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 |
|---|---|---|---|---|---|---|
| 25.021 | 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 | FIT_TO_TEMPLATE WHOLEMOLECULES COORDINATION ENERGY FIXEDATOM OPES_METAD_EXPLORE CENTER GROUP UPPER_WALLS MATHEVAL DISTANCE PRINT ANGLE | opes vatom generic function colvar core bias |
| 25.006 | Characterizing the conformational ensemble of PROTAC degraders in solutions via atomistic simulations | methods | Enhanced sampling, Atomistic simulations, Conformational ensemble, PROTACs, Targeted Protein Degradation, Chamelonic molecules | Shikshya Bhusal, Omar Valsson | WHOLEMOLECULES VOLUME DUMPATOMS READ ENERGY UPDATE_IF INCLUDE CENTER MOLINFO GYRATION DISTANCE PBMETAD PRINT RESTART TORSION | vatom generic colvar setup 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 | COM FLUSH COORDINATION COMBINE LOWER_WALLS FIXEDATOM DISTANCE RESTRAINT GROUP METAD DISTANCES PRINT UPPER_WALLS UNITS ANGLE COORDINATIONNUMBER | vatom generic function colvar core setup multicolvar symfunc bias |
| 21.043 | Predicting the Conformational Variability of Oncogenic GTP-bound G12D Mutated KRas-4B Proteins at Cell Membranes | chemistry | well-tempered metadynamics, KRas-4B, anionic membrane, conformational variability | Huixia Lu | FIT_TO_TEMPLATE FIXEDATOM METAD PRINT TORSION | generic bias vatom colvar |
| 21.030 | Thermodynamic Basis for Stabilization of Helical Peptoids by Chiral Sidechains | bio | parallel bias parallel tempered metadynamics in WTE, synthetic foldamers, self-assembly, peptoid secondary structure | Jim Pfaendtner | COM COORDINATION ENERGY INCLUDE PRINT METAD GYRATION DISTANCE PBMETAD ALPHABETA TORSION | vatom generic colvar multicolvar bias |
| 21.025 | Computational and biochemical analysis of type IV pilus dynamics and stability | bio | molecular dynamics, calcium binding, Type IV pilus | Yasaman Karami | DISTANCE PRINT LOWER_WALLS UPPER_WALLS | generic colvar bias |
| 19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Max Bonomi | WHOLEMOLECULES BIASVALUE EMMI GROUP MOLINFO PRINT | generic isdb bias core |
| 25.027 | Enhanced-sampling MD simulations of a protein-peptide complex integrating SAXS and XL-MS experimental information | bio | steered MD, metadynamics, SAXS, XL-MS, ensemble reconstruction | Mattia Bernetti | METAD SAXS GROUP PRINT CENTER INCLUDE MOLINFO UPPER_WALLS DISTANCE GYRATION WHOLEMOLECULES MOVINGRESTRAINT | vatom generic core colvar 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 | PRINT GROUP BAIES BIASVALUE | bias core generic isdb |
| 25.002 | M3_PCV-ABMD | chemistry | Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor | Gian Marco Elisi | ABMD PRINT UNITS PATHMSD UPPER_WALLS ENDPLUMED | colvar generic bias setup |
| 24.003 | Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations | chemistry | steered molecular dynamics, foldamers, peptoids, bio-inspired | Kaylyn Torkelson | COM COORDINATION PRINT TORSION INCLUDE DISTANCE GYRATION ALPHABETA WHOLEMOLECULES MOVINGRESTRAINT | vatom generic colvar multicolvar bias |
| 24.002 | Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes | chemistry | metadynamics, ligand design, solvent extraction | Xiaoyu Wang | METAD PRINT TORSION UNITS RESTART | colvar generic bias setup |
| 23.031 | Identifying small molecules binding sites in RNA conformational ensembles with SHAMAN | bio | RNA, metadynamics, probes, mixed-solvent MD, small molecules, binding sites | Max Bonomi | METAD DISTANCES POSITION GROUP PRINT FIT_TO_TEMPLATE CENTER UPPER_WALLS MOLINFO SHADOW WRAPAROUND WHOLEMOLECULES | vatom generic core colvar isdb multicolvar bias |
| 23.021 | Into the Dynamics of Rotaxanes at Atomistic Resolution | materials | metadynamics, rotaxanes, molecular shuttles, molecular machines | Luigi Leanza | METAD PRINT TORSION CENTER UPPER_WALLS MATHEVAL DISTANCE FIXEDATOM CUSTOM | vatom function generic colvar bias |
| 23.009 | Deep Learning Collective Variables from Transition Path Ensemble | methods | TPI-Deep-TDA, Deep-TDA, Transition Path, OPES, OPES Flooding, Machine Learning, Protein folding, Ligand binding | Dhiman Ray | PRINT OPES_METAD PYTORCH_MODEL MATHEVAL DISTANCE FIXEDATOM RMSD CONTACTMAP WHOLEMOLECULES COORDINATION COMMITTOR CUSTOM ENDPLUMED COMBINE GROUP FIT_TO_TEMPLATE CENTER INCLUDE MOLINFO ENERGY UPPER_WALLS ANGLE LOWER_WALLS | vatom function opes generic pytorch core colvar bias |
| 23.007 | Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains | bio | metadynamics, peptoids, parallel-bias metadynamics | Jim Pfaendtner | PBMETAD COM COORDINATION PRINT TORSION INCLUDE GYRATION RESTRAINT WHOLEMOLECULES | colvar vatom bias generic |
| 22.043 | Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES | bio | OPES, RNA, Tetraloop, Folding | Gül Zerze | OPES_EXPANDED PRINT ECV_UMBRELLAS_LINE ENERGY CONTACTMAP ECV_MULTITHERMAL WHOLEMOLECULES | opes colvar generic |
| 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 PRINT CELL COMMITTOR UPPER_WALLS MATHEVAL LOWER_WALLS DRMSD CUSTOM | function colvar generic bias |
| 22.031 | Rare Event Kinetics from Adaptive Bias Enhanced Sampling | methods | OPES Flooding, Kinetics, Rate, OPES, Machine Learning | Dhiman Ray | PRINT OPES_METAD PYTORCH_MODEL DISTANCE RMSD BIASVALUE CONTACTMAP WHOLEMOLECULES POSITION TORSION COMMITTOR CUSTOM ENDPLUMED COMBINE GROUP UNITS MOLINFO INCLUDE ENERGY CONSTANT | function opes generic pytorch core colvar setup bias |
| 22.013 | Ligand dissociation from PreQ1 riboswitch | bio | ligand, RNA, metadynamics, pRAVE | Yihang Wang | METAD COMBINE COM PRINT COMMITTOR MOLINFO DISTANCE COORDINATIONNUMBER RMSD WHOLEMOLECULES | vatom function generic symfunc colvar bias |
| 22.012 | Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT | bio | contact maps, protein-protein interactions | Isabell-Louise Grothaus | PRINT DISTANCE CONTACTMAP CENTER | colvar generic vatom |
| 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 | METAD LOAD PRINT WHOLEMOLECULES | generic bias setup |
| 21.048 | Enhancing ligand exploration within a channel pore and fenestrations using metadynamics | bio | well-tempered metadynamics, protein-ligand enhanced sampling, sodium channel, Nav, small molecule drug | Elaine Tao | METAD COM PRINT TORSION UNITS UPPER_WALLS DISTANCE LOWER_WALLS CUSTOM | vatom function generic colvar setup bias |
| 21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Adriana Pietropaolo | PBMETAD CONSTANT PRINT TORSION MATHEVAL RESTART BIASVALUE WHOLEMOLECULES | function generic colvar setup bias |
| 21.002 | Phase equilibrium of water with hexagonal and cubic ice using the SCAN functional | materials | ice, water, SCAN, OPES, VES, multithermal, crystallization, environment similarity, refcv, reweighting | Pablo Piaggi | OPES_EXPANDED VOLUME BF_LEGENDRE TD_UNIFORM PRINT UPPER_WALLS Q6 MATHEVAL OPT_AVERAGED_SGD VES_LINEAR_EXPANSION ECV_UMBRELLAS_LINE ECV_MULTITHERMAL_MULTIBARIC RESTART ENVIRONMENTSIMILARITY ENERGY | function opes envsim generic symfunc colvar setup bias ves |
| 20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Michele Invernizzi | PRINT MATHEVAL ECV_UMBRELLAS_LINE RMSD ECV_MULTITHERMAL_MULTIBARIC WHOLEMOLECULES POSITION TORSION CUSTOM ENDPLUMED ECV_MULTITHERMAL ECV_LINEAR OPES_EXPANDED UNITS MOLINFO ENVIRONMENTSIMILARITY Q6 ENERGY VOLUME UPPER_WALLS LOAD | function opes generic symfunc colvar setup bias envsim |
| 20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Glen Hocky | GROUP FISST PRINT UNITS MATHEVAL DISTANCE GYRATION BIASVALUE RESTRAINT ENERGY | function generic fisst core colvar setup bias |
| 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 | METAD COM CONSTANT GROUP PRINT PROJECTION_ON_AXIS INCLUDE UPPER_WALLS MOLINFO MATHEVAL DISTANCE LOWER_WALLS LOAD BIASVALUE CONTACTMAP FUNCPATHGENERAL WHOLEMOLECULES | vatom function generic core colvar setup bias |
| 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 | ABMD PRINT CONVERT_TO_FES DISTANCE REWEIGHT_METAD READ CONTACTMAP WHOLEMOLECULES DUMPGRID ENDPLUMED METAD HISTOGRAM COMBINE MOLINFO COM FLUSH FUNCPATHMSD UPPER_WALLS LOWER_WALLS | vatom function gridtools generic colvar bias |
| 19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | METAD COM PRINT UPPER_WALLS MOLINFO DISTANCE GYRATION ENERGY | generic vatom bias colvar |
| 19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | DISTANCES METAD COMBINE FLUSH PRINT UNITS UPPER_WALLS DISTANCE RESTART | function generic colvar setup multicolvar bias |
| 19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Jim Pfaendtner | METAD GROUP COORDINATION EXTERNAL ENERGY | core colvar bias |
| 19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Haochuan Chen | PRINT DRR TORSION | colvar generic drr |
| 19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Kresten Lindorff-Larsen | METAD COMBINE FLUSH PRINT COMMITTOR MOLINFO ALPHABETA | function multicolvar generic bias |
| 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 | PBMETAD GROUP COORDINATION PRINT CS2BACKBONE INCLUDE MOLINFO CENTER DISTANCE GYRATION ALPHABETA METAINFERENCE WHOLEMOLECULES | vatom generic core colvar isdb multicolvar bias |
| 25.023 | Molecular simulations of Tau-protein oligomers | bio | metadynamics, proteins, aggregation | Giovanni Bussi | RESTART PRINT CUSTOM METAD CONTACTMAP RESTRAINT RMSD FLUSH | generic function setup colvar bias |
| 25.014 | Atomic resolution ensembles of intrinsically disordered proteins with Alphafold | bio | bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement | Vincent Schnapka | BIASVALUE BAIES GROUP PRINT | core generic bias isdb |
| 24.023 | Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21. A Machine-Learning-Aided Enhanced Sampling Study | bio | RNA, miRNA, OneOPES, ligand binding, conformational changes | Valerio Rizzi | ECV_MULTITHERMAL RESTART PRINT COORDINATION COMBINE CUSTOM TORSION GROUP DISTANCE ENERGY OPES_EXPANDED OPES_METAD_EXPLORE | generic opes function setup core colvar |
| 24.018 | A new route to the prebiotic synthesis of glycine via ab initio-based machine learning calculations | chemistry | prebiotic chemistry, glycine, Strecker synthesis, ab initio calculations, machine learning | Léon HUET | DISTANCE PRINT | generic colvar |
| 24.008 | yCD Metadynamics | bio | volume-based MetaD, path CVs, infrequent MetaD, product release | James McCarty | MOLINFO FIT_TO_TEMPLATE HISTOGRAM PRINT COORDINATION WRAPAROUND RMSD FLUSH FIXEDATOM COMMITTOR READ MATHEVAL ENDPLUMED REWEIGHT_METAD COM GROUP METAD PATH WHOLEMOLECULES CONVERT_TO_FES INCLUDE UPPER_WALLS CONTACTMAP DISTANCE DUMPGRID | generic mapping gridtools function vatom core colvar bias |
| 23.045 | Minute-timescale simulations of G Protein Coupled Receptor A2A activation mechanism reveal a receptor pseudo-active state | bio | Path CVs Metadynamics, GPCRs activation transition | Vittorio Limongelli | MOLINFO PRINT INCLUDE UPPER_WALLS ALPHARMSD METAD CONTACTMAP LOWER_WALLS DISTANCE PATHMSD FUNCPATHMSD | generic function secondarystructure colvar bias |
| 23.035 | An Extended Metadynamics Protocol for Binding/Unbinding of Peptide Ligands to Class A G-Protein Coupled Receptors | bio | G protein coupled receptor, peptide ligands, metadynamics, multiple-walker | Timothy Clark | PRINT UPPER_WALLS CENTER CONSTANT BIASVALUE METAD LOWER_WALLS DISTANCE MATHEVAL WHOLEMOLECULES | generic function vatom colvar bias |
| 23.028 | Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process | chemistry | Ammonia decomposition; Dynamics;OPES; Neural Network potential | Manyi Yang | FIXEDATOM COMMITTOR PRINT OPES_METAD COM COORDINATIONNUMBER UPPER_WALLS CUSTOM ZDISTANCES GROUP LOWER_WALLS DISTANCE MATHEVAL ENERGY FLUSH UNITS DISTANCES | generic opes function symfunc vatom setup core multicolvar colvar bias |
| 23.014 | Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 | bio | metadynamics, oligomerization, chemokine receptors, GPCR, membrane | Vittorio Limongelli | PRINT COM COMBINE UPPER_WALLS TORSION METAD DISTANCE WHOLEMOLECULES FLUSH | generic function vatom colvar bias |
| 23.006 | Transcription factor unbinding | bio | metadynamics, DNA, conformational changes | Malin Lüking | MOLINFO ANGLE PRINT COM ALPHARMSD DUMPFORCES METAD CONTACTMAP DISTANCE | generic vatom secondarystructure colvar 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 | MOLINFO RESTART PRINT COORDINATION COM UPPER_WALLS TORSION GROUP EMMI BIASVALUE PBMETAD RMSD WHOLEMOLECULES | generic vatom setup core colvar bias isdb |
| 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 | MOLINFO YANGLES PRINT COM XANGLES UPPER_WALLS ZANGLES CUSTOM COMBINE TORSION METAD LOWER_WALLS DISTANCE MATHEVAL WHOLEMOLECULES ALPHABETA | generic function vatom multicolvar colvar bias |
| 22.006 | Peptide framework for screening the effects of amino acids on assembly | bio | metadynamics, peptides | Andrew White | GYRATION HISTOGRAM CONVERT_TO_FES PRINT COM INCLUDE COMBINE REWEIGHT_BIAS GROUP METAD DUMPGRID DISTANCES | generic gridtools function vatom core multicolvar 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 | GYRATION PRINT UPPER_WALLS GROUP METAD LOWER_WALLS WHOLEMOLECULES ALPHABETA ENDPLUMED | generic core multicolvar 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 | GYRATION MOLINFO PRINT COORDINATION ENERGY UPPER_WALLS GROUP PARABETARMSD ALPHARMSD METAD LOWER_WALLS RANDOM_EXCHANGES WHOLEMOLECULES ANTIBETARMSD DIHCOR | generic core multicolvar secondarystructure colvar bias |
| 21.018 | Localized Volume-based Metadynamics | bio | LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification | Riccardo Capelli | HISTOGRAM PRINT COORDINATION RMSD FLUSH FIXEDATOM READ MATHEVAL ENDPLUMED REWEIGHT_METAD COM GROUP METAD WHOLEMOLECULES CONVERT_TO_FES UPPER_WALLS DISTANCE DUMPGRID POSITION | generic gridtools function vatom core colvar bias |
| 20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Faidon Brotzakis | HISTOGRAM CONVERT_TO_FES MOLINFO READ WHOLEMOLECULES PRINT GROUP EMMI BIASVALUE RMSD DUMPGRID DISTANCES | generic gridtools core multicolvar colvar bias isdb |
| 20.010 | Phase equilibrium of liquid water and hexagonal ice from enhanced sampling molecular dynamics simulations | materials | water, ice, TIP4P, crystallization, EnvironmentSimilarity, RefCV, kernel, VES, variationally enhanced sampling | Pablo Piaggi | OPT_DUMMY ENVIRONMENTSIMILARITY RESTART Q6 PRINT OPT_AVERAGED_SGD UPPER_WALLS VES_LINEAR_EXPANSION TD_WELLTEMPERED VOLUME MATHEVAL BF_LEGENDRE | generic envsim function symfunc setup ves colvar bias |
| 20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Carlo Camilloni | GYRATION METAINFERENCE MOLINFO PRINT SAXS ALPHABETA TORSION STATS CENTER ENSEMBLE PBMETAD DISTANCE WHOLEMOLECULES FLUSH | generic function vatom multicolvar colvar bias isdb |
| 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 | HISTOGRAM CONVERT_TO_FES READ PRINT COM COMBINE UPPER_WALLS METAD LOWER_WALLS ABMD DISTANCE MATHEVAL DUMPGRID ENDPLUMED REWEIGHT_METAD | generic gridtools function vatom colvar bias |
| 19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Valerio Rizzi | UNITS RESTART PRINT COMBINE COORDINATIONNUMBER EXTERNAL GROUP METAD FLUSH ENDPLUMED | generic function symfunc setup core bias |
| 19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Matteo Salvalaglio | PRINT INCLUDE GROUP CENTER DISTANCE ENDPLUMED | core generic colvar vatom |
| 19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Jakub Rydzewski | RESTART PRINT UPPER_WALLS METAD LOWER_WALLS PATHMSD UNITS | generic bias colvar setup |
| 19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_SIMULATED_ANNEALING PRINT MAZE_OPTIMIZER_BIAS MAZE_LOSS POSITION UNITS | generic maze colvar setup |
| 19.059 | cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide | bio | bias-exchange metadynamics, cis-trans isomerization | Fabrizio Marinelli | PRINT INCLUDE TORSION METAD RANDOM_EXCHANGES | generic bias colvar |
| 19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Gareth Tribello | UNITS PRINT FCCUBIC CELL UPPER_WALLS METAD ENDPLUMED | generic symfunc setup colvar bias |
| 19.048 | Understanding Ligand Binding Selectivity in a Prototypical GPCR Family | bio | metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | PRINT COM UPPER_WALLS BIASVALUE CONSTANT METAD LOWER_WALLS DISTANCE MATHEVAL WHOLEMOLECULES | generic function vatom colvar bias |
| 19.040 | Optimal Metric for Path Collective Variables | bio | metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path | Francesco Luigi Gervasio | PRINT TORSION METAD MATHEVAL ENDPLUMED | generic bias colvar function |
| 19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Glen Hocky | EDS PRINT COMBINE TORSION DISTANCE RESTRAINT | generic function colvar bias eds |
| 19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Giovanni Bussi | MOLINFO ANGLE PRINT COMBINE INCLUDE UPPER_WALLS METAD ERMSD RANDOM_EXCHANGES DISTANCE LOWER_WALLS FLUSH DISTANCES | generic function multicolvar colvar bias |
| 25.017 | Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity | bio | EMMIVox, cryo-EM, allostery, decamer, filament, ensemble refinement, glutamine synthetase | Samuel Hoff | MOLINFO PRINT EMMIVOX BIASVALUE GROUP WHOLEMOLECULES | isdb bias generic core |
| 24.024 | Host-Guest binding free energies à la carte, an automated OneOPES protocol | bio | OneOPES, ligand binding, binding free energy,SAMPL challenge, host-guest | Valerio Rizzi | ENERGY PRINT TORSION DISTANCE CENTER FIT_TO_TEMPLATE OPES_METAD_EXPLORE MATHEVAL ENDPLUMED COORDINATION UPPER_WALLS ANGLE FIXEDATOM GROUP OPES_EXPANDED LOWER_WALLS WHOLEMOLECULES ECV_MULTITHERMAL | bias opes function vatom core generic colvar |
| 24.022 | Integrating Path Sampling with Enhanced Sampling for Rare-event Kinetics | methods | OPES Flooding, Weighted Ensemble, Metadynamics, Kinetics, Infrequent Metadynamics, Integrated Sampling | Dhiman Ray | CUSTOM CENTER MATHEVAL OPES_METAD METAD COORDINATION FIXEDATOM CONTACTMAP RMSD DISTANCE ANGLE UPPER_WALLS TORSION COMMITTOR GROUP WHOLEMOLECULES COMBINE MOLINFO PRINT ENDPLUMED FIT_TO_TEMPLATE | bias opes generic vatom function core colvar |
| 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 | ENERGY PRINT DISTANCE OPES_METAD UPPER_WALLS COORDINATION | opes generic colvar bias |
| 24.016 | Cryo-EM guided simulations of ribozyme | bio | metainference, cryo-EM | Giovanni Bussi | MOLINFO PRINT INCLUDE EMMIVOX BIASVALUE RESTRAINT GROUP WHOLEMOLECULES ERMSD | isdb bias core 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 | MOLINFO PRINT COM BIASVALUE DISTANCE CENTER COORDINATION METAD UPPER_WALLS GROUP DEBUG LOWER_WALLS GHBFIX COMBINE | bias vatom function core generic colvar |
| 23.046 | Lasso Peptides - HLDA CV | bio | metadynamics, protein folding, HLDA, harmonic | Gabriel da Hora | PRINT UNITS DISTANCE METAD WHOLEMOLECULES COMBINE | bias function generic setup colvar |
| 23.037 | Estimating binding free energy of solid binding peptides without extensive sampling | bio | metadynamics, solid binding peptides | Xin Qi | MOLINFO PRINT COM PBMETAD DISTANCE GYRATION UPPER_WALLS LOWER_WALLS | bias generic vatom colvar |
| 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 | MOLINFO PRINT BIASVALUE WHOLEMOLECULES METAD COORDINATION GHBFIX ERMSD COMBINE | bias generic function colvar |
| 23.023 | Rational design of novel biomimetic sequence-defined polymers for mineralization applications | methods | metadynamics, surface binding, biomimetic mineralization | Kaylyn Torkelson | PRINT COM PBMETAD DISTANCE GYRATION COORDINATION UPPER_WALLS | bias generic vatom colvar |
| 23.020 | FEP simulations of ATOX1 homodimer | chemistry | parallel bias metadynamics, FEP, free-energy of metal ion dissociation | Adriana Pietropaolo | PRINT PBMETAD BIASVALUE DISTANCE CONSTANT MATHEVAL ANGLE WHOLEMOLECULES | bias generic function colvar |
| 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 | PRINT RESTART ECV_UMBRELLAS_LINE HISTOGRAM UPPER_WALLS DUMPGRID OPES_EXPANDED ENVIRONMENTSIMILARITY LOWER_WALLS | bias opes generic envsim gridtools setup |
| 23.000 | Atomistic simulations of RNA tetraloop folding via PTWTE-WTM | bio | parallel tempering, well-tempered metadynamics, well-tempered ensemble, RNA, Tetraloop, Folding | Gül Zerze | ENERGY PRINT CONTACTMAP METAD UPPER_WALLS LOWER_WALLS WHOLEMOLECULES | bias generic colvar |
| 22.020 | Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix–Junction–Helix RNA | bio | RNA force field, Helix-Junction-Helix RNA, SAXS, Well tempered metadynamics | Weiwei He | PRINT TORSION COM DISTANCE METAD GROUP WHOLEMOLECULES | bias vatom core generic colvar |
| 21.039 | Deep learning the slow modes for rare events sampling | methods | collective variables, machine learning, slow modes, deep-tica, opes | Luigi Bonati | ENERGY UNITS LOAD FLUSH OPES_METAD CONTACTMAP RMSD PYTORCH_MODEL DISTANCE OPES_EXPANDED ENVIRONMENTSIMILARITY TORSION VOLUME Q6 GROUP WHOLEMOLECULES ECV_MULTITHERMAL MOLINFO COMBINE PRINT INCLUDE ENDPLUMED | symfunc pytorch opes function envsim core generic setup colvar |
| 21.038 | Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics | materials | metadynamics, SGOOP, nucleation, urea | Ziyue Zou | ENERGY PRINT INCLUDE VOLUME LOAD CENTER COORDINATIONNUMBER METAD GROUP COMBINE | symfunc bias vatom function core generic setup colvar |
| 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 PRINT TORSION RESTART FLUSH EXTERNAL | bias generic setup colvar |
| 21.015 | Coarse-grained metadynamics and umbrella sampling simulations to investigate interactions of carbohydrate-binding modules with chitin | bio | metadynamics, umbrella sampling, coarse-grained, MARTINI, chitin, carbohydrate-binding module | Gaston Courtade | PRINT RESTART CENTER POSITION MATHEVAL COORDINATION METAD REWEIGHT_BIAS RESTRAINT WHOLEMOLECULES | bias vatom function generic setup colvar |
| 20.032 | Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil | materials | clustering, conformational isomers | Matteo Salvalaglio | PRINT ENDPLUMED TORSION | generic colvar |
| 20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Cristina Paissoni | MOLINFO PRINT ENSEMBLE INCLUDE BIASVALUE DISTANCE CENTER STATS SAXS RESTRAINT GROUP WHOLEMOLECULES | isdb bias vatom function core generic colvar |
| 19.080 | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | methods | ves, variationally enhanced sampling, vibrational excitation, chemical reactions | Kristof Bal | PRINT UNITS TD_GRID DISTANCE CONVERT_TO_FES HISTOGRAM TD_WELLTEMPERED FLUSH EXTERNAL COORDINATION ANGLE UPPER_WALLS BF_CHEBYSHEV VES_LINEAR_EXPANSION DUMPGRID LOWER_WALLS OPT_AVERAGED_SGD COMBINE | ves bias generic function gridtools setup colvar |
| 19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Sandro Bottaro | MOLINFO PRINT TORSION DISTANCE METAD WHOLEMOLECULES RMSD ERMSD | bias generic colvar |
| 19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Kim E. Jelfs | PRINT COM RESTART DISTANCE CENTER UPPER_WALLS METAD GROUP LOWER_WALLS | bias vatom core generic setup colvar |
| 19.050 | Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes | chemistry | metadynamics, membranes, Willard Chandler surface | Gareth Tribello | PRINT RESTART CONVERT_TO_FES HISTOGRAM UPPER_WALLS DUMPGRID REWEIGHT_BIAS DISTANCE_FROM_CONTOUR READ METAD COMBINE | bias generic function contour gridtools setup |
| 19.032 | Chemical reaction in solution using path collective variables based on coordination patterns | chemistry | chemical reactions, solutions, metadynamics, coordination patterns | Fabio Pietrucci | PRINT RESTART FLUSH DISTANCES UPPER_WALLS METAD PATH | multicolvar bias mapping generic setup |
| 19.025 | Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide | bio | metainference, NMR, protein dynamics, force-fields | Carlo Camilloni | MOLINFO PRINT TORSION JCOUPLING PBMETAD ENSEMBLE BIASVALUE GYRATION CS2BACKBONE ENDPLUMED FLUSH WHOLEMOLECULES STATS RDC METAINFERENCE | isdb bias function generic colvar |
| 19.023 | RECT | methods | metadynamics, replica exchange | Giovanni Bussi | PRINT TORSION GYRATION METAD WHOLEMOLECULES | bias generic colvar |
| 19.009 | RNA tetraloops folding | bio | metadynamics, RNA, folding | Giovanni Bussi | MOLINFO PRINT ENDPLUMED METAD WHOLEMOLECULES RMSD ERMSD | bias generic colvar |
| 25.028 | Designing transferable transition state guided collective variable via interpretable machine learning model for enhanced sampling. A case study on polymer collapse transition | bio | metadynamics, polymer collapse transition, transferable CV,interpretable ML-model | Saikat Dhibar and Biman Jana | MATHEVAL LOWER_WALLS GROUP PRINT CENTER COMBINE COORDINATION WHOLEMOLECULES GYRATION METAD UPPER_WALLS DISTANCE | colvar generic vatom function core bias |
| 25.012 | A Machine Learning-Driven, Probability-Based Approach to Enzyme Catalysis | bio | enzyme catalysis, transition state, structure-activity relationship, free energy surface, reaction mechanism, water, alpha-amylase, sugar, QM/MM MD, OPES, committor function, machine learning | Sudip Das | UNITS MATHEVAL FLUSH POSITION PRINT INCLUDE TORSION CUSTOM LOAD COORDINATION CELL COMBINE BIASVALUE OPES_METAD ENERGY DISTANCE | colvar setup generic function opes bias |
| 25.008 | Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting | methods | metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting | Dhiman Ray | UNITS LOWER_WALLS POSITION PRINT GROUP RMSD TORSION CUSTOM PYTORCH_MODEL OPES_METAD WHOLEMOLECULES BIASVALUE METAD UPPER_WALLS ENDPLUMED MOLINFO ENERGY DISTANCE | colvar setup generic pytorch function opes core bias |
| 24.035 | Data efficient machine learning potentials for modeling catalytic reactivity via active learning and enhanced sampling | chemistry | opes, catalysis, ammonia, machine learning potentials | Luigi Bonati | COMMITTOR UNITS LOWER_WALLS PRINT GROUP CUSTOM COORDINATION OPES_METAD RESTART UPPER_WALLS DISTANCE | colvar setup generic function opes core bias |
| 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 | DUMPMASSCHARGE PARABETARMSD GROUP RMSD PRINT CENTER COORDINATION WHOLEMOLECULES EMMI BIASVALUE UPPER_WALLS COM MOLINFO ALPHARMSD DISTANCE PBMETAD DUMPATOMS | colvar secondarystructure generic vatom isdb core bias |
| 24.026 | Constant pH metadynamics of RNA oligomers | bio | metadynamics, pH, RNA | Giovanni Bussi | PRINT TORSION RESTART PUCKERING METAD MOLINFO | colvar setup generic 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 | PATH FIXEDATOM LOWER_WALLS PRINT GROUP CENTER TORSION CUSTOM FIT_TO_TEMPLATE COORDINATION WHOLEMOLECULES RESTART PYTORCH_MODEL UPPER_WALLS OPES_METAD DISTANCE | colvar setup generic mapping vatom pytorch function 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 | MATHEVAL LOWER_WALLS PRINT RMSD OPES_EXPANDED INCLUDE OPES_METAD_EXPLORE WRAPAROUND WHOLEMOLECULES BIASVALUE COM UPPER_WALLS CONTACTMAP PROJECTION_ON_AXIS TORSION COORDINATION RESTART ECV_MULTITHERMAL MOLINFO ENERGY GROUP CUSTOM METAD CONSTANT | colvar setup generic vatom function opes core bias |
| 24.000 | Ammonia Decomposition on Non-stoichiometric Lithium Imide | chemistry | ammonia decomposition, non-stoichiometric lithium imide, machine learning interatomic potentials, enhanced sampling, heterogeneous catalysis | Francesco Mambretti | UNITS ZDISTANCES FIXEDATOM FLUSH GROUP PRINT COORDINATIONNUMBER OPES_METAD UPPER_WALLS DISTANCE | colvar setup generic symfunc vatom multicolvar opes core bias |
| 23.036 | Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? | bio | NaCl, nucleation, metadynamics | Ruiyu Wang | VOLUME MATHEVAL PRINT Q4 COORDINATIONNUMBER COMBINE Q6 METAD ENERGY | colvar generic symfunc function bias |
| 23.024 | Permutationally Invariant Networks for Enhanced Sampling (PINES) | methods | collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent | Nicholas Herringer | LOAD PRINT PBMETAD | setup generic bias |
| 23.011 | OneOPES, a combined enhanced sampling method to rule them all | bio | OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding | Valerio Rizzi | PRINT TORSION OPES_METAD_EXPLORE ECV_MULTITHERMAL METAD ENDPLUMED OPES_EXPANDED MOLINFO ENERGY DISTANCE | colvar bias opes generic |
| 23.010 | An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G‑Protein-Coupled Receptor Ligands | bio | GPCR, binding free energy, free energy surface | Timothy Clark | MATHEVAL LOWER_WALLS PRINT WHOLEMOLECULES BIASVALUE UPPER_WALLS METAD CONSTANT DISTANCE | colvar function bias generic |
| 22.025 | Bubble nucleation rate predictions in a Lennard-Jones fluid | materials | free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation | Kristof Bal | UNITS VOLUME COMMITTOR ANN FLUSH CONVERT_TO_FES PRINT MOVINGRESTRAINT COORDINATIONNUMBER CUSTOM LOAD DUMPGRID BIASVALUE UPPER_WALLS REWEIGHT_BIAS HISTOGRAM RESTRAINT | colvar setup bias generic symfunc function annfunc gridtools |
| 22.009 | Glycosylation in calixarenes capsule | chemistry | Metadynamics, glycosylation, supramolecular catalysis | GiovanniMaria Piccini | UNITS MATHEVAL LOWER_WALLS FLUSH ANGLE GROUP RMSD PRINT FIT_TO_TEMPLATE COORDINATION WHOLEMOLECULES COMBINE BRIDGE UPPER_WALLS METAD DISTANCES DISTANCE | colvar setup generic adjmat multicolvar function core bias |
| 21.049 | Multiple-path-metadynamics and PathMaps | methods | path-CV, metadynamics, multiple-walker, multiple paths, pathmap | Alberto Pérez-de-Alba-Ortíz | UNITS LOWER_WALLS PRINT MOVINGRESTRAINT TORSION CUSTOM LOAD COMBINE UPPER_WALLS METAD ENSEMBLE CONSTANT RESTRAINT | colvar setup generic function bias |
| 21.045 | QM/MM metadynamics of thiol-disulfide exchange between methylthiolate and dimethyldisulfide in water with an imposed external electrostatic potential (ESP) | chemistry | metadynamics, QM/MM, electrostatic potential, thiol-disulfide exchange | Denis Maag | LOWER_WALLS PRINT COORDINATIONNUMBER COMBINE COORDINATION UPPER_WALLS METAD DISTANCE | colvar generic symfunc function bias |
| 21.033 | Multiple-path-metadynamics applied to DNA base-pairing transitions | bio | path-CV, metadynamics, multiple-walker, dna | Alberto Pérez-de-Alba-Ortíz | PRINT MOVINGRESTRAINT INCLUDE COMBINE UPPER_WALLS METAD CONSTANT RESTRAINT | function bias generic |
| 21.019 | Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations | materials | Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen | Matteo Salvalaglio | MATHEVAL KDE PRINT COM DISTANCE TORSIONS | colvar generic vatom multicolvar function gridtools |
| 21.016 | MD SAXS GTPase associated center | bio | metadynamics, RNA, folding, SAXS | Giovanni Bussi | ERMSD LOWER_WALLS GROUP PRINT INCLUDE CUSTOM SAXS WHOLEMOLECULES GYRATION UPPER_WALLS METAD MOLINFO | colvar generic isdb function core bias |
| 21.014 | how to determine statistically accurate conformational ensembles | bio | metadynamics, metainference, errors, cv, SAXS, ensemble determination | Cristina Paissoni | CONTACTMAP ALPHABETA PRINT CENTER TORSION STATS SAXS ANTIBETARMSD WHOLEMOLECULES GYRATION BIASVALUE METAD ENSEMBLE MOLINFO PBMETAD | colvar secondarystructure generic vatom isdb multicolvar function bias |
| 20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Valerio Rizzi | MATHEVAL FIXEDATOM ANGLE PRINT GROUP CENTER FIT_TO_TEMPLATE COORDINATION WHOLEMOLECULES PYTORCH_MODEL OPES_METAD UPPER_WALLS ENDPLUMED ENERGY DISTANCE | colvar generic vatom pytorch function opes core bias |
| 20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Vojtech Spiwok | PRINT TORSION METAD | colvar bias generic |
| 20.002 | Exploring conformational dynamics of the extracellular Venus flytrap domain of the GABAB receptor, a path-metadynamics study | bio | Metadynamics, path CVs | Riccardo Ocello | GROUP PRINT WHOLEMOLECULES RESTART METAD UPPER_WALLS MOLINFO PATHMSD | colvar setup generic core bias |
| 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 | LOWER_WALLS PRINT COORDINATIONNUMBER GYRATION METAD UPPER_WALLS ENDPLUMED DISTANCES ENERGY | colvar generic symfunc multicolvar bias |
| 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 | UNITS LOWER_WALLS FLUSH POSITION GROUP PRINT COORDINATION RESTART UPPER_WALLS METAD | colvar setup generic core bias |
| 19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | UNITS FLUSH PRINT COMBINE UPPER_WALLS METAD ENERGY DISTANCE | colvar setup generic function bias |
| 19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Carlo Camilloni | LOWER_WALLS FLUSH ALPHABETA GROUP CS2BACKBONE PRINT ANTIBETARMSD WHOLEMOLECULES RESTART BIASVALUE UPPER_WALLS ENDPLUMED MOLINFO PBMETAD | secondarystructure setup generic isdb multicolvar core bias |
| 19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Paolo Raiteri | UNITS MATHEVAL FLUSH PRINT RESTART UPPER_WALLS METAD DISTANCE | colvar setup generic function bias |
| 19.035 | Dimerization of GPCRs from coarse-grained umbrella sampling | bio | Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization | Davide Provasi | GROUP PRINT TORSION COM RESTRAINT DISTANCE | colvar generic vatom core bias |
| 19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Matteo Salvalaglio | COMMITTOR LOWER_WALLS PRINT CENTER TORSION UPPER_WALLS METAD DISTANCE | colvar bias generic vatom |
| 19.013 | RNA FF FITTING | methods | force field, RNA | Giovanni Bussi | MATHEVAL TORSION INCLUDE PUCKERING BIASVALUE CONSTANT MOLINFO | colvar function bias generic |
| 19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Carlo Camilloni | DIHCOR ALPHABETA GROUP PRINT RDC CENTER TORSION DHENERGY STATS WHOLEMOLECULES UPPER_WALLS METAINFERENCE ENDPLUMED ENSEMBLE MOLINFO RESTRAINT DISTANCE PBMETAD | colvar generic vatom isdb multicolvar function core bias |
| 19.003 | EMMI ClpP | bio | metainference, cryo-EM | Max Bonomi | GROUP PRINT EMMI BIASVALUE MOLINFO | isdb bias core generic |
| 25.029 | Energetic Constraints in the Enzymatic Depolymerization of Crystalline PET from enhanced molecular simulations | bio | HREX-Metadynamics, PETase, crystalline PET, amorphous PET, conformational ensembles, substrate binding, chain detachment | Ania Di Pede-Mattatelli and Francesco Colizzi | MOLINFO DISTANCE HISTOGRAM METAD COM LOWER_WALLS DUMPGRID REWEIGHT_BIAS FIXEDATOM PRINT WHOLEMOLECULES CONVERT_TO_FES UPPER_WALLS | bias gridtools colvar generic vatom |
| 25.026 | Deciphering the Molecular Mechanisms of Startle Disease - the Role of the Asn46Lys Mutation in the Glycine Receptor | bio | metadynamics, glycine receptors, funnel metadynamics | Jacob Adam Clark | METAD COM FUNNEL LOWER_WALLS FUNNEL_PS PRINT UPPER_WALLS | bias generic vatom funnel |
| 24.034 | Umbrella sampling of ion in transporter SLC26A7 | bio | umbrella sampling, transporter, ions | Xiaoli Lu | PRINT RESTRAINT POSITION UNITS | bias setup colvar generic |
| 24.013 | Estimating Free Energy Surfaces and their Convergence from multiple, independent static and history-dependent biased molecular-dynamics simulations with Mean Force Integration | methods | Mean Force Integration, Convergence, FES, Umbrella Sampling | Matteo Salvalaglio | MOLINFO DISTANCE COORDINATIONNUMBER TORSION BIASVALUE METAD RESTART FLUSH RESTRAINT ENERGY MATHEVAL PRINT COMMITTOR | function symfunc bias colvar generic setup |
| 24.006 | Water vapor condensation | chemistry | metadynamics, homogeneous condensation, chemical potential | Shenghui Zhong | COORDINATIONNUMBER CLUSTER_PROPERTIES METAD DFSCLUSTERING CONTACT_MATRIX CLUSTER_NATOMS UNITS PRINT UPPER_WALLS | adjmat symfunc bias generic clusters setup |
| 23.026 | Machine Learning Nucleation Collective Variables with Graph Neural Networks | chemistry | Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks | Florian Dietrich | COORDINATIONNUMBER MOVINGRESTRAINT COMBINE METAD MFILTER_MORE Q6 LOWER_WALLS GROUP PRINT LOCAL_Q6 | core function symfunc bias generic multicolvar |
| 23.022 | A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar | methods | collective variables, machine learning, toy model | Enrico Trizio | BIASVALUE ENDPLUMED LOWER_WALLS CUSTOM PYTORCH_MODEL OPES_METAD UNITS PRINT POSITION UPPER_WALLS | function bias colvar generic setup pytorch opes |
| 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 | BIASVALUE METAD TIME LOWER_WALLS CUSTOM PATHMSD FLUSH UNITS PRINT UPPER_WALLS DRR | function bias colvar generic setup drr |
| 23.008 | PBMetaD simulations of Histatin5 | bio | metadynamics, IDP, Rg, PPII | Francesco Pesce | MOLINFO TORSION GYRATION PBMETAD GROUP PRINT WHOLEMOLECULES | core bias colvar generic |
| 23.002 | Critical comparison of general-purpose collective variables for crystal nucleation | methods | metadynamics, umbrella sampling, commitor, entropy, PIV | Julien Lam | PIV PAIRENTROPY METAD Q6 CUSTOM VOLUME ENERGY RESTRAINT UNITS PRINT LOCAL_AVERAGE FUNCPATHMSD UPPER_WALLS Q4 | function bias gridtools symfunc colvar generic setup piv |
| 22.030 | Mixing physics across temperatures with generative artificial intelligence | methods | REMD, Generative AI, DDPM | Yihang Wang | PRINT WHOLEMOLECULES TORSION | colvar generic |
| 22.028 | N-glycan conformer distributions in atomistic simulation | bio | REST2, RECT, N-glycan, pucker | Isabell Grothaus | MOLINFO TORSION HISTOGRAM METAD READ DUMPGRID PUCKERING PRINT CONVERT_TO_FES | bias gridtools colvar generic |
| 21.047 | Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations | materials | pair entropy, metadynamics, ves, solids, crystallization | Pablo Piaggi | PAIRENTROPY COMBINE METAD RESTART LOAD BF_LEGENDRE VES_LINEAR_EXPANSION TD_WELLTEMPERED VOLUME ENERGY PRINT OPT_AVERAGED_SGD | ves function bias gridtools colvar generic setup |
| 21.037 | Molecular Dynamics simulations of RBD/hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain | Max Bonomi | RMSD DISTANCE PRINT | colvar generic |
| 21.035 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, interface | Aaron Finney | DISTANCE LOAD RESTRAINT GROUP FIXEDATOM PRINT | core bias colvar generic vatom setup |
| 21.032 | Metal-coupled folding mechanism to metallothionein | bio | parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination | Manuel-Peris Diaz | PBMETAD GROUP UNITS WHOLEMOLECULES COORDINATION | core bias colvar generic setup |
| 21.031 | Photo-switchable sulfonulureas in KATP channel | bio | metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels | Katarzyna Walczewska-Szewc | DISTANCE METAD COM LOWER_WALLS UNITS PRINT WHOLEMOLECULES UPPER_WALLS | bias colvar generic vatom setup |
| 21.020 | Reweighted Jarzynski sampling | methods | free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions | Kristof Bal | COORDINATIONNUMBER DISTANCE MOVINGRESTRAINT VES_LINEAR_EXPANSION OPES_METAD CONSTANT CONVERT_TO_FES OPT_AVERAGED_SGD REWEIGHT_METAD COMBINE METAD ANN LOAD FLUSH REWEIGHT_BIAS RESTRAINT UNITS PRINT UPPER_WALLS BIASVALUE HISTOGRAM BF_CHEBYSHEV DUMPGRID CUSTOM TD_WELLTEMPERED | ves function symfunc bias gridtools colvar generic setup annfunc opes |
| 21.006 | OPES, On-the-fly Probability Enhanced Sampling Method | methods | opes, alanine dipeptide, well-tempered, multithermal, multiumbrella | Michele Invernizzi | TORSION ENDPLUMED ECV_MULTITHERMAL OPES_METAD ENERGY PRINT OPES_EXPANDED ECV_UMBRELLAS_LINE | opes colvar generic |
| 21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Kresten Lindorff-Larsen | MOLINFO ALPHARMSD BIASVALUE GYRATION EEFSOLV CENTER PBMETAD FLUSH GROUP PRINT WHOLEMOLECULES METAINFERENCE SAXS | secondarystructure isdb core bias colvar generic vatom |
| 21.000 | Uremic toxin time scale dynamics | bio | uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs) | Jim Pfaendtner | DISTANCE COM GROUP PRINT WHOLEMOLECULES | core vatom colvar generic |
| 20.001 | Conformational stability and dynamics in solution and in crystals report similarly on unfolding and aggregation propensity of amyloidogenic proteins | bio | metainference, metadynamics, NMR, protein dynamics, b2m, protein crystals | Carlo Camilloni | MOLINFO ALPHABETA ENDPLUMED BIASVALUE CS2BACKBONE PBMETAD LOWER_WALLS FLUSH GROUP PRINT WHOLEMOLECULES UPPER_WALLS ANTIBETARMSD | secondarystructure isdb core bias generic multicolvar |
| 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 | RESTART VES_LINEAR_EXPANSION READ LOWER_WALLS TD_MULTITHERMAL_MULTIBARIC REWEIGHT_TEMP_PRESS ENERGY CONVERT_TO_FES OPT_AVERAGED_SGD BF_LEGENDRE COMBINE OPT_DUMMY LOAD CELL REWEIGHT_BIAS MATHEVAL PRINT UPPER_WALLS HISTOGRAM Q6 DUMPGRID TD_WELLTEMPERED VOLUME | ves function bias gridtools symfunc colvar generic setup |
| 19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | MOLINFO DISTANCE METAD COM GYRATION ENERGY PRINT UPPER_WALLS | bias vatom colvar generic |
| 19.076 | Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones | bio | molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics | Salvatore Assenza | MOVINGRESTRAINT ENDPLUMED GYRATION UNITS PRINT | bias setup colvar generic |
| 19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Michele Invernizzi | TORSION ENDPLUMED METAD OPES_METAD UNITS PRINT POSITION EXTERNAL | bias colvar generic setup opes |
| 19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Wei Chen | COMBINE COM RESTRAINT ANN POSITION | function bias colvar vatom annfunc |
| 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 | DISTANCE METAD COM ENERGY PRINT UPPER_WALLS | bias vatom colvar generic |
| 19.030 | Coarse-Grained MetaDynamics (CG-MetaD) | bio | Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy | Vittorio Limongelli | DISTANCE METAD COM LOWER_WALLS PRINT WHOLEMOLECULES UPPER_WALLS | bias vatom colvar generic |
| 19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Elena Papaleo | MOLINFO ALPHABETA METAD GYRATION LOWER_WALLS GROUP PRINT WHOLEMOLECULES UPPER_WALLS | core bias colvar generic multicolvar |
| 19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Pratyush Tiwary | DISTANCE ALPHABETA TORSION COMBINE RESTART COM PRINT WHOLEMOLECULES COMMITTOR EXTERNAL | function bias colvar generic vatom setup multicolvar |
| 19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Riccardo Capelli | REWEIGHT_METAD HISTOGRAM METAD ENDPLUMED COM READ DUMPGRID FLUSH FIT_TO_TEMPLATE WRAPAROUND GROUP MATHEVAL PRINT WHOLEMOLECULES CONVERT_TO_FES POSITION UPPER_WALLS COORDINATION | core function bias gridtools colvar generic vatom |
| 19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Carlo Camilloni | MOLINFO DISTANCE UPPER_WALLS BIASVALUE ENDPLUMED CENTER RMSD STATS RESTRAINT GROUP INCLUDE PRINT WHOLEMOLECULES SAXS | isdb core function bias colvar generic vatom |
| 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 | GROUP OPES_EXPANDED GHOST COORDINATION COMBINE ECV_MULTITHERMAL CENTER RMSD CUSTOM OPES_METAD_EXPLORE DISTANCE MOLINFO PRINT ENERGY | function colvar generic opes vatom core |
| 25.015 | Assessment of Force Fields for Describing Conformational Polymorphic Crystals of ROY | materials | Molecular crystal, Force Field, Collective Variable | Pradip Si and Omar Valsson | SMAC DUMPMULTICOLVAR TORSIONS DISTANCES PRINT | symfunc multicolvar generic |
| 25.013 | Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices | bio | umbrella sampling, temperature ramping | Alexander Berlaga | RESTRAINT GYRATION PRINT DISTANCE PYTORCH_MODEL | bias pytorch colvar generic |
| 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 | GROUP COORDINATIONNUMBER OPES_METAD FIXEDATOM ZDISTANCES DISTANCES CUSTOM COMMITTOR DISTANCE UPPER_WALLS FLUSH PRINT UNITS | symfunc function colvar setup bias generic opes vatom core multicolvar |
| 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 | bias function colvar 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 | GROUP CONVERT_TO_FES TORSION ANGLE COORDINATION HISTOGRAM DUMPGRID PRINT DISTANCE WHOLEMOLECULES | core colvar generic gridtools |
| 24.030 | NMR guided simulation of dsRBD | bio | Metainference, NMR, protein dynamics | Debadutta Patra | GROUP RDC ALPHABETA DISTANCE ENSEMBLE PRINT STATS MOLINFO FLUSH WHOLEMOLECULES METAINFERENCE | function colvar generic core multicolvar isdb |
| 24.029 | Combination of OPES and OPES-Explore | methods | OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin | Dhiman Ray | OPES_METAD ENDPLUMED OPES_METAD_EXPLORE DISTANCE FLUSH WHOLEMOLECULES UPPER_WALLS ENERGY PYTORCH_MODEL GROUP POSITION CONTACTMAP FIT_TO_TEMPLATE RMSD MATHEVAL INCLUDE UNITS COORDINATION FIXEDATOM CENTER CUSTOM BIASVALUE METAD COMBINE LOWER_WALLS PRINT MOLINFO | function colvar setup bias pytorch generic opes vatom core |
| 24.010 | Oxytocin metadynamics simulation | bio | metadynamics, oxytocin, peptide | Jan Beránek | METAD TORSION RESTART PRINT FLUSH WHOLEMOLECULES | bias setup colvar generic |
| 24.009 | Weighted Shape Gaussian Mixture Models | bio | metadynamics, clustering | Glen Hocky | GROUP METAD TORSION PRINT UNITS | setup colvar bias generic core |
| 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 | TORSION COMBINE LOWER_WALLS OPES_METAD UPPER_WALLS CUSTOM COMMITTOR PRINT DISTANCE FLUSH UNITS | function colvar setup bias generic opes |
| 23.044 | Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition | materials | metadynamics, interlocked molecules | Luigi Leanza | GROUP METAD CONVERT_TO_FES COORDINATION ENDPLUMED DUMPGRID HISTOGRAM COMMITTOR PRINT READ | colvar bias generic core gridtools |
| 23.025 | Probing ion binding to G-quadruplexes and related events | chemistry | metadynamics, repulsive potential, nucleic acids, G-quadruplexes | Marcelo Poleto | GROUP POSITION METAD COM FIT_TO_TEMPLATE RESTART DUMPATOMS WRAPAROUND LOWER_WALLS MATHEVAL UPPER_WALLS DISTANCES PRINT DISTANCE FLUSH WHOLEMOLECULES UNITS | function colvar setup bias generic vatom core multicolvar |
| 23.019 | Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors | bio | binding pathway, binding energy, sketch-map, drug development | Raitis Bobrovs | PATHMSD METAD COM VORONOI SKETCHMAP_PROJECTION COLLECT_FRAMES TRANSPOSE VSTACK LANDMARK_SELECT_FPS CUSTOM DISSIMILARITIES PRINT DISTANCE UPPER_WALLS WHOLEMOLECULES SKETCHMAP | function colvar landmarks bias valtools generic vatom dimred matrixtools |
| 23.018 | Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention | materials | metadynamics, surface binding, peptide adsorption | Kaylyn Torkelson | COM PBMETAD GYRATION PRINT DISTANCE UPPER_WALLS | vatom bias colvar generic |
| 23.015 | MPCs aggregation | bio | opes_explore, dimerization, MPCs, self-assembly | Vikas Tiwari | GROUP METAD COM COORDINATION LOWER_WALLS CENTER OPES_METAD_EXPLORE CUSTOM PRINT DISTANCE UPPER_WALLS WHOLEMOLECULES | function colvar bias generic opes vatom core |
| 23.005 | A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs | bio | metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A | Timothy Clark | METAD CONVERT_TO_FES REWEIGHT_METAD RMSD MATHEVAL DUMPGRID HISTOGRAM PRINT DISTANCE MOLINFO WHOLEMOLECULES READ | function colvar bias generic gridtools |
| 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 | EXTRACV METAD TORSION PRINT READ | bias colvar generic |
| 22.045 | Binding mode and mechanism of enzymatic polyethylene terephthalate degradation | bio | metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation | Francesco Colizzi | METAD ANGLE COM MOVINGRESTRAINT LOWER_WALLS PRINT DISTANCE UPPER_WALLS WHOLEMOLECULES | vatom bias colvar generic |
| 22.040 | From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure | bio | SARS-CoV-2, Spike, Omicron | Miłosz Wieczór | METAD PCAVARS LOWER_WALLS PRINT UPPER_WALLS WHOLEMOLECULES | bias mapping generic |
| 22.029 | Angiotensin-1-7_Metadynamics | bio | Metadynamics, Angiotensin-(1-7), peptide | L.-América Chi | GROUP METAD COORDINATION GYRATION LOWER_WALLS UPPER_WALLS PRINT FLUSH WHOLEMOLECULES | core bias colvar generic |
| 22.019 | Exploring aspartic protease inhibitor binding to design selective antimalarials | bio | ligand binding, loop opening, path CV, funnel metadynamics, drug development | Raitis Bobrovs | PATHMSD METAD COM FUNNEL_PS LOWER_WALLS FUNNEL PRINT DISTANCE UPPER_WALLS WHOLEMOLECULES | funnel colvar bias generic vatom |
| 22.003 | Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling | methods | opes, metadynamics, reweighting, alanine, muller | Michele Invernizzi | POSITION OPES_EXPANDED METAD TORSION ECV_UMBRELLAS_FILE PBMETAD ECV_MULTITHERMAL LOWER_WALLS OPES_METAD ENDPLUMED CUSTOM OPES_METAD_EXPLORE BIASVALUE UPPER_WALLS PRINT UNITS ENERGY | function colvar setup bias generic opes |
| 21.017 | All-atom simulations of the Vav1 AD construct | bio | metadynamics, parallel-bias, well-tempered | Simone Orioli | GROUP METAD CONTACTMAP WHOLEMOLECULES RESTART PBMETAD ALPHABETA REWEIGHT_BIAS PRINT MOLINFO ALPHARMSD | setup colvar bias generic core secondarystructure multicolvar |
| 21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Tarak Karmakar | LOAD GROUP LOWER_WALLS OPES_METAD MATHEVAL UPPER_WALLS PRINT FLUSH PYTORCH_MODEL | function setup bias pytorch generic opes core |
| 20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Max Bonomi | COORDINATION PBMETAD GYRATION DIHCOR ALPHABETA PRINT MOLINFO INCLUDE WHOLEMOLECULES | bias multicolvar colvar generic |
| 20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Matteo Salvalaglio | METAD LOWER_WALLS MATHEVAL CELL VOLUME UPPER_WALLS PRINT ENERGY | bias function colvar generic |
| 20.016 | Predicting polymorphism in molecular crystals using orientational entropy | materials | metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy | Pablo Piaggi | LOAD GROUP METAD CENTER INCLUDE VOLUME UPPER_WALLS PRINT | setup colvar bias generic vatom core |
| 20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Jim Pfaendtner | GROUP RESTART COORDINATION CENTER DISTANCES PRINT DISTANCE WHOLEMOLECULES | setup colvar generic vatom core multicolvar |
| 20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Luigi Bonati | LOAD GROUP TORSION COM LOWER_WALLS OPES_METAD ENDPLUMED MATHEVAL UPPER_WALLS PRINT DISTANCE FLUSH UNITS PYTORCH_MODEL | function setup colvar bias pytorch generic opes vatom core |
| 19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Valerio Rizzi | GROUP METAD RESTART COORDINATIONNUMBER COMBINE ENDPLUMED UPPER_WALLS DISTANCES PRINT FLUSH UNITS | symfunc function setup bias generic core multicolvar |
| 19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Giovanni Bussi | COORDINATION RESTRAINT LOWER_WALLS ENDPLUMED DISTANCE WHOLEMOLECULES | bias colvar generic |
| 19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Giovanni Bussi | METAD TORSION COM MAXENT COORDINATION SORT MATHEVAL INCLUDE PRINT DISTANCE MOLINFO FLUSH WHOLEMOLECULES | function colvar bias generic vatom |
| 19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Mattia Bernetti | PATHMSD METAD LOWER_WALLS PRINT UPPER_WALLS WHOLEMOLECULES | bias colvar generic |
| 19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Kim Jelfs | INPLANEDISTANCES COM RESTART MOVINGRESTRAINT DISTANCES PRINT FLUSH | setup bias generic vatom multicolvar |
| 19.056 | maze | methods | maze, ligand unbinding | Jakub Rydzewski | POSITION MAZE_OPTIMIZER_BIAS MAZE_SIMULATED_ANNEALING PRINT UNITS MAZE_LOSS | generic setup colvar maze |
| 19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | GiovanniMaria Piccini | METAD COMBINE LOWER_WALLS UPPER_WALLS PRINT DISTANCE FLUSH UNITS ENERGY | function setup colvar bias generic |
| 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 METAD TORSION COM REWEIGHT_METAD BRIDGE COMBINE LOWER_WALLS RMSD ALPHABETA FUNNEL DISTANCES PRINT DISTANCE MOLINFO UPPER_WALLS WHOLEMOLECULES | function colvar funnel bias generic vatom adjmat core multicolvar |
| 19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Davide Provasi | FUNCPATHMSD METAD COM CONTACTMAP RMSD ENDPLUMED PRINT DISTANCE WHOLEMOLECULES | function colvar bias generic vatom |
| 19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Matteo Salvalaglio | METAD TORSION COMBINE LOWER_WALLS ENDPLUMED MATHEVAL CELL VOLUME PRINT UPPER_WALLS ENERGY | bias function colvar generic |
| 19.004 | MI Ubiquitin | bio | metainference, NMR | Max Bonomi | GROUP CS2BACKBONE RDC PRINT MOLINFO WHOLEMOLECULES METAINFERENCE | core isdb generic |
| 25.025 | Enhanced Sampling of Ligand Binding Coupled to RNA Conformational Dynamics | bio | OPES, OPES Flooding , Metadynamics, RNA, Ligand binding, Free Energy, Kinetics, Funnel | Revanth Elangovan and Dhiman Ray | PRINT GROUP FUNNEL LOWER_WALLS FUNNEL_PS WHOLEMOLECULES TORSION WRAPAROUND MATHEVAL COORDINATION METAD COMMITTOR UPPER_WALLS COM RMSD CUSTOM CENTER OPES_METAD | vatom opes generic funnel bias core function colvar |
| 25.010 | Kinetic rates calculation with Ratchet&Pawl MD | methods | kinetics, ligand binding, ABMD, ratchet&pawl MD | Riccardo Capelli | PRINT GROUP WHOLEMOLECULES ABMD DISTANCE COMMITTOR FLUSH COM | vatom generic bias core colvar |
| 24.028 | All-atom simulations of RNA-membrane interactions | bio | metadynamics, membrane, RNA | Giovanni Bussi | GYRATION COMBINE PRINT GROUP MATHEVAL LOWER_WALLS SORT WHOLEMOLECULES POSITION MOLINFO METAD DISTANCES DISTANCE UPPER_WALLS PUCKERING GHOST CENTER | multicolvar vatom generic bias core function colvar |
| 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 | GYRATION COMBINE PRINT WHOLEMOLECULES TORSION COORDINATION DISTANCE CUSTOM ALPHARMSD MOLINFO OPES_METAD | opes generic secondarystructure function colvar |
| 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 | PRINT GROUP EMMIVOX INCLUDE WHOLEMOLECULES WRAPAROUND BIASVALUE DISTANCE UPPER_WALLS MOLINFO | isdb generic bias core colvar |
| 23.040 | Supramolecular capsules assembly dynamics | chemistry | Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics | Riccardo Capelli | PRINT GROUP WHOLEMOLECULES POSITION METAD DISTANCES DISTANCE FLUSH COM CUSTOM CENTER UNITS | multicolvar vatom generic bias core function setup colvar |
| 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 | PRINT HISTOGRAM REWEIGHT_METAD MATHEVAL CONVERT_TO_FES WHOLEMOLECULES METAD DISTANCE DUMPGRID RMSD READ MOLINFO | gridtools generic bias function colvar |
| 22.041 | Skipping the Replica Exchange Ladder with Normalizing Flows | methods | OPES, alanine, normalizing flows, replica exchange | Michele Invernizzi | ENERGY PRINT TORSION OPES_EXPANDED POSITION ENDPLUMED ECV_MULTITHERMAL UNITS OPES_METAD | setup colvar generic opes |
| 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 | PRINT RMSD | colvar generic |
| 22.021 | Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn Løland Bore | PRINT LOWER_WALLS INCLUDE OPES_EXPANDED UPPER_WALLS ENVIRONMENTSIMILARITY ECV_UMBRELLAS_LINE | generic envsim opes bias |
| 22.018 | Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations | bio | ligand binding, docking, EMMI, LAT1 | Max Bonomi | PRINT GROUP EMMIVOX WHOLEMOLECULES LOAD BIASVALUE MOLINFO | isdb generic core setup 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 | FIXEDATOM PRINT GROUP MATHEVAL LOWER_WALLS WHOLEMOLECULES PYTORCH_MODEL COORDINATION DISTANCE UPPER_WALLS COMMITTOR RMSD CUSTOM CENTER OPES_METAD FIT_TO_TEMPLATE | vatom opes colvar generic pytorch core function bias |
| 22.015 | Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome | bio | photodynamics, bacteriophytochrome, variationally enhanced sampling | Jakub Rydzewski | PRINT VES_LINEAR_EXPANSION TD_UNIFORM TORSION OPT_AVERAGED_SGD BF_FOURIER | colvar generic ves |
| 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 | PRINT ANGLE WHOLEMOLECULES TORSION COORDINATION METAD DISTANCE UPPER_WALLS FLUSH ALPHABETA ALPHARMSD MOLINFO | multicolvar generic bias secondarystructure colvar |
| 22.004 | Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques | chemistry | reaction discovery, OPES, collective variables | Umberto Raucci | PRINT GROUP MATHEVAL LOWER_WALLS LOAD PYTORCH_MODEL OPES_METAD_EXPLORE COORDINATION DISTANCE UPPER_WALLS CUSTOM COM UNITS OPES_METAD | vatom opes colvar generic pytorch core function setup bias |
| 22.000 | Amyloid precursor protein processing by human γ-secretase | bio | Bias Exchange Metadynamics, Helix unfolding, coupled binding | Xiaoli Lu | CONTACTMAP PRINT UNITS RANDOM_EXCHANGES INCLUDE MOLINFO COORDINATION METAD DISTANCE ALPHARMSD CENTER ANTIBETARMSD | vatom generic bias secondarystructure setup colvar |
| 21.050 | N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity | methods | bio | Isabell Louise Grothaus | DISTANCE PRINT CENTER | colvar vatom generic |
| 21.041 | Nucleating a Different Coordination in a Crystal under Pressure. A Study of the B1−B2 Transition in NaCl by Metadynamics | methods | metadynamics, structural phase transitions, pressure-induced phase transition, martensitic transitions | Matej Badin | COMBINE PRINT VOLUME COORDINATION METAD ENDPLUMED CUSTOM | colvar generic bias function |
| 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 | PRINT GROUP WHOLEMOLECULES MOLINFO BIASVALUE EMMI DISTANCE UPPER_WALLS COM RESTART | isdb vatom generic bias core setup colvar |
| 21.026 | Probing allosteric regulations with coevolution-driven molecular simulations | bio | metadynamics, coevolution, allostery, adenylate cyclase | Francesco Colizzi | PRINT WHOLEMOLECULES METAD DISTANCE PATHMSD UPPER_WALLS COM UNITS | vatom generic bias setup colvar |
| 21.023 | Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling | methods | enhanced sampling, collective variables, machine learning | Jakub Rydzewski | ENERGY REWEIGHT_METAD PRINT INCLUDE TORSION BIASVALUE METAD DISTANCE CONSTANT CUSTOM UNITS | generic bias function setup colvar |
| 21.013 | Role of vibrational excitation in heterogeneous catalysis | chemistry | catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption | Kristof Bal | VES_LINEAR_EXPANSION CONVERT_TO_FES LOWER_WALLS TD_GRID LOAD REWEIGHT_BIAS METAD DISTANCES UPPER_WALLS EXTERNAL HISTOGRAM COORDINATION DISTANCE DUMPGRID RESTRAINT COMBINE UWALLS FLUSH UNITS PRINT REWEIGHT_METAD BF_CHEBYSHEV ANGLES OPT_AVERAGED_SGD COORDINATIONNUMBER | multicolvar gridtools colvar generic ves symfunc function setup bias |
| 20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Adriana Pietropaolo | PRINT PBMETAD WHOLEMOLECULES COORDINATION CENTER | colvar generic vatom bias |
| 20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Pratyush Tiwary | COMBINE PRINT WHOLEMOLECULES TORSION MOLINFO METAD DISTANCE UPPER_WALLS RMSD RESTART | generic bias function setup colvar |
| 20.006 | Class B GPCR activation mechanism | bio | metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | ENERGY COMBINE PRINT CENTER MATHEVAL LOWER_WALLS WHOLEMOLECULES METAD DISTANCE UPPER_WALLS RMSD MOLINFO | vatom colvar generic function bias |
| 19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Matteo Salvalaglio | PRINT HISTOGRAM REWEIGHT_METAD MATHEVAL CONVERT_TO_FES TORSION BIASVALUE REWEIGHT_BIAS METAD DISTANCE COMMITTOR DUMPGRID READ EXTERNAL | gridtools generic bias function colvar |
| 19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Gareth Tribello | FOURIER_TRANSFORM FCCUBIC GROUP FIND_CONTOUR_SURFACE MORE_THAN DUMPGRID MULTICOLVARDENS CENTER UNITS | vatom contour symfunc gridtools fourier core function setup |
| 19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Gabriele Cesare Sosso | CONTACT_MATRIX OUTPUT_CLUSTER Q6 CLUSTER_WITHSURFACE DFSCLUSTERING MFILTER_MORE ENDPLUMED COMMITTOR FLUSH LOCAL_Q6 CLUSTER_NATOMS | multicolvar symfunc generic clusters adjmat |
| 19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Matteo Salvalaglio | GYRATION PRINT ENDPLUMED METAD COORDINATIONNUMBER DISTANCES RESTART | multicolvar symfunc generic bias setup colvar |
| 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 | DISTANCE PRINT UPPER_WALLS OPES_METAD_EXPLORE GROUP OPES_EXPANDED GHOST CUSTOM PATHMSD LOWER_WALLS RMSD COORDINATION ENERGY ECV_MULTITHERMAL DISTANCES CENTER | opes colvar multicolvar core generic bias function vatom |
| 25.018 | Metainference simulation for dimerization of RNA binding protein | bio | Metainference, Metadynamics, SAXS, protein dimer | Debadutta Patra | PBMETAD METAINFERENCE DISTANCE UPPER_WALLS PRINT TORSION SAXS FLUSH STATS MOLINFO ENSEMBLE GYRATION WHOLEMOLECULES CENTER | colvar generic bias function isdb vatom |
| 25.009 | Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water | chemistry | metadynamics, nitrate photolysis | Kam-Tung Chan | METAD DISTANCE UPPER_WALLS PRINT GROUP RESTART FLUSH DUMPGRID CUSTOM REWEIGHT_METAD COORDINATION HISTOGRAM READ | gridtools colvar core generic bias function setup |
| 25.000 | Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer | bio | metadynamics, pathCV | Sahithya Sridharan Iyer | METAD RESTART COM DISTANCE GROUP FUNCPATHGENERAL UPPER_WALLS PRINT MOLINFO WHOLEMOLECULES | colvar core generic bias function setup vatom |
| 24.032 | DeepLNE++ | methods | PATHCV, OPES | Thorben Fröhlking | COMBINE DISTANCE PRINT GROUP TORSION CUSTOM LOAD COORDINATION ENERGY OPES_METAD | opes colvar core generic function setup |
| 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 | DRR METAD PRINT UPPER_WALLS FLUSH PYTORCH_MODEL LOWER_WALLS MOLINFO COORDINATION RMSD WHOLEMOLECULES | pytorch colvar generic bias drr |
| 24.007 | SWISH-X | bio | swish-x, SWISH-X, swish, expanded SWISH | Alberto Borsatto | PRINT UPPER_WALLS OPES_EXPANDED CONTACTMAP MOLINFO ECV_MULTITHERMAL ENERGY WHOLEMOLECULES INCLUDE | opes colvar bias generic |
| 24.004 | Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables | materials | metadynamics, nucleation, machine learning | Ziyue Zou | METAD RESTART PRINT GROUP LOAD INCLUDE | setup bias core generic |
| 23.034 | Urea nucleation in water: do long-range forces matter? | materials | LMF theory, Metadynamics, Nucleation | Ziyue Zou | METAD PRINT GROUP INCLUDE COORDINATIONNUMBER LOAD CENTER | core generic bias symfunc setup vatom |
| 23.030 | Data Driven Classification of Ligand Unbinding Pathways | bio | OPES Explore, OPES Flooding, Benzene T4 Lysozyme, Ligand unbinding, Pathway classification, Kinetics, Residence time | Dhiman Ray | ENDPLUMED PRINT MOLINFO OPES_METAD CENTER FIT_TO_TEMPLATE DISTANCE TORSION COMMITTOR WHOLEMOLECULES UPPER_WALLS OPES_METAD_EXPLORE GROUP FLUSH POSITION MATHEVAL WRAPAROUND CUSTOM COORDINATION COM UNITS LOWER_WALLS ENERGY BIASVALUE | opes colvar core generic bias function setup vatom |
| 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 | DISTANCE PRINT UPPER_WALLS GROUP CENTER SAXS WRAPAROUND STATS ENSEMBLE MOLINFO RMSD BIASVALUE | colvar core generic bias function isdb vatom |
| 23.027 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, DFS, Q3, Pair Entropy | Aaron Finney | FIXEDATOM CLUSTER_DISTRIBUTION Q3 LOCAL_AVERAGE PRINT CONTACT_MATRIX GROUP CLUSTER_NATOMS DUMPGRID COORDINATIONNUMBER RESTRAINT UNITS DENSITY LOAD AROUND HISTOGRAM LOCAL_Q3 DFSCLUSTERING | gridtools core generic bias symfunc adjmat clusters setup volumes vatom |
| 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 | FIXEDATOM DISTANCE PRINT OPES_METAD_EXPLORE UPPER_WALLS GROUP TORSION PATH CUSTOM PYTORCH_MODEL UNITS LOWER_WALLS COORDINATION FIT_TO_TEMPLATE OPES_METAD WHOLEMOLECULES CENTER | mapping opes pytorch colvar core generic bias function setup vatom |
| 23.001 | Quantum phase diagram of water | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn-Løland Bore | RESTART UPPER_WALLS PRINT OPES_EXPANDED ENVIRONMENTSIMILARITY LOWER_WALLS ECV_UMBRELLAS_LINE INCLUDE | opes envsim generic bias setup |
| 22.044 | Colloid Crystallisation Analyses | materials | Q4, Q6, Pair Entropy, DFS | Aaron Finney | COMBINE LOCAL_AVERAGE MFILTER_MORE PRINT GROUP Q4 CLUSTER_NATOMS LOCAL_Q4 COORDINATIONNUMBER DFSCLUSTERING LOCAL_Q6 MFILTER_LESS CONTACT_MATRIX Q6 | multicolvar core generic function symfunc adjmat clusters |
| 22.039 | Driving and characterizing nucleation of urea and glycine polymorphs in water | bio | metadynamics, nucleation, amino acids, polymorphism | Eric Beyerle | COMBINE METAD PRINT GROUP Q4 PAIRENTROPY MATHEVAL INCLUDE COORDINATIONNUMBER LOAD CENTER Q6 | gridtools core generic bias symfunc function setup vatom |
| 22.037 | Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site | chemistry | metadynamics, DNA, abasic | Mike Jones | METAD DISTANCE DISTANCES PRINT | colvar bias multicolvar generic |
| 22.036 | Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction | bio | Well-tempered MetaDynamics with Hamiltonian Replica Exchange | Miroslav Krepl | GHBFIX COMBINE METAD PRINT UPPER_WALLS GROUP FLUSH CUSTOM LOAD MOLINFO COORDINATION BIASVALUE | colvar core generic bias function setup |
| 22.024 | Conformational Entropy as a Potential Liability of Computationally Designed Antibodies | bio | metadynamics, conformational entropy, antibody, nanobody | Thomas Löhr | PBMETAD RESTART PRINT COM ALPHARMSD TORSION ANTIBETARMSD MOLINFO WHOLEMOLECULES ALPHABETA | colvar multicolvar generic bias secondarystructure setup vatom |
| 22.016 | Homogeneous ice nucleation in an ab initio machine learning model of water | chemistry | ice, water, nucleation, seeding, environment similarity, interfacial free energy, interfaces | Pablo Piaggi | VOLUME RESTART PRINT UPPER_WALLS CUSTOM ENVIRONMENTSIMILARITY DUMPGRID ENERGY AROUND OPES_METAD HISTOGRAM | opes gridtools colvar generic envsim bias function setup volumes |
| 21.051 | Automatic learning of hydrogen-bond fixes in an AMBER RNA force field | methods | force field, RNA | Giovanni Bussi | COMBINE METAD PRINT MOLINFO COORDINATION ERMSD WHOLEMOLECULES BIASVALUE | colvar bias function generic |
| 21.044 | NaCl nucleation | chemistry | metadynamics, DFS clustering | Aaron Finney | FIXEDATOM CLUSTER_DISTRIBUTION COMBINE METAD PRINT MFILTER_MORE GROUP CONTACT_MATRIX CLUSTER_NATOMS COORDINATIONNUMBER DUMPGRID DFSCLUSTERING LOCAL_Q6 HISTOGRAM INSPHERE Q6 | gridtools multicolvar core generic bias function symfunc adjmat clusters volumes vatom |
| 21.042 | Peptoid-mediated Au nanocrystal growth | materials | parallel-bias metadynamics, peptoid, Au | Xin Qi | PBMETAD COM UPPER_WALLS DISTANCE PRINT MOLINFO GYRATION | colvar bias vatom generic |
| 21.028 | From Enhanced Sampling to Reaction Profiles | methods | collective variables, multi-state, machine learning, Deep-TDA | Enrico Trizio | FIXEDATOM ENDPLUMED PRINT OPES_METAD FIT_TO_TEMPLATE CENTER DISTANCE TORSION DISTANCES WHOLEMOLECULES UPPER_WALLS GROUP MATHEVAL PYTORCH_MODEL COORDINATION UNITS LOWER_WALLS LOAD ANGLE | opes pytorch colvar multicolvar core generic bias function setup vatom |
| 21.027 | EGFR activating mutations mechanism | bio | metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA | Francesco Gervasio | METAD DISTANCE UPPER_WALLS PRINT ALPHARMSD MATHEVAL CONTACTMAP MOLINFO LOWER_WALLS ENERGY WHOLEMOLECULES INCLUDE | colvar generic bias function secondarystructure |
| 21.011 | CmuMD simulations of NaCl(aq) at graphite | chemistry | CmuMD, DFS clustering | Aaron Finney | FIXEDATOM CLUSTER_DISTRIBUTION PRINT CONTACT_MATRIX GROUP CLUSTER_NATOMS MFILTER_MORE MULTICOLVARDENS COORDINATIONNUMBER DUMPGRID RESTRAINT LOAD DENSITY AROUND DFSCLUSTERING | gridtools multicolvar core generic bias symfunc adjmat clusters setup volumes vatom |
| 21.004 | Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy | bio | machine learning, well-tempered metadynamics, path collective variable, potential of mean force, standard binding free energy calculations, host-guest, protein-ligand unbinding | Dorothea Gobbo | METAD RESTART UPPER_WALLS PRINT PATHMSD LOWER_WALLS WHOLEMOLECULES | setup colvar bias generic |
| 20.030 | Converging experimental and computational views of the knotting mechanism of the smallest knotted protein | bio | phi-values, transition state, knotted proteins | Cristina Paissoni | COMBINE PRINT STATS RESTRAINT MOLINFO COORDINATION WHOLEMOLECULES | colvar bias function generic |
| 20.028 | Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane | bio | metadynamics, KRas-4B, anionic membrane | Huixia Lu | METAD RESTART DISTANCE PRINT FIT_TO_TEMPLATE CENTER | colvar generic bias setup vatom |
| 20.027 | Allosteric Regulation of SARS-CoV-2 Protease. Towards Informed Structure-Based Drug Discovery | bio | SARS-CoV2, MPro, Covid-19, Molecular Dynamics, Metadynamics, Computer-Aided Drug Discovery | Khaled Abdel-Maksoud | TORSION METAD DISTANCE PRINT | bias colvar generic |
| 20.008 | Simulating solvation and acidity in complex mixtures with first-principles accuracy. The case of CH3SO3H and H2O2 in phenol | chemistry | proton trasfer, metadynamics | Kevin Rossi | METAD PRINT CUSTOM UNITS DISTANCES COORDINATION | multicolvar colvar generic bias function setup |
| 19.075 | PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python | other | Python, automatic differentiation | Toni Giorgino | ENDPLUMED COMBINE DISTANCE PRINT GROUP TORSION CUSTOM RESTRAINT ANGLE CENTER DUMPDERIVATIVES | colvar core generic bias function vatom |
| 19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Jim Pfaendtner | METAD PRINT GYRATION ENERGY WHOLEMOLECULES | colvar bias generic |
| 19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Cristina Paissoni | ENDPLUMED PBMETAD COMBINE PRINT GROUP BIASVALUE SAXS MATHEVAL INCLUDE STATS MOLINFO ENSEMBLE COORDINATION ALPHABETA ANGLE WHOLEMOLECULES CENTER | colvar multicolvar core generic bias function isdb vatom |
| 19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Silvio Pipolo | METAD PRINT UPPER_WALLS FUNCPATHMSD PIV LOWER_WALLS CELL | colvar generic piv bias function |
| 19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Max Bonomi | PRINT GROUP MOLINFO EMMI BIASVALUE | bias isdb core generic |
| 19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Michele Invernizzi | ENDPLUMED METAD RESTART PRINT TORSION POSITION VES_DELTA_F UNITS LOAD ENERGY | colvar generic bias ves setup |
| 25.024 | Sampling glycan-glycan interactions for B22 calculations | bio | B22, glycan, carbohydrates, distance, REST2, metadynamics, RECT, replica exchange | Isabell Louise Grothaus | DISTANCE RESTRAINT COMBINE PRINT METAD COM POSITION | function bias vatom colvar generic |
| 25.022 | Imidazole Diffusion in SALEM-2 MOF | materials | OPES, Diffusion, Ring opening, MOFs, Machine Learning Potentials | Sudheesh Kumar Ethirajan | MOLINFO CENTER PROJECTION_ON_AXIS ENDPLUMED DISTANCE UNITS WHOLEMOLECULES DISTANCES OPES_METAD PRINT GROUP | setup core vatom colvar generic multicolvar opes |
| 25.011 | Chiral perovskite nucleation | chemistry | metadynamics, chiral perovskites, nucleation | Adriana Pietropaolo | LOWER_WALLS RESTART PBMETAD DISTANCE UNITS PRINT MULTI_RMSD UPPER_WALLS MATHEVAL | function bias setup colvar generic |
| 25.007 | Shaping the glycan landscape. Hidden relationships between linkage and ring distortion induced by carbohydrate-active enzmyes | bio | REST-RECT, REST2, glycan, enzyme, CAZyme, steered | Isabell Grothaus | MOLINFO RESTART DISTANCE RESTRAINT PUCKERING PRINT METAD MOVINGRESTRAINT TORSION | colvar generic bias setup |
| 25.003 | Surrogate Model CV | methods | Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding | Sompriya Chatterjee | MOLINFO ENDPLUMED DISTANCE OPES_METAD PYTORCH_MODEL COMBINE PRINT WHOLEMOLECULES ENERGY COMMITTOR GROUP CUSTOM TORSION MATHEVAL | function core pytorch colvar generic opes |
| 24.031 | DeepLNE | methods | PATHCV, OPES, OneOPES | Thorben Fröhlking | MOLINFO RESTART OPES_EXPANDED PYTORCH_MODEL COMBINE OPES_METAD_EXPLORE COORDINATION PRINT ENERGY VOLUME ECV_MULTITHERMAL ERMSD | function setup pytorch colvar generic opes |
| 24.027 | Proline cis and trans subensembles of a disordered peptide | bio | intrinsically disordered proteins, proline cis trans isomerisation, metadynamics, collective variables | Alice Pettitt | MOLINFO INCLUDE PBMETAD ANTIBETARMSD DISTANCE ENDPLUMED WHOLEMOLECULES FLUSH COMBINE DIHCOR COORDINATION PRINT ALPHARMSD PARABETARMSD GYRATION GROUP TORSION | function bias core secondarystructure colvar generic multicolvar |
| 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 | LOAD PRINT METAD COMMITTOR GROUP TORSION | bias setup core colvar generic |
| 24.011 | Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble | methods | committor, machine learning | Peilin Kang | WHOLEMOLECULES RMSD UPPER_WALLS MOLINFO INCLUDE LOAD PRINT TORSION MATHEVAL ENDPLUMED UNITS BIASVALUE ENERGY GROUP CELL CUSTOM POSITION LOWER_WALLS DISTANCE COORDINATION | function bias setup core colvar 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 | INCLUDE SELECT_COMPONENTS SUM FLUSH PRINT METAD TRANSPOSE MATHEVAL | function matrixtools bias valtools generic |
| 23.039 | Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation | chemistry | metadynamics, ligand dissociation | Eric Beyerle | MOLINFO CENTER DISTANCE RESTRAINT COMBINE DUMPMASSCHARGE PRINT METAD UPPER_WALLS FIXEDATOM | function bias vatom colvar generic |
| 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 | MOLINFO DISTANCE WHOLEMOLECULES PRINT METAD RMSD MATHEVAL | colvar generic bias function |
| 22.038 | Enhanced Sampling Aided Design of Molecular Photoswitches | chemistry | reaction discovery, OPES explore, graph CV | Umberto Raucci | UNITS PYTORCH_MODEL OPES_METAD_EXPLORE COORDINATION PRINT CUSTOM | function setup pytorch colvar generic opes |
| 22.035 | Deciphering the alphabet of disorder — Glu and Asp act differently on local but not global properties | bio | intrinsically disordered proteins, parallel bias metadynamics, protein | Kresten Lindorff-Larsen | MOLINFO PBMETAD WHOLEMOLECULES GYRATION TORSION | colvar generic bias |
| 22.032 | Reciprocal barrier restraint. Application to path-meta-eABF | methods | restraint, upper wall, lower wall, path colvar, meta-eABF, metadynamics, DRR, protein conformational transition, PROTAC | Istvan Kolossvary | DRR FLUSH PRINT METAD BIASVALUE PATHMSD CUSTOM | function bias drr colvar generic |
| 22.026 | Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification | materials | Peptoid, silica | Jim Pfaendtner | MOLINFO PBMETAD DISTANCE PRINT UPPER_WALLS GYRATION COM | colvar generic bias vatom |
| 22.022 | Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir | bio | RMSD, protein-ligand interactions | Isabell Grothaus | RMSD PRINT | colvar generic |
| 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 | LOWER_WALLS DISTANCE UNITS COMBINE FLUSH COORDINATION METAD UPPER_WALLS GYRATION COM COORDINATIONNUMBER | function bias setup vatom symfunc colvar generic |
| 22.002 | GAMBES_SAMPL5_RATES | other | GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding | Jayashrita Debnath | ANGLE CENTER FIT_TO_TEMPLATE ENDPLUMED DISTANCE WHOLEMOLECULES PYTORCH_MODEL FLUSH LOAD COORDINATION PRINT ENERGY UPPER_WALLS FIXEDATOM COMMITTOR GROUP MATHEVAL | function generic bias setup core vatom colvar pytorch |
| 22.001 | Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials | methods | enhanced sampling, variationally enhanced sampling, ves, metadynamics, bias representation, wavelets, adam | Benjamin Pampel | VES_OUTPUT_BASISFUNCTIONS OPT_ADAM BF_WAVELETS UPPER_WALLS INCLUDE TD_WELLTEMPERED PRINT BF_LEGENDRE BF_GAUSSIANS UNITS FLUSH TD_UNIFORM ENERGY POSITION VES_LINEAR_EXPANSION DISTANCE BF_CUBIC_B_SPLINES COORDINATION OPT_AVERAGED_SGD METAD BF_CHEBYSHEV | ves bias setup colvar generic |
| 21.052 | On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets | materials | Ibuprofen, unbinding, WTmetaD | Matteo Salvalaglio | CENTER ENDPLUMED DISTANCE PRINT METAD COMMITTOR TORSION COORDINATIONNUMBER | bias vatom symfunc colvar generic |
| 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 | RANDOM_EXCHANGES INCLUDE PBMETAD ENDPLUMED PRINT METAD TORSION | colvar generic bias |
| 21.022 | Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly | materials | parallel bias metadynamics, adsorption, peptide | Xin Qi | MOLINFO LOWER_WALLS PBMETAD DISTANCE PRINT ENERGY UPPER_WALLS GYRATION COM | colvar generic bias vatom |
| 21.012 | NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition | bio | funnel metadynamics | Jim Pfaendtner | FUNNEL FUNNEL_PS LOWER_WALLS DISTANCE PRINT METAD UPPER_WALLS COM | bias colvar vatom funnel generic |
| 21.010 | Step by Step Strecker Amino Acid Synthesis from Ab Initio Prebiotic Chemistry | chemistry | Strecker reaction, free energy landscape, ab initio molecular dynamics, glycine, prebiotic synthesis | Théo Magrino | generic | |
| 21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Kristof Bal | HISTOGRAM CONVERT_TO_FES UNITS FLUSH REWEIGHT_METAD PRINT LOAD DUMPGRID METAD MOVINGRESTRAINT UPPER_WALLS COMMITTOR COORDINATIONNUMBER | bias setup gridtools symfunc generic |
| 21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Tarsis Ferreira | RANDOM_EXCHANGES MOLINFO INCLUDE LOWER_WALLS HISTOGRAM DISTANCE WHOLEMOLECULES PUCKERING REWEIGHT_METAD PRINT COORDINATION DUMPGRID METAD ENERGY UPPER_WALLS GROUP | bias core gridtools colvar generic |
| 20.034 | Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations | bio | RNA, SARS-CoV-2, partial tempering | Sandro Bottaro | MOLINFO CENTER RESTART DISTANCE PRINT ABMD ERMSD TORSION | bias setup vatom colvar generic |
| 20.024 | Gaussian Mixture Based Enhanced Sampling (GAMBES) | methods | enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias | Jayashrita Debnath | LOWER_WALLS DISTANCE UNITS DISTANCES COMBINE LOAD PRINT ENERGY UPPER_WALLS GROUP TORSION | function bias setup core colvar generic multicolvar |
| 20.018 | Free energy barriers from biased molecular dynamics simulations | methods | kinetics, free energy barriers, chemical reactions, nucleation, metadynamics | Kristof Bal | CONVERT_TO_FES UPPER_WALLS REWEIGHT_BIAS PAIRENTROPY LOAD PRINT HISTOGRAM SPRINT UNITS FLUSH DENSITY REWEIGHT_METAD Q6 ENERGY VOLUME CONTACT_MATRIX CENTER LOWER_WALLS DISTANCE COMBINE DUMPGRID COORDINATION METAD LOCAL_AVERAGE COORDINATIONNUMBER | function bias sprint adjmat setup gridtools volumes vatom symfunc colvar 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 MOLINFO WHOLEMOLECULES LOAD PRINT BIASVALUE EMMIVOX GROUP | bias setup core generic isdb |
| 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 | WHOLEMOLECULES DIHCOR ENSEMBLE MOLINFO INCLUDE PBMETAD ANTIBETARMSD PRINT TORSION ENDPLUMED FLUSH METAINFERENCE PARABETARMSD GYRATION GROUP CS2BACKBONE COMBINE STATS COORDINATION ALPHARMSD | function bias core secondarystructure isdb colvar generic multicolvar |
| 19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Luigi Bonati | ENDPLUMED UNITS LOAD PRINT Q6 ENERGY ENVIRONMENTSIMILARITY POSITION TORSION | setup envsim symfunc colvar generic |
| 19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Gareth Tribello | LOWER_WALLS ENDPLUMED UNITS PRINT FCCUBIC METAD UPPER_WALLS CELL AROUND | bias setup volumes symfunc colvar generic |
| 19.049 | Determining the sizes of solid/liquid clusters in MD trajectories of nucleation | methods | nucleation, metadynamics, clustering, Steinhardt order parameters | Gareth Tribello | CLUSTER_PROPERTIES OUTER_PRODUCT MORE_THAN DISTANCES CLUSTER_NATOMS PRINT Q6 METAD LOCAL_Q6 ONES MATRIX_VECTOR_PRODUCT COORDINATIONNUMBER CLUSTER_DISTRIBUTION SMAC DFSCLUSTERING OUTPUT_CLUSTER CUSTOM CONTACT_MATRIX | function matrixtools clusters bias adjmat symfunc generic multicolvar |
| 19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Vittorio Limongelli | FUNNEL FUNNEL_PS LOWER_WALLS DISTANCE WHOLEMOLECULES PRINT METAD RMSD UPPER_WALLS COM | bias colvar vatom funnel generic |
| 19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Mattia Bernetti | MOLINFO ENDPLUMED WHOLEMOLECULES PRINT METAD ENERGY ALPHARMSD GYRATION | secondarystructure colvar generic bias |
| 19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Adriana Pietropaolo | WHOLEMOLECULES PRINT METAD BIASVALUE CONSTANT TORSION MATHEVAL | colvar generic bias function |