Browse the eggs in PLUMED-NEST
PLUMED-NEST provides all the data needed to reproduce the results of a PLUMED-enhanced molecular dynamics simulation or analysis contained in a published paper. Furthermore, PLUMED-NEST monitors the compatibility of the provided PLUMED input files with the current and development versions of the code and integrates links from these files to the PLUMED manual.
Here is the list of projects already deposited in PLUMED-NEST, while a complete bibliography can be found here.
| plumID | Name | Category | Keywords | Contributor | Actions | Modules |
|---|---|---|---|---|---|---|
| 25.014 | Atomic resolution ensembles of intrinsically disordered and multi-domain proteins with Alphafold | bio | bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement | Vincent Schnapka | PRINT BAIES BIASVALUE GROUP | generic isdb core bias |
| 25.013 | Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices | bio | umbrella sampling, temperature ramping | Alexander Berlaga | PYTORCH_MODEL PRINT GYRATION RESTRAINT DISTANCE | generic bias colvar pytorch |
| 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 METAD PRINT MOVINGRESTRAINT PUCKERING RESTART RESTRAINT DISTANCE TORSION | generic colvar setup bias |
| 25.000 | Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer | bio | metadynamics, pathCV | Sahithya Sridharan Iyer | MOLINFO GROUP METAD PRINT UPPER_WALLS WHOLEMOLECULES FUNCPATHGENERAL COM RESTART DISTANCE | bias function colvar generic core vatom setup |
| 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 MOLINFO ENERGY METAD PRINT COMMITTOR MATHEVAL RESTART RESTRAINT FLUSH DISTANCE TORSION BIASVALUE | bias function colvar generic symfunc setup |
| 24.002 | Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes | chemistry | metadynamics, ligand design, solvent extraction | Xiaoyu Wang | UNITS METAD PRINT RESTART TORSION | bias setup colvar generic |
| 23.024 | Permutationally Invariant Networks for Enhanced Sampling (PINES) | methods | collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent | Nicholas Herringer | LOAD PBMETAD PRINT | bias setup generic |
| 23.022 | A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar | methods | collective variables, machine learning, toy model | Enrico Trizio | UNITS PYTORCH_MODEL ENDPLUMED LOWER_WALLS PRINT UPPER_WALLS POSITION BIASVALUE OPES_METAD CUSTOM | bias function opes colvar pytorch generic setup |
| 22.044 | Colloid Crystallisation Analyses | materials | Q4, Q6, Pair Entropy, DFS | Aaron Finney | COORDINATIONNUMBER GROUP DFSCLUSTERING LOCAL_AVERAGE PRINT Q6 Q4 COMBINE CLUSTER_NATOMS LOCAL_Q4 MFILTER_MORE LOCAL_Q6 CONTACT_MATRIX MFILTER_LESS | function multicolvar adjmat generic core clusters symfunc |
| 22.007 | Characterization of a natural variant of human NDP52 and its functional consequences on mitophagy | bio | metadynamics, well-tempered, protein-protein interactions, disordered proteins, mutations autophagy | Elena Papaleo | MOLINFO METAD PRINT UPPER_WALLS WHOLEMOLECULES ANGLE ALPHARMSD COORDINATION ALPHABETA FLUSH DISTANCE TORSION | secondarystructure bias multicolvar colvar generic |
| 22.006 | Peptide framework for screening the effects of amino acids on assembly | bio | metadynamics, peptides | Andrew White | DISTANCES CONVERT_TO_FES GROUP METAD PRINT INCLUDE REWEIGHT_BIAS COM GYRATION COMBINE HISTOGRAM DUMPGRID | bias function multicolvar gridtools colvar generic core vatom |
| 21.040 | A structural ensemble of a tau-microtubule complex reveals regulatory tau phosphorylation and acetylation mechanisms | bio | EMMI, CryoEM, tau-microtubules, post-translational modifications, chemical mutagenesis, structural ensemble, Metainference | Faidon Brotzakis | MOLINFO GROUP PRINT UPPER_WALLS WHOLEMOLECULES EMMI COM RESTART DISTANCE BIASVALUE | bias colvar generic core isdb vatom setup |
| 21.017 | All-atom simulations of the Vav1 AD construct | bio | metadynamics, parallel-bias, well-tempered | Simone Orioli | MOLINFO GROUP PBMETAD METAD PRINT WHOLEMOLECULES CONTACTMAP RESTART ALPHARMSD ALPHABETA REWEIGHT_BIAS | secondarystructure bias multicolvar colvar generic core setup |
| 21.010 | Step by Step Strecker Amino Acid Synthesis from Ab Initio Prebiotic Chemistry | chemistry | Strecker reaction, free energy landscape, ab initio molecular dynamics, glycine, prebiotic synthesis | Théo Magrino | generic | |
| 20.014 | 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 | ENDPLUMED METAINFERENCE ALPHARMSD FLUSH PARABETARMSD TORSION GROUP ANTIBETARMSD PRINT INCLUDE WHOLEMOLECULES GYRATION CS2BACKBONE MOLINFO COMBINE ENSEMBLE PBMETAD DIHCOR STATS COORDINATION | secondarystructure bias function multicolvar colvar generic core isdb |
| 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 | MOLINFO LOWER_WALLS GROUP METAD DISTANCE PRINT UPPER_WALLS INCLUDE PROJECTION_ON_AXIS LOAD WHOLEMOLECULES FUNCPATHGENERAL MATHEVAL COM CONTACTMAP CONSTANT BIASVALUE | bias function colvar vatom generic core setup |
| 19.075 | PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python | other | Python, automatic differentiation | Toni Giorgino | ENDPLUMED GROUP DUMPDERIVATIVES PRINT ANGLE RESTRAINT COMBINE CENTER DISTANCE TORSION CUSTOM | bias function colvar generic core vatom |
| 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 | DISTANCES COORDINATIONNUMBER ENERGY ENDPLUMED LOWER_WALLS METAD PRINT UPPER_WALLS GYRATION | bias multicolvar colvar generic symfunc |
| 19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Giovanni Bussi | MOLINFO METAD PRINT INCLUDE WHOLEMOLECULES MATHEVAL COM SORT COORDINATION FLUSH DISTANCE TORSION MAXENT | bias function colvar generic vatom |
| 19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Matteo Salvalaglio | ENDPLUMED GROUP PRINT INCLUDE CENTER DISTANCE | generic core vatom colvar |
| 19.059 | cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide | bio | bias-exchange metadynamics, cis-trans isomerization | Fabrizio Marinelli | METAD PRINT INCLUDE TORSION RANDOM_EXCHANGES | bias colvar generic |
| 19.040 | Optimal Metric for Path Collective Variables | bio | metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path | Francesco Luigi Gervasio | ENDPLUMED METAD PRINT MATHEVAL TORSION | generic function colvar bias |
| 19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Carlo Camilloni | MOLINFO ENDPLUMED GROUP PRINT UPPER_WALLS INCLUDE STATS WHOLEMOLECULES RESTRAINT SAXS CENTER RMSD DISTANCE BIASVALUE | bias function colvar generic core isdb vatom |
| 19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Carlo Camilloni | MOLINFO ENDPLUMED DHENERGY GROUP RDC PBMETAD METAINFERENCE PRINT DIHCOR UPPER_WALLS STATS WHOLEMOLECULES RESTRAINT CENTER ENSEMBLE ALPHABETA DISTANCE TORSION | bias function multicolvar colvar generic core isdb vatom |
| 25.009 | Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water | chemistry | metadynamics, nitrate photolysis | Kam-Tung Chan | READ REWEIGHT_METAD DUMPGRID GROUP METAD PRINT UPPER_WALLS DISTANCE COORDINATION HISTOGRAM RESTART FLUSH CUSTOM | function colvar generic setup core bias gridtools |
| 25.008 | Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting | methods | metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting | Dhiman Ray | GROUP METAD RMSD MOLINFO PRINT UPPER_WALLS DISTANCE WHOLEMOLECULES TORSION BIASVALUE LOWER_WALLS ENERGY ENDPLUMED PYTORCH_MODEL OPES_METAD POSITION UNITS CUSTOM | function colvar generic setup opes core bias pytorch |
| 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 | GROUP RMSD MOLINFO PBMETAD UPPER_WALLS EMMI DISTANCE PRINT PARABETARMSD COORDINATION WHOLEMOLECULES DUMPMASSCHARGE COM ALPHARMSD BIASVALUE CENTER DUMPATOMS | vatom isdb secondarystructure colvar generic core bias |
| 24.025 | Correlating Enzymatic Reactivity for Different Substrates using Transferable Data-Driven Collective Variables | bio | enzymatic reactivity, k_cat, transfer learning, data-driven CVs, catalysis, ligand-binding modes, water, alpha-amylase, sugar, classical MD, OPES, machine learning, Deep TDA CV, path CV | Sudip Das | GROUP PRINT UPPER_WALLS DISTANCE COORDINATION WHOLEMOLECULES FIT_TO_TEMPLATE TORSION PATH LOWER_WALLS RESTART CENTER PYTORCH_MODEL FIXEDATOM OPES_METAD CUSTOM | vatom function colvar generic mapping setup opes core bias pytorch |
| 24.024 | Host-Guest binding free energies à la carte, an automated OneOPES protocol | bio | OneOPES, ligand binding, binding free energy,SAMPL challenge, host-guest | Valerio Rizzi | GROUP PRINT ECV_MULTITHERMAL UPPER_WALLS DISTANCE ANGLE FIT_TO_TEMPLATE WHOLEMOLECULES COORDINATION TORSION LOWER_WALLS ENERGY OPES_METAD_EXPLORE ENDPLUMED CENTER MATHEVAL FIXEDATOM OPES_EXPANDED | vatom function colvar generic opes core bias |
| 24.017 | Absolute Binding Free Energies with OneOPES | methods | protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy | Francesco Gervasio | ECV_MULTITHERMAL UPPER_WALLS CONSTANT LOWER_WALLS RESTART WRAPAROUND INCLUDE CUSTOM GROUP RMSD METAD PRINT WHOLEMOLECULES TORSION BIASVALUE OPES_EXPANDED MOLINFO COORDINATION COM OPES_METAD_EXPLORE ENERGY CONTACTMAP PROJECTION_ON_AXIS MATHEVAL | function vatom colvar generic setup opes core bias |
| 24.005 | Learning Markovian Dynamics with Spectral Maps | methods | spectral map, collective variables, machine learning | Jakub Rydzewski | PRINT DISTANCE BIASVALUE UNITS CUSTOM | function colvar generic setup bias |
| 24.004 | Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables | materials | metadynamics, nucleation, machine learning | Ziyue Zou | GROUP METAD LOAD PRINT RESTART INCLUDE | core generic setup bias |
| 23.044 | Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition | materials | metadynamics, interlocked molecules | Luigi Leanza | GROUP METAD READ DUMPGRID PRINT CONVERT_TO_FES COMMITTOR COORDINATION HISTOGRAM ENDPLUMED | colvar generic core bias gridtools |
| 23.033 | DNA G-quadruplex and G-hairpin folding with ST-metaD protocol | bio | DNA, G4, GQ, quadruplex, hairpin, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | ERMSD METAD MOLINFO COMBINE PRINT COORDINATION WHOLEMOLECULES BIASVALUE GHBFIX | generic function colvar 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 | METAD COLLECT_FRAMES PRINT PATHMSD UPPER_WALLS DISTANCE WHOLEMOLECULES COM DISSIMILARITIES SKETCHMAP VSTACK SKETCHMAP_PROJECTION LANDMARK_SELECT_FPS TRANSPOSE VORONOI CUSTOM | vatom function colvar generic landmarks valtools matrixtools bias dimred |
| 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 | GROUP PRINT UPPER_WALLS DISTANCE COORDINATION FIT_TO_TEMPLATE WHOLEMOLECULES TORSION PATH LOWER_WALLS OPES_METAD_EXPLORE PYTORCH_MODEL CENTER FIXEDATOM OPES_METAD UNITS CUSTOM | vatom function colvar generic mapping setup opes core bias pytorch |
| 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 | METAD CELL PRINT UPPER_WALLS COMMITTOR DRMSD LOWER_WALLS MATHEVAL CUSTOM | generic function colvar bias |
| 22.029 | Angiotensin-1-7_Metadynamics | bio | Metadynamics, Angiotensin-(1-7), peptide | L.-América Chi | GROUP METAD PRINT UPPER_WALLS COORDINATION WHOLEMOLECULES LOWER_WALLS FLUSH GYRATION | core generic colvar bias |
| 22.017 | Water regulates the residence time of Benzamidine in Trypsin | bio | ligand binding, water, opes, benzamidine trypsin, unbinding rates, machine learning, Deep-LDA, Deep-TICA | Narjes Ansari | GROUP RMSD PRINT UPPER_WALLS DISTANCE COMMITTOR FIT_TO_TEMPLATE WHOLEMOLECULES COORDINATION LOWER_WALLS CENTER PYTORCH_MODEL MATHEVAL FIXEDATOM OPES_METAD CUSTOM | vatom function colvar generic opes core bias pytorch |
| 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 | METAD COMBINE UPPER_WALLS DISTANCE COORDINATIONNUMBER COORDINATION COM LOWER_WALLS FLUSH GYRATION UNITS | function vatom colvar generic setup symfunc bias |
| 22.002 | GAMBES_SAMPL5_RATES | other | GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding | Jayashrita Debnath | GROUP LOAD PRINT UPPER_WALLS DISTANCE ANGLE COMMITTOR FIT_TO_TEMPLATE WHOLEMOLECULES COORDINATION ENERGY ENDPLUMED CENTER PYTORCH_MODEL MATHEVAL FIXEDATOM FLUSH | vatom function colvar generic setup core bias pytorch |
| 21.050 | N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity | methods | bio | Isabell Louise Grothaus | DISTANCE PRINT CENTER | vatom colvar generic |
| 21.035 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, interface | Aaron Finney | GROUP LOAD PRINT DISTANCE RESTRAINT FIXEDATOM | vatom colvar generic setup core bias |
| 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 | ALPHABETA METAD PBMETAD PRINT DISTANCE COORDINATION TORSION COM ENERGY GYRATION INCLUDE | vatom colvar generic bias multicolvar |
| 21.028 | From Enhanced Sampling to Reaction Profiles | methods | collective variables, multi-state, machine learning, Deep-TDA | Enrico Trizio | UPPER_WALLS LOWER_WALLS OPES_METAD GROUP LOAD PRINT DISTANCE WHOLEMOLECULES TORSION PYTORCH_MODEL FIXEDATOM COORDINATION ENDPLUMED ANGLE FIT_TO_TEMPLATE DISTANCES CENTER MATHEVAL UNITS | vatom function colvar generic setup opes core bias multicolvar pytorch |
| 21.022 | Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly | materials | parallel bias metadynamics, adsorption, peptide | Xin Qi | PBMETAD PRINT MOLINFO UPPER_WALLS DISTANCE COM LOWER_WALLS ENERGY GYRATION | generic colvar bias vatom |
| 21.006 | OPES, On-the-fly Probability Enhanced Sampling Method | methods | opes, alanine dipeptide, well-tempered, multithermal, multiumbrella | Michele Invernizzi | PRINT ECV_MULTITHERMAL ECV_UMBRELLAS_LINE TORSION ENERGY ENDPLUMED OPES_METAD OPES_EXPANDED | opes colvar generic |
| 21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Tarak Karmakar | GROUP LOAD PRINT UPPER_WALLS LOWER_WALLS PYTORCH_MODEL FLUSH MATHEVAL OPES_METAD | function generic setup opes core bias pytorch |
| 20.028 | Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane | bio | metadynamics, KRas-4B, anionic membrane | Huixia Lu | METAD PRINT DISTANCE FIT_TO_TEMPLATE RESTART CENTER | vatom colvar generic setup bias |
| 20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Matteo Salvalaglio | METAD CELL PRINT UPPER_WALLS LOWER_WALLS ENERGY VOLUME MATHEVAL | generic function colvar bias |
| 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 | PRINT UPPER_WALLS ENVIRONMENTSIMILARITY TD_WELLTEMPERED BF_LEGENDRE VES_LINEAR_EXPANSION RESTART VOLUME OPT_AVERAGED_SGD MATHEVAL OPT_DUMMY Q6 | function colvar generic setup envsim symfunc ves bias |
| 19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | METAD MOLINFO PRINT UPPER_WALLS DISTANCE COM ENERGY GYRATION | generic colvar bias vatom |
| 19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Sandro Bottaro | ERMSD RMSD METAD MOLINFO PRINT DISTANCE WHOLEMOLECULES TORSION | generic colvar bias |
| 19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Jakub Rydzewski | METAD PRINT PATHMSD UPPER_WALLS LOWER_WALLS RESTART UNITS | generic colvar bias setup |
| 19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Mattia Bernetti | METAD PRINT PATHMSD UPPER_WALLS WHOLEMOLECULES LOWER_WALLS | generic colvar bias |
| 19.048 | Understanding Ligand Binding Selectivity in a Prototypical GPCR Family | bio | metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | METAD PRINT UPPER_WALLS DISTANCE CONSTANT WHOLEMOLECULES COM BIASVALUE LOWER_WALLS MATHEVAL | function vatom colvar generic bias |
| 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 | GROUP RMSD ALPHABETA METAD MOLINFO FUNNEL UPPER_WALLS BRIDGE DISTANCE COMBINE REWEIGHT_METAD PRINT WHOLEMOLECULES TORSION COM LOWER_WALLS DISTANCES | function vatom colvar generic funnel core bias multicolvar adjmat |
| 19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Carlo Camilloni | GROUP ANTIBETARMSD ALPHABETA MOLINFO PBMETAD UPPER_WALLS PRINT WHOLEMOLECULES BIASVALUE LOWER_WALLS RESTART ENDPLUMED FLUSH CS2BACKBONE | isdb secondarystructure generic setup core bias multicolvar |
| 19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Elena Papaleo | GROUP METAD ALPHABETA MOLINFO PRINT UPPER_WALLS WHOLEMOLECULES LOWER_WALLS GYRATION | colvar generic core multicolvar bias |
| 19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Jim Pfaendtner | GROUP METAD COORDINATION ENERGY EXTERNAL | core colvar bias |
| 19.009 | RNA tetraloops folding | bio | metadynamics, RNA, folding | Giovanni Bussi | ERMSD RMSD METAD MOLINFO PRINT WHOLEMOLECULES ENDPLUMED | generic colvar bias |
| 19.003 | EMMI ClpP | bio | metainference, cryo-EM | Max Bonomi | GROUP PRINT EMMI MOLINFO BIASVALUE | core bias isdb generic |
| 25.019 | The Arch from the Stones. Understanding Protein Folding Energy Landscapes via Bio-inspired Collective Variables | bio | protein folding, OPES, OneOPES, binding free energy | Valerio Rizzi | COMBINE GHOST DISTANCE CENTER PRINT ECV_MULTITHERMAL OPES_EXPANDED CUSTOM GROUP COORDINATION MOLINFO OPES_METAD_EXPLORE ENERGY RMSD | opes vatom function core colvar 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 | EMMIVOX PRINT BIASVALUE GROUP MOLINFO WHOLEMOLECULES | generic core isdb bias |
| 25.016 | Advancing in silico drug design with Bayesian refinement of AlphaFold models | bio | bAIes, AlphaFold, Bayesian refinement, virtual screening, docking, small-molecule, enrichment | Samiran Sen | BIASVALUE BAIES GROUP PRINT | isdb generic bias core |
| 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 DISTANCE PRINT ECV_MULTITHERMAL OPES_EXPANDED CUSTOM GROUP RESTART COORDINATION OPES_METAD_EXPLORE ENERGY TORSION | opes core function setup colvar generic |
| 24.019 | Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning | bio | OPES, machine learning, protein folding, adaptive sampling | Mingyuan Zhang | COMBINE OPES_METAD ALPHARMSD DISTANCE TORSION PRINT GYRATION CUSTOM COORDINATION MOLINFO WHOLEMOLECULES | opes function generic colvar secondarystructure |
| 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 |
| 24.003 | Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations | chemistry | steered molecular dynamics, foldamers, peptoids, bio-inspired | Kaylyn Torkelson | DISTANCE ALPHABETA PRINT GYRATION MOVINGRESTRAINT COORDINATION INCLUDE WHOLEMOLECULES COM TORSION | vatom multicolvar colvar bias generic |
| 23.043 | Modeling the ferroelectric phase transition in barium titanate with DFT accuracy and converged sampling | materials | Barium Titanate, ferroelectric phase transition, Machine Learning, polarization order parameters | Lorenzo Gigli | MATHEVAL METAD TRANSPOSE SELECT_COMPONENTS FLUSH PRINT INCLUDE SUM | matrixtools function bias generic valtools |
| 23.034 | Urea nucleation in water: do long-range forces matter? | materials | LMF theory, Metadynamics, Nucleation | Ziyue Zou | COORDINATIONNUMBER METAD CENTER PRINT LOAD GROUP INCLUDE | symfunc vatom core setup bias generic |
| 23.014 | Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 | bio | metadynamics, oligomerization, chemokine receptors, GPCR, membrane | Vittorio Limongelli | COMBINE UPPER_WALLS METAD DISTANCE TORSION FLUSH PRINT COM WHOLEMOLECULES | vatom function colvar bias generic |
| 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 DRR METAD TIME FLUSH PATHMSD PRINT BIASVALUE CUSTOM UNITS LOWER_WALLS | function setup colvar bias generic drr |
| 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 | MATHEVAL UPPER_WALLS METAD DISTANCE PRINT BIASVALUE CONSTANT WHOLEMOLECULES LOWER_WALLS | generic colvar bias 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 | COMMITTOR DISTANCE PRINT FIXEDATOM CUSTOM MATHEVAL FIT_TO_TEMPLATE ANGLE CENTER ENDPLUMED GROUP COORDINATION MOLINFO LOWER_WALLS COMBINE OPES_METAD PYTORCH_MODEL INCLUDE ENERGY RMSD WHOLEMOLECULES UPPER_WALLS CONTACTMAP | pytorch opes function core vatom colvar bias generic |
| 23.007 | Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains | bio | metadynamics, peptoids, parallel-bias metadynamics | Jim Pfaendtner | RESTRAINT PBMETAD PRINT GYRATION COORDINATION INCLUDE WHOLEMOLECULES COM TORSION | generic colvar bias 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 | DUMPGRID MATHEVAL READ METAD DISTANCE REWEIGHT_METAD RMSD HISTOGRAM PRINT MOLINFO CONVERT_TO_FES WHOLEMOLECULES | function colvar bias generic gridtools |
| 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 METAD PRINT CONTACTMAP ENERGY WHOLEMOLECULES LOWER_WALLS | generic colvar bias |
| 22.041 | Skipping the Replica Exchange Ladder with Normalizing Flows | methods | OPES, alanine, normalizing flows, replica exchange | Michele Invernizzi | OPES_METAD ENDPLUMED PRINT ECV_MULTITHERMAL OPES_EXPANDED POSITION ENERGY UNITS TORSION | generic setup opes colvar |
| 22.038 | Enhanced Sampling Aided Design of Molecular Photoswitches | chemistry | reaction discovery, OPES explore, graph CV | Umberto Raucci | PRINT PYTORCH_MODEL OPES_METAD_EXPLORE CUSTOM COORDINATION UNITS | pytorch opes function setup colvar 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 | PBMETAD TORSION GYRATION MOLINFO WHOLEMOLECULES | generic colvar bias |
| 22.033 | Reciprocal barrier restraint. Application to PROTAC passive permeability prediction | methods | PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR | Istvan Kolossvary | DRR METAD DISTANCE FLUSH PRINT BIASVALUE CUSTOM COM UNITS | function vatom setup colvar bias generic drr |
| 22.019 | Exploring aspartic protease inhibitor binding to design selective antimalarials | bio | ligand binding, loop opening, path CV, funnel metadynamics, drug development | Raitis Bobrovs | UPPER_WALLS METAD DISTANCE FUNNEL PATHMSD PRINT FUNNEL_PS COM WHOLEMOLECULES LOWER_WALLS | vatom funnel colvar bias generic |
| 22.011 | Accelerating all-atom simulations and gaining mechanistic understanding of biophysical systems through State Predictive Information Bottleneck | methods | metadynamics, membrane permeation, protein folding | Shams Mehdi | MATHEVAL YANGLES UPPER_WALLS COMBINE METAD DISTANCE COM ALPHABETA TORSION PRINT XANGLES CUSTOM MOLINFO ZANGLES WHOLEMOLECULES LOWER_WALLS | vatom function multicolvar colvar bias generic |
| 22.004 | Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques | chemistry | reaction discovery, OPES, collective variables | Umberto Raucci | MATHEVAL UPPER_WALLS OPES_METAD DISTANCE PRINT PYTORCH_MODEL LOAD CUSTOM OPES_METAD_EXPLORE COORDINATION GROUP COM UNITS LOWER_WALLS | pytorch opes function core vatom setup colvar bias generic |
| 21.048 | Enhancing ligand exploration within a channel pore and fenestrations using metadynamics | bio | well-tempered metadynamics, protein-ligand enhanced sampling, sodium channel, Nav, small molecule drug | Elaine Tao | UPPER_WALLS METAD DISTANCE PRINT CUSTOM COM UNITS TORSION LOWER_WALLS | vatom function setup colvar bias generic |
| 20.015 | Rational design of ASCT2 inhibitors using an integrated experimental-computational approach | bio | ASCT2 transporter, small-molecules, cryo-EM, metainference | Max Bonomi | DUMPATOMS EMMIVOX PRINT LOAD BIASVALUE GROUP MOLINFO WHOLEMOLECULES | core isdb setup bias generic |
| 19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Valerio Rizzi | EXTERNAL COMBINE COORDINATIONNUMBER METAD FLUSH ENDPLUMED PRINT GROUP RESTART UNITS | symfunc core function setup bias generic |
| 19.056 | maze | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_SIMULATED_ANNEALING MAZE_LOSS PRINT MAZE_OPTIMIZER_BIAS POSITION UNITS | maze setup generic colvar |
| 19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Gareth Tribello | CELL UPPER_WALLS METAD FCCUBIC ENDPLUMED PRINT AROUND UNITS LOWER_WALLS | symfunc setup colvar bias generic volumes |
| 19.041 | Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces | bio | metadynamics, collective variables, conformational changes, multiple walkers, Well-Tempered MetaD, peptide, binding, phosphorylation, post-transitional motif, sio2, adsorption | Jim Pfaendtner | UPPER_WALLS METAD DISTANCE PRINT ENERGY COM | generic colvar bias vatom |
| 19.030 | Coarse-Grained MetaDynamics (CG-MetaD) | bio | Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy | Vittorio Limongelli | UPPER_WALLS METAD DISTANCE PRINT COM WHOLEMOLECULES LOWER_WALLS | generic colvar bias vatom |
| 19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Mattia Bernetti | ALPHARMSD METAD ENDPLUMED PRINT GYRATION MOLINFO ENERGY WHOLEMOLECULES | secondarystructure generic colvar bias |
| 19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Kresten Lindorff-Larsen | COMBINE COMMITTOR METAD ALPHABETA FLUSH PRINT MOLINFO | generic multicolvar bias function |
| 19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Adriana Pietropaolo | MATHEVAL METAD TORSION PRINT BIASVALUE CONSTANT WHOLEMOLECULES | generic colvar bias function |
| 19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Matteo Salvalaglio | UPPER_WALLS COMMITTOR METAD DISTANCE CENTER PRINT TORSION LOWER_WALLS | generic colvar bias vatom |
| 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 | UPPER_WALLS FIT_TO_TEMPLATE GROUP OPES_METAD_EXPLORE PRINT MATHEVAL CENTER FIXEDATOM DISTANCE ANGLE ENERGY WHOLEMOLECULES COORDINATION | function colvar bias vatom core generic opes |
| 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 VOLUME PRINT CENTER READ PBMETAD INCLUDE GYRATION DISTANCE ENERGY RESTART | colvar vatom setup bias generic |
| 24.001 | A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations | bio | OPES, OPES-Flooding, QM/MM, Kinetics, Enzyme Catalysis | Dhiman Ray | UPPER_WALLS TORSION CUSTOM LOWER_WALLS FLUSH PRINT UNITS COMBINE DISTANCE COMMITTOR OPES_METAD | function colvar bias setup generic opes |
| 23.038 | Determinants of Neutral Antagonism and Inverse Agonism in the β2-adrenergic receptor | bio | protein coupled receptor, beta-adrenergic, receptor activation, antagonism, inverse agonism, metadynamics | Timothy Clark | PRINT MATHEVAL RMSD METAD DISTANCE WHOLEMOLECULES MOLINFO | function generic colvar bias |
| 23.031 | Identifying small molecules binding sites in RNA conformational ensembles with SHAMAN | bio | RNA, metadynamics, probes, mixed-solvent MD, small molecules, binding sites | Max Bonomi | UPPER_WALLS FIT_TO_TEMPLATE WRAPAROUND GROUP PRINT CENTER METAD DISTANCES WHOLEMOLECULES SHADOW MOLINFO POSITION | colvar isdb multicolvar vatom bias core generic |
| 23.030 | Data Driven Classification of Ligand Unbinding Pathways | bio | OPES Explore, OPES Flooding, Benzene T4 Lysozyme, Ligand unbinding, Pathway classification, Kinetics, Residence time | Dhiman Ray | LOWER_WALLS WRAPAROUND ENDPLUMED OPES_METAD MATHEVAL FIT_TO_TEMPLATE OPES_METAD_EXPLORE UNITS CENTER COMMITTOR GROUP UPPER_WALLS TORSION CUSTOM FLUSH COM PRINT DISTANCE ENERGY WHOLEMOLECULES POSITION BIASVALUE COORDINATION MOLINFO | function colvar bias setup vatom core generic opes |
| 23.016 | Activation/deactivation free-energy profiles for the β2-adrenergic receptor: Ligand modes of action | bio | G protein coupled receptor, beta-adrenergic, receptor activation, partial agonism, metadynamics | Timothy Clark | REWEIGHT_METAD HISTOGRAM DUMPGRID PRINT MATHEVAL RMSD METAD DISTANCE CONVERT_TO_FES READ WHOLEMOLECULES MOLINFO | function colvar bias generic gridtools |
| 23.015 | MPCs aggregation | bio | opes_explore, dimerization, MPCs, self-assembly | Vikas Tiwari | UPPER_WALLS LOWER_WALLS CUSTOM COORDINATION OPES_METAD_EXPLORE PRINT COM CENTER METAD DISTANCE WHOLEMOLECULES GROUP | function colvar bias vatom core generic opes |
| 23.008 | PBMetaD simulations of Histatin5 | bio | metadynamics, IDP, Rg, PPII | Francesco Pesce | TORSION PRINT PBMETAD GYRATION WHOLEMOLECULES GROUP MOLINFO | generic colvar bias core |
| 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 | UPPER_WALLS LOWER_WALLS HISTOGRAM DUMPGRID ENVIRONMENTSIMILARITY OPES_EXPANDED ECV_UMBRELLAS_LINE PRINT RESTART | bias setup generic envsim gridtools opes |
| 22.040 | From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure | bio | SARS-CoV-2, Spike, Omicron | Miłosz Wieczór | UPPER_WALLS LOWER_WALLS PCAVARS PRINT METAD WHOLEMOLECULES | generic bias mapping |
| 22.037 | Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site | chemistry | metadynamics, DNA, abasic | Mike Jones | METAD DISTANCES DISTANCE PRINT | multicolvar colvar bias generic |
| 22.028 | N-glycan conformer distributions in atomistic simulation | bio | REST2, RECT, N-glycan, pucker | Isabell Grothaus | TORSION HISTOGRAM DUMPGRID PUCKERING PRINT CONVERT_TO_FES METAD READ MOLINFO | generic colvar gridtools bias |
| 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 | TORSION GROUP PRINT COM METAD DISTANCE WHOLEMOLECULES | colvar vatom bias core generic |
| 22.003 | Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling | methods | opes, metadynamics, reweighting, alanine, muller | Michele Invernizzi | UPPER_WALLS TORSION LOWER_WALLS ECV_MULTITHERMAL OPES_EXPANDED CUSTOM ECV_UMBRELLAS_FILE BIASVALUE OPES_METAD_EXPLORE PRINT UNITS METAD ENDPLUMED PBMETAD ENERGY OPES_METAD POSITION | function colvar bias setup generic opes |
| 21.051 | Automatic learning of hydrogen-bond fixes in an AMBER RNA force field | methods | force field, RNA | Giovanni Bussi | ERMSD COORDINATION BIASVALUE PRINT METAD COMBINE WHOLEMOLECULES MOLINFO | function generic colvar bias |
| 21.046 | Ubiquitin Interacting Motifs, Duality Between Structured and Disordered Motifs | bio | wt metadynamics, ubiquitin, ataxin-3, short linear motifs, ubiquitin binding motif, moonlight functions, intrinsic disorder | Elena Papaleo | UPPER_WALLS LOWER_WALLS GROUP ALPHABETA PRINT METAD GYRATION ENDPLUMED WHOLEMOLECULES | colvar multicolvar bias core generic |
| 21.045 | QM/MM metadynamics of thiol-disulfide exchange between methylthiolate and dimethyldisulfide in water with an imposed external electrostatic potential (ESP) | chemistry | metadynamics, QM/MM, electrostatic potential, thiol-disulfide exchange | Denis Maag | UPPER_WALLS LOWER_WALLS PRINT COORDINATIONNUMBER METAD DISTANCE COMBINE COORDINATION | function symfunc colvar bias generic |
| 21.043 | Predicting the Conformational Variability of Oncogenic GTP-bound G12D Mutated KRas-4B Proteins at Cell Membranes | chemistry | well-tempered metadynamics, KRas-4B, anionic membrane, conformational variability | Huixia Lu | TORSION FIT_TO_TEMPLATE PRINT METAD FIXEDATOM | generic vatom colvar bias |
| 21.036 | Modelling the structure and interactions of intrinsically disordered peptides with multiple-replica, metadynamics-based sampling methods and force-field combinations | bio | Bias Exchange Metadynamics, PTWTE-metaD | Matteo Salvalaglio | UPPER_WALLS LOWER_WALLS DIHCOR PARABETARMSD GROUP PRINT RANDOM_EXCHANGES METAD GYRATION ANTIBETARMSD WHOLEMOLECULES ENERGY ALPHARMSD COORDINATION MOLINFO | colvar multicolvar bias core generic secondarystructure |
| 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 | TORSION PRINT RANDOM_EXCHANGES METAD ENDPLUMED INCLUDE PBMETAD | generic colvar bias |
| 21.032 | Metal-coupled folding mechanism to metallothionein | bio | parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination | Manuel-Peris Diaz | GROUP UNITS PBMETAD WHOLEMOLECULES COORDINATION | colvar bias setup core generic |
| 21.015 | Coarse-grained metadynamics and umbrella sampling simulations to investigate interactions of carbohydrate-binding modules with chitin | bio | metadynamics, umbrella sampling, coarse-grained, MARTINI, chitin, carbohydrate-binding module | Gaston Courtade | COORDINATION RESTRAINT PRINT CENTER METAD REWEIGHT_BIAS WHOLEMOLECULES MATHEVAL POSITION RESTART | function colvar vatom bias setup generic |
| 21.014 | how to determine statistically accurate conformational ensembles | bio | metadynamics, metainference, errors, cv, SAXS, ensemble determination | Cristina Paissoni | TORSION ENSEMBLE SAXS BIASVALUE ALPHABETA PRINT CONTACTMAP CENTER METAD GYRATION PBMETAD ANTIBETARMSD STATS WHOLEMOLECULES MOLINFO | function colvar isdb multicolvar bias vatom generic secondarystructure |
| 21.012 | NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition | bio | funnel metadynamics | Jim Pfaendtner | UPPER_WALLS LOWER_WALLS FUNNEL_PS FUNNEL COM PRINT METAD DISTANCE | colvar funnel vatom bias generic |
| 21.011 | CmuMD simulations of NaCl(aq) at graphite | chemistry | CmuMD, DFS clustering | Aaron Finney | CLUSTER_NATOMS DUMPGRID RESTRAINT DFSCLUSTERING LOAD DENSITY CLUSTER_DISTRIBUTION AROUND PRINT COORDINATIONNUMBER MFILTER_MORE FIXEDATOM CONTACT_MATRIX MULTICOLVARDENS GROUP | gridtools symfunc multicolvar clusters bias setup vatom core generic adjmat volumes |
| 21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Kristof Bal | UPPER_WALLS HISTOGRAM FLUSH DUMPGRID LOAD UNITS PRINT COORDINATIONNUMBER MOVINGRESTRAINT CONVERT_TO_FES METAD COMMITTOR REWEIGHT_METAD | symfunc bias setup generic gridtools |
| 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 | UPPER_WALLS LOWER_WALLS PRINT METAD PATHMSD WHOLEMOLECULES RESTART | generic colvar bias setup |
| 21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Kresten Lindorff-Larsen | FLUSH SAXS BIASVALUE GROUP PRINT CENTER EEFSOLV GYRATION PBMETAD ALPHARMSD WHOLEMOLECULES MOLINFO METAINFERENCE | colvar isdb vatom bias core generic secondarystructure |
| 20.005 | Muscarinic M2 receptor/ligand Frequency-Adaptive Metadynamics and QM/MM calculations | bio | Frequency-adaptive metadynamics, multiple-walkers metadynamics, well-tempered metadynamics, GPCR, receptor, Adiabatic Bias MD | Riccardo Capelli | LOWER_WALLS CONTACTMAP CONVERT_TO_FES ENDPLUMED ABMD UPPER_WALLS FLUSH COM PRINT METAD DISTANCE READ WHOLEMOLECULES REWEIGHT_METAD FUNCPATHMSD HISTOGRAM DUMPGRID COMBINE MOLINFO | function colvar vatom bias generic gridtools |
| 20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Luigi Bonati | UPPER_WALLS TORSION LOWER_WALLS FLUSH LOAD PRINT UNITS COM MATHEVAL DISTANCE ENDPLUMED OPES_METAD GROUP PYTORCH_MODEL | function colvar pytorch vatom bias setup core generic opes |
| 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 | UPPER_WALLS LOWER_WALLS HISTOGRAM DUMPGRID COM PRINT ABMD CONVERT_TO_FES METAD DISTANCE ENDPLUMED READ COMBINE MATHEVAL REWEIGHT_METAD | function colvar vatom bias generic gridtools |
| 19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Giovanni Bussi | COORDINATION LOWER_WALLS RESTRAINT ENDPLUMED DISTANCE WHOLEMOLECULES | generic colvar bias |
| 19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Matteo Salvalaglio | TORSION HISTOGRAM DUMPGRID BIASVALUE PRINT EXTERNAL CONVERT_TO_FES METAD DISTANCE READ REWEIGHT_BIAS COMMITTOR MATHEVAL REWEIGHT_METAD | function colvar bias generic gridtools |
| 19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Jim Pfaendtner | PRINT METAD GYRATION ENERGY WHOLEMOLECULES | generic colvar bias |
| 19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Kim Jelfs | FLUSH COM MOVINGRESTRAINT PRINT DISTANCES INPLANEDISTANCES RESTART | multicolvar vatom setup bias generic |
| 19.045 | Adsorption free energy of Ca/CO3 ions on calcite steps in contact with water | materials | metadynamics, well-tempered, multiple walkers, LAMMPS | Marco De La Pierre | UPPER_WALLS LOWER_WALLS COORDINATION FLUSH UNITS PRINT METAD GROUP POSITION RESTART | colvar bias setup core generic |
| 19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | UPPER_WALLS FLUSH PRINT UNITS DISTANCES DISTANCE METAD COMBINE RESTART | function colvar multicolvar bias setup generic |
| 19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Vittorio Limongelli | UPPER_WALLS LOWER_WALLS FUNNEL_PS FUNNEL COM PRINT RMSD METAD DISTANCE WHOLEMOLECULES | colvar funnel vatom bias generic |
| 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 PRINT COM DISTANCE GROUP | colvar vatom bias core generic |
| 19.032 | Chemical reaction in solution using path collective variables based on coordination patterns | chemistry | chemical reactions, solutions, metadynamics, coordination patterns | Fabio Pietrucci | UPPER_WALLS FLUSH PATH PRINT DISTANCES METAD RESTART | mapping multicolvar bias setup generic |
| 19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Riccardo Capelli | UPPER_WALLS HISTOGRAM FIT_TO_TEMPLATE FLUSH DUMPGRID WRAPAROUND GROUP COM PRINT MATHEVAL CONVERT_TO_FES METAD READ ENDPLUMED WHOLEMOLECULES COORDINATION REWEIGHT_METAD POSITION | function colvar vatom bias core generic gridtools |
| 19.004 | MI Ubiquitin | bio | metainference, NMR | Max Bonomi | RDC PRINT CS2BACKBONE WHOLEMOLECULES GROUP MOLINFO METAINFERENCE | generic isdb core |
| 19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Max Bonomi | BIASVALUE PRINT EMMI GROUP MOLINFO | generic bias isdb core |
| 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 | LOWER_WALLS COORDINATION UPPER_WALLS ECV_MULTITHERMAL OPES_EXPANDED OPES_METAD_EXPLORE DISTANCES GROUP ENERGY RMSD PATHMSD DISTANCE CENTER CUSTOM GHOST PRINT | generic vatom multicolvar core colvar function opes bias |
| 25.018 | Metainference simulation for dimerization of RNA binding protein | bio | Metainference, Metadynamics, SAXS, protein dimer | Debadutta Patra | SAXS UPPER_WALLS PBMETAD FLUSH METAINFERENCE MOLINFO CENTER TORSION WHOLEMOLECULES DISTANCE STATS ENSEMBLE PRINT GYRATION | generic vatom colvar function bias isdb |
| 25.001 | RNA G-quadruplex folding with ST-metaD protocol | bio | RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | METAD COMBINE MOLINFO WHOLEMOLECULES ERMSD | colvar bias generic function |
| 24.006 | Water vapor condensation | chemistry | metadynamics, homogeneous condensation, chemical potential | Shenghui Zhong | UPPER_WALLS COORDINATIONNUMBER METAD CLUSTER_NATOMS DFSCLUSTERING CONTACT_MATRIX UNITS CLUSTER_PROPERTIES PRINT | clusters generic adjmat setup bias symfunc |
| 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 | LOWER_WALLS CONTACTMAP FUNCPATHMSD UPPER_WALLS METAD DISTANCE MOLINFO PATHMSD INCLUDE PRINT ALPHARMSD | generic secondarystructure colvar function bias |
| 23.037 | Estimating binding free energy of solid binding peptides without extensive sampling | bio | metadynamics, solid binding peptides | Xin Qi | LOWER_WALLS UPPER_WALLS PBMETAD MOLINFO COM DISTANCE PRINT GYRATION | colvar bias generic vatom |
| 23.036 | Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? | bio | NaCl, nucleation, metadynamics | Ruiyu Wang | COORDINATIONNUMBER METAD MATHEVAL Q4 COMBINE ENERGY VOLUME Q6 PRINT | generic colvar function bias symfunc |
| 23.020 | FEP simulations of ATOX1 homodimer | chemistry | parallel bias metadynamics, FEP, free-energy of metal ion dissociation | Adriana Pietropaolo | MATHEVAL PBMETAD BIASVALUE CONSTANT ANGLE WHOLEMOLECULES DISTANCE PRINT | colvar function generic bias |
| 23.006 | Transcription factor unbinding | bio | metadynamics, DNA, conformational changes | Malin Lüking | CONTACTMAP METAD MOLINFO COM ANGLE DISTANCE DUMPFORCES PRINT ALPHARMSD | generic vatom secondarystructure colvar bias |
| 23.003 | Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations | methods | metadynamics, alchemical variable, alchemical free energy calculations | Wei-Tse Hsu | METAD READ EXTRACV TORSION PRINT | colvar bias generic |
| 22.043 | Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES | bio | OPES, RNA, Tetraloop, Folding | Gül Zerze | CONTACTMAP ECV_MULTITHERMAL OPES_EXPANDED ENERGY ECV_UMBRELLAS_LINE WHOLEMOLECULES PRINT | colvar generic opes |
| 22.042 | Metadynamics of NSP10 and variants | bio | metadynamics, NSP10, crystal structure, variants | Shozeb Haider | METAD TORSION PRINT | colvar bias generic |
| 22.036 | Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction | bio | Well-tempered MetaDynamics with Hamiltonian Replica Exchange | Miroslav Krepl | COORDINATION GHBFIX UPPER_WALLS METAD BIASVALUE COMBINE GROUP MOLINFO LOAD FLUSH CUSTOM PRINT | generic core colvar function setup 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 | COORDINATION UPPER_WALLS RESTART PBMETAD BIASVALUE GROUP MOLINFO COM RMSD WHOLEMOLECULES EMMI TORSION PRINT | generic vatom core colvar setup bias isdb |
| 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 | LOWER_WALLS UPPER_WALLS OPES_EXPANDED ECV_UMBRELLAS_LINE ENVIRONMENTSIMILARITY INCLUDE PRINT | opes bias generic envsim |
| 22.018 | Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations | bio | ligand binding, docking, EMMI, LAT1 | Max Bonomi | BIASVALUE GROUP MOLINFO EMMIVOX WHOLEMOLECULES LOAD PRINT | generic core setup bias isdb |
| 22.001 | Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials | methods | enhanced sampling, variationally enhanced sampling, ves, metadynamics, bias representation, wavelets, adam | Benjamin Pampel | BF_CUBIC_B_SPLINES TD_WELLTEMPERED POSITION BF_CHEBYSHEV OPT_ADAM ENERGY OPT_AVERAGED_SGD UNITS BF_WAVELETS FLUSH UPPER_WALLS VES_LINEAR_EXPANSION VES_OUTPUT_BASISFUNCTIONS INCLUDE TD_UNIFORM COORDINATION BF_GAUSSIANS METAD DISTANCE PRINT BF_LEGENDRE | generic ves colvar setup bias |
| 21.049 | Multiple-path-metadynamics and PathMaps | methods | path-CV, metadynamics, multiple-walker, multiple paths, pathmap | Alberto Pérez-de-Alba-Ortíz | LOWER_WALLS UPPER_WALLS METAD COMBINE CONSTANT TORSION UNITS LOAD RESTRAINT ENSEMBLE CUSTOM MOVINGRESTRAINT PRINT | generic colvar function setup bias |
| 21.019 | Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations | materials | Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen | Matteo Salvalaglio | KDE MATHEVAL COM DISTANCE TORSIONS PRINT | gridtools generic vatom multicolvar colvar function |
| 21.018 | Localized Volume-based Metadynamics | bio | LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification | Riccardo Capelli | ENDPLUMED HISTOGRAM DUMPGRID POSITION COM FIXEDATOM REWEIGHT_METAD FLUSH UPPER_WALLS MATHEVAL READ RMSD COORDINATION METAD CONVERT_TO_FES GROUP WHOLEMOLECULES DISTANCE PRINT | gridtools generic vatom core colvar function bias |
| 20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Adriana Pietropaolo | COORDINATION PBMETAD WHOLEMOLECULES CENTER PRINT | colvar bias generic vatom |
| 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 | COORDINATION COMBINE MOLINFO WHOLEMOLECULES RESTRAINT STATS PRINT | colvar function generic bias |
| 20.026 | Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor | bio | Metadynamics, Umbrella sampling | Brandon Peters | MULTI_RMSD METAD HISTOGRAM CONVERT_TO_FES DUMPGRID RESTRAINT REWEIGHT_METAD PRINT | colvar bias generic gridtools |
| 20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Valerio Rizzi | COORDINATION UPPER_WALLS ENDPLUMED FIT_TO_TEMPLATE MATHEVAL OPES_METAD GROUP ENERGY ANGLE FIXEDATOM WHOLEMOLECULES DISTANCE CENTER PYTORCH_MODEL PRINT | generic vatom core colvar function opes bias pytorch |
| 20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Vojtech Spiwok | METAD TORSION PRINT | colvar bias generic |
| 20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Max Bonomi | COORDINATION PBMETAD MOLINFO ALPHABETA WHOLEMOLECULES INCLUDE DIHCOR PRINT GYRATION | colvar bias generic multicolvar |
| 20.001 | Conformational stability and dynamics in solution and in crystals report similarly on unfolding and aggregation propensity of amyloidogenic proteins | bio | metainference, metadynamics, NMR, protein dynamics, b2m, protein crystals | Carlo Camilloni | LOWER_WALLS UPPER_WALLS ENDPLUMED PBMETAD BIASVALUE CS2BACKBONE GROUP ANTIBETARMSD MOLINFO ALPHABETA WHOLEMOLECULES PRINT FLUSH | generic secondarystructure multicolvar core bias isdb |
| 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 REWEIGHT_TEMP_PRESS LOAD DUMPGRID TD_WELLTEMPERED LOWER_WALLS ENERGY OPT_AVERAGED_SGD UPPER_WALLS VES_LINEAR_EXPANSION MATHEVAL COMBINE READ VOLUME CELL TD_MULTITHERMAL_MULTIBARIC RESTART OPT_DUMMY CONVERT_TO_FES REWEIGHT_BIAS Q6 PRINT BF_LEGENDRE | gridtools generic ves colvar function setup bias symfunc |
| 19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Kim E. Jelfs | LOWER_WALLS UPPER_WALLS METAD RESTART GROUP COM DISTANCE CENTER PRINT | generic vatom core colvar setup bias |
| 19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Cristina Paissoni | COORDINATION SAXS ENDPLUMED MATHEVAL PBMETAD BIASVALUE COMBINE GROUP MOLINFO CENTER ANGLE ALPHABETA WHOLEMOLECULES INCLUDE STATS ENSEMBLE PRINT | generic vatom multicolvar core colvar function bias isdb |
| 19.050 | Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes | chemistry | metadynamics, membranes, Willard Chandler surface | Gareth Tribello | UPPER_WALLS METAD HISTOGRAM RESTART CONVERT_TO_FES COMBINE READ REWEIGHT_BIAS DUMPGRID DISTANCE_FROM_CONTOUR PRINT | gridtools generic function setup bias contour |
| 19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Davide Provasi | CONTACTMAP FUNCPATHMSD ENDPLUMED METAD COM RMSD WHOLEMOLECULES DISTANCE PRINT | generic vatom colvar function bias |
| 19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Gabriele Cesare Sosso | ENDPLUMED CLUSTER_NATOMS COMMITTOR CLUSTER_WITHSURFACE DFSCLUSTERING OUTPUT_CLUSTER CONTACT_MATRIX MFILTER_MORE Q6 LOCAL_Q6 FLUSH | clusters generic multicolvar adjmat symfunc |
| 19.023 | RECT | methods | metadynamics, replica exchange | Giovanni Bussi | METAD WHOLEMOLECULES TORSION PRINT GYRATION | colvar bias generic |
| 19.013 | RNA FF FITTING | methods | force field, RNA | Giovanni Bussi | MATHEVAL BIASVALUE MOLINFO CONSTANT INCLUDE TORSION PUCKERING | colvar function generic bias |
| 19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Max Bonomi | BIASVALUE GROUP MOLINFO WHOLEMOLECULES EMMI PRINT | bias generic isdb core |
| 24.030 | NMR guided simulation of dsRBD | bio | Metainference, NMR, protein dynamics | Debadutta Patra | GROUP ALPHABETA STATS FLUSH MOLINFO METAINFERENCE PRINT DISTANCE ENSEMBLE RDC WHOLEMOLECULES | core multicolvar isdb function generic colvar |
| 24.027 | Proline cis and trans subensembles of a disordered peptide | bio | intrinsically disordered proteins, proline cis trans isomerisation, metadynamics, collective variables | Alice Pettitt | COMBINE GROUP DIHCOR FLUSH ANTIBETARMSD MOLINFO PARABETARMSD COORDINATION PBMETAD PRINT ENDPLUMED DISTANCE INCLUDE GYRATION ALPHARMSD TORSION WHOLEMOLECULES | core multicolvar function bias generic colvar secondarystructure |
| 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 | COMBINE OPES_METAD METAD COMMITTOR WHOLEMOLECULES RMSD GROUP FIXEDATOM MOLINFO PRINT DISTANCE TORSION ANGLE UPPER_WALLS CENTER MATHEVAL CUSTOM COORDINATION ENDPLUMED FIT_TO_TEMPLATE CONTACTMAP | core opes function bias generic vatom colvar |
| 24.008 | yCD Metadynamics | bio | volume-based MetaD, path CVs, infrequent MetaD, product release | James McCarty | DUMPGRID METAD COMMITTOR COM READ CONVERT_TO_FES WHOLEMOLECULES RMSD GROUP WRAPAROUND MOLINFO FIXEDATOM PRINT DISTANCE UPPER_WALLS FLUSH PATH INCLUDE REWEIGHT_METAD MATHEVAL COORDINATION ENDPLUMED FIT_TO_TEMPLATE HISTOGRAM CONTACTMAP | core function bias gridtools generic vatom colvar mapping |
| 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 GROUP UPPER_WALLS OPES_METAD FLUSH COORDINATIONNUMBER FIXEDATOM PRINT DISTANCE ZDISTANCES | core multicolvar opes vatom bias symfunc generic setup colvar |
| 23.035 | An Extended Metadynamics Protocol for Binding/Unbinding of Peptide Ligands to Class A G-Protein Coupled Receptors | bio | G protein coupled receptor, peptide ligands, metadynamics, multiple-walker | Timothy Clark | CONSTANT UPPER_WALLS MATHEVAL LOWER_WALLS CENTER BIASVALUE METAD PRINT DISTANCE WHOLEMOLECULES | function bias generic vatom colvar |
| 23.011 | OneOPES, a combined enhanced sampling method to rule them all | bio | OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding | Valerio Rizzi | OPES_METAD_EXPLORE METAD MOLINFO ECV_MULTITHERMAL OPES_EXPANDED PRINT ENDPLUMED ENERGY DISTANCE TORSION | generic colvar bias opes |
| 23.001 | Quantum phase diagram of water | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn-Løland Bore | ENVIRONMENTSIMILARITY UPPER_WALLS LOWER_WALLS OPES_EXPANDED PRINT RESTART INCLUDE ECV_UMBRELLAS_LINE | opes bias envsim generic setup |
| 22.045 | Binding mode and mechanism of enzymatic polyethylene terephthalate degradation | bio | metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation | Francesco Colizzi | ANGLE MOVINGRESTRAINT COM UPPER_WALLS LOWER_WALLS METAD PRINT DISTANCE WHOLEMOLECULES | vatom colvar generic bias |
| 22.039 | Driving and characterizing nucleation of urea and glycine polymorphs in water | bio | metadynamics, nucleation, amino acids, polymorphism | Eric Beyerle | COMBINE PAIRENTROPY GROUP Q6 CENTER MATHEVAL METAD Q4 COORDINATIONNUMBER PRINT INCLUDE LOAD | core function bias gridtools setup symfunc generic vatom |
| 22.025 | Bubble nucleation rate predictions in a Lennard-Jones fluid | materials | free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation | Kristof Bal | UNITS DUMPGRID MOVINGRESTRAINT UPPER_WALLS FLUSH BIASVALUE CUSTOM COORDINATIONNUMBER REWEIGHT_BIAS RESTRAINT COMMITTOR ANN PRINT VOLUME HISTOGRAM LOAD CONVERT_TO_FES | annfunc function bias gridtools symfunc generic setup colvar |
| 22.013 | Ligand dissociation from PreQ1 riboswitch | bio | ligand, RNA, metadynamics, pRAVE | Yihang Wang | COMBINE RMSD COM METAD MOLINFO COORDINATIONNUMBER COMMITTOR PRINT DISTANCE WHOLEMOLECULES | function bias symfunc generic vatom colvar |
| 22.009 | Glycosylation in calixarenes capsule | chemistry | Metadynamics, glycosylation, supramolecular catalysis | GiovanniMaria Piccini | COMBINE UNITS GROUP ANGLE RMSD UPPER_WALLS MATHEVAL LOWER_WALLS METAD FLUSH BRIDGE DISTANCES COORDINATION PRINT FIT_TO_TEMPLATE DISTANCE WHOLEMOLECULES | core multicolvar function bias adjmat generic setup colvar |
| 21.033 | Multiple-path-metadynamics applied to DNA base-pairing transitions | bio | path-CV, metadynamics, multiple-walker, dna | Alberto Pérez-de-Alba-Ortíz | COMBINE MOVINGRESTRAINT CONSTANT UPPER_WALLS METAD RESTRAINT PRINT INCLUDE | function generic bias |
| 21.031 | Photo-switchable sulfonulureas in KATP channel | bio | metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels | Katarzyna Walczewska-Szewc | UNITS UPPER_WALLS LOWER_WALLS METAD PRINT COM DISTANCE WHOLEMOLECULES | bias setup generic vatom colvar |
| 21.025 | Computational and biochemical analysis of type IV pilus dynamics and stability | bio | molecular dynamics, calcium binding, Type IV pilus | Yasaman Karami | DISTANCE LOWER_WALLS PRINT UPPER_WALLS | colvar generic bias |
| 21.023 | Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling | methods | enhanced sampling, collective variables, machine learning | Jakub Rydzewski | UNITS INCLUDE CONSTANT METAD BIASVALUE CUSTOM ENERGY PRINT DISTANCE REWEIGHT_METAD TORSION | function bias generic setup colvar |
| 21.020 | Reweighted Jarzynski sampling | methods | free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions | Kristof Bal | COMBINE MOVINGRESTRAINT DUMPGRID OPES_METAD METAD BF_CHEBYSHEV CONVERT_TO_FES OPT_AVERAGED_SGD CONSTANT RESTRAINT PRINT DISTANCE LOAD UPPER_WALLS FLUSH COORDINATIONNUMBER TD_WELLTEMPERED ANN VES_LINEAR_EXPANSION REWEIGHT_METAD UNITS BIASVALUE CUSTOM REWEIGHT_BIAS HISTOGRAM | opes ves annfunc function bias gridtools symfunc generic setup colvar |
| 21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Tarsis Ferreira | GROUP DUMPGRID UPPER_WALLS WHOLEMOLECULES LOWER_WALLS METAD REWEIGHT_METAD MOLINFO ENERGY PUCKERING COORDINATION PRINT DISTANCE INCLUDE HISTOGRAM RANDOM_EXCHANGES | core bias gridtools generic colvar |
| 20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Jim Pfaendtner | GROUP CENTER DISTANCES COORDINATION PRINT DISTANCE RESTART WHOLEMOLECULES | core multicolvar setup generic vatom colvar |
| 20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Carlo Camilloni | SAXS CENTER ALPHABETA STATS FLUSH MOLINFO PBMETAD METAINFERENCE PRINT DISTANCE ENSEMBLE GYRATION TORSION WHOLEMOLECULES | multicolvar isdb function bias generic vatom colvar |
| 19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | GiovanniMaria Piccini | COMBINE UNITS UPPER_WALLS LOWER_WALLS METAD FLUSH PRINT ENERGY DISTANCE | function bias generic setup colvar |
| 19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Gareth Tribello | UNITS GROUP MULTICOLVARDENS FIND_CONTOUR_SURFACE DUMPGRID FOURIER_TRANSFORM CENTER MORE_THAN FCCUBIC | core vatom fourier function gridtools symfunc contour setup |
| 19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | COMBINE UNITS UPPER_WALLS METAD FLUSH PRINT ENERGY DISTANCE | function bias generic setup colvar |
| 19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Paolo Raiteri | UNITS UPPER_WALLS MATHEVAL METAD FLUSH PRINT DISTANCE RESTART | function bias generic setup colvar |
| 19.025 | Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide | bio | metainference, NMR, protein dynamics, force-fields | Carlo Camilloni | RDC WHOLEMOLECULES STATS FLUSH BIASVALUE MOLINFO PBMETAD PRINT ENDPLUMED METAINFERENCE ENSEMBLE CS2BACKBONE GYRATION TORSION JCOUPLING | isdb function bias generic colvar |
| 19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Haochuan Chen | TORSION PRINT DRR | drr colvar generic |
| 19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Matteo Salvalaglio | COMBINE UPPER_WALLS MATHEVAL LOWER_WALLS METAD CELL PRINT ENDPLUMED ENERGY VOLUME TORSION | colvar function generic bias |
| 25.005 | Mechanism of Nanocluster Formation from Machine-Learned Potential-based Simulations | chemistry | WT-metadynamics, metal nanoclusters, nucleation, neural network potential, deepMD | Vikas Tiwari, Tarak Karmakar | GROUP FLUSH METAD ANGLE UPPER_WALLS RESTRAINT DISTANCE UNITS FIXEDATOM LOWER_WALLS COORDINATION COORDINATIONNUMBER COMBINE DISTANCES COM PRINT | colvar function multicolvar setup bias vatom generic core symfunc |
| 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 | POSITION COORDINATION PRINT DISTANCE COMBINE CELL ENERGY FLUSH MATHEVAL BIASVALUE LOAD TORSION INCLUDE OPES_METAD UNITS CUSTOM | bias colvar setup opes function generic |
| 25.011 | Chiral perovskite nucleation | chemistry | metadynamics, chiral perovskites, nucleation | Adriana Pietropaolo | UPPER_WALLS DISTANCE PRINT MULTI_RMSD LOWER_WALLS RESTART MATHEVAL PBMETAD UNITS | bias colvar setup function generic |
| 25.003 | Surrogate Model CV | methods | Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding | Sompriya Chatterjee | DISTANCE PRINT COMBINE COMMITTOR ENERGY GROUP MOLINFO MATHEVAL WHOLEMOLECULES TORSION PYTORCH_MODEL ENDPLUMED OPES_METAD CUSTOM | colvar opes pytorch function core generic |
| 24.036 | Leveraging cryptic ligand envelopes through enhanced molecular simulations | bio | HREX, conformational heterogeneity, drug discovery, ligand binding, plitidepsin, aplidin, ligand-target complexes, cryptic ligand envelope | Francesco Colizzi | HISTOGRAM DISTANCE PRINT CONVERT_TO_FES COORDINATION ANGLE GROUP WHOLEMOLECULES DUMPGRID TORSION | gridtools core generic colvar |
| 24.034 | Umbrella sampling of ion in transporter SLC26A7 | bio | umbrella sampling, transporter, ions | Xiaoli Lu | POSITION UNITS PRINT RESTRAINT | setup bias generic colvar |
| 24.032 | DeepLNE++ | methods | PATHCV, OPES | Thorben Fröhlking | COORDINATION DISTANCE PRINT COMBINE ENERGY GROUP LOAD TORSION OPES_METAD CUSTOM | colvar setup opes function core generic |
| 24.029 | Combination of OPES and OPES-Explore | methods | OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin | Dhiman Ray | UPPER_WALLS COMBINE FLUSH LOWER_WALLS WHOLEMOLECULES FIXEDATOM CUSTOM RMSD POSITION DISTANCE PRINT MOLINFO CENTER OPES_METAD_EXPLORE METAD ENERGY GROUP PYTORCH_MODEL INCLUDE CONTACTMAP UNITS COORDINATION MATHEVAL BIASVALUE ENDPLUMED OPES_METAD FIT_TO_TEMPLATE | vatom bias colvar setup opes pytorch function core generic |
| 24.028 | All-atom simulations of RNA-membrane interactions | bio | metadynamics, membrane, RNA | Giovanni Bussi | UPPER_WALLS POSITION DISTANCE PRINT COMBINE GROUP DISTANCES MOLINFO LOWER_WALLS SORT PUCKERING CENTER WHOLEMOLECULES MATHEVAL GYRATION METAD GHOST | vatom bias colvar multicolvar function core generic |
| 24.009 | Weighted Shape Gaussian Mixture Models | bio | metadynamics, clustering | Glen Hocky | PRINT GROUP TORSION METAD UNITS | bias colvar setup core generic |
| 24.007 | SWISH-X | bio | swish-x, SWISH-X, swish, expanded SWISH | Alberto Borsatto | UPPER_WALLS PRINT ENERGY MOLINFO WHOLEMOLECULES OPES_EXPANDED INCLUDE CONTACTMAP ECV_MULTITHERMAL | opes colvar bias generic |
| 23.041 | Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference | methods | EMMIVox, cryo-EM, single-structure refinement, ensemble refinement, Bayesian inference, B-factors, structural ensembles | Samuel Hoff | UPPER_WALLS EMMIVOX PRINT DISTANCE GROUP WRAPAROUND MOLINFO WHOLEMOLECULES BIASVALUE INCLUDE | bias colvar isdb core generic |
| 23.027 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, DFS, Q3, Pair Entropy | Aaron Finney | COORDINATIONNUMBER HISTOGRAM CLUSTER_NATOMS LOCAL_AVERAGE PRINT GROUP AROUND Q3 DUMPGRID DENSITY FIXEDATOM DFSCLUSTERING CLUSTER_DISTRIBUTION LOAD RESTRAINT UNITS LOCAL_Q3 CONTACT_MATRIX | clusters vatom bias setup gridtools adjmat symfunc volumes core generic |
| 23.026 | Machine Learning Nucleation Collective Variables with Graph Neural Networks | chemistry | Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks | Florian Dietrich | COORDINATIONNUMBER MFILTER_MORE PRINT Q6 COMBINE GROUP LOWER_WALLS LOCAL_Q6 MOVINGRESTRAINT METAD | bias multicolvar symfunc function core generic |
| 23.025 | Probing ion binding to G-quadruplexes and related events | chemistry | metadynamics, repulsive potential, nucleic acids, G-quadruplexes | Marcelo Poleto | UPPER_WALLS POSITION DISTANCE PRINT COM DUMPATOMS FLUSH GROUP WRAPAROUND DISTANCES LOWER_WALLS WHOLEMOLECULES MATHEVAL FIT_TO_TEMPLATE RESTART METAD UNITS | vatom bias colvar multicolvar setup function core generic |
| 23.012 | JAK2 2D meta-eABF PMF with statistical analysis | bio | 2D meta-eABF, path CV, PMF | Istvan Kolossvary | UPPER_WALLS PRINT FLUSH PATHMSD LOWER_WALLS BIASVALUE METAD DRR CUSTOM | bias colvar drr function generic |
| 23.002 | Critical comparison of general-purpose collective variables for crystal nucleation | methods | metadynamics, umbrella sampling, commitor, entropy, PIV | Julien Lam | VOLUME UPPER_WALLS PAIRENTROPY PRINT Q6 LOCAL_AVERAGE ENERGY Q4 FUNCPATHMSD PIV RESTRAINT METAD UNITS CUSTOM | bias colvar setup gridtools symfunc function piv generic |
| 22.031 | Rare Event Kinetics from Adaptive Bias Enhanced Sampling | methods | OPES Flooding, Kinetics, Rate, OPES, Machine Learning | Dhiman Ray | COMBINE WHOLEMOLECULES CUSTOM RMSD POSITION DISTANCE PRINT MOLINFO CONSTANT ENERGY GROUP PYTORCH_MODEL INCLUDE CONTACTMAP UNITS COMMITTOR BIASVALUE TORSION ENDPLUMED OPES_METAD | bias colvar setup opes pytorch function core generic |
| 22.026 | Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification | materials | Peptoid, silica | Jim Pfaendtner | UPPER_WALLS DISTANCE PRINT COM MOLINFO PBMETAD GYRATION | generic vatom bias colvar |
| 22.024 | Conformational Entropy as a Potential Liability of Computationally Designed Antibodies | bio | metadynamics, conformational entropy, antibody, nanobody | Thomas Löhr | ANTIBETARMSD ALPHARMSD PRINT COM RESTART MOLINFO WHOLEMOLECULES ALPHABETA PBMETAD TORSION | vatom bias colvar multicolvar setup secondarystructure generic |
| 21.042 | Peptoid-mediated Au nanocrystal growth | materials | parallel-bias metadynamics, peptoid, Au | Xin Qi | UPPER_WALLS DISTANCE PRINT COM MOLINFO PBMETAD GYRATION | generic vatom bias 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 | VOLUME COORDINATION PRINT COMBINE ENDPLUMED METAD CUSTOM | function bias generic colvar |
| 21.013 | Role of vibrational excitation in heterogeneous catalysis | chemistry | catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption | Kristof Bal | UPPER_WALLS COMBINE FLUSH LOWER_WALLS ANGLES OPT_AVERAGED_SGD RESTRAINT HISTOGRAM REWEIGHT_BIAS DISTANCE PRINT LOAD METAD CONVERT_TO_FES EXTERNAL DISTANCES DUMPGRID UNITS TD_GRID VES_LINEAR_EXPANSION COORDINATIONNUMBER REWEIGHT_METAD COORDINATION BF_CHEBYSHEV UWALLS | ves bias colvar multicolvar setup gridtools symfunc function generic |
| 21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Adriana Pietropaolo | PRINT CONSTANT RESTART MATHEVAL WHOLEMOLECULES PBMETAD BIASVALUE TORSION | bias colvar setup function generic |
| 20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Faidon Brotzakis | HISTOGRAM PRINT CONVERT_TO_FES GROUP DISTANCES MOLINFO WHOLEMOLECULES DUMPGRID BIASVALUE EMMI READ RMSD | bias colvar multicolvar isdb gridtools core generic |
| 20.032 | Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil | materials | clustering, conformational isomers | Matteo Salvalaglio | PRINT TORSION ENDPLUMED | colvar generic |
| 20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Cristina Paissoni | STATS DISTANCE PRINT GROUP MOLINFO SAXS WHOLEMOLECULES ENSEMBLE CENTER BIASVALUE RESTRAINT INCLUDE | vatom bias colvar isdb function core generic |
| 20.024 | Gaussian Mixture Based Enhanced Sampling (GAMBES) | methods | enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias | Jayashrita Debnath | UPPER_WALLS DISTANCE PRINT COMBINE ENERGY GROUP DISTANCES LOWER_WALLS LOAD TORSION UNITS | bias colvar multicolvar setup function core generic |
| 20.018 | Free energy barriers from biased molecular dynamics simulations | methods | kinetics, free energy barriers, chemical reactions, nucleation, metadynamics | Kristof Bal | UPPER_WALLS LOCAL_AVERAGE COMBINE FLUSH LOWER_WALLS REWEIGHT_BIAS HISTOGRAM DISTANCE PRINT SPRINT CENTER LOAD METAD CONTACT_MATRIX CONVERT_TO_FES ENERGY DUMPGRID UNITS VOLUME COORDINATIONNUMBER REWEIGHT_METAD PAIRENTROPY COORDINATION Q6 DENSITY | sprint vatom bias colvar setup gridtools adjmat symfunc volumes function generic |
| 20.016 | Predicting polymorphism in molecular crystals using orientational entropy | materials | metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy | Pablo Piaggi | VOLUME UPPER_WALLS PRINT GROUP CENTER LOAD INCLUDE METAD | vatom bias colvar setup core generic |
| 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 PRINT COMBINE ENERGY LOWER_WALLS MOLINFO WHOLEMOLECULES MATHEVAL CENTER METAD RMSD | vatom bias colvar function generic |
| 19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Wei Chen | POSITION COM ANN COMBINE RESTRAINT | vatom bias colvar function annfunc |
| 19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Giovanni Bussi | UPPER_WALLS ERMSD DISTANCE PRINT RANDOM_EXCHANGES COMBINE FLUSH ANGLE LOWER_WALLS DISTANCES MOLINFO INCLUDE METAD | bias colvar multicolvar function generic |
| 25.010 | Kinetic rates calculation with Ratchet&Pawl MD | methods | kinetics, ligand binding, ABMD, ratchet&pawl MD | Riccardo Capelli | COM DISTANCE GROUP ABMD PRINT WHOLEMOLECULES COMMITTOR FLUSH | bias core generic vatom colvar |
| 25.004 | Machine Learning-Driven Molecular Dynamics Unveil a Bulk Phase Transformation Driving Ammonia Synthesis on Barium Hydride | chemistry | OPES, OPES flooding, Catalysis, Ammonia Synthesis | Axel Tosello Gardini | ZDISTANCES CUSTOM DISTANCE OPES_METAD GROUP PRINT UPPER_WALLS UNITS FIXEDATOM COMMITTOR COORDINATIONNUMBER DISTANCES FLUSH | function bias opes core generic colvar symfunc vatom multicolvar setup |
| 25.002 | M3_PCV-ABMD | chemistry | Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor | Gian Marco Elisi | ENDPLUMED PATHMSD ABMD PRINT UNITS UPPER_WALLS | setup bias generic colvar |
| 24.035 | Data efficient machine learning potentials for modeling catalytic reactivity via active learning and enhanced sampling | chemistry | opes, catalysis, ammonia, machine learning potentials | Luigi Bonati | CUSTOM DISTANCE RESTART OPES_METAD COORDINATION GROUP LOWER_WALLS PRINT UNITS UPPER_WALLS COMMITTOR | function bias opes core generic colvar setup |
| 24.031 | DeepLNE | methods | PATHCV, OPES, OneOPES | Thorben Fröhlking | OPES_METAD_EXPLORE RESTART MOLINFO COORDINATION OPES_EXPANDED COMBINE VOLUME PRINT ENERGY ERMSD ECV_MULTITHERMAL PYTORCH_MODEL | function opes pytorch generic colvar setup |
| 24.021 | Ab initio machine learning simulation of calcium carbonate from aqueous solutions to the solid state | chemistry | ion pairing, caco3, opes, proton transfer, crystallization | Pablo Piaggi | DISTANCE OPES_METAD COORDINATION PRINT UPPER_WALLS ENERGY | bias generic colvar opes |
| 24.016 | Cryo-EM guided simulations of ribozyme | bio | metainference, cryo-EM | Giovanni Bussi | RESTRAINT INCLUDE MOLINFO GROUP PRINT EMMIVOX WHOLEMOLECULES ERMSD BIASVALUE | bias core isdb generic colvar |
| 24.012 | Molecular simulations to investigate the impact of N6-methylation in RNA recognition | bio | metadynamics, alchemistry, RNA modification, RNA:protein interactions | Giovanni Bussi | GHBFIX DISTANCE METAD COM MOLINFO COORDINATION CENTER COMBINE GROUP UPPER_WALLS LOWER_WALLS DEBUG PRINT BIASVALUE | function bias core generic vatom colvar |
| 23.040 | Supramolecular capsules assembly dynamics | chemistry | Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics | Riccardo Capelli | CUSTOM DISTANCE COM METAD GROUP CENTER PRINT UNITS POSITION WHOLEMOLECULES DISTANCES FLUSH | function bias core generic multicolvar vatom colvar setup |
| 23.039 | Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation | chemistry | metadynamics, ligand dissociation | Eric Beyerle | RESTRAINT DISTANCE METAD MOLINFO CENTER COMBINE PRINT UPPER_WALLS DUMPMASSCHARGE FIXEDATOM | function bias generic vatom colvar |
| 23.029 | An accurate and efficient SAXS/SANS implementation including solvation layer effects suitable for restrained Molecular Dynamics simulations | bio | SAXS, SANS, SAS, metainference, proteins, nucleic-acid | Federico Ballabio | STATS RMSD DISTANCE MOLINFO CENTER GROUP PRINT WRAPAROUND UPPER_WALLS SAXS ENSEMBLE BIASVALUE | function bias core isdb generic vatom colvar |
| 23.023 | Rational design of novel biomimetic sequence-defined polymers for mineralization applications | methods | metadynamics, surface binding, biomimetic mineralization | Kaylyn Torkelson | COM DISTANCE COORDINATION GYRATION UPPER_WALLS PRINT PBMETAD | vatom generic bias colvar |
| 23.018 | Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention | materials | metadynamics, surface binding, peptide adsorption | Kaylyn Torkelson | COM DISTANCE GYRATION UPPER_WALLS PRINT PBMETAD | vatom generic bias colvar |
| 22.032 | Reciprocal barrier restraint. Application to path-meta-eABF | methods | restraint, upper wall, lower wall, path colvar, meta-eABF, metadynamics, DRR, protein conformational transition, PROTAC | Istvan Kolossvary | CUSTOM METAD PATHMSD PRINT DRR BIASVALUE FLUSH | drr function bias generic colvar |
| 22.030 | Mixing physics across temperatures with generative artificial intelligence | methods | REMD, Generative AI, DDPM | Yihang Wang | PRINT TORSION WHOLEMOLECULES | generic colvar |
| 22.022 | Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir | bio | RMSD, protein-ligand interactions | Isabell Grothaus | PRINT RMSD | generic colvar |
| 22.000 | Amyloid precursor protein processing by human γ-secretase | bio | Bias Exchange Metadynamics, Helix unfolding, coupled binding | Xiaoli Lu | CONTACTMAP DISTANCE INCLUDE METAD MOLINFO COORDINATION CENTER PRINT RANDOM_EXCHANGES UNITS ANTIBETARMSD ALPHARMSD | bias secondarystructure generic vatom colvar setup |
| 21.044 | NaCl nucleation | chemistry | metadynamics, DFS clustering | Aaron Finney | Q6 HISTOGRAM CLUSTER_DISTRIBUTION METAD CLUSTER_NATOMS DUMPGRID GROUP COMBINE PRINT DFSCLUSTERING LOCAL_Q6 FIXEDATOM MFILTER_MORE COORDINATIONNUMBER CONTACT_MATRIX INSPHERE | clusters function bias core generic volumes symfunc vatom adjmat multicolvar gridtools |
| 21.037 | Molecular Dynamics simulations of RBD/hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain | Max Bonomi | PRINT RMSD DISTANCE | generic colvar |
| 21.027 | EGFR activating mutations mechanism | bio | metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA | Francesco Gervasio | CONTACTMAP DISTANCE INCLUDE METAD MOLINFO ALPHARMSD LOWER_WALLS UPPER_WALLS PRINT ENERGY WHOLEMOLECULES MATHEVAL | function bias secondarystructure generic colvar |
| 21.016 | MD SAXS GTPase associated center | bio | metadynamics, RNA, folding, SAXS | Giovanni Bussi | CUSTOM INCLUDE METAD MOLINFO GROUP GYRATION UPPER_WALLS LOWER_WALLS PRINT ERMSD WHOLEMOLECULES SAXS | function bias core isdb generic colvar |
| 21.000 | Uremic toxin time scale dynamics | bio | uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs) | Jim Pfaendtner | COM DISTANCE GROUP PRINT WHOLEMOLECULES | core vatom generic colvar |
| 20.034 | Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations | bio | RNA, SARS-CoV-2, partial tempering | Sandro Bottaro | DISTANCE RESTART TORSION MOLINFO CENTER ABMD PRINT ERMSD | bias generic vatom colvar setup |
| 20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Michele Invernizzi | LOAD UNITS POSITION ECV_MULTITHERMAL RMSD Q6 ENDPLUMED PRINT ENERGY TORSION MOLINFO OPES_EXPANDED VOLUME ECV_UMBRELLAS_LINE WHOLEMOLECULES ECV_MULTITHERMAL_MULTIBARIC MATHEVAL CUSTOM ECV_LINEAR UPPER_WALLS ENVIRONMENTSIMILARITY | function bias envsim opes generic symfunc colvar setup |
| 20.021 | Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins. | bio | phi-values, restrained MD, transition-state, protein folding, disordered proteins, protein evolution | Cristina Paissoni | RESTRAINT STATS MOLINFO COORDINATION PRINT WHOLEMOLECULES | function bias generic colvar |
| 20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Pratyush Tiwary | DISTANCE RESTART TORSION METAD MOLINFO COMBINE PRINT UPPER_WALLS WHOLEMOLECULES RMSD | function bias generic colvar setup |
| 20.002 | Exploring conformational dynamics of the extracellular Venus flytrap domain of the GABAB receptor, a path-metadynamics study | bio | Metadynamics, path CVs | Riccardo Ocello | RESTART PATHMSD METAD MOLINFO GROUP PRINT UPPER_WALLS WHOLEMOLECULES | bias core generic colvar setup |
| 19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Valerio Rizzi | ENDPLUMED RESTART METAD GROUP COMBINE PRINT UPPER_WALLS UNITS COORDINATIONNUMBER DISTANCES FLUSH | function bias core generic symfunc multicolvar setup |
| 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 | setup bias generic colvar |
| 19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | COM METAD DISTANCE MOLINFO GYRATION UPPER_WALLS PRINT ENERGY | vatom generic bias colvar |
| 19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Luigi Bonati | Q6 LOAD ENDPLUMED TORSION PRINT UNITS POSITION ENERGY ENVIRONMENTSIMILARITY | envsim generic symfunc colvar setup |
| 19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Gareth Tribello | ENDPLUMED METAD PRINT UPPER_WALLS UNITS CELL FCCUBIC | bias generic symfunc colvar setup |
| 19.049 | Determining the sizes of solid/liquid clusters in MD trajectories of nucleation | methods | nucleation, metadynamics, clustering, Steinhardt order parameters | Gareth Tribello | OUTPUT_CLUSTER Q6 CUSTOM MATRIX_VECTOR_PRODUCT CLUSTER_DISTRIBUTION METAD CLUSTER_NATOMS MORE_THAN ONES CLUSTER_PROPERTIES DFSCLUSTERING PRINT LOCAL_Q6 SMAC COORDINATIONNUMBER DISTANCES CONTACT_MATRIX OUTER_PRODUCT | clusters function bias matrixtools generic symfunc adjmat multicolvar |
| 19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Silvio Pipolo | PIV METAD FUNCPATHMSD LOWER_WALLS UPPER_WALLS PRINT CELL | piv function bias generic colvar |
| 19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Glen Hocky | RESTRAINT DISTANCE EDS TORSION COMBINE PRINT | function bias eds generic colvar |
| 19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Matteo Salvalaglio | ENDPLUMED RESTART METAD PRINT GYRATION COORDINATIONNUMBER DISTANCES | bias generic multicolvar symfunc colvar setup |
| 19.011 | Automatic Gradient Computation for Collective Variables | other | gradient, differentiation, curvature | Toni Giorgino | ENDPLUMED | generic |
| 19.005 | Cmyc small molecule interaction | bio | metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP | Gabriella Heller | ALPHABETA CS2BACKBONE METAINFERENCE INCLUDE DISTANCE MOLINFO COORDINATION GROUP CENTER GYRATION PRINT WHOLEMOLECULES PBMETAD | bias core isdb generic colvar vatom multicolvar |
| 25.015 | Assessment of Force Fields for Describing Conformational Polymorphic Crystals of ROY | materials | Molecular crystal, Force Field, Collective Variable | Pradip Si and Omar Valsson | PRINT DUMPMULTICOLVAR SMAC TORSIONS DISTANCES | multicolvar generic symfunc |
| 24.026 | Constant pH metadynamics of RNA oligomers | bio | metadynamics, pH, RNA | Giovanni Bussi | MOLINFO PUCKERING TORSION PRINT METAD RESTART | bias generic setup colvar |
| 24.020 | Graph Neural Network-State Predictive Information Bottleneck (GNN-SPIB) approach for learning molecular thermodynamics and kinetics | bio | LJ7, alanine, well-tempered metadynamics, infrequent metadynamics, machine learning | Ziyue Zou, Dedi Wang, Pratyush Tiwary | TORSION LOAD GROUP PRINT METAD COMMITTOR | setup bias generic core colvar |
| 24.014 | Learning Collective Variables with Synthetic Data Augmentation through Physics-inspired Geodesic Interpolation | methods | data augmentation, geodesic interpolation, collective variables, protein folding | Juno Nam | MOLINFO DRR LOWER_WALLS PYTORCH_MODEL RMSD FLUSH UPPER_WALLS WHOLEMOLECULES PRINT METAD COORDINATION | pytorch bias generic colvar drr |
| 24.011 | Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble | methods | committor, machine learning | Peilin Kang | MOLINFO INCLUDE POSITION LOWER_WALLS TORSION RMSD DISTANCE UPPER_WALLS WHOLEMOLECULES CUSTOM ENDPLUMED CELL LOAD UNITS PRINT COORDINATION MATHEVAL ENERGY BIASVALUE GROUP | setup function bias generic core colvar |
| 24.010 | Oxytocin metadynamics simulation | bio | metadynamics, oxytocin, peptide | Jan Beránek | TORSION FLUSH WHOLEMOLECULES PRINT METAD RESTART | bias generic setup colvar |
| 23.046 | Lasso Peptides - HLDA CV | bio | metadynamics, protein folding, HLDA, harmonic | Gabriel da Hora | COMBINE DISTANCE WHOLEMOLECULES UNITS PRINT METAD | setup function bias generic colvar |
| 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 ANN COMBINE POSITION WHOLEMOLECULES PRINT METAD FIT_TO_TEMPLATE ALPHARMSD | function bias generic secondarystructure colvar annfunc |
| 23.028 | Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process | chemistry | Ammonia decomposition; Dynamics;OPES; Neural Network potential | Manyi Yang | CUSTOM MATHEVAL COORDINATIONNUMBER ENERGY LOWER_WALLS FLUSH DISTANCE COM UPPER_WALLS GROUP FIXEDATOM UNITS OPES_METAD PRINT ZDISTANCES COMMITTOR DISTANCES | setup function generic bias core multicolvar colvar opes symfunc vatom |
| 23.021 | Into the Dynamics of Rotaxanes at Atomistic Resolution | materials | metadynamics, rotaxanes, molecular shuttles, molecular machines | Luigi Leanza | MATHEVAL TORSION DISTANCE UPPER_WALLS CENTER FIXEDATOM METAD PRINT CUSTOM | function generic bias colvar vatom |
| 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 | generic colvar |
| 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 | AROUND HISTOGRAM ENERGY VOLUME UPPER_WALLS DUMPGRID PRINT OPES_METAD ENVIRONMENTSIMILARITY RESTART CUSTOM | volumes gridtools setup function generic bias envsim colvar opes |
| 22.015 | Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome | bio | photodynamics, bacteriophytochrome, variationally enhanced sampling | Jakub Rydzewski | TD_UNIFORM BF_FOURIER TORSION VES_LINEAR_EXPANSION PRINT OPT_AVERAGED_SGD | generic ves colvar |
| 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 | CONTACTMAP CENTER PRINT DISTANCE | vatom generic colvar |
| 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 WHOLEMOLECULES PRINT METAD | bias generic setup |
| 21.052 | On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets | materials | Ibuprofen, unbinding, WTmetaD | Matteo Salvalaglio | COORDINATIONNUMBER ENDPLUMED TORSION DISTANCE CENTER PRINT METAD COMMITTOR | bias generic colvar symfunc vatom |
| 21.047 | Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations | materials | pair entropy, metadynamics, ves, solids, crystallization | Pablo Piaggi | ENERGY VOLUME COMBINE RESTART BF_LEGENDRE LOAD TD_WELLTEMPERED VES_LINEAR_EXPANSION PRINT METAD OPT_AVERAGED_SGD PAIRENTROPY | gridtools setup function generic bias colvar ves |
| 21.039 | Deep learning the slow modes for rare events sampling | methods | collective variables, machine learning, slow modes, deep-tica, opes | Luigi Bonati | MOLINFO Q6 VOLUME INCLUDE OPES_EXPANDED COMBINE TORSION RMSD ECV_MULTITHERMAL DISTANCE WHOLEMOLECULES OPES_METAD CONTACTMAP ENDPLUMED LOAD UNITS PRINT ENERGY PYTORCH_MODEL FLUSH GROUP ENVIRONMENTSIMILARITY | setup function pytorch generic core envsim colvar opes symfunc |
| 21.038 | Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics | materials | metadynamics, SGOOP, nucleation, urea | Ziyue Zou | COORDINATIONNUMBER ENERGY VOLUME INCLUDE COMBINE LOAD CENTER GROUP METAD PRINT | setup function generic bias core colvar symfunc vatom |
| 21.029 | Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs | bio | metadynamics, small peptide, machine learning | Pratyush Tiwary | MOLINFO ENERGY EXTERNAL TORSION FLUSH PRINT RESTART | bias generic setup colvar |
| 21.026 | Probing allosteric regulations with coevolution-driven molecular simulations | bio | metadynamics, coevolution, allostery, adenylate cyclase | Francesco Colizzi | PATHMSD DISTANCE COM WHOLEMOLECULES UNITS UPPER_WALLS METAD PRINT | setup bias generic colvar vatom |
| 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 | MATHEVAL TD_UNIFORM ECV_MULTITHERMAL_MULTIBARIC Q6 ENERGY VOLUME BF_LEGENDRE ECV_UMBRELLAS_LINE VES_LINEAR_EXPANSION UPPER_WALLS PRINT OPES_EXPANDED OPT_AVERAGED_SGD ENVIRONMENTSIMILARITY RESTART | setup function ves bias generic envsim colvar opes symfunc |
| 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 | bias generic colvar |
| 20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Glen Hocky | MATHEVAL ENERGY BIASVALUE RESTRAINT FISST DISTANCE GYRATION UNITS GROUP PRINT | setup function bias generic core colvar fisst |
| 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 PRINT METAD COORDINATION CUSTOM DISTANCES | setup function bias generic multicolvar colvar |
| 19.080 | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | methods | ves, variationally enhanced sampling, vibrational excitation, chemical reactions | Kristof Bal | TD_GRID BF_CHEBYSHEV HISTOGRAM LOWER_WALLS COMBINE CONVERT_TO_FES FLUSH DISTANCE TD_WELLTEMPERED UPPER_WALLS ANGLE UNITS VES_LINEAR_EXPANSION PRINT COORDINATION OPT_AVERAGED_SGD DUMPGRID EXTERNAL | gridtools setup function generic bias colvar ves |
| 19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Michele Invernizzi | ENDPLUMED TORSION POSITION UNITS PRINT METAD OPES_METAD EXTERNAL | setup bias generic colvar opes |
| 19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Jakub Rydzewski | POSITION UNITS PRINT MAZE_LOSS MAZE_SIMULATED_ANNEALING MAZE_OPTIMIZER_BIAS | maze generic setup colvar |
| 19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Pratyush Tiwary | ALPHABETA COMBINE TORSION RESTART DISTANCE COM WHOLEMOLECULES PRINT COMMITTOR EXTERNAL | setup function generic bias multicolvar colvar vatom |
| 19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Michele Invernizzi | ENERGY VES_DELTA_F ENDPLUMED TORSION POSITION LOAD UNITS PRINT METAD RESTART | setup bias generic colvar ves |