Bal K. | REWEIGHT_BIAS CONVERT_TO_FES ANN RESTRAINT COMMITTOR COORDINATIONNUMBER UPPER_WALLS CONTACT_MATRIX LESS_THAN UNITS LOAD FLUSH VOLUME DUMPGRID MOVINGRESTRAINT GROUP ONES MATRIX_VECTOR_PRODUCT HISTOGRAM BIASVALUE SUM PRINT CUSTOM MEAN | annfunc adjmat function symfunc core matrixtools generic bias setup colvar gridtools |
| 22.015 | Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome | bio | photodynamics, bacteriophytochrome, variationally enhanced sampling | Rydzewski J. | VES_LINEAR_EXPANSION TD_UNIFORM TORSION PRINT BF_FOURIER OPT_AVERAGED_SGD | colvar generic ves |
| 22.004 | Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques | chemistry | reaction discovery, OPES, collective variables | Raucci U. | GROUP MATHEVAL OPES_METAD DISTANCE OPES_METAD_EXPLORE LOWER_WALLS COM UPPER_WALLS LOAD PYTORCH_MODEL PRINT COORDINATION UNITS CUSTOM | function core vatom opes pytorch generic bias colvar setup |
| 21.047 | Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations | materials | pair entropy, metadynamics, ves, solids, crystallization | Piaggi P. | VES_LINEAR_EXPANSION TD_WELLTEMPERED COMBINE VOLUME ENERGY PAIRENTROPY METAD PRINT RESTART BF_LEGENDRE LOAD OPT_AVERAGED_SGD | ves function generic bias setup colvar gridtools |
| 21.037 | Molecular Dynamics simulations of RBD/hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain | Bonomi M. | DISTANCE PRINT RMSD | generic colvar |
| 21.027 | EGFR activating mutations mechanism | bio | metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA | Gervasio F. | MATHEVAL INCLUDE DISTANCE MOLINFO PRINT SECONDARY_STRUCTURE_RMSD CONTACTMAP ENERGY UPPER_WALLS SUM ALPHARMSD LESS_THAN METAD LOWER_WALLS WHOLEMOLECULES | function generic bias colvar secondarystructure |
| 21.017 | All-atom simulations of the Vav1 AD construct | bio | metadynamics, parallel-bias, well-tempered | Orioli S. | CUSTOM ALPHABETA GROUP REWEIGHT_BIAS MOLINFO SECONDARY_STRUCTURE_RMSD CONSTANT PRINT COMBINE PBMETAD CONTACTMAP METAD ALPHARMSD SUM TORSION LESS_THAN RESTART WHOLEMOLECULES | function core multicolvar generic bias colvar setup secondarystructure |
| 21.007 | Sampling enhancement by metadynamics driven by machine learning and de novo protein modelling | bio | metadynamics, machine learning, protein folding | Spiwok V. | MATHEVAL MOLINFO POSITION SECONDARY_STRUCTURE_RMSD COMBINE FIT_TO_TEMPLATE SUM ALPHARMSD LESS_THAN WHOLEMOLECULES | function generic colvar secondarystructure |
| 20.032 | Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil | materials | clustering, conformational isomers | Salvalaglio M. | ENDPLUMED TORSION PRINT | generic colvar |
| 20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Invernizzi M. | MORE_THAN ECV_UMBRELLAS_LINE DISTANCE_MATRIX ENDPLUMED OPES_EXPANDED TORSION WHOLEMOLECULES Q6 SPHERICAL_HARMONIC MOLINFO ECV_MULTITHERMAL_MULTIBARIC ENVIRONMENTSIMILARITY UPPER_WALLS ECV_LINEAR CONTACT_MATRIX ECV_MULTITHERMAL UNITS LOAD MATHEVAL VOLUME GROUP POSITION ONES MATRIX_VECTOR_PRODUCT COMBINE ENERGY RMSD SUM PRINT CUSTOM MEAN | function symfunc core matrixtools opes generic bias setup colvar adjmat envsim |
| 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 | Gervasio F. | GROUP MATHEVAL INCLUDE DISTANCE CONSTANT PRINT MOLINFO COM CONTACTMAP PROJECTION_ON_AXIS UPPER_WALLS LOAD BIASVALUE METAD LOWER_WALLS FUNCPATHGENERAL WHOLEMOLECULES | function bias vatom generic core colvar setup |
| 20.002 | Exploring conformational dynamics of the extracellular Venus flytrap domain of the GABAB receptor, a path-metadynamics study | bio | Metadynamics, path CVs | Ocello R. | GROUP MOLINFO PATHMSD UPPER_WALLS METAD PRINT RESTART WHOLEMOLECULES | core generic bias colvar setup |
| 19.076 | Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones | bio | molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics | Assenza S. | MOVINGRESTRAINT ENDPLUMED PRINT UNITS GYRATION | generic colvar setup bias |
| 19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Rydzewski J. | POSITION MAZE_SIMULATED_ANNEALING PRINT MAZE_LOSS UNITS MAZE_OPTIMIZER_BIAS | maze generic colvar setup |
| 19.056 | maze | methods | maze, ligand unbinding | Rydzewski J. | POSITION MAZE_SIMULATED_ANNEALING PRINT MAZE_LOSS UNITS MAZE_OPTIMIZER_BIAS | maze generic colvar setup |
| 19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Provasi D. | DISTANCE CONTACTMAP COM FUNCPATHMSD RMSD ENDPLUMED METAD PRINT WHOLEMOLECULES | function vatom generic bias colvar |
| 19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Sosso G. | MFILTER_MORE DFSCLUSTERING FLUSH Q6 CLUSTER_WITHSURFACE CLUSTER_NATOMS OUTPUT_CLUSTER LOCAL_Q6 CONTACT_MATRIX ENDPLUMED COMMITTOR | symfunc multicolvar generic clusters adjmat |
| 19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Salvalaglio M. | MATHEVAL CELL COMBINE LOWER_WALLS VOLUME ENERGY METAD UPPER_WALLS ENDPLUMED TORSION PRINT | function generic colvar bias |
| 19.006 | Flying Gaussian proof | methods | flying Gaussians, alanine dipeptide | Spiwok V. | TORSION PRINT METAD | generic colvar bias |
| 24.012 | Molecular simulations to investigate the impact of N6-methylation in RNA recognition | bio | metadynamics, alchemistry, RNA modification, RNA:protein interactions | Bussi G. | MOLINFO UPPER_WALLS GROUP GHBFIX COORDINATION LOWER_WALLS COMBINE DEBUG CENTER BIASVALUE DISTANCE PRINT METAD COM | core bias generic vatom function colvar |
| 24.002 | Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes | chemistry | metadynamics, ligand design, solvent extraction | Wang X. | RESTART UNITS PRINT METAD TORSION | bias setup generic colvar |
| 23.038 | Determinants of Neutral Antagonism and Inverse Agonism in the β2-adrenergic receptor | bio | protein coupled receptor, beta-adrenergic, receptor activation, antagonism, inverse agonism, metadynamics | Clark T. | MOLINFO MATHEVAL RMSD WHOLEMOLECULES DISTANCE PRINT METAD | bias colvar generic function |
| 23.028 | Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process | chemistry | Ammonia decomposition; Dynamics;OPES; Neural Network potential | Yang M. | DISTANCES MEAN LOWER_WALLS CENTER COMMITTOR ZDISTANCES UPPER_WALLS GROUP SUM MATHEVAL UNITS PRINT COORDINATIONNUMBER CONTACT_MATRIX DISTANCE FIXEDATOM LESS_THAN OPES_METAD FLUSH CUSTOM MATRIX_VECTOR_PRODUCT ENERGY ONES COM | core opes setup multicolvar bias generic vatom function adjmat symfunc matrixtools colvar |
| 23.018 | Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention | materials | metadynamics, surface binding, peptide adsorption | Torkelson K. | GYRATION DISTANCE PBMETAD PRINT UPPER_WALLS COM | bias colvar generic vatom |
| 23.008 | PBMetaD simulations of Histatin5 | bio | metadynamics, IDP, Rg, PPII | Pesce F. | MOLINFO GROUP GYRATION WHOLEMOLECULES PBMETAD PRINT TORSION | core bias generic colvar |
| 22.044 | Colloid Crystallisation Analyses | materials | Q4, Q6, Pair Entropy, DFS | Finney A. | Q4 CLUSTER_NATOMS GROUP LOCAL_Q6 CONTACT_MATRIX Q6 COMBINE MFILTER_LESS MFILTER_MORE PRINT LOCAL_Q4 COORDINATIONNUMBER DFSCLUSTERING LOCAL_AVERAGE | core multicolvar generic clusters function adjmat symfunc |
| 22.034 | Rationalising the difference in crystallisability of two Sulflowers using efficient in silico methods | materials | metadynamics, crystallizability, crystal structure prediction, sulflower, persulforated coronene | Salvalaglio M. | DRMSD CUSTOM LOWER_WALLS SUM MATHEVAL CELL COMMITTOR METAD CONSTANT DISTANCE PRINT UPPER_WALLS | generic bias colvar function |
| 22.024 | Conformational Entropy as a Potential Liability of Computationally Designed Antibodies | bio | metadynamics, conformational entropy, antibody, nanobody | Löhr T. | MOLINFO CUSTOM COM RESTART SECONDARY_STRUCTURE_RMSD COMBINE SUM ALPHABETA WHOLEMOLECULES ANTIBETARMSD CONSTANT PRINT PBMETAD ALPHARMSD LESS_THAN TORSION | setup multicolvar bias generic vatom function secondarystructure colvar |
| 22.014 | Quasi Liquid Layer Order Parameters | materials | Quasi-Liquid Layer, Steinhardt Order Parameter, Entropy Fingerprint | Shi J. | Q3 ENDPLUMED DUMPGRID LOCAL_Q3 Q4 LOAD HISTOGRAM PAIRENTROPIES LOCAL_Q6 Q6 UNITS DUMPMULTICOLVAR LOCAL_Q4 LOCAL_AVERAGE | setup multicolvar generic symfunc gridtools |
| 22.003 | Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling | methods | opes, metadynamics, reweighting, alanine, muller | Invernizzi M. | UPPER_WALLS ENDPLUMED POSITION CUSTOM ENERGY LOWER_WALLS UNITS ECV_MULTITHERMAL OPES_EXPANDED OPES_METAD_EXPLORE BIASVALUE PBMETAD PRINT ECV_UMBRELLAS_FILE METAD OPES_METAD TORSION | opes setup bias generic function colvar |
| 21.046 | Ubiquitin Interacting Motifs, Duality Between Structured and Disordered Motifs | bio | wt metadynamics, ubiquitin, ataxin-3, short linear motifs, ubiquitin binding motif, moonlight functions, intrinsic disorder | Papaleo E. | ENDPLUMED CUSTOM GROUP GYRATION LOWER_WALLS COMBINE SUM ALPHABETA WHOLEMOLECULES METAD CONSTANT PRINT UPPER_WALLS TORSION | core multicolvar bias generic function colvar |
| 21.036 | Modelling the structure and interactions of intrinsically disordered peptides with multiple-replica, metadynamics-based sampling methods and force-field combinations | bio | Bias Exchange Metadynamics, PTWTE-metaD | Salvalaglio M. | GYRATION LOWER_WALLS LOWEST ALPHARMSD UPPER_WALLS MOLINFO GROUP COORDINATION SUM DIHCOR WHOLEMOLECULES ANTIBETARMSD PRINT RANDOM_EXCHANGES LESS_THAN METAD DIHEDRAL_CORRELATION SECONDARY_STRUCTURE_RMSD ENERGY PARABETARMSD | core multicolvar bias generic function secondarystructure colvar |
| 21.026 | Probing allosteric regulations with coevolution-driven molecular simulations | bio | metadynamics, coevolution, allostery, adenylate cyclase | Colizzi F. | UPPER_WALLS UNITS WHOLEMOLECULES PATHMSD DISTANCE PRINT METAD COM | setup bias generic vatom colvar |
| 21.016 | MD SAXS GTPase associated center | bio | metadynamics, RNA, folding, SAXS | Bussi G. | MOLINFO CUSTOM SAXS GROUP GYRATION LOWER_WALLS CENTER ERMSD WHOLEMOLECULES INCLUDE METAD PRINT UPPER_WALLS | core bias generic vatom isdb function colvar |
| 21.006 | OPES, On-the-fly Probability Enhanced Sampling Method | methods | opes, alanine dipeptide, well-tempered, multithermal, multiumbrella | Invernizzi M. | ENDPLUMED ECV_UMBRELLAS_LINE ENERGY ECV_MULTITHERMAL OPES_EXPANDED PRINT OPES_METAD TORSION | opes generic colvar |
| 20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Pietropaolo A. | COORDINATION CENTER WHOLEMOLECULES PBMETAD PRINT | bias colvar generic vatom |
| 20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Pfaendtner J. | DISTANCES CUSTOM GROUP RESTART COORDINATION SUM CENTER WHOLEMOLECULES DISTANCE PRINT | core setup multicolvar generic vatom function colvar |
| 20.001 | Conformational stability and dynamics in solution and in crystals report similarly on unfolding and aggregation propensity of amyloidogenic proteins | bio | metainference, metadynamics, NMR, protein dynamics, b2m, protein crystals | Camilloni C. | LOWER_WALLS CS2BACKBONE UPPER_WALLS TORSION MOLINFO ENDPLUMED GROUP SUM WHOLEMOLECULES ANTIBETARMSD BIASVALUE PRINT ALPHABETA CONSTANT LESS_THAN FLUSH CUSTOM SECONDARY_STRUCTURE_RMSD COMBINE PBMETAD | core multicolvar bias generic isdb function secondarystructure colvar |
| 19.075 | PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python | other | Python, automatic differentiation | Giorgino T. | ENDPLUMED CUSTOM GROUP ANGLE RESTRAINT COMBINE CENTER DUMPDERIVATIVES DISTANCE PRINT TORSION | core bias generic vatom function colvar |
| 19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Chen W. | POSITION RESTRAINT COMBINE ANN COM | bias vatom function annfunc colvar |
| 19.055 | Flying Gaussian method | methods | flying Gaussians, alanine dipeptide, peptide bond, Met-enkephalin | Spiwok V. | COMBINE MATHEVAL DISTANCE PRINT METAD TORSION | generic bias colvar function |
| 19.045 | Adsorption free energy of Ca/CO3 ions on calcite steps in contact with water | materials | metadynamics, well-tempered, multiple walkers, LAMMPS | Pierre M. | POSITION FLUSH GROUP RESTART COORDINATION LOWER_WALLS UNITS METAD PRINT UPPER_WALLS | core setup bias generic colvar |
| 19.035 | Dimerization of GPCRs from coarse-grained umbrella sampling | bio | Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization | Provasi D. | GROUP COM RESTRAINT DISTANCE PRINT TORSION | core bias generic vatom colvar |
| 19.025 | Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide | bio | metainference, NMR, protein dynamics, force-fields | Camilloni C. | MOLINFO ENDPLUMED JCOUPLING FLUSH RDC STATS METAINFERENCE GYRATION WHOLEMOLECULES BIASVALUE CS2BACKBONE PBMETAD ENSEMBLE PRINT TORSION | bias generic isdb function colvar |
| 19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Salvalaglio M. | LOWER_WALLS CENTER COMMITTOR METAD DISTANCE PRINT UPPER_WALLS TORSION | bias generic colvar vatom |
| 19.005 | Cmyc small molecule interaction | bio | metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP | Heller G. | MOLINFO GROUP METAINFERENCE COORDINATION GYRATION ALPHABETA CENTER INCLUDE WHOLEMOLECULES CS2BACKBONE DISTANCE PBMETAD PRINT | core multicolvar bias generic vatom isdb colvar |
| 24.011 | Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble | methods | committor, machine learning | Kang P. | LOWER_WALLS ENERGY LOAD MOLINFO WHOLEMOLECULES CUSTOM CELL PRINT INCLUDE RMSD BIASVALUE POSITION COORDINATION UNITS DISTANCE TORSION ENDPLUMED MATHEVAL GROUP UPPER_WALLS | core setup colvar bias generic function |
| 24.001 | A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations | bio | OPES, OPES-Flooding, QM/MM, Kinetics, Enzyme Catalysis | Ray D. | LOWER_WALLS PRINT OPES_METAD FLUSH TORSION CUSTOM COMMITTOR COMBINE DISTANCE UNITS UPPER_WALLS | setup opes colvar bias generic function |
| 23.037 | Estimating binding free energy of solid binding peptides without extensive sampling | bio | metadynamics, solid binding peptides | Qi X. | LOWER_WALLS PRINT MOLINFO COM GYRATION DISTANCE UPPER_WALLS PBMETAD | vatom bias generic colvar |
| 23.027 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, DFS, Q3, Pair Entropy | Finney A. | LOAD SPHERICAL_HARMONIC FIXEDATOM MATRIX_PRODUCT CUSTOM COMBINE PRINT Q3 MATRIX_VECTOR_PRODUCT LOCAL_AVERAGE DENSITY KDE CLUSTER_NATOMS HISTOGRAM AROUND DFSCLUSTERING COORDINATIONNUMBER OUTER_PRODUCT HIGHEST UNITS ACCUMULATE CONTACT_MATRIX RESTRAINT SUM ONES MEAN CLUSTER_DISTRIBUTION DUMPGRID LOCAL_Q3 VSTACK TRANSPOSE GROUP CLUSTER_WEIGHTS MORE_THAN | gridtools core setup volumes vatom clusters symfunc valtools matrixtools adjmat bias generic function |
| 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 | Das S. | LOWER_WALLS PYTORCH_MODEL FIXEDATOM WHOLEMOLECULES CUSTOM LOWEST COMBINE PRINT COORDINATION UNITS PATH FIT_TO_TEMPLATE CENTER SUM DISTANCE TORSION GROUP OPES_METAD CONSTANT PDB2CONSTANT OPES_METAD_EXPLORE EUCLIDEAN_DISTANCE UPPER_WALLS | core mapping setup vatom opes colvar bias refdist pytorch generic function |
| 23.007 | Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains | bio | metadynamics, peptoids, parallel-bias metadynamics | Pfaendtner J. | INCLUDE RESTRAINT WHOLEMOLECULES COM GYRATION COORDINATION TORSION PRINT PBMETAD | vatom bias generic colvar |
| 22.043 | Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES | bio | OPES, RNA, Tetraloop, Folding | Zerze G. | ENERGY ECV_MULTITHERMAL OPES_EXPANDED CONTACTMAP WHOLEMOLECULES ECV_UMBRELLAS_LINE PRINT | opes generic colvar |
| 22.033 | Reciprocal barrier restraint. Application to PROTAC passive permeability prediction | methods | PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR | Kolossvary I. | PRINT BIASVALUE FLUSH COM CUSTOM DISTANCE UNITS METAD DRR | setup drr vatom colvar bias generic function |
| 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 | Brotzakis F. | EMMI PRINT MOLINFO GROUP RMSD BIASVALUE WHOLEMOLECULES COM RESTART COORDINATION TORSION UPPER_WALLS PBMETAD | core setup vatom colvar isdb bias generic |
| 22.013 | Ligand dissociation from PreQ1 riboswitch | bio | ligand, RNA, metadynamics, pRAVE | Wang Y. | MATRIX_VECTOR_PRODUCT CONTACT_MATRIX MOLINFO GROUP METAD RMSD WHOLEMOLECULES COM SUM ONES COORDINATIONNUMBER MEAN CUSTOM COMMITTOR COMBINE DISTANCE PRINT | core vatom symfunc colvar matrixtools bias adjmat generic function |
| 22.002 | GAMBES_SAMPL5_RATES | other | GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding | Debnath J. | MATHEVAL PYTORCH_MODEL LOAD ENERGY PRINT FIT_TO_TEMPLATE GROUP CENTER FIXEDATOM FLUSH WHOLEMOLECULES ENDPLUMED COMMITTOR COORDINATION DISTANCE ANGLE UPPER_WALLS | core setup vatom colvar bias pytorch generic function |
| 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 | Maag D. | LOWER_WALLS MATRIX_VECTOR_PRODUCT PRINT CONTACT_MATRIX METAD GROUP COMBINE ONES COORDINATIONNUMBER MEAN COORDINATION DISTANCE UPPER_WALLS | core symfunc colvar matrixtools adjmat bias generic function |
| 21.035 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, interface | Finney A. | LOAD GROUP RESTRAINT FIXEDATOM DISTANCE PRINT | core setup vatom colvar bias generic |
| 21.025 | Computational and biochemical analysis of type IV pilus dynamics and stability | bio | molecular dynamics, calcium binding, Type IV pilus | Karami Y. | LOWER_WALLS DISTANCE UPPER_WALLS PRINT | bias generic colvar |
| 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 | Courtade G. | MATHEVAL METAD RESTRAINT CENTER WHOLEMOLECULES POSITION RESTART REWEIGHT_BIAS COORDINATION PRINT | setup vatom colvar bias generic function |
| 21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Karmakar T. | LOWER_WALLS PYTORCH_MODEL MATHEVAL LOAD PRINT GROUP OPES_METAD FLUSH UPPER_WALLS | core setup opes bias pytorch generic function |
| 20.030 | Converging experimental and computational views of the knotting mechanism of the smallest knotted protein | bio | phi-values, transition state, knotted proteins | Paissoni C. | MOLINFO RESTRAINT COMBINE WHOLEMOLECULES COORDINATION STATS PRINT | bias generic colvar function |
| 20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Bonomi M. | INCLUDE MOLINFO CONSTANT COMBINE WHOLEMOLECULES SUM DIHEDRAL_CORRELATION ALPHABETA CUSTOM DIHCOR GYRATION COORDINATION TORSION PRINT PBMETAD | multicolvar colvar bias generic function |
| 20.010 | Phase equilibrium of liquid water and hexagonal ice from enhanced sampling molecular dynamics simulations | materials | water, ice, TIP4P, crystallization, EnvironmentSimilarity, RefCV, kernel, VES, variationally enhanced sampling | Piaggi P. | SPHERICAL_HARMONIC CUSTOM COMBINE ENVIRONMENTSIMILARITY PRINT MATRIX_VECTOR_PRODUCT OPT_AVERAGED_SGD VOLUME BF_LEGENDRE CONTACT_MATRIX SUM ONES RESTART MEAN MATHEVAL TD_WELLTEMPERED GROUP OPT_DUMMY Q6 VES_LINEAR_EXPANSION DISTANCE_MATRIX UPPER_WALLS MORE_THAN | core setup envsim symfunc colvar matrixtools adjmat bias ves generic function |
| 20.000 | Muscarinic M2 receptor-ligand funnel metadynamics | bio | multiple walker metadynamics, well-tempered metadynamics, funnel metadynamics, MC-HLDA, GPCR, receptor, Adiabatic Bias MD | Capelli R. | LOWER_WALLS CONVERT_TO_FES CUSTOM ABMD COMBINE PRINT KDE HISTOGRAM ACCUMULATE METAD COM ONES ENDPLUMED DISTANCE REWEIGHT_METAD DUMPGRID MATHEVAL READ UPPER_WALLS | gridtools vatom colvar bias generic function |
| 19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Bussi G. | LOWER_WALLS RESTRAINT WHOLEMOLECULES ENDPLUMED COORDINATION DISTANCE | bias generic colvar |
| 19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Pfaendtner J. | UPPER_WALLS ENERGY PRINT MOLINFO COM GYRATION DISTANCE METAD | vatom bias generic colvar |
| 19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | Piccini G. | LOWER_WALLS ENERGY PRINT METAD FLUSH COMBINE DISTANCE UNITS UPPER_WALLS | setup colvar bias generic function |
| 19.044 | Multithermal-multibaric simulations using VES | methods | ves, Wang Landau, multicanonical, water, density anomaly | Piaggi P. | ENERGY CONVERT_TO_FES CUSTOM COMBINE PRINT KDE OPT_AVERAGED_SGD HISTOGRAM VOLUME ACCUMULATE BF_LEGENDRE TD_MULTITHERMAL_MULTIBARIC ONES RESTART REWEIGHT_BIAS DUMPGRID REWEIGHT_TEMP_PRESS OPT_DUMMY READ VES_LINEAR_EXPANSION AVERAGE | gridtools setup colvar bias ves generic function |
| 19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Pfaendtner J. | ENERGY GROUP EXTERNAL COORDINATION METAD | core bias colvar |
| 19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Salvalaglio M. | MATRIX_VECTOR_PRODUCT PRINT CONTACT_MATRIX GROUP CENTER DISTANCE SUM ONES RESTART COORDINATIONNUMBER MEAN DISTANCES LOWEST GYRATION ENDPLUMED METAD MORE_THAN | core multicolvar setup vatom symfunc colvar matrixtools adjmat bias generic function |
| 19.004 | MI Ubiquitin | bio | metainference, NMR | Bonomi M. | METAINFERENCE CS2BACKBONE MOLINFO GROUP RDC WHOLEMOLECULES PRINT | core generic isdb |
| 24.010 | Oxytocin metadynamics simulation | bio | metadynamics, oxytocin, peptide | Beránek J. | WHOLEMOLECULES PRINT TORSION RESTART FLUSH METAD | colvar generic 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 | Mambretti F. | ZDISTANCES FIXEDATOM SUM CENTER PRINT ONES UPPER_WALLS OPES_METAD UNITS MATRIX_VECTOR_PRODUCT MEAN DISTANCE CONTACT_MATRIX CUSTOM COORDINATIONNUMBER GROUP FLUSH | core opes multicolvar matrixtools bias generic function symfunc setup colvar vatom adjmat |
| 23.036 | Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? | bio | NaCl, nucleation, metadynamics | Wang R. | SUM PRINT CUSTOM ONES VOLUME METAD MATRIX_VECTOR_PRODUCT MEAN CONTACT_MATRIX ENERGY Q6 MATHEVAL Q4 COMBINE COORDINATIONNUMBER GROUP MORE_THAN SPHERICAL_HARMONIC | core matrixtools bias generic function colvar symfunc adjmat |
| 23.026 | Machine Learning Nucleation Collective Variables with Graph Neural Networks | chemistry | Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks | Dietrich F. | MATRIX_PRODUCT MEAN COORDINATIONNUMBER MFILTER_MORE MOVINGRESTRAINT GROUP LOCAL_Q6 SPHERICAL_HARMONIC SUM ONES MATRIX_VECTOR_PRODUCT CONTACT_MATRIX Q6 COMBINE OUTER_PRODUCT METAD PRINT CUSTOM TRANSPOSE VSTACK MORE_THAN LOWER_WALLS | core valtools matrixtools multicolvar bias generic function symfunc adjmat |
| 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 | Clark T. | ACCUMULATE WHOLEMOLECULES READ PRINT RMSD ONES METAD KDE HISTOGRAM DISTANCE DUMPGRID REWEIGHT_METAD MATHEVAL CUSTOM CONVERT_TO_FES MOLINFO | gridtools bias generic function colvar |
| 23.006 | Transcription factor unbinding | bio | metadynamics, DNA, conformational changes | Lüking M. | LESS_THAN SUM PRINT DUMPFORCES METAD COM DISTANCE ALPHARMSD MOLINFO CONTACTMAP ANGLE SECONDARY_STRUCTURE_RMSD | bias secondarystructure generic function colvar vatom |
| 22.042 | Metadynamics of NSP10 and variants | bio | metadynamics, NSP10, crystal structure, variants | Haider S. | TORSION PRINT METAD | colvar generic bias |
| 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 | Kolossvary I. | PRINT METAD DRR PATHMSD CUSTOM FLUSH BIASVALUE | bias generic function colvar drr |
| 22.022 | Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir | bio | RMSD, protein-ligand interactions | Grothaus I. | PRINT RMSD | colvar generic |
| 22.012 | Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT | bio | contact maps, protein-protein interactions | Grothaus I. | CENTER PRINT CONTACTMAP DISTANCE | 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 | Pampel B. | UPPER_WALLS VES_LINEAR_EXPANSION TD_WELLTEMPERED COORDINATION INCLUDE FLUSH UNITS BF_WAVELETS ENERGY BF_CUBIC_B_SPLINES OPT_AVERAGED_SGD VES_OUTPUT_BASISFUNCTIONS POSITION BF_CHEBYSHEV METAD BF_LEGENDRE PRINT DISTANCE OPT_ADAM BF_GAUSSIANS TD_UNIFORM | bias generic colvar ves setup |
| 21.044 | NaCl nucleation | chemistry | metadynamics, DFS clustering | Finney A. | ACCUMULATE DFSCLUSTERING MATRIX_PRODUCT CLUSTER_DISTRIBUTION MEAN COORDINATIONNUMBER MFILTER_MORE HIGHEST CLUSTER_NATOMS GROUP KDE DUMPGRID LOCAL_Q6 SPHERICAL_HARMONIC LESS_THAN SUM INSPHERE ONES MATRIX_VECTOR_PRODUCT CONTACT_MATRIX Q6 COMBINE OUTER_PRODUCT METAD FIXEDATOM PRINT BETWEEN HISTOGRAM CLUSTER_WEIGHTS CUSTOM TRANSPOSE VSTACK MORE_THAN | core valtools matrixtools multicolvar gridtools bias volumes clusters generic function vatom symfunc adjmat |
| 21.034 | Efficient sampling of high-dimensional free energy landscapes using adaptive reinforced dynamics | bio | reinforced dynamics, bias-exchange metadynamics, parallel-bias metadynamics | Wang D. | PRINT TORSION ENDPLUMED PBMETAD RANDOM_EXCHANGES INCLUDE METAD | colvar generic bias |
| 21.024 | Property map collective variable as a useful tool for force field correction | chemistry | molecular mechanics | Spiwok V. | WHOLEMOLECULES PRINT TORSION PROPERTYMAP BIASVALUE METAD | colvar generic bias |
| 21.014 | how to determine statistically accurate conformational ensembles | bio | metadynamics, metainference, errors, cv, SAXS, ensemble determination | Paissoni C. | ENSEMBLE TORSION PBMETAD ALPHABETA CONSTANT STATS GYRATION SECONDARY_STRUCTURE_RMSD WHOLEMOLECULES LESS_THAN SUM SAXS COMBINE METAD MOLINFO CENTER PRINT ANTIBETARMSD CONTACTMAP CUSTOM BIASVALUE | isdb multicolvar bias secondarystructure generic function colvar vatom |
| 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 | Gobbo D. | WHOLEMOLECULES PRINT UPPER_WALLS PATHMSD LOWER_WALLS RESTART METAD | colvar generic bias setup |
| 20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Paissoni C. | WHOLEMOLECULES CENTER PRINT STATS ENSEMBLE DISTANCE RESTRAINT SAXS BIASVALUE INCLUDE GROUP MOLINFO | isdb core bias generic function colvar vatom |
| 20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Salvalaglio M. | PRINT UPPER_WALLS VOLUME CELL METAD ENERGY MATHEVAL LOWER_WALLS | colvar generic function bias |
| 20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Camilloni C. | WHOLEMOLECULES CENTER SUM CUSTOM PRINT STATS FLUSH ENSEMBLE DISTANCE METAINFERENCE TORSION SAXS PBMETAD ALPHABETA COMBINE CONSTANT GYRATION MOLINFO | isdb multicolvar bias generic function colvar vatom |
| 19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Rizzi V. | UPPER_WALLS MEAN COORDINATIONNUMBER FLUSH UNITS RESTART SUM ONES MATRIX_VECTOR_PRODUCT CONTACT_MATRIX ENDPLUMED COMBINE METAD CENTER PRINT DISTANCE DISTANCES CUSTOM GROUP | vatom core matrixtools multicolvar bias generic function setup colvar symfunc adjmat |
| 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 | Salvalaglio M. | UPPER_WALLS MEAN COORDINATIONNUMBER LOWEST GYRATION ENERGY SUM ONES MATRIX_VECTOR_PRODUCT CONTACT_MATRIX ENDPLUMED METAD CENTER PRINT DISTANCE DISTANCES GROUP MORE_THAN LOWER_WALLS | core matrixtools multicolvar bias generic function vatom colvar symfunc adjmat |
| 19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Bernetti M. | WHOLEMOLECULES PRINT UPPER_WALLS METAD PATHMSD LOWER_WALLS | colvar generic bias |
| 19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Tribello G. | ACCUMULATE MULTICOLVARDENS ARGS2VATOM FIND_CONTOUR_SURFACE MASS UNITS KDE DUMPGRID FOURIER_TRANSFORM FCCUBIC POSITION SUM ONES MATRIX_VECTOR_PRODUCT CONTACT_MATRIX CENTER CHARGE DISTANCES FCCUBIC_FUNC CUSTOM GROUP MORE_THAN | contour core gridtools matrixtools multicolvar generic function symfunc fourier setup colvar vatom adjmat |
| 19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | Piccini G. | PRINT UPPER_WALLS UNITS DISTANCE DISTANCES COMBINE RESTART FLUSH METAD | multicolvar bias generic function colvar setup |
| 19.023 | RECT | methods | metadynamics, replica exchange | Bussi G. | WHOLEMOLECULES PRINT TORSION GYRATION METAD | colvar generic bias |
| 19.013 | RNA FF FITTING | methods | force field, RNA | Bussi G. | PUCKERING CONSTANT TORSION MATHEVAL BIASVALUE INCLUDE MOLINFO | colvar generic function bias |
| 19.003 | EMMI ClpP | bio | metainference, cryo-EM | Bonomi M. | PRINT EMMI MOLINFO GROUP BIASVALUE | generic isdb bias core |
| 24.009 | Weighted Shape Gaussian Mixture Models | bio | metadynamics, clustering | Hocky G. | METAD TORSION UNITS PRINT GROUP | colvar setup core generic bias |
| 23.046 | Lasso Peptides - HLDA CV | bio | metadynamics, protein folding, HLDA, harmonic | Hora G. | COMBINE DISTANCE METAD PRINT UNITS WHOLEMOLECULES | colvar setup function generic bias |
| 23.035 | An Extended Metadynamics Protocol for Binding/Unbinding of Peptide Ligands to Class A G-Protein Coupled Receptors | bio | G protein coupled receptor, peptide ligands, metadynamics, multiple-walker | Clark T. | DISTANCE BIASVALUE CONSTANT UPPER_WALLS LOWER_WALLS CENTER MATHEVAL METAD PRINT WHOLEMOLECULES | colvar function vatom generic bias |
| 23.025 | Probing ion binding to G-quadruplexes and related events | chemistry | metadynamics, repulsive potential, nucleic acids, G-quadruplexes | Poleto M. | DISTANCE UPPER_WALLS METAD POSITION WHOLEMOLECULES FIT_TO_TEMPLATE COM CENTER LOWEST MATHEVAL FLUSH UNITS PRINT LOWER_WALLS DISTANCES RESTART WRAPAROUND DUMPATOMS GROUP | colvar multicolvar setup function vatom core generic bias |
| 23.015 | MPCs aggregation | bio | opes_explore, dimerization, MPCs, self-assembly | Tiwari V. | DISTANCE CUSTOM COORDINATION UPPER_WALLS LOWER_WALLS COM CENTER METAD PRINT OPES_METAD_EXPLORE WHOLEMOLECULES GROUP | colvar opes function vatom core generic bias |
| 23.005 | A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs | bio | metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A | Clark T. | ONES READ RMSD DISTANCE HISTOGRAM CUSTOM MOLINFO MATHEVAL ACCUMULATE DUMPGRID METAD PRINT REWEIGHT_METAD KDE WHOLEMOLECULES CONVERT_TO_FES | colvar gridtools bias generic function |
| 22.041 | Skipping the Replica Exchange Ladder with Normalizing Flows | methods | OPES, alanine, normalizing flows, replica exchange | Invernizzi M. | ENERGY ECV_MULTITHERMAL OPES_EXPANDED OPES_METAD POSITION TORSION UNITS PRINT ENDPLUMED | colvar setup generic opes |
| 22.031 | Rare Event Kinetics from Adaptive Bias Enhanced Sampling | methods | OPES Flooding, Kinetics, Rate, OPES, Machine Learning | Ray D. | DISTANCE INCLUDE POSITION WHOLEMOLECULES ENERGY PYTORCH_MODEL UNITS PRINT CONSTANT CUSTOM MOLINFO CONTACTMAP COMMITTOR BIASVALUE RMSD COMBINE OPES_METAD TORSION GROUP ENDPLUMED | colvar bias setup opes core generic pytorch function |
| 22.021 | Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Bore S. | ONES MORE_THAN CUSTOM UPPER_WALLS LOWER_WALLS ECV_UMBRELLAS_LINE OPES_EXPANDED INCLUDE DISTANCE_MATRIX ENVIRONMENTSIMILARITY SUM MEAN PRINT GROUP MATRIX_VECTOR_PRODUCT | envsim core opes function adjmat generic bias matrixtools |
| 22.011 | Accelerating all-atom simulations and gaining mechanistic understanding of biophysical systems through State Predictive Information Bottleneck | methods | metadynamics, membrane permeation, protein folding | Mehdi S. | DISTANCE ZANGLES UPPER_WALLS YANGLES METAD MEAN WHOLEMOLECULES COM MATHEVAL PRINT CONSTANT CUSTOM LOWER_WALLS MOLINFO ALPHABETA SUM COMBINE XANGLES TORSION | multicolvar colvar function vatom generic bias |
| 22.000 | Amyloid precursor protein processing by human γ-secretase | bio | Bias Exchange Metadynamics, Helix unfolding, coupled binding | Lu X. | ANTIBETARMSD RANDOM_EXCHANGES CONTACTMAP DISTANCE COORDINATION ALPHARMSD CENTER MOLINFO INCLUDE METAD SECONDARY_STRUCTURE_RMSD LESS_THAN SUM UNITS PRINT | colvar secondarystructure setup function vatom generic 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 | Lu H. | METAD PRINT TORSION FIXEDATOM FIT_TO_TEMPLATE | colvar generic bias vatom |
| 21.033 | Multiple-path-metadynamics applied to DNA base-pairing transitions | bio | path-CV, metadynamics, multiple-walker, dna | Pérez-de-Alba-Ortíz A. | RESTRAINT COMBINE DISTANCE CONSTANT CUSTOM UPPER_WALLS MOVINGRESTRAINT CENTER LOAD INCLUDE METAD PRINT TORSION UNITS WHOLEMOLECULES | colvar setup function vatom generic bias |
| 21.023 | Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling | methods | enhanced sampling, collective variables, machine learning | Rydzewski J. | ENERGY DISTANCE BIASVALUE CONSTANT CUSTOM TORSION INCLUDE METAD REWEIGHT_METAD UNITS PRINT | colvar setup function generic bias |
| 21.013 | Role of vibrational excitation in heterogeneous catalysis | chemistry | catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption | Bal K. | UWALLS DISTANCE ANGLES UPPER_WALLS OPT_AVERAGED_SGD LOAD METAD MEAN COORDINATIONNUMBER REWEIGHT_BIAS ONES CONTACT_MATRIX DUMPGRID BF_CHEBYSHEV FLUSH REWEIGHT_METAD UNITS PRINT CONVERT_TO_FES MATRIX_VECTOR_PRODUCT CUSTOM LOWER_WALLS VES_LINEAR_EXPANSION ACCUMULATE COORD_ANGLES DISTANCES KDE TD_GRID COMBINE HISTOGRAM RESTRAINT COORDINATION EXTERNAL GROUP | multicolvar colvar gridtools core setup symfunc function adjmat generic bias matrixtools ves |
| 21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Lindorff-Larsen K. | METAINFERENCE BIASVALUE EEFSOLV GYRATION ALPHARMSD CENTER MOLINFO PRINT SAXS FLUSH PBMETAD WHOLEMOLECULES GROUP | colvar secondarystructure isdb vatom core generic bias |
| 20.028 | Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane | bio | metadynamics, KRas-4B, anionic membrane | Lu H. | DISTANCE CENTER METAD PRINT RESTART FIT_TO_TEMPLATE | colvar setup vatom generic bias |
| 20.018 | Free energy barriers from biased molecular dynamics simulations | methods | kinetics, free energy barriers, chemical reactions, nucleation, metadynamics | Bal K. | DISTANCE UPPER_WALLS LOAD LOCAL_AVERAGE METAD COORDINATIONNUMBER REWEIGHT_BIAS ENERGY CONTACT_MATRIX CENTER DUMPGRID FLUSH REWEIGHT_METAD DENSITY UNITS PRINT CONVERT_TO_FES Q6 LOWER_WALLS SPRINT COMBINE HISTOGRAM COORDINATION VOLUME PAIRENTROPY | colvar gridtools setup symfunc function vatom volumes sprint adjmat generic bias |
| 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 | Rossi K. | DISTANCE CUSTOM COORDINATION CENTER DISTANCES METAD SUM UNITS PRINT GROUP | multicolvar colvar setup function vatom core generic bias |
| 19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Rizzi V. | ONES MEAN ENDPLUMED COMBINE CONTACT_MATRIX CUSTOM FLUSH COORDINATIONNUMBER METAD RESTART EXTERNAL SUM UNITS PRINT GROUP MATRIX_VECTOR_PRODUCT | core setup symfunc function adjmat generic bias matrixtools |
| 19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Bussi G. | DISTANCE FLUSH COORDINATION COM MOLINFO SORT MATHEVAL INCLUDE PRINT METAD MAXENT TORSION WHOLEMOLECULES | colvar function vatom generic bias |
| 19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Pfaendtner J. | ENERGY GYRATION METAD PRINT WHOLEMOLECULES | colvar generic bias |
| 19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Tribello G. | ONES MEAN ENDPLUMED CONTACT_MATRIX FCCUBIC_FUNC CUSTOM MORE_THAN UPPER_WALLS FCCUBIC METAD CELL SUM UNITS PRINT GROUP MATRIX_VECTOR_PRODUCT | colvar core setup symfunc function adjmat generic bias matrixtools |
| 19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | Piccini G. | ENERGY COMBINE DISTANCE UPPER_WALLS METAD FLUSH UNITS PRINT | colvar setup function generic bias |
| 19.032 | Chemical reaction in solution using path collective variables based on coordination patterns | chemistry | chemical reactions, solutions, metadynamics, coordination patterns | Pietrucci F. | PATH UPPER_WALLS DISTANCES METAD RESTART FLUSH PRINT | multicolvar mapping setup generic bias |
| 19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Chen H. | DRR TORSION PRINT | colvar generic drr |
| 19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Camilloni C. | STATS RESTRAINT RMSD DISTANCE BIASVALUE UPPER_WALLS CENTER MOLINFO INCLUDE PRINT SAXS WHOLEMOLECULES GROUP ENDPLUMED | colvar isdb function vatom core generic bias |
| 19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Bonomi M. | BIASVALUE MOLINFO EMMI PRINT GROUP | isdb generic bias core |
| 24.008 | yCD Metadynamics | bio | volume-based MetaD, path CVs, infrequent MetaD, product release | McCarty J. | PATH UPPER_WALLS INCLUDE ENDPLUMED PRINT FLUSH COMMITTOR HISTOGRAM METAD COORDINATION CONTACTMAP COMBINE COM DISTANCE WRAPAROUND WHOLEMOLECULES MATHEVAL GPATH GROUP RMSD REWEIGHT_METAD CONVERT_TO_FES DUMPGRID FIT_TO_TEMPLATE FIXEDATOM READ MOLINFO | gridtools mapping generic vatom function colvar core 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 | Limongelli V. | SECONDARY_STRUCTURE_RMSD FUNCPATHMSD LOWER_WALLS DISTANCE ALPHARMSD UPPER_WALLS METAD INCLUDE SUM PATHMSD MOLINFO CONTACTMAP PRINT LESS_THAN | generic secondarystructure function colvar bias |
| 23.034 | Urea nucleation in water: do long-range forces matter? | materials | LMF theory, Metadynamics, Nucleation | Zou Z. | CUSTOM CONTACT_MATRIX ONES MATRIX_VECTOR_PRODUCT METAD MEAN INCLUDE COORDINATIONNUMBER GROUP CENTER MORE_THAN SUM PRINT LOAD | generic symfunc matrixtools vatom setup adjmat function core bias |
| 23.024 | Permutationally Invariant Networks for Enhanced Sampling (PINES) | methods | collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent | Herringer N. | PRINT LOAD PBMETAD | setup generic bias |
| 23.014 | Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 | bio | metadynamics, oligomerization, chemokine receptors, GPCR, membrane | Limongelli V. | COMBINE COM DISTANCE UPPER_WALLS TORSION WHOLEMOLECULES METAD PRINT FLUSH | generic vatom function colvar bias |
| 23.004 | Melting curves of ice polymorphs in the vicinity of the liquid-liquid critical point | chemistry | water, liquid-liquid transition, second critical point, ice, polymorphs, melting curves, environment similarity, opes, density-functional theory, scan, machine learning potential | Piaggi P. | MATRIX_VECTOR_PRODUCT UPPER_WALLS MORE_THAN PRINT HISTOGRAM ONES ENVIRONMENTSIMILARITY ACCUMULATE LOWER_WALLS CUSTOM ECV_UMBRELLAS_LINE OPES_EXPANDED GROUP KDE DUMPGRID DISTANCE_MATRIX MEAN SUM RESTART | gridtools generic opes matrixtools setup adjmat function envsim core bias |
| 22.040 | From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure | bio | SARS-CoV-2, Spike, Omicron | Wieczór M. | LOWER_WALLS CUSTOM MATRIX_VECTOR_PRODUCT COMBINE BIASVALUE UPPER_WALLS WHOLEMOLECULES METAD PRINT CONSTANT RMSD SUM PCAVARS SELECT_COMPONENTS | mapping generic matrixtools function colvar valtools bias |
| 22.030 | Mixing physics across temperatures with generative artificial intelligence | methods | REMD, Generative AI, DDPM | Wang Y. | TORSION WHOLEMOLECULES PRINT | generic colvar |
| 22.020 | Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix–Junction–Helix RNA | bio | RNA force field, Helix-Junction-Helix RNA, SAXS, Well tempered metadynamics | He W. | COM DISTANCE TORSION WHOLEMOLECULES METAD GROUP PRINT | generic vatom colvar core bias |
| 22.009 | Glycosylation in calixarenes capsule | chemistry | Metadynamics, glycosylation, supramolecular catalysis | Piccini G. | BRIDGE UPPER_WALLS BRIDGE_MATRIX ANGLE PRINT FLUSH METAD COORDINATION CENTER LOWER_WALLS COMBINE DISTANCE DISTANCES WHOLEMOLECULES MATHEVAL GROUP RMSD FIT_TO_TEMPLATE MEAN UNITS SUM | generic vatom setup adjmat function colvar core multicolvar bias |
| 21.052 | On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets | materials | Ibuprofen, unbinding, WTmetaD | Salvalaglio M. | COMMITTOR CONTACT_MATRIX ONES DISTANCE MATRIX_VECTOR_PRODUCT TORSION METAD MEAN COORDINATIONNUMBER ENDPLUMED GROUP PRINT CENTER | generic symfunc matrixtools vatom adjmat function colvar core bias |
| 21.042 | Peptoid-mediated Au nanocrystal growth | materials | parallel-bias metadynamics, peptoid, Au | Qi X. | COM DISTANCE UPPER_WALLS GYRATION PBMETAD MOLINFO PRINT | bias colvar generic vatom |
| 21.032 | Metal-coupled folding mechanism to metallothionein | bio | parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination | Diaz M. | MATRIX_VECTOR_PRODUCT COORDINATIONNUMBER MORE_THAN PRINT HISTOGRAM REWEIGHT_BIAS CONTACT_MATRIX ONES COORDINATION ACCUMULATE DRMSD CUSTOM COMBINE DISTANCE WHOLEMOLECULES CONSTANT GROUP REWEIGHT_METAD CONVERT_TO_FES HIGHEST KDE DUMPGRID MFILTER_MORE MEAN UNITS PBMETAD READ SUM | gridtools generic symfunc matrixtools setup adjmat function colvar core multicolvar bias |
| 21.022 | Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly | materials | parallel bias metadynamics, adsorption, peptide | Qi X. | LOWER_WALLS COM DISTANCE UPPER_WALLS GYRATION PBMETAD MOLINFO PRINT ENERGY | vatom generic colvar bias |
| 21.012 | NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition | bio | funnel metadynamics | Pfaendtner J. | LOWER_WALLS FUNNEL_PS COM DISTANCE UPPER_WALLS METAD PRINT FUNNEL | generic funnel vatom colvar bias |
| 21.002 | Phase equilibrium of water with hexagonal and cubic ice using the SCAN functional | materials | ice, water, SCAN, OPES, VES, multithermal, crystallization, environment similarity, refcv, reweighting | Piaggi P. | MATRIX_VECTOR_PRODUCT ECV_MULTITHERMAL_MULTIBARIC TD_UNIFORM UPPER_WALLS OPT_AVERAGED_SGD MORE_THAN PRINT VOLUME CONTACT_MATRIX ONES ENVIRONMENTSIMILARITY Q6 CUSTOM VES_LINEAR_EXPANSION ECV_UMBRELLAS_LINE COMBINE MATHEVAL BF_LEGENDRE OPES_EXPANDED GROUP DISTANCE_MATRIX MEAN SUM RESTART ENERGY SPHERICAL_HARMONIC | generic opes symfunc matrixtools setup adjmat function colvar envsim core ves bias |
| 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 | Abdel-Maksoud K. | DISTANCE PRINT TORSION METAD | generic colvar bias |
| 20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Hocky G. | DISTANCE BIASVALUE MATHEVAL GYRATION RESTRAINT UNITS GROUP PRINT ENERGY FISST | generic setup function fisst colvar core bias |
| 20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Tiwary P. | COMBINE DISTANCE UPPER_WALLS TORSION WHOLEMOLECULES METAD RMSD MOLINFO RESTART PRINT | generic setup function colvar bias |
| 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 | Piaggi P. | CELL UPPER_WALLS OPT_AVERAGED_SGD PRINT LOAD VOLUME HISTOGRAM REWEIGHT_BIAS ONES TD_WELLTEMPERED ACCUMULATE Q6 LOWER_WALLS CUSTOM VES_LINEAR_EXPANSION COMBINE MATHEVAL BF_LEGENDRE CONVERT_TO_FES REWEIGHT_TEMP_PRESS KDE DUMPGRID OPT_DUMMY READ TD_MULTITHERMAL_MULTIBARIC RESTART ENERGY | gridtools generic symfunc setup function colvar ves bias |
| 19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Salvalaglio M. | COMMITTOR HISTOGRAM REWEIGHT_BIAS DUMPGRID DISTANCE BIASVALUE MATHEVAL TORSION METAD READ EXTERNAL CONVERT_TO_FES REWEIGHT_METAD PRINT | gridtools generic function colvar bias |
| 19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Jelfs K. | LOWER_WALLS COM DISTANCE UPPER_WALLS METAD GROUP RESTART PRINT CENTER | generic vatom setup colvar core bias |
| 19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Tribello G. | CELL MATRIX_VECTOR_PRODUCT UPPER_WALLS FCCUBIC ENDPLUMED MORE_THAN PRINT LESS_THAN FCCUBIC_FUNC CONTACT_MATRIX ONES METAD LOWER_WALLS CUSTOM AROUND GROUP MEAN UNITS SUM | generic symfunc matrixtools volumes adjmat function setup colvar core 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 | Pfaendtner J. | COM DISTANCE UPPER_WALLS METAD PRINT ENERGY | bias colvar generic vatom |
| 19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Pipolo S. | LOWER_WALLS CELL FUNCPATHMSD PIV UPPER_WALLS METAD PRINT | generic function colvar piv bias |
| 19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Hocky G. | COMBINE DISTANCE TORSION EDS PRINT RESTRAINT | generic eds function colvar bias |
| 19.011 | Automatic Gradient Computation for Collective Variables | other | gradient, differentiation, curvature | Giorgino T. | ENDPLUMED | generic |
| 19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Bussi G. | LOWER_WALLS COMBINE RANDOM_EXCHANGES DISTANCE DISTANCES UPPER_WALLS LOWEST METAD INCLUDE ANGLE CENTER GROUP MOLINFO PRINT FLUSH ERMSD | generic vatom function colvar core multicolvar bias |
| 24.007 | SWISH-X | bio | swish-x, SWISH-X, swish, expanded SWISH | Borsatto A. | PRINT ECV_MULTITHERMAL MOLINFO WHOLEMOLECULES CONTACTMAP INCLUDE UPPER_WALLS OPES_EXPANDED ENERGY | colvar bias opes generic |
| 23.044 | Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition | materials | metadynamics, interlocked molecules | Leanza L. | KDE PRINT ONES COORDINATION CUSTOM CONVERT_TO_FES HISTOGRAM COMMITTOR ENDPLUMED ACCUMULATE DUMPGRID GROUP READ METAD | bias function generic core colvar gridtools |
| 23.033 | DNA G-quadruplex and G-hairpin folding with ST-metaD protocol | bio | DNA, G4, GQ, quadruplex, hairpin, folding, metadynamics, REST2, ST-metaD | Pokorná P. | PRINT COORDINATION MOLINFO WHOLEMOLECULES ERMSD GHBFIX COMBINE BIASVALUE METAD | colvar function bias generic |
| 23.023 | Rational design of novel biomimetic sequence-defined polymers for mineralization applications | methods | metadynamics, surface binding, biomimetic mineralization | Torkelson K. | PRINT COORDINATION GYRATION DISTANCE PBMETAD COM UPPER_WALLS | colvar bias generic vatom |
| 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 | Kolossvary I. | PRINT TIME CUSTOM PATHMSD DRR FLUSH UPPER_WALLS UNITS LOWER_WALLS BIASVALUE METAD | drr bias function generic colvar setup |
| 23.003 | Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations | methods | metadynamics, alchemical variable, alchemical free energy calculations | Hsu W. | PRINT EXTRACV PUT TORSION READ METAD | colvar bias generic core |
| 22.039 | Driving and characterizing nucleation of urea and glycine polymorphs in water | bio | metadynamics, nucleation, amino acids, polymorphism | Beyerle E. | MORE_THAN PAIRENTROPY CENTER MATHEVAL MATRIX_VECTOR_PRODUCT COMBINE Q6 ONES CUSTOM PRINT COORDINATIONNUMBER INCLUDE METAD MEAN GROUP CONTACT_MATRIX SPHERICAL_HARMONIC Q4 SUM LOAD | bias vatom function generic gridtools core setup adjmat matrixtools symfunc |
| 22.029 | Angiotensin-1-7_Metadynamics | bio | Metadynamics, Angiotensin-(1-7), peptide | Chi L. | PRINT COORDINATION WHOLEMOLECULES GYRATION FLUSH UPPER_WALLS GROUP METAD LOWER_WALLS | colvar bias generic core |
| 22.019 | Exploring aspartic protease inhibitor binding to design selective antimalarials | bio | ligand binding, loop opening, path CV, funnel metadynamics, drug development | Bobrovs R. | PRINT FUNNEL_PS PATHMSD WHOLEMOLECULES FUNNEL DISTANCE COM UPPER_WALLS LOWER_WALLS METAD | bias vatom generic colvar funnel |
| 22.008 | Ab initio metadynamics determination of temperature-dependent free-energy landscape in ultrasmall silver clusters | materials | Well tempered metadynamics, ab-initio, ase | Sucerquia D. | CONTACT_MATRIX ONES COORDINATION CUSTOM COORDINATIONNUMBER GYRATION FLUSH DISTANCE COM MATRIX_VECTOR_PRODUCT UPPER_WALLS COMBINE MEAN UNITS GROUP METAD LOWER_WALLS | bias vatom function generic core colvar setup adjmat matrixtools symfunc |
| 21.051 | Automatic learning of hydrogen-bond fixes in an AMBER RNA force field | methods | force field, RNA | Bussi G. | PRINT COORDINATION MOLINFO WHOLEMOLECULES ERMSD COMBINE BIASVALUE METAD | colvar function bias 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 | Badin M. | PRINT CUSTOM COORDINATION VOLUME COMBINE ENDPLUMED METAD | colvar function bias generic |
| 21.031 | Photo-switchable sulfonulureas in KATP channel | bio | metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels | Walczewska-Szewc K. | PRINT WHOLEMOLECULES DISTANCE COM UPPER_WALLS UNITS METAD LOWER_WALLS | bias vatom generic colvar setup |
| 21.021 | ATLAS | methods | Machine Learning, Metadynamics | Giberti F. | CONTACT_MATRIX PRINT ONES COORDINATION COORDINATIONNUMBER WHOLEMOLECULES MATHEVAL TORSION GYRATION DISTANCE MATRIX_VECTOR_PRODUCT MEAN GROUP UNITS DUMPATOMS BIASVALUE METAD | bias function generic core colvar setup adjmat matrixtools symfunc |
| 21.011 | CmuMD simulations of NaCl(aq) at graphite | chemistry | CmuMD, DFS clustering | Finney A. | KDE MORE_THAN RESTRAINT MATRIX_VECTOR_PRODUCT DFSCLUSTERING PRINT ONES DISTANCES CUSTOM COORDINATIONNUMBER CLUSTER_WEIGHTS CLUSTER_DISTRIBUTION AROUND CLUSTER_NATOMS DENSITY HIGHEST MEAN MULTICOLVARDENS GROUP CONTACT_MATRIX FIXEDATOM SUM ACCUMULATE LOAD MFILTER_MORE DUMPGRID | bias vatom function multicolvar generic gridtools core volumes setup adjmat clusters matrixtools symfunc |
| 21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Ferreira T. | KDE REWEIGHT_METAD PUCKERING WHOLEMOLECULES RANDOM_EXCHANGES UPPER_WALLS LOWER_WALLS PRINT ONES COORDINATION CUSTOM INCLUDE METAD MOLINFO HISTOGRAM DISTANCE GROUP ENERGY ACCUMULATE DUMPGRID | bias function generic gridtools colvar core |
| 20.026 | Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor | bio | Metadynamics, Umbrella sampling | Peters B. | KDE PRINT REWEIGHT_METAD CUSTOM ONES CONVERT_TO_FES DUMPGRID WHOLEMOLECULES HISTOGRAM RESTRAINT RMSD_VECTOR ACCUMULATE MULTI_RMSD CONSTANT CONCATENATE COMBINE POSITION METAD | valtools bias function generic gridtools colvar |
| 20.016 | Predicting polymorphism in molecular crystals using orientational entropy | materials | metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy | Piaggi P. | PRINT VOLUME CENTER LOAD INCLUDE UPPER_WALLS GROUP METAD | bias vatom generic core colvar setup |
| 20.006 | Class B GPCR activation mechanism | bio | metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding | Gervasio F. | PRINT MOLINFO WHOLEMOLECULES RMSD CENTER MATHEVAL DISTANCE UPPER_WALLS COMBINE LOWER_WALLS ENERGY METAD | bias vatom function generic colvar |
| 19.080 | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | methods | ves, variationally enhanced sampling, vibrational excitation, chemical reactions | Bal K. | KDE CONVERT_TO_FES OPT_AVERAGED_SGD UPPER_WALLS COMBINE EXTERNAL LOWER_WALLS PRINT ONES COORDINATION CUSTOM VES_LINEAR_EXPANSION FLUSH BF_CHEBYSHEV HISTOGRAM DISTANCE TD_WELLTEMPERED TD_GRID ANGLE ACCUMULATE DUMPGRID UNITS | bias ves function generic gridtools colvar setup |
| 19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Bottaro S. | PRINT MOLINFO WHOLEMOLECULES RMSD ERMSD TORSION DISTANCE METAD | colvar bias generic |
| 19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Bonati L. | PRINT ENVIRONMENTSIMILARITY Q6 POSITION TORSION LOAD UNITS ENDPLUMED ENERGY | envsim generic colvar setup symfunc |
| 19.050 | Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes | chemistry | metadynamics, membranes, Willard Chandler surface | Tribello G. | KDE PRINT ONES CUSTOM CONVERT_TO_FES RESTART HISTOGRAM REWEIGHT_BIAS ACCUMULATE DUMPGRID UPPER_WALLS DISTANCE_FROM_CONTOUR READ COMBINE METAD | contour bias function generic gridtools setup |
| 19.040 | Optimal Metric for Path Collective Variables | bio | metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path | Gervasio F. | PRINT TORSION MATHEVAL ENDPLUMED METAD | colvar function bias generic |
| 19.030 | Coarse-Grained MetaDynamics (CG-MetaD) | bio | Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy | Limongelli V. | PRINT WHOLEMOLECULES DISTANCE COM UPPER_WALLS LOWER_WALLS METAD | colvar bias generic vatom |
| 19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Bernetti M. | PRINT SECONDARY_STRUCTURE_RMSD ALPHARMSD MOLINFO WHOLEMOLECULES LESS_THAN SUM GYRATION ENDPLUMED ENERGY METAD | bias secondarystructure function generic colvar |
| 19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Camilloni C. | WHOLEMOLECULES CENTER DIHCOR RESTRAINT PBMETAD CONSTANT UPPER_WALLS COMBINE ENSEMBLE PRINT STATS CUSTOM RDC DIHEDRAL_CORRELATION MOLINFO TORSION DISTANCE ALPHABETA GROUP DHENERGY SUM METAINFERENCE ENDPLUMED | bias vatom function multicolvar generic core isdb colvar |
| 19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Invernizzi M. | PRINT POSITION VES_DELTA_F RESTART TORSION LOAD UNITS ENDPLUMED ENERGY METAD | bias ves generic colvar setup |