Browse the eggs in PLUMED-NEST
PLUMED-NEST provides all the data needed to reproduce the results of a PLUMED-enhanced molecular dynamics simulation or analysis contained in a published paper. Furthermore, PLUMED-NEST monitors the compatibility of the provided PLUMED input files with the current and development versions of the code and integrates links from these files to the PLUMED manual.
Here is the list of projects already deposited in PLUMED-NEST, while a complete bibliography can be found here.
| plumID | Name | Category | Keywords | Contributor | Actions | Modules |
|---|---|---|---|---|---|---|
| 26.004 | Resolving the ambiguous binding site of quercetin at the calcineurin subunit junction using funnel metadynamics with deep learning collective variables | bio | metadynamics, funnel metadynamics, DeepTICA | Jason Loo | UPPER_WALLS GROUP METAD COORDINATION LOWER_WALLS RMSD FUNNEL_PS WHOLEMOLECULES PRINT WRAPAROUND ENERGY COM MATHEVAL PYTORCH_MODEL FUNNEL DISTANCE | vatom function pytorch bias generic funnel colvar core |
| 25.022 | Imidazole Diffusion in SALEM-2 MOF | materials | OPES, Diffusion, Ring opening, MOFs, Machine Learning Potentials | Sudheesh Kumar Ethirajan | CENTER GROUP MOLINFO OPES_METAD PRINT WHOLEMOLECULES ENDPLUMED PROJECTION_ON_AXIS DISTANCES UNITS DISTANCE | vatom multicolvar generic colvar core setup opes |
| 25.019 | The Arch from the Stones. Understanding Protein Folding Energy Landscapes via Bio-inspired Collective Variables | bio | protein folding, OPES, OneOPES, binding free energy | Valerio Rizzi | CUSTOM GROUP COORDINATION OPES_METAD_EXPLORE MOLINFO RMSD PRINT ECV_MULTITHERMAL GHOST COMBINE ENERGY DISTANCE OPES_EXPANDED CENTER | vatom function generic colvar core opes |
| 25.009 | Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water | chemistry | metadynamics, nitrate photolysis | Kam-Tung Chan | CUSTOM UPPER_WALLS GROUP METAD DUMPGRID RESTART COORDINATION PRINT HISTOGRAM FLUSH REWEIGHT_METAD READ DISTANCE | function bias generic colvar gridtools core setup |
| 25.003 | Surrogate Model CV | methods | Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding | Sompriya Chatterjee | CUSTOM GROUP MOLINFO OPES_METAD PRINT WHOLEMOLECULES ENDPLUMED TORSION ENERGY COMBINE MATHEVAL PYTORCH_MODEL DISTANCE COMMITTOR | function pytorch generic colvar core opes |
| 24.031 | DeepLNE | methods | PATHCV, OPES, OneOPES | Thorben Fröhlking | VOLUME RESTART COORDINATION OPES_METAD_EXPLORE MOLINFO ECV_MULTITHERMAL PRINT COMBINE ENERGY OPES_EXPANDED PYTORCH_MODEL ERMSD | function pytorch generic colvar setup opes |
| 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 | CUSTOM COORDINATION MOLINFO OPES_METAD PRINT WHOLEMOLECULES TORSION COMBINE GYRATION DISTANCE ALPHARMSD | secondarystructure function generic colvar opes |
| 24.014 | Learning Collective Variables with Synthetic Data Augmentation through Physics-inspired Geodesic Interpolation | methods | data augmentation, geodesic interpolation, collective variables, protein folding | Juno Nam | UPPER_WALLS PYTORCH_MODEL METAD DRR COORDINATION MOLINFO RMSD PRINT WHOLEMOLECULES FLUSH LOWER_WALLS | pytorch bias generic colvar drr |
| 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 | METAD DUMPGRID CONVERT_TO_FES MOLINFO RMSD PRINT WHOLEMOLECULES MATHEVAL HISTOGRAM REWEIGHT_METAD READ DISTANCE | function bias generic colvar gridtools |
| 23.011 | OneOPES, a combined enhanced sampling method to rule them all | bio | OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding | Valerio Rizzi | METAD OPES_METAD_EXPLORE MOLINFO ECV_MULTITHERMAL PRINT ENDPLUMED TORSION ENERGY OPES_EXPANDED DISTANCE | colvar opes generic bias |
| 23.000 | Atomistic simulations of RNA tetraloop folding via PTWTE-WTM | bio | parallel tempering, well-tempered metadynamics, well-tempered ensemble, RNA, Tetraloop, Folding | Gül Zerze | UPPER_WALLS CONTACTMAP METAD PRINT WHOLEMOLECULES ENERGY LOWER_WALLS | colvar generic bias |
| 22.042 | Metadynamics of NSP10 and variants | bio | metadynamics, NSP10, crystal structure, variants | Shozeb Haider | TORSION METAD PRINT | colvar generic bias |
| 22.027 | Molecular Dynamics simulations of BANAL-236 RBD-hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, BANAL-236, receptor-binding domain | Max Bonomi | RMSD PRINT | colvar generic |
| 22.024 | Conformational Entropy as a Potential Liability of Computationally Designed Antibodies | bio | metadynamics, conformational entropy, antibody, nanobody | Thomas Löhr | RESTART MOLINFO PRINT WHOLEMOLECULES TORSION COM ALPHABETA ANTIBETARMSD PBMETAD ALPHARMSD | vatom secondarystructure bias multicolvar generic colvar setup |
| 22.015 | Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome | bio | photodynamics, bacteriophytochrome, variationally enhanced sampling | Jakub Rydzewski | BF_FOURIER OPT_AVERAGED_SGD PRINT TORSION VES_LINEAR_EXPANSION TD_UNIFORM | colvar generic ves |
| 21.052 | On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets | materials | Ibuprofen, unbinding, WTmetaD | Matteo Salvalaglio | METAD PRINT ENDPLUMED TORSION DISTANCE COORDINATIONNUMBER CENTER COMMITTOR | vatom bias generic colvar symfunc |
| 21.051 | Automatic learning of hydrogen-bond fixes in an AMBER RNA force field | methods | force field, RNA | Giovanni Bussi | METAD COORDINATION MOLINFO PRINT WHOLEMOLECULES BIASVALUE COMBINE ERMSD | colvar function 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 | Huixia Lu | METAD PRINT FIT_TO_TEMPLATE TORSION FIXEDATOM | colvar generic vatom bias |
| 21.040 | A structural ensemble of a tau-microtubule complex reveals regulatory tau phosphorylation and acetylation mechanisms | bio | EMMI, CryoEM, tau-microtubules, post-translational modifications, chemical mutagenesis, structural ensemble, Metainference | Faidon Brotzakis | UPPER_WALLS GROUP RESTART MOLINFO PRINT WHOLEMOLECULES BIASVALUE COM EMMI DISTANCE | vatom bias generic colvar core setup 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 | Jim Pfaendtner | INCLUDE METAD COORDINATION PRINT TORSION ENERGY COM ALPHABETA GYRATION PBMETAD DISTANCE | vatom bias multicolvar generic colvar |
| 21.016 | MD SAXS GTPase associated center | bio | metadynamics, RNA, folding, SAXS | Giovanni Bussi | INCLUDE CUSTOM UPPER_WALLS GROUP METAD MOLINFO PRINT WHOLEMOLECULES ERMSD GYRATION LOWER_WALLS SAXS | function bias generic colvar core isdb |
| 20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Cristina Paissoni | INCLUDE CENTER GROUP MOLINFO PRINT WHOLEMOLECULES BIASVALUE RESTRAINT ENSEMBLE STATS SAXS DISTANCE | vatom function bias generic colvar core isdb |
| 20.024 | Gaussian Mixture Based Enhanced Sampling (GAMBES) | methods | enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias | Jayashrita Debnath | UPPER_WALLS GROUP PRINT TORSION LOAD COMBINE ENERGY DISTANCES LOWER_WALLS UNITS DISTANCE | function bias multicolvar generic colvar core setup |
| 20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Max Bonomi | INCLUDE COORDINATION MOLINFO PRINT WHOLEMOLECULES ALPHABETA GYRATION DIHCOR PBMETAD | colvar multicolvar generic bias |
| 20.015 | Rational design of ASCT2 inhibitors using an integrated experimental-computational approach | bio | ASCT2 transporter, small-molecules, cryo-EM, metainference | Max Bonomi | GROUP MOLINFO PRINT WHOLEMOLECULES BIASVALUE DUMPATOMS LOAD EMMIVOX | bias generic core setup isdb |
| 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 | UPPER_WALLS METAD PRINT ENDPLUMED ENERGY COORDINATIONNUMBER GYRATION DISTANCES LOWER_WALLS | bias multicolvar generic colvar symfunc |
| 19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Matteo Salvalaglio | METAD DUMPGRID EXTERNAL CONVERT_TO_FES PRINT BIASVALUE TORSION MATHEVAL HISTOGRAM REWEIGHT_BIAS REWEIGHT_METAD READ DISTANCE COMMITTOR | function bias generic colvar gridtools |
| 19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Jakub Rydzewski | UPPER_WALLS METAD RESTART PRINT PATHMSD LOWER_WALLS UNITS | colvar generic setup 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 | INCLUDE METAD PRINT RANDOM_EXCHANGES TORSION | colvar generic bias |
| 19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Gareth Tribello | UPPER_WALLS METAD CELL FCCUBIC PRINT ENDPLUMED UNITS | bias generic colvar symfunc setup |
| 19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | UPPER_WALLS METAD PRINT ENERGY COMBINE FLUSH UNITS DISTANCE | function bias generic colvar setup |
| 19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Elena Papaleo | UPPER_WALLS GROUP METAD MOLINFO PRINT WHOLEMOLECULES ALPHABETA GYRATION LOWER_WALLS | bias multicolvar generic colvar core |
| 19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Adriana Pietropaolo | METAD PRINT WHOLEMOLECULES BIASVALUE TORSION MATHEVAL CONSTANT | colvar function generic bias |
| 19.005 | Cmyc small molecule interaction | bio | metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP | Gabriella Heller | INCLUDE CENTER CS2BACKBONE GROUP COORDINATION MOLINFO PRINT WHOLEMOLECULES METAINFERENCE ALPHABETA GYRATION PBMETAD DISTANCE | vatom bias multicolvar generic colvar core isdb |
| 19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Max Bonomi | GROUP MOLINFO PRINT BIASVALUE EMMI | isdb core generic bias |
| 26.013 | Characterizing Partially Unfolded States of the C-Terminal Domain in WT and 3PA Mouse Prion Protein | bio | parallel-bias metadynamics, PBMetaD, metadynamics, mouse prion protein, prion protein, protein folding, partially unfolded states, molecular dynamics | Sonali M. Jadhav | COORDINATION DUMPMASSCHARGE ALPHARMSD INCLUDE PRINT GYRATION WHOLEMOLECULES GROUP COM CONTACTMAP MOLINFO DISTANCE PBMETAD | colvar secondarystructure vatom core generic bias |
| 25.023 | Molecular simulations of Tau-protein oligomers | bio | metadynamics, proteins, aggregation | Giovanni Bussi | REWEIGHT_BIAS CUSTOM RESTRAINT FLUSH PRINT RMSD CONTACTMAP CONVERT_TO_FES METAD DUMPGRID RESTART HISTOGRAM | setup colvar gridtools generic function bias |
| 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 | CUSTOM COORDINATION UNITS PRINT UPPER_WALLS LOWER_WALLS COMMITTOR GROUP OPES_METAD DISTANCE RESTART | setup colvar opes generic core function bias |
| 24.018 | A new route to the prebiotic synthesis of glycine via ab initio-based machine learning calculations | chemistry | prebiotic chemistry, glycine, Strecker synthesis, ab initio calculations, machine learning | Léon HUET | DISTANCE PRINT | generic colvar |
| 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 | COORDINATIONNUMBER RESTRAINT BIASVALUE ENERGY FLUSH TORSION PRINT COMMITTOR MATHEVAL METAD MOLINFO DISTANCE RESTART | setup colvar symfunc generic function bias |
| 24.010 | Oxytocin metadynamics simulation | bio | metadynamics, oxytocin, peptide | Jan Beránek | FLUSH TORSION PRINT WHOLEMOLECULES METAD RESTART | setup generic colvar bias |
| 23.037 | Estimating binding free energy of solid binding peptides without extensive sampling | bio | metadynamics, solid binding peptides | Xin Qi | PRINT UPPER_WALLS LOWER_WALLS COM GYRATION MOLINFO DISTANCE PBMETAD | colvar vatom generic bias |
| 23.036 | Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? | bio | NaCl, nucleation, metadynamics | Ruiyu Wang | VOLUME COORDINATIONNUMBER Q4 COMBINE ENERGY PRINT Q6 MATHEVAL METAD | colvar symfunc generic function bias |
| 23.019 | Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors | bio | binding pathway, binding energy, sketch-map, drug development | Raitis Bobrovs | PATHMSD CUSTOM LANDMARK_SELECT_FPS SKETCHMAP VORONOI VSTACK PRINT UPPER_WALLS TRANSPOSE COM WHOLEMOLECULES COLLECT_FRAMES METAD DISSIMILARITIES SKETCHMAP_PROJECTION DISTANCE | colvar dimred vatom landmarks generic function valtools matrixtools bias |
| 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 | CUSTOM PATH COORDINATION OPES_METAD_EXPLORE FIT_TO_TEMPLATE FIXEDATOM UNITS TORSION PRINT UPPER_WALLS LOWER_WALLS WHOLEMOLECULES GROUP CENTER OPES_METAD DISTANCE PYTORCH_MODEL | setup colvar opes pytorch vatom generic mapping function core bias |
| 23.007 | Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains | bio | metadynamics, peptoids, parallel-bias metadynamics | Jim Pfaendtner | COORDINATION RESTRAINT TORSION INCLUDE PRINT COM WHOLEMOLECULES GYRATION PBMETAD | vatom generic colvar bias |
| 23.006 | Transcription factor unbinding | bio | metadynamics, DNA, conformational changes | Malin Lüking | ALPHARMSD PRINT DUMPFORCES COM CONTACTMAP METAD MOLINFO ANGLE DISTANCE | colvar secondarystructure vatom generic bias |
| 23.002 | Critical comparison of general-purpose collective variables for crystal nucleation | methods | metadynamics, umbrella sampling, commitor, entropy, PIV | Julien Lam | FUNCPATHMSD VOLUME Q4 CUSTOM PAIRENTROPY RESTRAINT PIV ENERGY UNITS PRINT UPPER_WALLS Q6 METAD LOCAL_AVERAGE | setup colvar piv symfunc gridtools generic function bias |
| 22.043 | Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES | bio | OPES, RNA, Tetraloop, Folding | Gül Zerze | ECV_MULTITHERMAL OPES_EXPANDED ENERGY PRINT ECV_UMBRELLAS_LINE WHOLEMOLECULES CONTACTMAP | opes generic colvar |
| 22.039 | Driving and characterizing nucleation of urea and glycine polymorphs in water | bio | metadynamics, nucleation, amino acids, polymorphism | Eric Beyerle | COORDINATIONNUMBER Q4 COMBINE PAIRENTROPY INCLUDE PRINT Q6 GROUP CENTER MATHEVAL METAD LOAD | setup symfunc vatom gridtools core generic function bias |
| 22.026 | Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification | materials | Peptoid, silica | Jim Pfaendtner | PRINT UPPER_WALLS GYRATION COM MOLINFO DISTANCE PBMETAD | colvar vatom generic bias |
| 22.023 | Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy | bio | CryoEM, MEMMI,EMMI, Metadynamics, Metainference, IAPP, structural ensemble | Faidon Brotzakis | EMMI COORDINATION BIASVALUE TORSION PRINT UPPER_WALLS RMSD COM WHOLEMOLECULES GROUP MOLINFO RESTART PBMETAD | setup colvar vatom generic isdb core bias |
| 22.022 | Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir | bio | RMSD, protein-ligand interactions | Isabell Grothaus | RMSD PRINT | generic colvar |
| 22.018 | Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations | bio | ligand binding, docking, EMMI, LAT1 | Max Bonomi | BIASVALUE PRINT EMMIVOX WHOLEMOLECULES GROUP MOLINFO LOAD | setup core isdb generic bias |
| 22.013 | Ligand dissociation from PreQ1 riboswitch | bio | ligand, RNA, metadynamics, pRAVE | Yihang Wang | COORDINATIONNUMBER COMBINE PRINT RMSD COM WHOLEMOLECULES COMMITTOR METAD MOLINFO DISTANCE | colvar symfunc vatom generic function bias |
| 21.042 | Peptoid-mediated Au nanocrystal growth | materials | parallel-bias metadynamics, peptoid, Au | Xin Qi | PRINT UPPER_WALLS GYRATION COM MOLINFO DISTANCE PBMETAD | colvar vatom generic bias |
| 21.039 | Deep learning the slow modes for rare events sampling | methods | collective variables, machine learning, slow modes, deep-tica, opes | Luigi Bonati | ENERGY PRINT Q6 CONTACTMAP LOAD VOLUME OPES_EXPANDED ENDPLUMED COMBINE FLUSH RMSD ENVIRONMENTSIMILARITY PYTORCH_MODEL TORSION WHOLEMOLECULES GROUP MOLINFO ECV_MULTITHERMAL UNITS INCLUDE OPES_METAD DISTANCE | setup colvar symfunc opes pytorch generic core function envsim |
| 21.017 | All-atom simulations of the Vav1 AD construct | bio | metadynamics, parallel-bias, well-tempered | Simone Orioli | REWEIGHT_BIAS ALPHARMSD PRINT ALPHABETA WHOLEMOLECULES CONTACTMAP GROUP METAD MOLINFO RESTART PBMETAD | multicolvar setup colvar secondarystructure generic core bias |
| 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 | REWEIGHT_BIAS COORDINATION RESTRAINT POSITION PRINT WHOLEMOLECULES MATHEVAL CENTER METAD RESTART | setup colvar vatom generic function bias |
| 20.032 | Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil | materials | clustering, conformational isomers | Matteo Salvalaglio | ENDPLUMED TORSION PRINT | generic colvar |
| 20.030 | Converging experimental and computational views of the knotting mechanism of the smallest knotted protein | bio | phi-values, transition state, knotted proteins | Cristina Paissoni | COMBINE COORDINATION RESTRAINT PRINT WHOLEMOLECULES MOLINFO STATS | bias generic colvar 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 | Gabriella Heller | PRINT PARABETARMSD STATS ENSEMBLE COMBINE ENDPLUMED ALPHARMSD FLUSH DIHCOR METAINFERENCE ANTIBETARMSD TORSION GYRATION WHOLEMOLECULES GROUP MOLINFO COORDINATION INCLUDE CS2BACKBONE PBMETAD | multicolvar colvar secondarystructure generic isdb function core bias |
| 19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Valerio Rizzi | COORDINATIONNUMBER ENDPLUMED COMBINE DISTANCES FLUSH UNITS PRINT UPPER_WALLS GROUP METAD RESTART | multicolvar setup symfunc generic core function bias |
| 19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Valerio Rizzi | COORDINATIONNUMBER EXTERNAL ENDPLUMED COMBINE FLUSH UNITS PRINT GROUP METAD RESTART | setup symfunc generic core function bias |
| 19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Sandro Bottaro | TORSION PRINT ERMSD RMSD WHOLEMOLECULES METAD MOLINFO DISTANCE | generic colvar bias |
| 19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | ENERGY PRINT UPPER_WALLS GYRATION COM METAD MOLINFO DISTANCE | vatom generic colvar 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 | ENERGY PRINT UPPER_WALLS COM METAD DISTANCE | vatom generic colvar bias |
| 19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Glen Hocky | COMBINE RESTRAINT TORSION PRINT DISTANCE EDS | colvar generic function eds bias |
| 19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Matteo Salvalaglio | VOLUME ENDPLUMED COMBINE ENERGY TORSION PRINT CELL UPPER_WALLS LOWER_WALLS METAD MATHEVAL | bias generic colvar function |
| 26.001 | Molecular simulations Alx riboswitch | bio | RNA, riboswitch | Giovanni Bussi | MOLINFO MOVINGRESTRAINT ERMSD PRINT RESTRAINT MATHEVAL DISTANCE | generic colvar bias function |
| 25.026 | Deciphering the Molecular Mechanisms of Startle Disease - the Role of the Asn46Lys Mutation in the Glycine Receptor | bio | metadynamics, glycine receptors, funnel metadynamics | Jacob Adam Clark | FUNNEL_PS METAD FUNNEL UPPER_WALLS LOWER_WALLS PRINT COM | vatom generic bias funnel |
| 25.016 | Advancing in silico drug design with Bayesian refinement of AlphaFold models | bio | bAIes, AlphaFold, Bayesian refinement, virtual screening, docking, small-molecule, enrichment | Samiran Sen | BAIES BIASVALUE GROUP PRINT | core isdb bias 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 | MOLINFO RESTART METAD MOVINGRESTRAINT TORSION PUCKERING PRINT RESTRAINT DISTANCE | setup generic colvar 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 | MOLINFO CUSTOM ANGLE GROUP CONTACTMAP FIXEDATOM MATHEVAL COMMITTOR UPPER_WALLS WHOLEMOLECULES TORSION COORDINATION DISTANCE OPES_METAD METAD COMBINE PRINT ENDPLUMED RMSD FIT_TO_TEMPLATE CENTER | generic bias opes colvar function vatom core |
| 23.029 | An accurate and efficient SAXS/SANS implementation including solvation layer effects suitable for restrained Molecular Dynamics simulations | bio | SAXS, SANS, SAS, metainference, proteins, nucleic-acid | Federico Ballabio | MOLINFO RMSD ENSEMBLE UPPER_WALLS GROUP WRAPAROUND STATS PRINT BIASVALUE SAXS CENTER DISTANCE | generic isdb bias colvar function vatom core |
| 23.025 | Probing ion binding to G-quadruplexes and related events | chemistry | metadynamics, repulsive potential, nucleic acids, G-quadruplexes | Marcelo Poleto | RESTART DUMPATOMS METAD POSITION UPPER_WALLS WHOLEMOLECULES LOWER_WALLS GROUP WRAPAROUND FIT_TO_TEMPLATE COM PRINT DISTANCES UNITS FLUSH MATHEVAL DISTANCE | generic bias multicolvar colvar setup function vatom core |
| 23.021 | Into the Dynamics of Rotaxanes at Atomistic Resolution | materials | metadynamics, rotaxanes, molecular shuttles, molecular machines | Luigi Leanza | CUSTOM METAD UPPER_WALLS TORSION PRINT FIXEDATOM CENTER MATHEVAL DISTANCE | generic bias colvar function vatom |
| 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 RMSD READ METAD DUMPGRID WHOLEMOLECULES HISTOGRAM PRINT REWEIGHT_METAD CONVERT_TO_FES MATHEVAL DISTANCE | generic bias gridtools colvar function |
| 22.031 | Rare Event Kinetics from Adaptive Bias Enhanced Sampling | methods | OPES Flooding, Kinetics, Rate, OPES, Machine Learning | Dhiman Ray | MOLINFO CUSTOM GROUP CONTACTMAP CONSTANT COMMITTOR WHOLEMOLECULES INCLUDE TORSION UNITS DISTANCE OPES_METAD POSITION COMBINE BIASVALUE PRINT ENDPLUMED RMSD ENERGY PYTORCH_MODEL | generic bias opes colvar pytorch setup function core |
| 22.019 | Exploring aspartic protease inhibitor binding to design selective antimalarials | bio | ligand binding, loop opening, path CV, funnel metadynamics, drug development | Raitis Bobrovs | FUNNEL_PS PATHMSD METAD FUNNEL UPPER_WALLS WHOLEMOLECULES LOWER_WALLS PRINT COM DISTANCE | generic bias colvar funnel vatom |
| 21.050 | N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity | methods | bio | Isabell Louise Grothaus | PRINT CENTER DISTANCE | vatom generic colvar |
| 21.048 | Enhancing ligand exploration within a channel pore and fenestrations using metadynamics | bio | well-tempered metadynamics, protein-ligand enhanced sampling, sodium channel, Nav, small molecule drug | Elaine Tao | CUSTOM METAD UPPER_WALLS LOWER_WALLS TORSION PRINT UNITS COM DISTANCE | generic bias colvar setup function vatom |
| 21.047 | Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations | materials | pair entropy, metadynamics, ves, solids, crystallization | Pablo Piaggi | RESTART METAD COMBINE LOAD OPT_AVERAGED_SGD BF_LEGENDRE ENERGY VES_LINEAR_EXPANSION PRINT TD_WELLTEMPERED PAIRENTROPY VOLUME | generic bias gridtools colvar setup function ves |
| 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 | MOLINFO METAD ANTIBETARMSD ALPHARMSD RANDOM_EXCHANGES UPPER_WALLS WHOLEMOLECULES LOWER_WALLS PARABETARMSD GROUP ENERGY GYRATION PRINT COORDINATION DIHCOR | generic bias multicolvar colvar secondarystructure core |
| 21.035 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, interface | Aaron Finney | LOAD GROUP PRINT RESTRAINT FIXEDATOM DISTANCE | generic bias colvar setup vatom core |
| 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 GROUP COORDINATION UNITS | generic bias colvar setup core |
| 21.011 | CmuMD simulations of NaCl(aq) at graphite | chemistry | CmuMD, DFS clustering | Aaron Finney | CLUSTER_DISTRIBUTION DENSITY DUMPGRID AROUND LOAD GROUP COORDINATIONNUMBER PRINT CLUSTER_NATOMS DFSCLUSTERING RESTRAINT MFILTER_MORE MULTICOLVARDENS CONTACT_MATRIX FIXEDATOM | generic bias volumes multicolvar clusters gridtools adjmat setup vatom core symfunc |
| 21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Kristof Bal | DUMPGRID METAD COMMITTOR MOVINGRESTRAINT UPPER_WALLS LOAD HISTOGRAM PRINT COORDINATIONNUMBER UNITS FLUSH REWEIGHT_METAD CONVERT_TO_FES | generic bias gridtools setup symfunc |
| 21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Tarsis Ferreira | MOLINFO DUMPGRID METAD RANDOM_EXCHANGES UPPER_WALLS LOWER_WALLS WHOLEMOLECULES GROUP INCLUDE ENERGY HISTOGRAM PUCKERING PRINT COORDINATION REWEIGHT_METAD DISTANCE | generic bias gridtools colvar core |
| 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 | DISTANCE PRINT METAD TORSION | generic colvar bias |
| 20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Glen Hocky | GROUP ENERGY GYRATION PRINT RESTRAINT BIASVALUE FISST UNITS MATHEVAL DISTANCE | generic bias colvar setup function fisst core |
| 20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Carlo Camilloni | MOLINFO ENSEMBLE METAINFERENCE WHOLEMOLECULES PBMETAD TORSION STATS GYRATION PRINT SAXS FLUSH CENTER DISTANCE ALPHABETA | generic isdb bias multicolvar colvar function vatom |
| 20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Luigi Bonati | ENDPLUMED OPES_METAD MATHEVAL UPPER_WALLS LOAD LOWER_WALLS GROUP TORSION PRINT UNITS FLUSH PYTORCH_MODEL COM DISTANCE | generic bias opes colvar pytorch setup function vatom 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 | HISTOGRAM MATHEVAL CELL OPT_DUMMY UPPER_WALLS LOWER_WALLS OPT_AVERAGED_SGD REWEIGHT_BIAS VOLUME RESTART READ COMBINE LOAD VES_LINEAR_EXPANSION PRINT Q6 TD_WELLTEMPERED CONVERT_TO_FES DUMPGRID TD_MULTITHERMAL_MULTIBARIC REWEIGHT_TEMP_PRESS BF_LEGENDRE ENERGY | generic bias gridtools colvar setup function ves symfunc |
| 19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Mattia Bernetti | PATHMSD METAD UPPER_WALLS WHOLEMOLECULES LOWER_WALLS PRINT | generic colvar bias |
| 19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Luigi Bonati | ENDPLUMED POSITION LOAD ENERGY TORSION PRINT Q6 UNITS ENVIRONMENTSIMILARITY | generic colvar setup envsim symfunc |
| 19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Cristina Paissoni | MOLINFO ENDPLUMED ENSEMBLE COMBINE WHOLEMOLECULES ANGLE PBMETAD GROUP INCLUDE STATS BIASVALUE PRINT COORDINATION SAXS CENTER MATHEVAL ALPHABETA | generic isdb bias multicolvar colvar function vatom core |
| 19.056 | maze | methods | maze, ligand unbinding | Jakub Rydzewski | POSITION MAZE_OPTIMIZER_BIAS MAZE_SIMULATED_ANNEALING PRINT UNITS MAZE_LOSS | setup generic colvar maze |
| 19.023 | RECT | methods | metadynamics, replica exchange | Giovanni Bussi | METAD WHOLEMOLECULES TORSION GYRATION PRINT | generic colvar bias |
| 19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Mattia Bernetti | MOLINFO ENDPLUMED METAD ALPHARMSD WHOLEMOLECULES ENERGY GYRATION PRINT | generic colvar bias secondarystructure |
| 19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Max Bonomi | MOLINFO WHOLEMOLECULES EMMI GROUP BIASVALUE PRINT | core generic isdb bias |
| 19.004 | MI Ubiquitin | bio | metainference, NMR | Max Bonomi | MOLINFO METAINFERENCE WHOLEMOLECULES GROUP CS2BACKBONE PRINT RDC | core generic isdb |
| 26.015 | Ensemble Dynamics | methods | State Exploration, Protein Folding, Drug Binding, Phase Transition | Florian M. Dietrich | OPES_METAD_EXPLORE UNITS GROUP DISTANCE CELL POSITION TORSION CUSTOM LOAD BIASVALUE PRINT | colvar bias function setup core generic opes |
| 26.014 | Dissociation free energy (DFE) calculationsfor GPR15L–polySia | bio | metadynamics, protein-carbohydrate interaction | Davide Luciano and Gaston Courtade | GROUP DISTANCE COM METAD UPPER_WALLS PRINT | colvar bias vatom core generic |
| 25.030 | Committor Regularization | methods | metadynamics, enhanced sampling, mlcvs, committor, machine learning | Florian Dietrich | METAD UNITS MOVINGRESTRAINT PRINT | bias generic setup |
| 25.027 | Enhanced-sampling MD simulations of a protein-peptide complex integrating SAXS and XL-MS experimental information | bio | steered MD, metadynamics, SAXS, XL-MS, ensemble reconstruction | Mattia Bernetti | CENTER MOVINGRESTRAINT GROUP DISTANCE WHOLEMOLECULES INCLUDE SAXS UPPER_WALLS METAD GYRATION MOLINFO PRINT | colvar bias isdb vatom core generic |
| 25.020 | Revealing Water-Mediated Activation Mechanisms in the Beta 1-Adrenergic Receptor via OneOPES-Enhanced Free Energy Landscapes | bio | OneOPES, GPCR, ADRB1, activation, microswitches, conformational changes, allostery | Valerio Rizzi | DISTANCES OPES_METAD_EXPLORE ECV_MULTITHERMAL CENTER OPES_EXPANDED GROUP DISTANCE PATHMSD RMSD ENERGY GHOST COORDINATION CUSTOM UPPER_WALLS LOWER_WALLS PRINT | colvar bias multicolvar function vatom core generic opes |
| 24.030 | NMR guided simulation of dsRBD | bio | Metainference, NMR, protein dynamics | Debadutta Patra | STATS GROUP ENSEMBLE DISTANCE WHOLEMOLECULES ALPHABETA FLUSH RDC MOLINFO METAINFERENCE PRINT | colvar isdb multicolvar function core generic |
| 24.025 | Correlating Enzymatic Reactivity for Different Substrates using Transferable Data-Driven Collective Variables | bio | enzymatic reactivity, k_cat, transfer learning, data-driven CVs, catalysis, ligand-binding modes, water, alpha-amylase, sugar, classical MD, OPES, machine learning, Deep TDA CV, path CV | Sudip Das | CENTER GROUP DISTANCE FIT_TO_TEMPLATE PATH RESTART WHOLEMOLECULES COORDINATION PYTORCH_MODEL TORSION CUSTOM FIXEDATOM OPES_METAD UPPER_WALLS LOWER_WALLS PRINT | colvar bias setup pytorch function mapping vatom core generic opes |
| 24.016 | Cryo-EM guided simulations of ribozyme | bio | metainference, cryo-EM | Giovanni Bussi | GROUP RESTRAINT WHOLEMOLECULES INCLUDE ERMSD EMMIVOX BIASVALUE MOLINFO PRINT | colvar bias isdb core 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 | CENTER GROUP DISTANCE DEBUG GHBFIX COORDINATION COM COMBINE METAD BIASVALUE UPPER_WALLS MOLINFO LOWER_WALLS PRINT | colvar bias function vatom core generic |
| 24.011 | Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble | methods | committor, machine learning | Peilin Kang | RMSD WHOLEMOLECULES LOAD MOLINFO DISTANCE ENDPLUMED INCLUDE PRINT UNITS CUSTOM UPPER_WALLS GROUP CELL ENERGY COORDINATION TORSION MATHEVAL BIASVALUE POSITION LOWER_WALLS | colvar bias function setup core generic |
| 23.044 | Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition | materials | metadynamics, interlocked molecules | Luigi Leanza | GROUP ENDPLUMED READ CONVERT_TO_FES HISTOGRAM COORDINATION COMMITTOR DUMPGRID METAD PRINT | colvar gridtools bias core generic |
| 23.039 | Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation | chemistry | metadynamics, ligand dissociation | Eric Beyerle | DUMPMASSCHARGE CENTER RESTRAINT DISTANCE FIXEDATOM COMBINE UPPER_WALLS METAD MOLINFO PRINT | colvar bias function vatom generic |
| 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 | GHBFIX WHOLEMOLECULES COORDINATION ERMSD COMBINE BIASVALUE METAD MOLINFO PRINT | colvar bias generic function |
| 23.032 | Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics | bio | metadynamics, tSNE, neural network, machine learning, trp-cage, folding | Vojtech Spiwok | MOLINFO FIT_TO_TEMPLATE ANN WHOLEMOLECULES COMBINE METAD POSITION ALPHARMSD PRINT | colvar secondarystructure bias function annfunc generic |
| 23.004 | Melting curves of ice polymorphs in the vicinity of the liquid-liquid critical point | chemistry | water, liquid-liquid transition, second critical point, ice, polymorphs, melting curves, environment similarity, opes, density-functional theory, scan, machine learning potential | Pablo Piaggi | OPES_EXPANDED ECV_UMBRELLAS_LINE RESTART DUMPGRID UPPER_WALLS HISTOGRAM ENVIRONMENTSIMILARITY LOWER_WALLS PRINT | gridtools bias setup envsim generic opes |
| 23.001 | Quantum phase diagram of water | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn-Løland Bore | OPES_EXPANDED ECV_UMBRELLAS_LINE RESTART INCLUDE UPPER_WALLS ENVIRONMENTSIMILARITY LOWER_WALLS PRINT | bias setup envsim generic opes |
| 22.037 | Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site | chemistry | metadynamics, DNA, abasic | Mike Jones | DISTANCES METAD DISTANCE PRINT | generic colvar bias multicolvar |
| 22.036 | Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction | bio | Well-tempered MetaDynamics with Hamiltonian Replica Exchange | Miroslav Krepl | UPPER_WALLS GROUP BIASVALUE GHBFIX COORDINATION FLUSH CUSTOM COMBINE LOAD METAD MOLINFO PRINT | colvar bias function setup core generic |
| 22.035 | Deciphering the alphabet of disorder — Glu and Asp act differently on local but not global properties | bio | intrinsically disordered proteins, parallel bias metadynamics, protein | Kresten Lindorff-Larsen | WHOLEMOLECULES TORSION PBMETAD GYRATION MOLINFO | colvar bias generic |
| 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 | GROUP DISTANCE WHOLEMOLECULES COM TORSION METAD PRINT | colvar bias vatom core generic |
| 22.009 | Glycosylation in calixarenes capsule | chemistry | Metadynamics, glycosylation, supramolecular catalysis | GiovanniMaria Piccini | BRIDGE DISTANCES UNITS GROUP DISTANCE ANGLE FIT_TO_TEMPLATE RMSD WHOLEMOLECULES COORDINATION FLUSH COMBINE MATHEVAL UPPER_WALLS METAD LOWER_WALLS PRINT | colvar adjmat bias multicolvar setup function core generic |
| 21.037 | Molecular Dynamics simulations of RBD/hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain | Max Bonomi | RMSD DISTANCE PRINT | colvar generic |
| 21.031 | Photo-switchable sulfonulureas in KATP channel | bio | metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels | Katarzyna Walczewska-Szewc | UNITS DISTANCE WHOLEMOLECULES COM UPPER_WALLS METAD LOWER_WALLS PRINT | colvar bias setup vatom generic |
| 21.019 | Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations | materials | Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen | Matteo Salvalaglio | DISTANCE COM TORSIONS PRINT MATHEVAL KDE | colvar gridtools multicolvar function vatom generic |
| 21.018 | Localized Volume-based Metadynamics | bio | LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification | Riccardo Capelli | RMSD WHOLEMOLECULES METAD DISTANCE ENDPLUMED READ HISTOGRAM PRINT UPPER_WALLS GROUP CONVERT_TO_FES COORDINATION DUMPGRID COM FLUSH MATHEVAL FIXEDATOM REWEIGHT_METAD POSITION | colvar gridtools bias function vatom core generic |
| 21.012 | NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition | bio | funnel metadynamics | Jim Pfaendtner | FUNNEL DISTANCE FUNNEL_PS COM METAD UPPER_WALLS LOWER_WALLS PRINT | colvar bias vatom funnel generic |
| 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 | TD_UNIFORM OPES_EXPANDED ECV_UMBRELLAS_LINE ENERGY RESTART VES_LINEAR_EXPANSION ECV_MULTITHERMAL_MULTIBARIC BF_LEGENDRE VOLUME UPPER_WALLS ENVIRONMENTSIMILARITY MATHEVAL Q6 OPT_AVERAGED_SGD PRINT | colvar ves bias setup function envsim symfunc generic opes |
| 20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Adriana Pietropaolo | CENTER WHOLEMOLECULES COORDINATION PBMETAD PRINT | colvar bias vatom generic |
| 20.026 | Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor | bio | Metadynamics, Umbrella sampling | Brandon Peters | MULTI_RMSD RESTRAINT CONVERT_TO_FES DUMPGRID METAD REWEIGHT_METAD HISTOGRAM PRINT | colvar bias gridtools generic |
| 20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Michele Invernizzi | ECV_UMBRELLAS_LINE RMSD WHOLEMOLECULES ECV_LINEAR ECV_MULTITHERMAL_MULTIBARIC VOLUME LOAD MOLINFO ENDPLUMED PRINT ECV_MULTITHERMAL UNITS OPES_EXPANDED CUSTOM UPPER_WALLS ENERGY TORSION MATHEVAL ENVIRONMENTSIMILARITY Q6 POSITION | colvar bias setup function envsim symfunc generic opes |
| 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 | FUNCPATHMSD WHOLEMOLECULES METAD MOLINFO ENDPLUMED DISTANCE READ HISTOGRAM PRINT ABMD COMBINE UPPER_WALLS CONVERT_TO_FES DUMPGRID COM FLUSH CONTACTMAP REWEIGHT_METAD LOWER_WALLS | colvar gridtools bias function vatom 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 | GROUP PATHMSD WHOLEMOLECULES RESTART METAD UPPER_WALLS MOLINFO PRINT | colvar bias setup core generic |
| 19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Giovanni Bussi | DISTANCE SORT WHOLEMOLECULES INCLUDE COORDINATION COM FLUSH TORSION MATHEVAL METAD MOLINFO MAXENT PRINT | colvar bias function vatom generic |
| 19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Michele Invernizzi | UNITS ENDPLUMED EXTERNAL TORSION OPES_METAD METAD POSITION PRINT | colvar bias setup generic opes |
| 19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Kim E. Jelfs | CENTER GROUP DISTANCE RESTART COM UPPER_WALLS METAD LOWER_WALLS PRINT | colvar bias setup vatom core generic |
| 19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Davide Provasi | ENDPLUMED FUNCPATHMSD DISTANCE RMSD WHOLEMOLECULES COM CONTACTMAP METAD PRINT | colvar bias function vatom generic |
| 19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Gabriele Cesare Sosso | CONTACT_MATRIX LOCAL_Q6 CLUSTER_NATOMS ENDPLUMED COMMITTOR OUTPUT_CLUSTER FLUSH DFSCLUSTERING CLUSTER_WITHSURFACE Q6 MFILTER_MORE | adjmat multicolvar symfunc generic clusters |
| 19.025 | Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide | bio | metainference, NMR, protein dynamics, force-fields | Carlo Camilloni | STATS ENDPLUMED ENSEMBLE WHOLEMOLECULES JCOUPLING CS2BACKBONE RDC FLUSH TORSION PBMETAD BIASVALUE GYRATION MOLINFO METAINFERENCE PRINT | colvar bias isdb function generic |
| 19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Matteo Salvalaglio | CENTER DISTANCE COMMITTOR TORSION UPPER_WALLS METAD LOWER_WALLS PRINT | colvar bias vatom generic |
| 19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Matteo Salvalaglio | DISTANCES ENDPLUMED RESTART METAD COORDINATIONNUMBER GYRATION PRINT | colvar bias multicolvar setup symfunc generic |
| 19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Carlo Camilloni | CENTER STATS GROUP DISTANCE RESTRAINT RMSD WHOLEMOLECULES INCLUDE ENDPLUMED SAXS BIASVALUE UPPER_WALLS MOLINFO PRINT | colvar bias isdb function vatom core generic |
| 19.011 | Automatic Gradient Computation for Collective Variables | other | gradient, differentiation, curvature | Toni Giorgino | ENDPLUMED | generic |
| 19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Michele Invernizzi | UNITS ENDPLUMED ENERGY RESTART VES_DELTA_F TORSION LOAD METAD POSITION PRINT | colvar ves bias setup generic |
| 26.010 | Solvation-Mediated Ammonia Synthesis in a Nanoheterogeneous Liquid Alloy | materials | OPES, Catalysis, Ammonia Synthesis | Axel Tosello Gardini | GROUP INCLUDE DISTANCES CUSTOM PRINT UPPER_WALLS OPES_METAD COORDINATION FLUSH DISTANCE COORDINATIONNUMBER OPES_METAD_EXPLORE UNITS | multicolvar core function symfunc setup bias generic colvar opes |
| 26.000 | OPES simulations of disordered proteins | bio | OPES, IDPs | Julian Streit | RESTART ENERGY PRINT OPES_EXPANDED ECV_MULTITHERMAL | setup generic colvar opes |
| 25.021 | All You Need Is Water. Converging Ligand Binding Simulations with Hydration Collective Variables | bio | OPES Explore, ligand binding, binding free energy, water, hydration CVs, SAMPL challenge, host-guest | Valerio Rizzi | GROUP WHOLEMOLECULES ENERGY PRINT UPPER_WALLS CENTER FIXEDATOM COORDINATION FIT_TO_TEMPLATE DISTANCE ANGLE MATHEVAL OPES_METAD_EXPLORE | core function bias vatom generic colvar opes |
| 25.018 | Metainference simulation for dimerization of RNA binding protein | bio | Metainference, Metadynamics, SAXS, protein dimer | Debadutta Patra | ENSEMBLE STATS MOLINFO TORSION WHOLEMOLECULES SAXS PBMETAD PRINT UPPER_WALLS CENTER GYRATION METAINFERENCE FLUSH DISTANCE | isdb function bias vatom generic colvar |
| 25.010 | Kinetic rates calculation with Ratchet&Pawl MD | methods | kinetics, ligand binding, ABMD, ratchet&pawl MD | Riccardo Capelli | WHOLEMOLECULES PRINT COM ABMD FLUSH DISTANCE COMMITTOR GROUP | core bias vatom generic colvar |
| 24.023 | Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21. A Machine-Learning-Aided Enhanced Sampling Study | bio | RNA, miRNA, OneOPES, ligand binding, conformational changes | Valerio Rizzi | COMBINE GROUP RESTART TORSION CUSTOM ENERGY PRINT OPES_EXPANDED COORDINATION DISTANCE ECV_MULTITHERMAL OPES_METAD_EXPLORE | core function setup generic colvar opes |
| 24.004 | Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables | materials | metadynamics, nucleation, machine learning | Ziyue Zou | INCLUDE RESTART PRINT LOAD METAD GROUP | bias setup generic core |
| 23.046 | Lasso Peptides - HLDA CV | bio | metadynamics, protein folding, HLDA, harmonic | Gabriel da Hora | COMBINE WHOLEMOLECULES PRINT DISTANCE METAD UNITS | function setup bias generic colvar |
| 23.031 | Identifying small molecules binding sites in RNA conformational ensembles with SHAMAN | bio | RNA, metadynamics, probes, mixed-solvent MD, small molecules, binding sites | Max Bonomi | WRAPAROUND POSITION MOLINFO DISTANCES WHOLEMOLECULES PRINT UPPER_WALLS CENTER SHADOW FIT_TO_TEMPLATE METAD GROUP | multicolvar isdb core bias vatom generic colvar |
| 22.025 | Bubble nucleation rate predictions in a Lennard-Jones fluid | materials | free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation | Kristof Bal | REWEIGHT_BIAS RESTRAINT MOVINGRESTRAINT VOLUME CUSTOM PRINT UPPER_WALLS LOAD DUMPGRID HISTOGRAM ANN BIASVALUE COMMITTOR FLUSH COORDINATIONNUMBER CONVERT_TO_FES UNITS | gridtools function symfunc setup bias annfunc generic colvar |
| 22.021 | Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn Løland Bore | ENVIRONMENTSIMILARITY INCLUDE PRINT UPPER_WALLS OPES_EXPANDED LOWER_WALLS ECV_UMBRELLAS_LINE | bias generic envsim opes |
| 22.005 | Collective Variable for Metadynamics Derived from AlphaFold Output | bio | AlphaFold, protein folding, protein structure prediction, metadynamics, deep learning, free energy simulation, collective variable | Vojtech Spiwok | LOAD METAD PRINT WHOLEMOLECULES | setup bias generic |
| 22.003 | Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling | methods | opes, metadynamics, reweighting, alanine, muller | Michele Invernizzi | POSITION TORSION ENDPLUMED ECV_UMBRELLAS_FILE ENERGY PRINT OPES_METAD PBMETAD CUSTOM UPPER_WALLS OPES_EXPANDED LOWER_WALLS BIASVALUE ECV_MULTITHERMAL METAD OPES_METAD_EXPLORE UNITS | function setup bias generic colvar opes |
| 21.046 | Ubiquitin Interacting Motifs, Duality Between Structured and Disordered Motifs | bio | wt metadynamics, ubiquitin, ataxin-3, short linear motifs, ubiquitin binding motif, moonlight functions, intrinsic disorder | Elena Papaleo | WHOLEMOLECULES ENDPLUMED ALPHABETA UPPER_WALLS PRINT GYRATION LOWER_WALLS METAD GROUP | multicolvar core bias generic colvar |
| 21.041 | Nucleating a Different Coordination in a Crystal under Pressure. A Study of the B1−B2 Transition in NaCl by Metadynamics | methods | metadynamics, structural phase transitions, pressure-induced phase transition, martensitic transitions | Matej Badin | COMBINE VOLUME CUSTOM ENDPLUMED PRINT COORDINATION METAD | function bias generic colvar |
| 21.023 | Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling | methods | enhanced sampling, collective variables, machine learning | Jakub Rydzewski | INCLUDE CONSTANT TORSION CUSTOM ENERGY PRINT BIASVALUE REWEIGHT_METAD DISTANCE METAD UNITS | function setup bias generic colvar |
| 21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Tarak Karmakar | PRINT UPPER_WALLS OPES_METAD LOAD LOWER_WALLS PYTORCH_MODEL FLUSH MATHEVAL GROUP | core function pytorch setup bias generic opes |
| 20.018 | Free energy barriers from biased molecular dynamics simulations | methods | kinetics, free energy barriers, chemical reactions, nucleation, metadynamics | Kristof Bal | DENSITY ENERGY Q6 LOAD CONTACT_MATRIX CONVERT_TO_FES PRINT COORDINATION METAD UNITS REWEIGHT_BIAS VOLUME CENTER HISTOGRAM REWEIGHT_METAD DISTANCE COORDINATIONNUMBER PAIRENTROPY COMBINE SPRINT UPPER_WALLS DUMPGRID LOWER_WALLS FLUSH LOCAL_AVERAGE | function symfunc setup bias generic sprint vatom gridtools colvar volumes adjmat |
| 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 ENDPLUMED PRINT GYRATION UNITS | colvar setup bias generic |
| 19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Matteo Salvalaglio | INCLUDE ENDPLUMED PRINT CENTER DISTANCE GROUP | vatom generic colvar core |
| 19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Jim Pfaendtner | WHOLEMOLECULES ENERGY PRINT GYRATION METAD | bias generic colvar |
| 19.048 | Understanding Ligand Binding Selectivity in a Prototypical GPCR Family | bio | metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | CONSTANT WHOLEMOLECULES PRINT UPPER_WALLS COM LOWER_WALLS BIASVALUE DISTANCE MATHEVAL METAD | function bias vatom generic colvar |
| 19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Carlo Camilloni | ENSEMBLE RESTRAINT STATS TORSION MOLINFO WHOLEMOLECULES PBMETAD ENDPLUMED ALPHABETA UPPER_WALLS PRINT DIHCOR CENTER RDC METAINFERENCE DHENERGY DISTANCE GROUP | multicolvar isdb core function bias vatom generic colvar |
| 26.007 | Metadynamics Simulations Reveal the Protonation-Dependent Conformational Landscape of GSK-3β Dual Inhibitors | chemistry | metadynamics, ligand unbinding, path CVs, funnel metadynamics | Gian Marco Elisi | UPPER_WALLS PATHMSD COM ANGLE DISTANCE RMSD METAD COMBINE UNITS FUNNEL MATHEVAL WHOLEMOLECULES LOWER_WALLS MOLINFO ENDPLUMED FUNNEL_PS PRINT | colvar bias vatom setup funnel generic function |
| 25.029 | Energetic Constraints in the Enzymatic Depolymerization of Crystalline PET from enhanced molecular simulations | bio | HREX-Metadynamics, PETase, crystalline PET, amorphous PET, conformational ensembles, substrate binding, chain detachment | Ania Di Pede-Mattatelli and Francesco Colizzi | UPPER_WALLS COM DISTANCE METAD REWEIGHT_BIAS DUMPGRID WHOLEMOLECULES CONVERT_TO_FES LOWER_WALLS MOLINFO HISTOGRAM FIXEDATOM PRINT | colvar bias vatom gridtools generic |
| 25.017 | Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity | bio | EMMIVox, cryo-EM, allostery, decamer, filament, ensemble refinement, glutamine synthetase | Samuel Hoff | GROUP BIASVALUE WHOLEMOLECULES MOLINFO EMMIVOX PRINT | generic isdb core bias |
| 25.006 | Characterizing the conformational ensemble of PROTAC degraders in solutions via atomistic simulations | methods | Enhanced sampling, Atomistic simulations, Conformational ensemble, PROTACs, Targeted Protein Degradation, Chamelonic molecules | Shikshya Bhusal, Omar Valsson | TORSION DUMPATOMS VOLUME UPDATE_IF DISTANCE CENTER INCLUDE GYRATION WHOLEMOLECULES RESTART MOLINFO ENERGY READ PBMETAD PRINT | colvar bias vatom setup generic |
| 25.000 | Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer | bio | metadynamics, pathCV | Sahithya Sridharan Iyer | UPPER_WALLS COM GROUP DISTANCE METAD WHOLEMOLECULES RESTART MOLINFO FUNCPATHGENERAL PRINT | colvar bias vatom setup generic core function |
| 24.034 | Umbrella sampling of ion in transporter SLC26A7 | bio | umbrella sampling, transporter, ions | Xiaoli Lu | UNITS POSITION RESTRAINT PRINT | generic setup colvar bias |
| 24.027 | Proline cis and trans subensembles of a disordered peptide | bio | intrinsically disordered proteins, proline cis trans isomerisation, metadynamics, collective variables | Alice Pettitt | COORDINATION DIHCOR TORSION PRINT GROUP ANTIBETARMSD DISTANCE INCLUDE PARABETARMSD COMBINE GYRATION WHOLEMOLECULES MOLINFO ALPHARMSD ENDPLUMED PBMETAD FLUSH | multicolvar colvar bias core generic secondarystructure function |
| 24.026 | Constant pH metadynamics of RNA oligomers | bio | metadynamics, pH, RNA | Giovanni Bussi | TORSION METAD PUCKERING RESTART MOLINFO PRINT | generic setup colvar bias |
| 24.008 | yCD Metadynamics | bio | volume-based MetaD, path CVs, infrequent MetaD, product release | James McCarty | COM MATHEVAL WRAPAROUND MOLINFO ENDPLUMED PRINT COORDINATION DISTANCE METAD INCLUDE FIXEDATOM UPPER_WALLS RMSD PATH DUMPGRID REWEIGHT_METAD WHOLEMOLECULES READ COMMITTOR FIT_TO_TEMPLATE GROUP CONTACTMAP CONVERT_TO_FES FLUSH HISTOGRAM | mapping colvar bias vatom gridtools generic core function |
| 23.040 | Supramolecular capsules assembly dynamics | chemistry | Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics | Riccardo Capelli | CUSTOM GROUP COM DISTANCE CENTER POSITION METAD DISTANCES UNITS WHOLEMOLECULES FLUSH PRINT | colvar bias multicolvar vatom setup core generic function |
| 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 | UPPER_WALLS DISTANCE METAD CENTER MATHEVAL CONSTANT BIASVALUE WHOLEMOLECULES LOWER_WALLS PRINT | colvar bias vatom generic function |
| 23.014 | Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 | bio | metadynamics, oligomerization, chemokine receptors, GPCR, membrane | Vittorio Limongelli | UPPER_WALLS TORSION COM DISTANCE METAD COMBINE WHOLEMOLECULES FLUSH PRINT | colvar bias vatom generic function |
| 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 | UPPER_WALLS CUSTOM PATHMSD TIME METAD UNITS BIASVALUE LOWER_WALLS DRR FLUSH PRINT | colvar bias setup generic drr function |
| 23.012 | JAK2 2D meta-eABF PMF with statistical analysis | bio | 2D meta-eABF, path CV, PMF | Istvan Kolossvary | UPPER_WALLS CUSTOM PATHMSD METAD BIASVALUE LOWER_WALLS DRR FLUSH PRINT | colvar bias generic drr function |
| 23.009 | Deep Learning Collective Variables from Transition Path Ensemble | methods | TPI-Deep-TDA, Deep-TDA, Transition Path, OPES, OPES Flooding, Machine Learning, Protein folding, Ligand binding | Dhiman Ray | CUSTOM MATHEVAL MOLINFO ENDPLUMED PRINT COORDINATION ANGLE DISTANCE INCLUDE COMBINE ENERGY FIXEDATOM PYTORCH_MODEL LOWER_WALLS UPPER_WALLS RMSD WHOLEMOLECULES OPES_METAD COMMITTOR FIT_TO_TEMPLATE GROUP CENTER CONTACTMAP | colvar bias vatom pytorch generic core opes function |
| 22.045 | Binding mode and mechanism of enzymatic polyethylene terephthalate degradation | bio | metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation | Francesco Colizzi | UPPER_WALLS COM ANGLE DISTANCE METAD MOVINGRESTRAINT WHOLEMOLECULES LOWER_WALLS PRINT | generic vatom colvar bias |
| 22.044 | Colloid Crystallisation Analyses | materials | Q4, Q6, Pair Entropy, DFS | Aaron Finney | COORDINATIONNUMBER MFILTER_LESS LOCAL_Q4 GROUP Q4 COMBINE CONTACT_MATRIX LOCAL_AVERAGE MFILTER_MORE LOCAL_Q6 CLUSTER_NATOMS DFSCLUSTERING Q6 PRINT | adjmat symfunc multicolvar clusters core generic function |
| 22.029 | Angiotensin-1-7_Metadynamics | bio | Metadynamics, Angiotensin-(1-7), peptide | L.-América Chi | COORDINATION UPPER_WALLS GROUP METAD GYRATION WHOLEMOLECULES LOWER_WALLS FLUSH PRINT | generic core colvar bias |
| 22.016 | Homogeneous ice nucleation in an ab initio machine learning model of water | chemistry | ice, water, nucleation, seeding, environment similarity, interfacial free energy, interfaces | Pablo Piaggi | UPPER_WALLS CUSTOM VOLUME DUMPGRID RESTART ENERGY OPES_METAD HISTOGRAM AROUND ENVIRONMENTSIMILARITY PRINT | colvar bias setup gridtools envsim generic volumes opes function |
| 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 | UPPER_WALLS CUSTOM TORSION COM ALPHABETA DISTANCE METAD COMBINE ZANGLES MATHEVAL WHOLEMOLECULES YANGLES LOWER_WALLS MOLINFO XANGLES PRINT | multicolvar colvar bias vatom generic function |
| 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 | COORDINATION MOLINFO UPPER_WALLS TORSION ALPHABETA ANGLE DISTANCE METAD WHOLEMOLECULES FLUSH ALPHARMSD PRINT | multicolvar colvar bias generic secondarystructure |
| 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 | VES_OUTPUT_BASISFUNCTIONS VES_LINEAR_EXPANSION PRINT COORDINATION TD_WELLTEMPERED DISTANCE METAD BF_WAVELETS INCLUDE UNITS OPT_ADAM ENERGY BF_CHEBYSHEV BF_GAUSSIANS UPPER_WALLS BF_CUBIC_B_SPLINES TD_UNIFORM POSITION OPT_AVERAGED_SGD BF_LEGENDRE FLUSH | colvar bias setup ves generic |
| 21.038 | Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics | materials | metadynamics, SGOOP, nucleation, urea | Ziyue Zou | COORDINATIONNUMBER VOLUME GROUP METAD CENTER COMBINE INCLUDE LOAD ENERGY PRINT | symfunc colvar bias vatom setup core generic function |
| 21.029 | Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs | bio | metadynamics, small peptide, machine learning | Pratyush Tiwary | TORSION FLUSH EXTERNAL RESTART MOLINFO ENERGY PRINT | setup colvar generic bias |
| 21.025 | Computational and biochemical analysis of type IV pilus dynamics and stability | bio | molecular dynamics, calcium binding, Type IV pilus | Yasaman Karami | UPPER_WALLS DISTANCE LOWER_WALLS PRINT | generic colvar bias |
| 21.000 | Uremic toxin time scale dynamics | bio | uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs) | Jim Pfaendtner | COM GROUP DISTANCE WHOLEMOLECULES PRINT | generic vatom colvar core |
| 20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Valerio Rizzi | COORDINATION UPPER_WALLS FIT_TO_TEMPLATE GROUP ANGLE DISTANCE CENTER MATHEVAL WHOLEMOLECULES ENERGY OPES_METAD ENDPLUMED FIXEDATOM PYTORCH_MODEL PRINT | colvar bias vatom pytorch generic core opes function |
| 20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Jim Pfaendtner | COORDINATION GROUP DISTANCE CENTER DISTANCES WHOLEMOLECULES RESTART PRINT | multicolvar colvar vatom setup generic 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 | UPPER_WALLS TD_WELLTEMPERED VOLUME OPT_DUMMY MATHEVAL RESTART BF_LEGENDRE VES_LINEAR_EXPANSION Q6 OPT_AVERAGED_SGD ENVIRONMENTSIMILARITY PRINT | symfunc colvar bias setup ves envsim generic function |
| 20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Pratyush Tiwary | UPPER_WALLS TORSION DISTANCE RMSD METAD COMBINE WHOLEMOLECULES RESTART MOLINFO PRINT | colvar bias setup generic function |
| 20.006 | Class B GPCR activation mechanism | bio | metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | UPPER_WALLS DISTANCE METAD RMSD COMBINE CENTER MATHEVAL WHOLEMOLECULES LOWER_WALLS MOLINFO ENERGY PRINT | colvar bias vatom generic function |
| 19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Wei Chen | RESTRAINT COM COMBINE ANN POSITION | colvar annfunc bias vatom function |
| 19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Kim Jelfs | COM MOVINGRESTRAINT DISTANCES INPLANEDISTANCES RESTART FLUSH PRINT | multicolvar bias vatom setup generic |
| 19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | GiovanniMaria Piccini | UPPER_WALLS DISTANCE METAD COMBINE UNITS LOWER_WALLS FLUSH ENERGY PRINT | colvar bias setup generic function |
| 19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Gareth Tribello | FOURIER_TRANSFORM GROUP CENTER MULTICOLVARDENS UNITS FCCUBIC FIND_CONTOUR_SURFACE DUMPGRID MORE_THAN | fourier symfunc vatom setup contour gridtools core function |
| 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 | COORDINATION UPPER_WALLS GROUP POSITION METAD UNITS RESTART LOWER_WALLS FLUSH PRINT | colvar bias setup generic core |
| 19.035 | Dimerization of GPCRs from coarse-grained umbrella sampling | bio | Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization | Davide Provasi | TORSION RESTRAINT COM GROUP DISTANCE PRINT | colvar bias vatom generic core |
| 19.030 | Coarse-Grained MetaDynamics (CG-MetaD) | bio | Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy | Vittorio Limongelli | UPPER_WALLS COM DISTANCE METAD WHOLEMOLECULES LOWER_WALLS PRINT | generic vatom colvar bias |
| 19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Riccardo Capelli | COORDINATION UPPER_WALLS FIT_TO_TEMPLATE GROUP COM POSITION METAD MATHEVAL DUMPGRID WRAPAROUND WHOLEMOLECULES REWEIGHT_METAD CONVERT_TO_FES FLUSH READ ENDPLUMED HISTOGRAM PRINT | colvar bias vatom gridtools generic core function |
| 19.013 | RNA FF FITTING | methods | force field, RNA | Giovanni Bussi | TORSION INCLUDE PUCKERING MATHEVAL CONSTANT BIASVALUE MOLINFO | bias colvar generic function |
| 26.012 | Buprenorphine Restricts the Conformational Landscape of the μ-Opioid Receptor | bio | OneOPES, GPCR, MOR, activation, euclidean path, conformational changes, allostery | Simone Aureli | RMSD PRINT PATH DISTANCE UPPER_WALLS ENERGY CENTER ECV_MULTITHERMAL VOLUME GROUP CUSTOM OPES_METAD_EXPLORE OPES_EXPANDED COORDINATION | core opes bias generic mapping colvar vatom function |
| 26.008 | Ensemble Dynamics | methods | State Exploration, Protein Folding, Drug Binding, Phase Transition | Florian M. Dietrich | UNITS PRINT DISTANCE CELL POSITION GROUP CUSTOM BIASVALUE TORSION OPES_METAD_EXPLORE LOAD | core opes generic bias colvar setup function |
| 26.002 | A Transferable and Robust Computational Framework for Class A GPCR Activation Free Energies | bio | OneOPES, GPCR, ADRB1, activation, euclidean path, microswitches, conformational changes, allostery | Valerio Rizzi | LOWER_WALLS PATHMSD RMSD PRINT PATH DISTANCE UPPER_WALLS ENERGY CENTER ECV_MULTITHERMAL VOLUME GROUP CUSTOM OPES_METAD_EXPLORE OPES_EXPANDED COORDINATION | core opes bias mapping generic colvar vatom function |
| 25.028 | Designing transferable transition state guided collective variable via interpretable machine learning model for enhanced sampling. A case study on polymer collapse transition | bio | metadynamics, polymer collapse transition, transferable CV,interpretable ML-model | Saikat Dhibar and Biman Jana | LOWER_WALLS COORDINATION PRINT DISTANCE UPPER_WALLS CENTER MATHEVAL GROUP COMBINE WHOLEMOLECULES METAD GYRATION | core bias generic colvar vatom function |
| 25.001 | RNA G-quadruplex folding with ST-metaD protocol | bio | RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | ERMSD MOLINFO COMBINE WHOLEMOLECULES METAD | bias generic function colvar |
| 24.029 | Combination of OPES and OPES-Explore | methods | OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin | Dhiman Ray | LOWER_WALLS RMSD PRINT UPPER_WALLS GROUP WHOLEMOLECULES METAD PYTORCH_MODEL DISTANCE MOLINFO FLUSH ENERGY FIXEDATOM COMBINE OPES_METAD_EXPLORE UNITS ENDPLUMED OPES_METAD MATHEVAL POSITION COORDINATION FIT_TO_TEMPLATE CENTER INCLUDE CONTACTMAP CUSTOM BIASVALUE | core opes bias generic colvar pytorch setup vatom function |
| 24.028 | All-atom simulations of RNA-membrane interactions | bio | metadynamics, membrane, RNA | Giovanni Bussi | LOWER_WALLS PUCKERING PRINT SORT DISTANCES DISTANCE UPPER_WALLS MOLINFO CENTER POSITION GROUP MATHEVAL COMBINE GHOST WHOLEMOLECULES METAD GYRATION | core bias generic colvar multicolvar vatom function |
| 24.002 | Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes | chemistry | metadynamics, ligand design, solvent extraction | Xiaoyu Wang | RESTART UNITS PRINT TORSION METAD | setup generic colvar bias |
| 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 | UNITS PRINT OPES_METAD DISTANCE UPPER_WALLS FLUSH FIXEDATOM GROUP ZDISTANCES COORDINATIONNUMBER | core opes symfunc generic bias colvar multicolvar setup vatom |
| 23.034 | Urea nucleation in water: do long-range forces matter? | materials | LMF theory, Metadynamics, Nucleation | Ziyue Zou | LOAD PRINT COORDINATIONNUMBER CENTER INCLUDE GROUP METAD | core symfunc generic bias setup vatom |
| 23.027 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, DFS, Q3, Pair Entropy | Aaron Finney | LOAD DUMPGRID HISTOGRAM UNITS CLUSTER_NATOMS CONTACT_MATRIX LOCAL_AVERAGE PRINT LOCAL_Q3 COORDINATIONNUMBER GROUP FIXEDATOM DENSITY AROUND CLUSTER_DISTRIBUTION RESTRAINT DFSCLUSTERING Q3 | volumes core adjmat symfunc generic bias clusters setup vatom gridtools |
| 23.024 | Permutationally Invariant Networks for Enhanced Sampling (PINES) | methods | collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent | Nicholas Herringer | LOAD PRINT PBMETAD PINES | setup generic pines bias |
| 23.022 | A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar | methods | collective variables, machine learning, toy model | Enrico Trizio | LOWER_WALLS UNITS ENDPLUMED PRINT OPES_METAD PYTORCH_MODEL UPPER_WALLS POSITION CUSTOM BIASVALUE | opes bias generic colvar setup pytorch function |
| 22.040 | From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure | bio | SARS-CoV-2, Spike, Omicron | Miłosz Wieczór | LOWER_WALLS PRINT UPPER_WALLS WHOLEMOLECULES PCAVARS METAD | bias mapping generic |
| 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 RMSD FIT_TO_TEMPLATE PRINT OPES_METAD DISTANCE UPPER_WALLS PYTORCH_MODEL CENTER COMMITTOR MATHEVAL FIXEDATOM GROUP WHOLEMOLECULES CUSTOM COORDINATION | core opes bias generic colvar pytorch vatom function |
| 22.012 | Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT | bio | contact maps, protein-protein interactions | Isabell-Louise Grothaus | PRINT CONTACTMAP DISTANCE CENTER | generic vatom colvar |
| 22.004 | Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques | chemistry | reaction discovery, OPES, collective variables | Umberto Raucci | LOWER_WALLS UNITS COM PRINT OPES_METAD DISTANCE PYTORCH_MODEL UPPER_WALLS MATHEVAL GROUP CUSTOM OPES_METAD_EXPLORE COORDINATION LOAD | core opes bias generic colvar setup pytorch vatom function |
| 21.049 | Multiple-path-metadynamics and PathMaps | methods | path-CV, metadynamics, multiple-walker, multiple paths, pathmap | Alberto Pérez-de-Alba-Ortíz | LOWER_WALLS LOAD MOVINGRESTRAINT UNITS CONSTANT PRINT UPPER_WALLS RESTRAINT CUSTOM TORSION COMBINE METAD ENSEMBLE | bias generic colvar setup function |
| 21.022 | Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly | materials | parallel bias metadynamics, adsorption, peptide | Xin Qi | LOWER_WALLS COM PRINT DISTANCE UPPER_WALLS ENERGY MOLINFO PBMETAD GYRATION | bias vatom colvar generic |
| 21.013 | Role of vibrational excitation in heterogeneous catalysis | chemistry | catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption | Kristof Bal | LOWER_WALLS EXTERNAL TD_GRID PRINT UPPER_WALLS VES_LINEAR_EXPANSION ANGLES OPT_AVERAGED_SGD METAD HISTOGRAM DISTANCE REWEIGHT_BIAS FLUSH RESTRAINT UWALLS COMBINE LOAD DUMPGRID UNITS CONVERT_TO_FES BF_CHEBYSHEV COORDINATION COORDINATIONNUMBER DISTANCES REWEIGHT_METAD | symfunc bias generic ves colvar multicolvar setup function gridtools |
| 21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Adriana Pietropaolo | RESTART CONSTANT PRINT MATHEVAL PBMETAD TORSION BIASVALUE WHOLEMOLECULES | generic bias colvar setup function |
| 21.006 | OPES, On-the-fly Probability Enhanced Sampling Method | methods | opes, alanine dipeptide, well-tempered, multithermal, multiumbrella | Michele Invernizzi | ENDPLUMED PRINT OPES_METAD ENERGY ECV_UMBRELLAS_LINE TORSION OPES_EXPANDED ECV_MULTITHERMAL | generic opes colvar |
| 20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Faidon Brotzakis | DUMPGRID HISTOGRAM RMSD EMMI READ PRINT CONVERT_TO_FES MOLINFO GROUP BIASVALUE WHOLEMOLECULES DISTANCES | core generic bias colvar multicolvar isdb gridtools |
| 20.028 | Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane | bio | metadynamics, KRas-4B, anionic membrane | Huixia Lu | RESTART FIT_TO_TEMPLATE PRINT DISTANCE CENTER METAD | generic bias colvar setup vatom |
| 20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Vojtech Spiwok | TORSION PRINT METAD | bias generic colvar |
| 20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Matteo Salvalaglio | LOWER_WALLS PRINT CELL ENERGY UPPER_WALLS VOLUME MATHEVAL METAD | bias generic function colvar |
| 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 | LOWER_WALLS LOAD COM PRINT CONSTANT DISTANCE UPPER_WALLS MOLINFO INCLUDE CONTACTMAP MATHEVAL GROUP PROJECTION_ON_AXIS FUNCPATHGENERAL BIASVALUE WHOLEMOLECULES METAD | core bias generic colvar setup vatom function |
| 19.080 | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | methods | ves, variationally enhanced sampling, vibrational excitation, chemical reactions | Kristof Bal | LOWER_WALLS EXTERNAL HISTOGRAM UNITS DUMPGRID TD_GRID PRINT ANGLE CONVERT_TO_FES DISTANCE UPPER_WALLS FLUSH VES_LINEAR_EXPANSION BF_CHEBYSHEV TD_WELLTEMPERED OPT_AVERAGED_SGD COMBINE COORDINATION | bias generic ves colvar setup function gridtools |
| 19.050 | Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes | chemistry | metadynamics, membranes, Willard Chandler surface | Gareth Tribello | DUMPGRID HISTOGRAM RESTART READ CONVERT_TO_FES PRINT REWEIGHT_BIAS UPPER_WALLS DISTANCE_FROM_CONTOUR COMBINE METAD | contour generic bias setup function gridtools |
| 19.040 | Optimal Metric for Path Collective Variables | bio | metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path | Francesco Luigi Gervasio | ENDPLUMED PRINT MATHEVAL TORSION METAD | bias generic function colvar |
| 19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Carlo Camilloni | LOWER_WALLS ALPHABETA RESTART ENDPLUMED PRINT UPPER_WALLS MOLINFO FLUSH ANTIBETARMSD GROUP PBMETAD WHOLEMOLECULES BIASVALUE CS2BACKBONE | core bias generic multicolvar secondarystructure setup isdb |
| 19.032 | Chemical reaction in solution using path collective variables based on coordination patterns | chemistry | chemical reactions, solutions, metadynamics, coordination patterns | Fabio Pietrucci | RESTART PRINT PATH UPPER_WALLS FLUSH METAD DISTANCES | generic mapping bias multicolvar setup |
| 19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Pratyush Tiwary | EXTERNAL ALPHABETA RESTART COM PRINT DISTANCE COMMITTOR TORSION COMBINE WHOLEMOLECULES | bias generic colvar multicolvar setup vatom function |
| 19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Jim Pfaendtner | EXTERNAL ENERGY GROUP COORDINATION METAD | bias core colvar |
| 19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Kresten Lindorff-Larsen | ALPHABETA PRINT MOLINFO FLUSH COMBINE COMMITTOR METAD | bias generic function multicolvar |
| 19.003 | EMMI ClpP | bio | metainference, cryo-EM | Max Bonomi | EMMI PRINT MOLINFO GROUP BIASVALUE | isdb generic core bias |
| 19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Giovanni Bussi | LOWER_WALLS ERMSD PRINT ANGLE DISTANCE UPPER_WALLS FLUSH MOLINFO INCLUDE RANDOM_EXCHANGES COMBINE METAD DISTANCES | bias generic colvar multicolvar function |
| 26.011 | Lets Stalk About Membranes. Committor-Based Enhanced Sampling of Stalk Formation. | bio | committor, machine learning, enhanced sampling, OPES, membrane fusion, stalk formation, nanoparticles | Giorgia Rossi | COORDINATION OPES_METAD_EXPLORE PRINT CUSTOM LOAD GROUP BIASVALUE CENTER LOWER_WALLS | core colvar generic setup function vatom opes bias |
| 26.006 | Metadynamics simulations of buried phosphorylation sites and proline isomerisation | bio | metadynamics | Julian Streit | COORDINATION PRINT WHOLEMOLECULES TORSION METAD MOLINFO | bias generic colvar |
| 25.025 | Enhanced Sampling of Ligand Binding Coupled to RNA Conformational Dynamics | bio | OPES, OPES Flooding , Metadynamics, RNA, Ligand binding, Free Energy, Kinetics, Funnel | Revanth Elangovan and Dhiman Ray | RMSD COMMITTOR COORDINATION UPPER_WALLS CENTER LOWER_WALLS DISTANCE PRINT OPES_METAD CUSTOM WRAPAROUND ENDPLUMED FUNNEL MATHEVAL GROUP WHOLEMOLECULES TORSION METAD FUNNEL_PS COM | core colvar function generic funnel opes vatom bias |
| 25.008 | Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting | methods | metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting | Dhiman Ray | DISTANCE ENDPLUMED PYTORCH_MODEL PRINT OPES_METAD UNITS CUSTOM GROUP WHOLEMOLECULES TORSION RMSD POSITION UPPER_WALLS METAD MOLINFO ENERGY BIASVALUE LOWER_WALLS | core colvar function generic setup pytorch opes bias |
| 24.036 | Leveraging cryptic ligand envelopes through enhanced molecular simulations | bio | HREX, conformational heterogeneity, drug discovery, ligand binding, plitidepsin, aplidin, ligand-target complexes, cryptic ligand envelope | Francesco Colizzi | DISTANCE HISTOGRAM ANGLE COORDINATION PRINT GROUP WHOLEMOLECULES TORSION DUMPGRID CONVERT_TO_FES | core generic gridtools colvar |
| 24.033 | Transient interactions between the fuzzy coat and the cross-b core of brain-derived Ab42 filaments | bio | CryoEM, MEMMI, Metadynamics, Metainference, Ab42 Fibrils, structural ensemble | Maria Milanesi | DISTANCE COORDINATION PRINT PARABETARMSD GROUP ALPHARMSD WHOLEMOLECULES DUMPATOMS RMSD UPPER_WALLS PBMETAD BIASVALUE MOLINFO CENTER EMMI DUMPMASSCHARGE COM | core colvar secondarystructure generic isdb vatom bias |
| 24.032 | DeepLNE++ | methods | PATHCV, OPES | Thorben Fröhlking | DISTANCE COORDINATION PRINT OPES_METAD CUSTOM LOAD GROUP TORSION COMBINE ENERGY | core colvar generic setup function opes |
| 24.024 | Host-Guest binding free energies à la carte, an automated OneOPES protocol | bio | OneOPES, ligand binding, binding free energy,SAMPL challenge, host-guest | Valerio Rizzi | FIXEDATOM DISTANCE ANGLE COORDINATION ENDPLUMED MATHEVAL OPES_METAD_EXPLORE PRINT ECV_MULTITHERMAL GROUP WHOLEMOLECULES OPES_EXPANDED TORSION UPPER_WALLS FIT_TO_TEMPLATE ENERGY CENTER LOWER_WALLS | core colvar generic function vatom 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 | DISTANCE COORDINATION OPES_METAD PRINT UPPER_WALLS ENERGY | opes bias generic colvar |
| 24.006 | Water vapor condensation | chemistry | metadynamics, homogeneous condensation, chemical potential | Shenghui Zhong | COORDINATIONNUMBER PRINT UNITS CONTACT_MATRIX UPPER_WALLS METAD CLUSTER_PROPERTIES DFSCLUSTERING CLUSTER_NATOMS | adjmat generic setup clusters symfunc bias |
| 24.003 | Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations | chemistry | steered molecular dynamics, foldamers, peptoids, bio-inspired | Kaylyn Torkelson | DISTANCE INCLUDE COORDINATION PRINT GYRATION MOVINGRESTRAINT WHOLEMOLECULES TORSION COM ALPHABETA | multicolvar colvar generic vatom 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 | DISTANCE INCLUDE FUNCPATHMSD PRINT ALPHARMSD CONTACTMAP UPPER_WALLS METAD MOLINFO PATHMSD LOWER_WALLS | colvar secondarystructure generic function 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 | DISTANCE MATHEVAL PRINT WHOLEMOLECULES RMSD METAD MOLINFO | function bias generic colvar |
| 23.026 | Machine Learning Nucleation Collective Variables with Graph Neural Networks | chemistry | Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks | Florian Dietrich | LOCAL_Q6 COORDINATIONNUMBER PRINT Q6 GROUP MFILTER_MORE MOVINGRESTRAINT COMBINE METAD LOWER_WALLS | core multicolvar generic symfunc function bias |
| 23.023 | Rational design of novel biomimetic sequence-defined polymers for mineralization applications | methods | metadynamics, surface binding, biomimetic mineralization | Kaylyn Torkelson | DISTANCE COORDINATION PRINT GYRATION PBMETAD UPPER_WALLS COM | bias generic vatom colvar |
| 23.018 | Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention | materials | metadynamics, surface binding, peptide adsorption | Kaylyn Torkelson | DISTANCE PRINT GYRATION PBMETAD UPPER_WALLS COM | bias generic vatom colvar |
| 23.015 | MPCs aggregation | bio | opes_explore, dimerization, MPCs, self-assembly | Vikas Tiwari | DISTANCE COORDINATION OPES_METAD_EXPLORE PRINT CUSTOM GROUP WHOLEMOLECULES UPPER_WALLS METAD CENTER LOWER_WALLS COM | core colvar generic function vatom opes 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 | DISTANCE MATHEVAL CONSTANT PRINT WHOLEMOLECULES UPPER_WALLS BIASVALUE METAD LOWER_WALLS | function bias generic colvar |
| 23.003 | Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations | methods | metadynamics, alchemical variable, alchemical free energy calculations | Wei-Tse Hsu | READ PRINT TORSION METAD EXTRACV | bias generic colvar |
| 22.034 | Rationalising the difference in crystallisability of two Sulflowers using efficient in silico methods | materials | metadynamics, crystallizability, crystal structure prediction, sulflower, persulforated coronene | Matteo Salvalaglio | CELL MATHEVAL PRINT CUSTOM UPPER_WALLS METAD LOWER_WALLS COMMITTOR DRMSD | function bias generic colvar |
| 22.030 | Mixing physics across temperatures with generative artificial intelligence | methods | REMD, Generative AI, DDPM | Yihang Wang | TORSION WHOLEMOLECULES PRINT | generic colvar |
| 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 | DISTANCE COORDINATION COORDINATIONNUMBER GYRATION UNITS COMBINE UPPER_WALLS METAD FLUSH LOWER_WALLS COM | colvar generic setup symfunc function vatom bias |
| 22.006 | Peptide framework for screening the effects of amino acids on assembly | bio | metadynamics, peptides | Andrew White | INCLUDE HISTOGRAM PRINT GYRATION GROUP COMBINE REWEIGHT_BIAS METAD DUMPGRID DISTANCES CONVERT_TO_FES COM | core multicolvar colvar generic bias function vatom gridtools |
| 22.000 | Amyloid precursor protein processing by human γ-secretase | bio | Bias Exchange Metadynamics, Helix unfolding, coupled binding | Xiaoli Lu | DISTANCE INCLUDE COORDINATION ANTIBETARMSD PRINT UNITS ALPHARMSD CONTACTMAP RANDOM_EXCHANGES METAD MOLINFO CENTER | colvar secondarystructure generic setup vatom bias |
| 21.044 | NaCl nucleation | chemistry | metadynamics, DFS clustering | Aaron Finney | FIXEDATOM LOCAL_Q6 HISTOGRAM COORDINATIONNUMBER PRINT Q6 GROUP MFILTER_MORE COMBINE CONTACT_MATRIX METAD INSPHERE DUMPGRID DFSCLUSTERING CLUSTER_DISTRIBUTION CLUSTER_NATOMS | core adjmat multicolvar generic clusters volumes symfunc bias function vatom gridtools |
| 21.034 | Efficient sampling of high-dimensional free energy landscapes using adaptive reinforced dynamics | bio | reinforced dynamics, bias-exchange metadynamics, parallel-bias metadynamics | Dongdong Wang | ENDPLUMED INCLUDE PRINT TORSION RANDOM_EXCHANGES PBMETAD METAD | bias generic colvar |
| 21.028 | From Enhanced Sampling to Reaction Profiles | methods | collective variables, multi-state, machine learning, Deep-TDA | Enrico Trizio | FIXEDATOM PYTORCH_MODEL COORDINATION UPPER_WALLS FIT_TO_TEMPLATE CENTER LOWER_WALLS DISTANCE ANGLE OPES_METAD PRINT ENDPLUMED MATHEVAL UNITS GROUP LOAD WHOLEMOLECULES TORSION DISTANCES | core multicolvar colvar function generic pytorch setup opes vatom bias |
| 21.020 | Reweighted Jarzynski sampling | methods | free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions | Kristof Bal | ANN BF_CHEBYSHEV BIASVALUE RESTRAINT CONVERT_TO_FES HISTOGRAM OPT_AVERAGED_SGD CONSTANT REWEIGHT_METAD COMBINE UPPER_WALLS DUMPGRID FLUSH TD_WELLTEMPERED VES_LINEAR_EXPANSION DISTANCE COORDINATIONNUMBER PRINT OPES_METAD CUSTOM UNITS MOVINGRESTRAINT LOAD REWEIGHT_BIAS METAD | annfunc colvar generic setup symfunc bias ves function opes gridtools |
| 21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Kresten Lindorff-Larsen | PRINT GYRATION GROUP ALPHARMSD WHOLEMOLECULES METAINFERENCE EEFSOLV PBMETAD SAXS BIASVALUE MOLINFO FLUSH CENTER | core colvar secondarystructure generic isdb vatom bias |
| 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 | COORDINATION PRINT WHOLEMOLECULES MOLINFO RESTRAINT STATS | function bias generic colvar |
| 20.016 | Predicting polymorphism in molecular crystals using orientational entropy | materials | metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy | Pablo Piaggi | INCLUDE PRINT VOLUME LOAD GROUP UPPER_WALLS METAD CENTER | core colvar generic setup vatom bias |
| 20.001 | Conformational stability and dynamics in solution and in crystals report similarly on unfolding and aggregation propensity of amyloidogenic proteins | bio | metainference, metadynamics, NMR, protein dynamics, b2m, protein crystals | Carlo Camilloni | ENDPLUMED ANTIBETARMSD PRINT GROUP WHOLEMOLECULES CS2BACKBONE PBMETAD UPPER_WALLS BIASVALUE MOLINFO FLUSH LOWER_WALLS ALPHABETA | core multicolvar secondarystructure generic isdb bias |
| 19.075 | PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python | other | Python, automatic differentiation | Toni Giorgino | DISTANCE ENDPLUMED ANGLE PRINT CUSTOM GROUP TORSION COMBINE DUMPDERIVATIVES CENTER RESTRAINT | core colvar generic function vatom bias |
| 19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_SIMULATED_ANNEALING PRINT UNITS POSITION MAZE_OPTIMIZER_BIAS MAZE_LOSS | maze generic colvar setup |
| 19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Paolo Raiteri | DISTANCE MATHEVAL PRINT UNITS UPPER_WALLS METAD FLUSH RESTART | colvar generic setup function bias |
| 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 | TORSIONS DUMPMULTICOLVAR SMAC DISTANCES PRINT | generic multicolvar symfunc |
| 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 | UPPER_WALLS METAD COM COORDINATIONNUMBER FLUSH FIXEDATOM COMBINE RESTRAINT DISTANCES LOWER_WALLS PRINT DISTANCE ANGLE GROUP UNITS COORDINATION | bias colvar vatom function multicolvar core generic symfunc setup |
| 25.002 | M3_PCV-ABMD | chemistry | Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor | Gian Marco Elisi | UPPER_WALLS ENDPLUMED ABMD PATHMSD PRINT UNITS | bias generic colvar setup |
| 24.020 | Graph Neural Network-State Predictive Information Bottleneck (GNN-SPIB) approach for learning molecular thermodynamics and kinetics | bio | LJ7, alanine, well-tempered metadynamics, infrequent metadynamics, machine learning | Ziyue Zou, Dedi Wang, Pratyush Tiwary | METAD LOAD TORSION PRINT COMMITTOR GROUP | bias colvar core generic setup |
| 23.043 | Modeling the ferroelectric phase transition in barium titanate with DFT accuracy and converged sampling | materials | Barium Titanate, ferroelectric phase transition, Machine Learning, polarization order parameters | Lorenzo Gigli | METAD SUM FLUSH TRANSPOSE INCLUDE PRINT SELECT_COMPONENTS MATHEVAL | bias function matrixtools generic valtools |
| 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 | FIT_TO_TEMPLATE LOWER_WALLS BIASVALUE TORSION PRINT MATHEVAL COMMITTOR COORDINATION UPPER_WALLS ENDPLUMED FLUSH OPES_METAD WRAPAROUND ENERGY OPES_METAD_EXPLORE GROUP DISTANCE CENTER COM CUSTOM MOLINFO POSITION UNITS WHOLEMOLECULES | bias colvar opes vatom function core generic setup |
| 23.028 | Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process | chemistry | Ammonia decomposition; Dynamics;OPES; Neural Network potential | Manyi Yang | UPPER_WALLS COM ZDISTANCES COORDINATIONNUMBER CUSTOM FLUSH OPES_METAD COMMITTOR FIXEDATOM DISTANCES ENERGY PRINT LOWER_WALLS DISTANCE GROUP UNITS MATHEVAL | bias opes colvar vatom function multicolvar core generic symfunc setup |
| 22.041 | Skipping the Replica Exchange Ladder with Normalizing Flows | methods | OPES, alanine, normalizing flows, replica exchange | Michele Invernizzi | ENDPLUMED OPES_EXPANDED ECV_MULTITHERMAL OPES_METAD TORSION POSITION ENERGY PRINT UNITS | colvar generic opes setup |
| 22.002 | GAMBES_SAMPL5_RATES | other | GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding | Jayashrita Debnath | UPPER_WALLS CENTER ENDPLUMED WHOLEMOLECULES FLUSH FIT_TO_TEMPLATE LOAD COMMITTOR FIXEDATOM ENERGY PRINT DISTANCE ANGLE GROUP COORDINATION MATHEVAL PYTORCH_MODEL | bias colvar vatom function core generic pytorch setup |
| 21.033 | Multiple-path-metadynamics applied to DNA base-pairing transitions | bio | path-CV, metadynamics, multiple-walker, dna | Alberto Pérez-de-Alba-Ortíz | UPPER_WALLS METAD MOVINGRESTRAINT COMBINE INCLUDE RESTRAINT CONSTANT PRINT | bias function generic |
| 21.014 | how to determine statistically accurate conformational ensembles | bio | metadynamics, metainference, errors, cv, SAXS, ensemble determination | Cristina Paissoni | CENTER METAD PBMETAD ALPHABETA CONTACTMAP BIASVALUE ENSEMBLE STATS MOLINFO TORSION SAXS ANTIBETARMSD PRINT GYRATION WHOLEMOLECULES | bias colvar secondarystructure vatom function multicolvar generic isdb |
| 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 | RESTART CENTER MOLINFO ABMD TORSION ERMSD PRINT DISTANCE | bias colvar vatom generic setup |
| 19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Silvio Pipolo | CELL UPPER_WALLS METAD FUNCPATHMSD PIV LOWER_WALLS PRINT | colvar bias function generic piv |
| 26.009 | Exploring the Conformational Landscape of HIV-1 TAR RNA by PT-WTE | bio | RNA, PT-WTE, HIV-1 TAR | Stefano Bosio | ENERGY WHOLEMOLECULES METAD MOLINFO PRINT GROUP | colvar generic core bias |
| 26.005 | Cryptic pocket discovery in Alzheimer disease risk proteins BIN1, PICALM, and CD2AP via well-tempered metadynamics | methods | cryptic pockets, Alzheimer disease, BIN1, PICALM, CD2AP, well-tempered metadynamics, endocytosis, clathrin-mediated trafficking, virtual screening | Cagrı Ozkurt | DISTANCE WHOLEMOLECULES METAD ANGLE PRINT | colvar generic bias |
| 25.024 | Sampling glycan-glycan interactions for B22 calculations | bio | B22, glycan, carbohydrates, distance, REST2, metadynamics, RECT, replica exchange | Isabell Louise Grothaus | DISTANCE COM COMBINE METAD POSITION RESTRAINT PRINT | bias colvar generic function vatom |
| 25.014 | Atomic resolution ensembles of intrinsically disordered proteins with Alphafold | bio | bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement | Vincent Schnapka | GROUP BAIES BIASVALUE PRINT | generic core bias isdb |
| 25.013 | Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices | bio | umbrella sampling, temperature ramping | Alexander Berlaga | DISTANCE RESTRAINT PRINT PYTORCH_MODEL GYRATION | colvar generic pytorch 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 | DISTANCE COMBINE MATHEVAL UNITS ENERGY INCLUDE TORSION FLUSH COORDINATION POSITION LOAD OPES_METAD CELL BIASVALUE PRINT CUSTOM | bias colvar generic function setup opes |
| 25.011 | Chiral perovskite nucleation | chemistry | metadynamics, chiral perovskites, nucleation | Adriana Pietropaolo | DISTANCE LOWER_WALLS UNITS MULTI_RMSD UPPER_WALLS PBMETAD PRINT MATHEVAL RESTART | bias colvar generic function setup |
| 25.004 | Machine Learning-Driven Molecular Dynamics Unveil a Bulk Phase Transformation Driving Ammonia Synthesis on Barium Hydride | chemistry | OPES, OPES flooding, Catalysis, Ammonia Synthesis | Axel Tosello Gardini | DISTANCE UNITS DISTANCES COMMITTOR UPPER_WALLS FIXEDATOM FLUSH OPES_METAD ZDISTANCES PRINT COORDINATIONNUMBER CUSTOM GROUP | symfunc bias colvar multicolvar generic setup function vatom core opes |
| 24.017 | Absolute Binding Free Energies with OneOPES | methods | protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy | Francesco Gervasio | ENERGY OPES_EXPANDED PROJECTION_ON_AXIS OPES_METAD_EXPLORE COM INCLUDE WHOLEMOLECULES MOLINFO BIASVALUE PRINT CUSTOM GROUP CONSTANT RMSD ECV_MULTITHERMAL CONTACTMAP LOWER_WALLS UPPER_WALLS TORSION METAD COORDINATION WRAPAROUND MATHEVAL RESTART | bias colvar generic function setup vatom core opes |
| 24.009 | Weighted Shape Gaussian Mixture Models | bio | metadynamics, clustering | Glen Hocky | UNITS TORSION METAD PRINT GROUP | bias colvar generic setup core |
| 24.007 | SWISH-X | bio | swish-x, SWISH-X, swish, expanded SWISH | Alberto Borsatto | ENERGY INCLUDE WHOLEMOLECULES UPPER_WALLS MOLINFO ECV_MULTITHERMAL OPES_EXPANDED CONTACTMAP PRINT | colvar generic bias opes |
| 24.005 | Learning Markovian Dynamics with Spectral Maps | methods | spectral map, collective variables, machine learning | Jakub Rydzewski | DISTANCE UNITS BIASVALUE PRINT CUSTOM | bias colvar generic function setup |
| 24.001 | A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations | bio | OPES, OPES-Flooding, QM/MM, Kinetics, Enzyme Catalysis | Dhiman Ray | DISTANCE COMBINE LOWER_WALLS UNITS COMMITTOR UPPER_WALLS TORSION FLUSH OPES_METAD PRINT CUSTOM | bias colvar generic function setup opes |
| 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 | DISTANCE INCLUDE WHOLEMOLECULES UPPER_WALLS MOLINFO WRAPAROUND EMMIVOX BIASVALUE PRINT GROUP | bias isdb colvar generic core |
| 23.020 | FEP simulations of ATOX1 homodimer | chemistry | parallel bias metadynamics, FEP, free-energy of metal ion dissociation | Adriana Pietropaolo | DISTANCE CONSTANT WHOLEMOLECULES PBMETAD ANGLE BIASVALUE PRINT MATHEVAL | colvar generic function bias |
| 23.008 | PBMetaD simulations of Histatin5 | bio | metadynamics, IDP, Rg, PPII | Francesco Pesce | WHOLEMOLECULES TORSION MOLINFO PBMETAD PRINT GYRATION GROUP | colvar generic core bias |
| 22.038 | Enhanced Sampling Aided Design of Molecular Photoswitches | chemistry | reaction discovery, OPES explore, graph CV | Umberto Raucci | UNITS COORDINATION PRINT OPES_METAD_EXPLORE PYTORCH_MODEL CUSTOM | pytorch colvar generic function setup opes |
| 22.033 | Reciprocal barrier restraint. Application to PROTAC passive permeability prediction | methods | PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR | Istvan Kolossvary | DISTANCE COM UNITS METAD DRR FLUSH BIASVALUE PRINT CUSTOM | drr bias colvar generic function setup vatom |
| 22.032 | Reciprocal barrier restraint. Application to path-meta-eABF | methods | restraint, upper wall, lower wall, path colvar, meta-eABF, metadynamics, DRR, protein conformational transition, PROTAC | Istvan Kolossvary | PATHMSD METAD DRR FLUSH BIASVALUE PRINT CUSTOM | drr bias colvar generic function |
| 22.028 | N-glycan conformer distributions in atomistic simulation | bio | REST2, RECT, N-glycan, pucker | Isabell Grothaus | DUMPGRID TORSION MOLINFO METAD READ CONVERT_TO_FES PUCKERING PRINT HISTOGRAM | colvar generic gridtools bias |
| 21.027 | EGFR activating mutations mechanism | bio | metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA | Francesco Gervasio | DISTANCE LOWER_WALLS ENERGY INCLUDE WHOLEMOLECULES UPPER_WALLS MOLINFO METAD CONTACTMAP PRINT ALPHARMSD MATHEVAL | bias colvar generic function secondarystructure |
| 21.026 | Probing allosteric regulations with coevolution-driven molecular simulations | bio | metadynamics, coevolution, allostery, adenylate cyclase | Francesco Colizzi | DISTANCE COM UNITS PATHMSD WHOLEMOLECULES METAD UPPER_WALLS PRINT | bias colvar generic setup vatom |
| 21.010 | Step by Step Strecker Amino Acid Synthesis from Ab Initio Prebiotic Chemistry | chemistry | Strecker reaction, free energy landscape, ab initio molecular dynamics, glycine, prebiotic synthesis | Théo Magrino | generic | |
| 21.004 | Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy | bio | machine learning, well-tempered metadynamics, path collective variable, potential of mean force, standard binding free energy calculations, host-guest, protein-ligand unbinding | Dorothea Gobbo | LOWER_WALLS PATHMSD WHOLEMOLECULES UPPER_WALLS METAD PRINT RESTART | colvar generic setup 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 | Kevin Rossi | UNITS DISTANCES METAD COORDINATION PRINT CUSTOM | bias colvar multicolvar generic setup 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 | Riccardo Capelli | DISTANCE COM COMBINE LOWER_WALLS DUMPGRID ABMD REWEIGHT_METAD HISTOGRAM UPPER_WALLS METAD READ CONVERT_TO_FES ENDPLUMED PRINT MATHEVAL | bias gridtools colvar generic function vatom |
| 19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | DISTANCE COM ENERGY UPPER_WALLS METAD MOLINFO PRINT GYRATION | colvar generic bias vatom |
| 19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Giovanni Bussi | DISTANCE LOWER_WALLS WHOLEMOLECULES COORDINATION RESTRAINT ENDPLUMED | colvar generic bias |
| 19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Gareth Tribello | LOWER_WALLS UNITS FCCUBIC UPPER_WALLS METAD AROUND ENDPLUMED CELL PRINT | symfunc volumes bias colvar generic setup |
| 19.049 | Determining the sizes of solid/liquid clusters in MD trajectories of nucleation | methods | nucleation, metadynamics, clustering, Steinhardt order parameters | Gareth Tribello | CLUSTER_NATOMS DISTANCES COORDINATIONNUMBER MATRIX_VECTOR_PRODUCT METAD OUTER_PRODUCT LOCAL_Q6 MORE_THAN Q6 OUTPUT_CLUSTER PRINT CLUSTER_DISTRIBUTION DFSCLUSTERING ONES CLUSTER_PROPERTIES SMAC CONTACT_MATRIX CUSTOM | symfunc bias clusters matrixtools multicolvar function generic adjmat |
| 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 | DISTANCE COM FUNNEL LOWER_WALLS RMSD DISTANCES COMBINE REWEIGHT_METAD WHOLEMOLECULES UPPER_WALLS MOLINFO TORSION ALPHABETA METAD BRIDGE PRINT GROUP | funnel bias colvar multicolvar function generic adjmat vatom core |
| 19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | DISTANCE COMBINE UNITS DISTANCES UPPER_WALLS METAD FLUSH PRINT RESTART | bias colvar multicolvar function setup generic |
| 19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Vittorio Limongelli | DISTANCE COM FUNNEL LOWER_WALLS RMSD WHOLEMOLECULES METAD UPPER_WALLS PRINT FUNNEL_PS | funnel bias colvar generic vatom |
| 19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Haochuan Chen | TORSION DRR PRINT | drr colvar generic |
| 19.009 | RNA tetraloops folding | bio | metadynamics, RNA, folding | Giovanni Bussi | RMSD WHOLEMOLECULES METAD MOLINFO ERMSD ENDPLUMED PRINT | colvar generic bias |