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 |
|---|---|---|---|---|---|---|
| 25.025 | 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 | WHOLEMOLECULES PRINT FUNNEL LOWER_WALLS METAD CUSTOM MATHEVAL COM OPES_METAD RMSD TORSION CENTER FUNNEL_PS COORDINATION COMMITTOR WRAPAROUND UPPER_WALLS GROUP | colvar opes bias funnel function vatom core generic |
| 25.015 | Assessment of Force Fields for Describing Conformational Polymorphic Crystals of ROY | materials | Molecular crystal, Force Field, Collective Variable | Pradip Si and Omar Valsson | PRINT DISTANCES DUMPMULTICOLVAR TORSIONS SMAC | symfunc multicolvar generic |
| 25.003 | Surrogate Model CV | methods | Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding | Sompriya Chatterjee | PRINT WHOLEMOLECULES MOLINFO ENERGY CUSTOM COMBINE OPES_METAD MATHEVAL TORSION DISTANCE COMMITTOR PYTORCH_MODEL ENDPLUMED GROUP | colvar pytorch opes function core generic |
| 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 | WHOLEMOLECULES PRINT MOLINFO DISTANCE CENTER COMMITTOR FIT_TO_TEMPLATE METAD ANGLE UPPER_WALLS MATHEVAL TORSION CONTACTMAP COORDINATION CUSTOM COMBINE OPES_METAD RMSD FIXEDATOM ENDPLUMED GROUP | colvar opes bias function vatom core generic |
| 24.017 | Absolute Binding Free Energies with OneOPES | methods | protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy | Francesco Gervasio | WHOLEMOLECULES PRINT MOLINFO OPES_METAD_EXPLORE ECV_MULTITHERMAL RESTART METAD PROJECTION_ON_AXIS UPPER_WALLS WRAPAROUND BIASVALUE LOWER_WALLS MATHEVAL COM CONSTANT INCLUDE CONTACTMAP TORSION COORDINATION CUSTOM RMSD OPES_EXPANDED ENERGY GROUP | colvar opes bias function vatom setup core generic |
| 24.013 | Estimating Free Energy Surfaces and their Convergence from multiple, independent static and history-dependent biased molecular-dynamics simulations with Mean Force Integration | methods | Mean Force Integration, Convergence, FES, Umbrella Sampling | Matteo Salvalaglio | PRINT RESTRAINT MOLINFO METAD MATHEVAL FLUSH TORSION DISTANCE COORDINATIONNUMBER COMMITTOR RESTART ENERGY BIASVALUE | colvar bias function symfunc setup generic |
| 24.004 | Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables | materials | metadynamics, nucleation, machine learning | Ziyue Zou | PRINT METAD INCLUDE RESTART GROUP LOAD | setup core generic bias |
| 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 | WHOLEMOLECULES PRINT MOLINFO INCLUDE DISTANCE EMMIVOX WRAPAROUND UPPER_WALLS GROUP BIASVALUE | colvar bias isdb core generic |
| 23.025 | Probing ion binding to G-quadruplexes and related events | chemistry | metadynamics, repulsive potential, nucleic acids, G-quadruplexes | Marcelo Poleto | WHOLEMOLECULES PRINT LOWER_WALLS FIT_TO_TEMPLATE METAD MATHEVAL COM UNITS DISTANCES POSITION FLUSH GROUP DISTANCE DUMPATOMS RESTART UPPER_WALLS WRAPAROUND | colvar bias multicolvar function vatom setup core generic |
| 23.021 | Into the Dynamics of Rotaxanes at Atomistic Resolution | materials | metadynamics, rotaxanes, molecular shuttles, molecular machines | Luigi Leanza | PRINT METAD CUSTOM MATHEVAL FIXEDATOM TORSION DISTANCE CENTER UPPER_WALLS | colvar bias function vatom generic |
| 23.020 | FEP simulations of ATOX1 homodimer | chemistry | parallel bias metadynamics, FEP, free-energy of metal ion dissociation | Adriana Pietropaolo | WHOLEMOLECULES PRINT MATHEVAL CONSTANT DISTANCE ANGLE BIASVALUE PBMETAD | function colvar generic bias |
| 23.012 | JAK2 2D meta-eABF PMF with statistical analysis | bio | 2D meta-eABF, path CV, PMF | Istvan Kolossvary | PATHMSD DRR PRINT LOWER_WALLS METAD CUSTOM FLUSH UPPER_WALLS BIASVALUE | drr colvar bias function generic |
| 23.002 | Critical comparison of general-purpose collective variables for crystal nucleation | methods | metadynamics, umbrella sampling, commitor, entropy, PIV | Julien Lam | PRINT RESTRAINT PAIRENTROPY ENERGY METAD CUSTOM FUNCPATHMSD Q6 UNITS Q4 PIV VOLUME LOCAL_AVERAGE UPPER_WALLS | colvar bias piv function generic symfunc setup gridtools |
| 22.005 | Collective Variable for Metadynamics Derived from AlphaFold Output | bio | AlphaFold, protein folding, protein structure prediction, metadynamics, deep learning, free energy simulation, collective variable | Vojtech Spiwok | WHOLEMOLECULES METAD PRINT LOAD | setup generic bias |
| 22.002 | GAMBES_SAMPL5_RATES | other | GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding | Jayashrita Debnath | WHOLEMOLECULES PRINT FIT_TO_TEMPLATE MATHEVAL ENDPLUMED UPPER_WALLS FIXEDATOM FLUSH CENTER GROUP COMMITTOR DISTANCE COORDINATION PYTORCH_MODEL ENERGY ANGLE LOAD | colvar pytorch bias function vatom setup core 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 | PRINT METAD CUSTOM COMBINE VOLUME COORDINATION ENDPLUMED | function colvar generic bias |
| 21.040 | A structural ensemble of a tau-microtubule complex reveals regulatory tau phosphorylation and acetylation mechanisms | bio | EMMI, CryoEM, tau-microtubules, post-translational modifications, chemical mutagenesis, structural ensemble, Metainference | Faidon Brotzakis | WHOLEMOLECULES PRINT MOLINFO COM EMMI DISTANCE RESTART UPPER_WALLS GROUP BIASVALUE | colvar bias vatom isdb setup core generic |
| 21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Adriana Pietropaolo | WHOLEMOLECULES PRINT MATHEVAL CONSTANT TORSION RESTART BIASVALUE PBMETAD | colvar bias function setup generic |
| 21.006 | OPES, On-the-fly Probability Enhanced Sampling Method | methods | opes, alanine dipeptide, well-tempered, multithermal, multiumbrella | Michele Invernizzi | PRINT ENERGY ECV_MULTITHERMAL OPES_METAD OPES_EXPANDED TORSION ECV_UMBRELLAS_LINE ENDPLUMED | colvar opes generic |
| 21.000 | Uremic toxin time scale dynamics | bio | uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs) | Jim Pfaendtner | WHOLEMOLECULES PRINT COM DISTANCE GROUP | vatom colvar core generic |
| 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 | PRINT DISTANCE METAD TORSION | colvar generic bias |
| 20.024 | Gaussian Mixture Based Enhanced Sampling (GAMBES) | methods | enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias | Jayashrita Debnath | PRINT LOWER_WALLS ENERGY COMBINE UNITS DISTANCES TORSION DISTANCE UPPER_WALLS GROUP LOAD | colvar bias multicolvar function setup core generic |
| 20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Glen Hocky | PRINT RESTRAINT GYRATION ENERGY MATHEVAL UNITS DISTANCE FISST GROUP BIASVALUE | fisst colvar bias function setup core generic |
| 20.010 | Phase equilibrium of liquid water and hexagonal ice from enhanced sampling molecular dynamics simulations | materials | water, ice, TIP4P, crystallization, EnvironmentSimilarity, RefCV, kernel, VES, variationally enhanced sampling | Pablo Piaggi | PRINT ENVIRONMENTSIMILARITY OPT_AVERAGED_SGD MATHEVAL Q6 TD_WELLTEMPERED VES_LINEAR_EXPANSION BF_LEGENDRE VOLUME RESTART UPPER_WALLS OPT_DUMMY | colvar ves bias function symfunc setup envsim generic |
| 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 | PRINT GYRATION ENERGY LOWER_WALLS METAD DISTANCES UPPER_WALLS COORDINATIONNUMBER ENDPLUMED | colvar bias multicolvar symfunc generic |
| 19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Michele Invernizzi | PRINT METAD OPES_METAD UNITS POSITION EXTERNAL TORSION ENDPLUMED | colvar opes bias setup generic |
| 19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Luigi Bonati | PRINT ENVIRONMENTSIMILARITY Q6 ENDPLUMED UNITS POSITION TORSION ENERGY LOAD | colvar symfunc setup envsim generic |
| 19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Gareth Tribello | PRINT CELL METAD UNITS UPPER_WALLS FCCUBIC ENDPLUMED | colvar bias symfunc setup 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 | WHOLEMOLECULES REWEIGHT_METAD MOLINFO FUNNEL LOWER_WALLS METAD PRINT COMBINE COM DISTANCES RMSD TORSION DISTANCE BRIDGE ALPHABETA UPPER_WALLS GROUP | colvar adjmat bias funnel multicolvar function vatom core generic |
| 19.045 | Adsorption free energy of Ca/CO3 ions on calcite steps in contact with water | materials | metadynamics, well-tempered, multiple walkers, LAMMPS | Marco De La Pierre | PRINT LOWER_WALLS METAD UNITS POSITION FLUSH COORDINATION RESTART UPPER_WALLS GROUP | colvar bias setup core generic |
| 19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Carlo Camilloni | WHOLEMOLECULES PRINT MOLINFO RESTRAINT ENSEMBLE METAINFERENCE RDC PBMETAD UPPER_WALLS TORSION DISTANCE DHENERGY CENTER ALPHABETA DIHCOR ENDPLUMED GROUP STATS | colvar bias multicolvar function vatom isdb core generic |
| 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 | FLUSH UNITS COORDINATION GROUP DISTANCES COMBINE ANGLE DISTANCE METAD PRINT RESTRAINT COM FIXEDATOM COORDINATIONNUMBER UPPER_WALLS LOWER_WALLS | symfunc colvar setup function generic vatom core bias multicolvar |
| 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 | ENERGY OPES_EXPANDED CENTER DISTANCE GHOST ECV_MULTITHERMAL CUSTOM GROUP COMBINE MOLINFO PRINT COORDINATION RMSD OPES_METAD_EXPLORE | colvar generic opes core function vatom |
| 25.010 | Kinetic rates calculation with Ratchet&Pawl MD | methods | kinetics, ligand binding, ABMD, ratchet&pawl MD | Riccardo Capelli | COMMITTOR ABMD DISTANCE FLUSH COM GROUP WHOLEMOLECULES PRINT | colvar generic bias core vatom |
| 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 | GYRATION ENERGY CENTER DISTANCE INCLUDE PBMETAD VOLUME UPDATE_IF WHOLEMOLECULES READ MOLINFO PRINT DUMPATOMS TORSION RESTART | colvar generic bias setup vatom |
| 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 DISTANCE OPES_METAD COORDINATION PRINT UPPER_WALLS | opes colvar generic bias |
| 24.009 | Weighted Shape Gaussian Mixture Models | bio | metadynamics, clustering | Glen Hocky | UNITS GROUP PRINT TORSION METAD | colvar generic bias setup core |
| 23.046 | Lasso Peptides - HLDA CV | bio | metadynamics, protein folding, HLDA, harmonic | Gabriel da Hora | DISTANCE UNITS COMBINE WHOLEMOLECULES PRINT METAD | colvar generic bias setup function |
| 23.031 | Identifying small molecules binding sites in RNA conformational ensembles with SHAMAN | bio | RNA, metadynamics, probes, mixed-solvent MD, small molecules, binding sites | Max Bonomi | CENTER GROUP DISTANCES WHOLEMOLECULES WRAPAROUND SHADOW FIT_TO_TEMPLATE POSITION MOLINFO PRINT UPPER_WALLS METAD | colvar generic isdb bias core vatom multicolvar |
| 23.026 | Machine Learning Nucleation Collective Variables with Graph Neural Networks | chemistry | Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks | Florian Dietrich | LOCAL_Q6 LOWER_WALLS MFILTER_MORE GROUP COMBINE COORDINATIONNUMBER Q6 MOVINGRESTRAINT PRINT METAD | generic bias symfunc core function multicolvar |
| 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 | DUMPGRID DISTANCE MATHEVAL REWEIGHT_METAD HISTOGRAM WHOLEMOLECULES READ MOLINFO PRINT CONVERT_TO_FES RMSD METAD | colvar generic bias function gridtools |
| 23.001 | Quantum phase diagram of water | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn-Løland Bore | OPES_EXPANDED INCLUDE LOWER_WALLS ECV_UMBRELLAS_LINE ENVIRONMENTSIMILARITY PRINT UPPER_WALLS RESTART | generic bias setup opes envsim |
| 22.033 | Reciprocal barrier restraint. Application to PROTAC passive permeability prediction | methods | PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR | Istvan Kolossvary | BIASVALUE DISTANCE FLUSH UNITS CUSTOM COM PRINT DRR METAD | colvar generic bias setup drr function vatom |
| 22.026 | Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification | materials | Peptoid, silica | Jim Pfaendtner | GYRATION DISTANCE PBMETAD COM MOLINFO PRINT UPPER_WALLS | colvar vatom generic bias |
| 22.007 | Characterization of a natural variant of human NDP52 and its functional consequences on mitophagy | bio | metadynamics, well-tempered, protein-protein interactions, disordered proteins, mutations autophagy | Elena Papaleo | ALPHARMSD ANGLE DISTANCE FLUSH ALPHABETA WHOLEMOLECULES MOLINFO PRINT COORDINATION UPPER_WALLS TORSION METAD | colvar generic bias secondarystructure multicolvar |
| 21.049 | Multiple-path-metadynamics and PathMaps | methods | path-CV, metadynamics, multiple-walker, multiple paths, pathmap | Alberto Pérez-de-Alba-Ortíz | CONSTANT LOWER_WALLS LOAD UNITS ENSEMBLE COMBINE CUSTOM RESTRAINT MOVINGRESTRAINT PRINT UPPER_WALLS TORSION METAD | colvar generic bias setup function |
| 21.042 | Peptoid-mediated Au nanocrystal growth | materials | parallel-bias metadynamics, peptoid, Au | Xin Qi | GYRATION DISTANCE PBMETAD COM MOLINFO PRINT UPPER_WALLS | colvar vatom generic 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 | ENERGY GYRATION METAD ALPHARMSD LOWER_WALLS DIHCOR PARABETARMSD GROUP WHOLEMOLECULES MOLINFO PRINT RANDOM_EXCHANGES UPPER_WALLS ANTIBETARMSD COORDINATION | colvar generic bias secondarystructure core multicolvar |
| 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 | GYRATION ENERGY DISTANCE INCLUDE PBMETAD COM ALPHABETA COORDINATION PRINT TORSION METAD | colvar generic bias vatom multicolvar |
| 21.027 | EGFR activating mutations mechanism | bio | metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA | Francesco Gervasio | ENERGY ALPHARMSD DISTANCE MATHEVAL LOWER_WALLS INCLUDE WHOLEMOLECULES MOLINFO CONTACTMAP PRINT UPPER_WALLS METAD | colvar generic bias secondarystructure function |
| 21.023 | Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling | methods | enhanced sampling, collective variables, machine learning | Jakub Rydzewski | BIASVALUE ENERGY CONSTANT DISTANCE INCLUDE REWEIGHT_METAD UNITS CUSTOM PRINT TORSION METAD | colvar generic bias setup function |
| 20.032 | Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil | materials | clustering, conformational isomers | Matteo Salvalaglio | ENDPLUMED PRINT TORSION | colvar 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 | STATS COMBINE WHOLEMOLECULES RESTRAINT MOLINFO PRINT COORDINATION | function colvar generic bias |
| 20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Matteo Salvalaglio | ENERGY CELL VOLUME MATHEVAL LOWER_WALLS PRINT UPPER_WALLS METAD | function colvar generic bias |
| 20.018 | Free energy barriers from biased molecular dynamics simulations | methods | kinetics, free energy barriers, chemical reactions, nucleation, metadynamics | Kristof Bal | DUMPGRID ENERGY LOCAL_AVERAGE FLUSH SPRINT PRINT CENTER REWEIGHT_METAD Q6 CONVERT_TO_FES UPPER_WALLS DISTANCE VOLUME UNITS HISTOGRAM COORDINATIONNUMBER CONTACT_MATRIX REWEIGHT_BIAS COORDINATION DENSITY LOWER_WALLS LOAD COMBINE PAIRENTROPY METAD | colvar generic bias setup sprint symfunc volumes function gridtools vatom adjmat |
| 20.016 | Predicting polymorphism in molecular crystals using orientational entropy | materials | metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy | Pablo Piaggi | VOLUME CENTER INCLUDE LOAD GROUP PRINT UPPER_WALLS METAD | colvar generic bias setup core vatom |
| 20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Carlo Camilloni | GYRATION SAXS METAINFERENCE CENTER DISTANCE STATS PBMETAD ENSEMBLE ALPHABETA FLUSH WHOLEMOLECULES MOLINFO PRINT TORSION | colvar generic bias isdb function vatom multicolvar |
| 19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | GYRATION ENERGY DISTANCE COM MOLINFO PRINT UPPER_WALLS METAD | colvar vatom generic bias |
| 19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Wei Chen | ANN COM COMBINE RESTRAINT POSITION | colvar bias annfunc function vatom |
| 19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Mattia Bernetti | LOWER_WALLS WHOLEMOLECULES PRINT PATHMSD UPPER_WALLS METAD | colvar generic bias |
| 19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | ENERGY DISTANCE FLUSH UNITS COMBINE PRINT UPPER_WALLS METAD | colvar generic bias setup function |
| 19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Vittorio Limongelli | UPPER_WALLS DISTANCE LOWER_WALLS COM WHOLEMOLECULES RMSD PRINT FUNNEL FUNNEL_PS METAD | colvar generic funnel bias vatom |
| 19.032 | Chemical reaction in solution using path collective variables based on coordination patterns | chemistry | chemical reactions, solutions, metadynamics, coordination patterns | Fabio Pietrucci | PATH FLUSH DISTANCES RESTART PRINT UPPER_WALLS METAD | generic bias setup mapping multicolvar |
| 19.025 | Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide | bio | metainference, NMR, protein dynamics, force-fields | Carlo Camilloni | BIASVALUE GYRATION CS2BACKBONE METAINFERENCE FLUSH RDC PBMETAD STATS ENSEMBLE WHOLEMOLECULES MOLINFO ENDPLUMED PRINT TORSION JCOUPLING | colvar generic isdb bias function |
| 25.018 | Metainference simulation for dimerization of RNA binding protein | bio | Metainference, Metadynamics, SAXS, protein dimer | Debadutta Patra | SAXS WHOLEMOLECULES TORSION UPPER_WALLS PRINT FLUSH CENTER GYRATION MOLINFO ENSEMBLE PBMETAD STATS DISTANCE METAINFERENCE | function isdb generic bias colvar vatom |
| 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 | TORSION PUCKERING MOVINGRESTRAINT RESTRAINT RESTART METAD DISTANCE MOLINFO PRINT | generic setup colvar bias |
| 23.036 | Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? | bio | NaCl, nucleation, metadynamics | Ruiyu Wang | COMBINE Q4 ENERGY VOLUME COORDINATIONNUMBER METAD Q6 MATHEVAL PRINT | function generic bias symfunc 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 | WHOLEMOLECULES COORDINATION COMBINE GHBFIX BIASVALUE METAD MOLINFO ERMSD PRINT | function bias colvar generic |
| 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 | WHOLEMOLECULES TORSION LOWER_WALLS UPPER_WALLS COORDINATION PYTORCH_MODEL FIXEDATOM PATH OPES_METAD_EXPLORE PRINT OPES_METAD FIT_TO_TEMPLATE GROUP CENTER DISTANCE UNITS CUSTOM | function mapping core generic opes setup bias pytorch colvar vatom |
| 23.011 | OneOPES, a combined enhanced sampling method to rule them all | bio | OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding | Valerio Rizzi | ECV_MULTITHERMAL TORSION ENDPLUMED ENERGY OPES_METAD_EXPLORE METAD DISTANCE MOLINFO OPES_EXPANDED PRINT | opes bias colvar generic |
| 23.004 | Melting curves of ice polymorphs in the vicinity of the liquid-liquid critical point | chemistry | water, liquid-liquid transition, second critical point, ice, polymorphs, melting curves, environment similarity, opes, density-functional theory, scan, machine learning potential | Pablo Piaggi | UPPER_WALLS LOWER_WALLS ENVIRONMENTSIMILARITY RESTART DUMPGRID ECV_UMBRELLAS_LINE OPES_EXPANDED HISTOGRAM PRINT | generic opes gridtools setup bias envsim |
| 22.043 | Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES | bio | OPES, RNA, Tetraloop, Folding | Gül Zerze | ECV_MULTITHERMAL WHOLEMOLECULES CONTACTMAP ENERGY ECV_UMBRELLAS_LINE OPES_EXPANDED PRINT | 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 | UPPER_WALLS LOWER_WALLS PRINT CELL COMMITTOR METAD CUSTOM MATHEVAL DRMSD | function colvar bias generic |
| 22.027 | Molecular Dynamics simulations of BANAL-236 RBD-hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, BANAL-236, receptor-binding domain | Max Bonomi | RMSD PRINT | colvar generic |
| 22.019 | Exploring aspartic protease inhibitor binding to design selective antimalarials | bio | ligand binding, loop opening, path CV, funnel metadynamics, drug development | Raitis Bobrovs | WHOLEMOLECULES UPPER_WALLS LOWER_WALLS COM PATHMSD PRINT METAD FUNNEL FUNNEL_PS DISTANCE | generic bias funnel colvar vatom |
| 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 | UPPER_WALLS LOWER_WALLS COORDINATION COMBINE COM FLUSH COORDINATIONNUMBER METAD GYRATION UNITS DISTANCE | function generic setup bias symfunc colvar vatom |
| 22.001 | Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials | methods | enhanced sampling, variationally enhanced sampling, ves, metadynamics, bias representation, wavelets, adam | Benjamin Pampel | OPT_AVERAGED_SGD TD_WELLTEMPERED UPPER_WALLS VES_OUTPUT_BASISFUNCTIONS FLUSH BF_WAVELETS BF_CHEBYSHEV METAD POSITION TD_UNIFORM VES_LINEAR_EXPANSION BF_LEGENDRE BF_CUBIC_B_SPLINES COORDINATION ENERGY BF_GAUSSIANS INCLUDE DISTANCE OPT_ADAM UNITS PRINT | generic setup bias colvar ves |
| 21.035 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, interface | Aaron Finney | FIXEDATOM RESTRAINT LOAD GROUP DISTANCE PRINT | core generic setup bias colvar vatom |
| 21.018 | Localized Volume-based Metadynamics | bio | LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification | Riccardo Capelli | CONVERT_TO_FES UPPER_WALLS ENDPLUMED FIXEDATOM RMSD FLUSH METAD REWEIGHT_METAD POSITION HISTOGRAM WHOLEMOLECULES COM MATHEVAL COORDINATION DISTANCE GROUP DUMPGRID READ PRINT | function core generic gridtools bias colvar vatom |
| 21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Tarsis Ferreira | WHOLEMOLECULES UPPER_WALLS LOWER_WALLS PUCKERING COORDINATION ENERGY RANDOM_EXCHANGES GROUP DUMPGRID INCLUDE METAD DISTANCE REWEIGHT_METAD MOLINFO HISTOGRAM PRINT | core generic gridtools bias colvar |
| 20.005 | Muscarinic M2 receptor/ligand Frequency-Adaptive Metadynamics and QM/MM calculations | bio | Frequency-adaptive metadynamics, multiple-walkers metadynamics, well-tempered metadynamics, GPCR, receptor, Adiabatic Bias MD | Riccardo Capelli | CONVERT_TO_FES UPPER_WALLS ENDPLUMED CONTACTMAP FLUSH METAD REWEIGHT_METAD HISTOGRAM WHOLEMOLECULES COM COMBINE MOLINFO ABMD DISTANCE LOWER_WALLS FUNCPATHMSD DUMPGRID READ PRINT | function generic gridtools bias colvar vatom |
| 19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Valerio Rizzi | UPPER_WALLS ENDPLUMED COMBINE RESTART FLUSH GROUP COORDINATIONNUMBER DISTANCES METAD UNITS PRINT | function core generic setup bias symfunc multicolvar |
| 19.080 | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | methods | ves, variationally enhanced sampling, vibrational excitation, chemical reactions | Kristof Bal | VES_LINEAR_EXPANSION OPT_AVERAGED_SGD CONVERT_TO_FES UPPER_WALLS TD_WELLTEMPERED DISTANCE COORDINATION COMBINE LOWER_WALLS FLUSH DUMPGRID BF_CHEBYSHEV ANGLE UNITS TD_GRID HISTOGRAM PRINT EXTERNAL | function generic gridtools setup bias colvar ves |
| 19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Kim Jelfs | MOVINGRESTRAINT COM RESTART FLUSH DISTANCES INPLANEDISTANCES PRINT | generic setup bias vatom multicolvar |
| 19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Cristina Paissoni | ALPHABETA SAXS WHOLEMOLECULES ENDPLUMED COORDINATION COMBINE BIASVALUE MATHEVAL GROUP INCLUDE CENTER ANGLE MOLINFO ENSEMBLE PBMETAD STATS PRINT | function core isdb generic bias colvar vatom multicolvar |
| 19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Gareth Tribello | UPPER_WALLS ENDPLUMED LOWER_WALLS AROUND CELL FCCUBIC METAD UNITS PRINT | volumes generic setup bias symfunc colvar |
| 19.050 | Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes | chemistry | metadynamics, membranes, Willard Chandler surface | Gareth Tribello | CONVERT_TO_FES UPPER_WALLS DISTANCE_FROM_CONTOUR COMBINE PRINT RESTART DUMPGRID METAD READ HISTOGRAM REWEIGHT_BIAS | function generic gridtools setup bias contour |
| 19.049 | Determining the sizes of solid/liquid clusters in MD trajectories of nucleation | methods | nucleation, metadynamics, clustering, Steinhardt order parameters | Gareth Tribello | OUTPUT_CLUSTER OUTER_PRODUCT MORE_THAN CLUSTER_DISTRIBUTION CLUSTER_NATOMS PRINT CONTACT_MATRIX DFSCLUSTERING COORDINATIONNUMBER SMAC Q6 CLUSTER_PROPERTIES CUSTOM ONES METAD DISTANCES LOCAL_Q6 MATRIX_VECTOR_PRODUCT | function matrixtools generic multicolvar bias symfunc adjmat clusters |
| 19.035 | Dimerization of GPCRs from coarse-grained umbrella sampling | bio | Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization | Davide Provasi | TORSION COM RESTRAINT GROUP DISTANCE PRINT | core generic bias colvar vatom |
| 19.004 | MI Ubiquitin | bio | metainference, NMR | Max Bonomi | WHOLEMOLECULES CS2BACKBONE GROUP MOLINFO RDC PRINT METAINFERENCE | core isdb generic |
| 25.022 | Imidazole Diffusion in SALEM-2 MOF | materials | OPES, Diffusion, Ring opening, MOFs, Machine Learning Potentials | Sudheesh Kumar Ethirajan | OPES_METAD CENTER WHOLEMOLECULES ENDPLUMED DISTANCE UNITS PROJECTION_ON_AXIS MOLINFO GROUP DISTANCES PRINT | generic setup colvar vatom opes core multicolvar |
| 25.020 | Revealing Water-Mediated Activation Mechanisms in the Beta 1-Adrenergic Receptor via OneOPES-Enhanced Free Energy Landscapes | bio | OneOPES, GPCR, ADRB1, activation, microswitches, conformational changes, allostery | Valerio Rizzi | DISTANCES RMSD CENTER LOWER_WALLS UPPER_WALLS ENERGY DISTANCE COORDINATION GROUP OPES_METAD_EXPLORE CUSTOM GHOST PATHMSD PRINT ECV_MULTITHERMAL OPES_EXPANDED | function generic bias colvar vatom opes core multicolvar |
| 25.013 | Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices | bio | umbrella sampling, temperature ramping | Alexander Berlaga | RESTRAINT GYRATION DISTANCE PRINT PYTORCH_MODEL | pytorch bias generic colvar |
| 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 | LOAD OPES_METAD BIASVALUE MATHEVAL ENERGY CELL DISTANCE POSITION UNITS COMBINE COORDINATION TORSION INCLUDE FLUSH CUSTOM PRINT | function generic setup colvar opes bias |
| 25.002 | M3_PCV-ABMD | chemistry | Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor | Gian Marco Elisi | ENDPLUMED ABMD UPPER_WALLS UNITS PATHMSD PRINT | bias generic setup colvar |
| 24.031 | DeepLNE | methods | PATHCV, OPES, OneOPES | Thorben Fröhlking | RESTART ENERGY OPES_EXPANDED COMBINE PYTORCH_MODEL COORDINATION MOLINFO OPES_METAD_EXPLORE ERMSD PRINT ECV_MULTITHERMAL VOLUME | function generic setup pytorch colvar opes |
| 24.006 | Water vapor condensation | chemistry | metadynamics, homogeneous condensation, chemical potential | Shenghui Zhong | CONTACT_MATRIX COORDINATIONNUMBER UPPER_WALLS CLUSTER_PROPERTIES DFSCLUSTERING UNITS CLUSTER_NATOMS PRINT METAD | generic setup adjmat clusters bias symfunc |
| 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 | bias generic setup |
| 23.019 | Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors | bio | binding pathway, binding energy, sketch-map, drug development | Raitis Bobrovs | LANDMARK_SELECT_FPS VORONOI COLLECT_FRAMES WHOLEMOLECULES UPPER_WALLS TRANSPOSE SKETCHMAP_PROJECTION DISTANCE DISSIMILARITIES VSTACK CUSTOM PATHMSD PRINT SKETCHMAP METAD COM | function generic colvar vatom dimred valtools landmarks bias matrixtools |
| 23.014 | Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 | bio | metadynamics, oligomerization, chemokine receptors, GPCR, membrane | Vittorio Limongelli | WHOLEMOLECULES UPPER_WALLS DISTANCE COMBINE TORSION FLUSH PRINT METAD COM | function generic colvar vatom 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 | CENTER DISTANCE COMMITTOR GROUP CUSTOM ANGLE MATHEVAL LOWER_WALLS CONTACTMAP PYTORCH_MODEL PRINT RMSD ENDPLUMED UPPER_WALLS COORDINATION INCLUDE FIXEDATOM FIT_TO_TEMPLATE WHOLEMOLECULES ENERGY COMBINE MOLINFO OPES_METAD | function generic pytorch colvar vatom opes core bias |
| 22.045 | Binding mode and mechanism of enzymatic polyethylene terephthalate degradation | bio | metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation | Francesco Colizzi | WHOLEMOLECULES LOWER_WALLS UPPER_WALLS ANGLE DISTANCE MOVINGRESTRAINT PRINT METAD COM | bias generic colvar vatom |
| 22.030 | Mixing physics across temperatures with generative artificial intelligence | methods | REMD, Generative AI, DDPM | Yihang Wang | TORSION PRINT WHOLEMOLECULES | generic colvar |
| 22.018 | Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations | bio | ligand binding, docking, EMMI, LAT1 | Max Bonomi | LOAD WHOLEMOLECULES BIASVALUE EMMIVOX MOLINFO GROUP PRINT | generic setup isdb core bias |
| 22.011 | Accelerating all-atom simulations and gaining mechanistic understanding of biophysical systems through State Predictive Information Bottleneck | methods | metadynamics, membrane permeation, protein folding | Shams Mehdi | MATHEVAL WHOLEMOLECULES LOWER_WALLS UPPER_WALLS ZANGLES DISTANCE YANGLES COMBINE XANGLES ALPHABETA TORSION MOLINFO CUSTOM PRINT METAD COM | function generic bias colvar vatom multicolvar |
| 22.004 | Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques | chemistry | reaction discovery, OPES, collective variables | Umberto Raucci | LOAD OPES_METAD MATHEVAL LOWER_WALLS UPPER_WALLS DISTANCE UNITS COORDINATION GROUP OPES_METAD_EXPLORE CUSTOM PRINT PYTORCH_MODEL COM | function generic setup pytorch colvar vatom opes core bias |
| 22.000 | Amyloid precursor protein processing by human γ-secretase | bio | Bias Exchange Metadynamics, Helix unfolding, coupled binding | Xiaoli Lu | CENTER DISTANCE UNITS ALPHARMSD CONTACTMAP COORDINATION RANDOM_EXCHANGES MOLINFO INCLUDE ANTIBETARMSD PRINT METAD | generic setup colvar vatom secondarystructure bias |
| 21.052 | On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets | materials | Ibuprofen, unbinding, WTmetaD | Matteo Salvalaglio | CENTER ENDPLUMED COORDINATIONNUMBER DISTANCE COMMITTOR TORSION PRINT METAD | generic colvar vatom bias symfunc |
| 21.039 | Deep learning the slow modes for rare events sampling | methods | collective variables, machine learning, slow modes, deep-tica, opes | Luigi Bonati | DISTANCE ENVIRONMENTSIMILARITY TORSION Q6 GROUP ECV_MULTITHERMAL VOLUME CONTACTMAP FLUSH PYTORCH_MODEL PRINT LOAD RMSD ENDPLUMED INCLUDE OPES_EXPANDED WHOLEMOLECULES ENERGY UNITS COMBINE MOLINFO OPES_METAD | function generic setup pytorch colvar opes envsim core symfunc |
| 21.034 | Efficient sampling of high-dimensional free energy landscapes using adaptive reinforced dynamics | bio | reinforced dynamics, bias-exchange metadynamics, parallel-bias metadynamics | Dongdong Wang | ENDPLUMED PBMETAD TORSION RANDOM_EXCHANGES INCLUDE PRINT METAD | bias generic colvar |
| 21.028 | From Enhanced Sampling to Reaction Profiles | methods | collective variables, multi-state, machine learning, Deep-TDA | Enrico Trizio | CENTER DISTANCE TORSION GROUP ANGLE MATHEVAL LOWER_WALLS PYTORCH_MODEL PRINT LOAD ENDPLUMED UPPER_WALLS COORDINATION FIXEDATOM FIT_TO_TEMPLATE WHOLEMOLECULES UNITS DISTANCES OPES_METAD | function generic setup pytorch colvar vatom multicolvar opes core bias |
| 21.022 | Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly | materials | parallel bias metadynamics, adsorption, peptide | Xin Qi | PBMETAD GYRATION LOWER_WALLS UPPER_WALLS ENERGY DISTANCE MOLINFO PRINT COM | bias generic colvar vatom |
| 21.020 | Reweighted Jarzynski sampling | methods | free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions | Kristof Bal | VES_LINEAR_EXPANSION COORDINATIONNUMBER DISTANCE CONSTANT REWEIGHT_METAD CUSTOM HISTOGRAM MOVINGRESTRAINT FLUSH REWEIGHT_BIAS LOAD OPT_AVERAGED_SGD RESTRAINT UPPER_WALLS OPES_METAD DUMPGRID BIASVALUE ANN UNITS COMBINE TD_WELLTEMPERED PRINT CONVERT_TO_FES BF_CHEBYSHEV METAD | function generic setup gridtools colvar opes ves annfunc bias symfunc |
| 21.017 | All-atom simulations of the Vav1 AD construct | bio | metadynamics, parallel-bias, well-tempered | Simone Orioli | REWEIGHT_BIAS RESTART WHOLEMOLECULES PBMETAD ALPHABETA CONTACTMAP ALPHARMSD MOLINFO GROUP PRINT METAD | generic bias setup colvar secondarystructure core multicolvar |
| 21.015 | Coarse-grained metadynamics and umbrella sampling simulations to investigate interactions of carbohydrate-binding modules with chitin | bio | metadynamics, umbrella sampling, coarse-grained, MARTINI, chitin, carbohydrate-binding module | Gaston Courtade | REWEIGHT_BIAS RESTART CENTER WHOLEMOLECULES MATHEVAL RESTRAINT POSITION COORDINATION PRINT METAD | function generic setup colvar vatom bias |
| 21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Kristof Bal | LOAD COORDINATIONNUMBER UPPER_WALLS COMMITTOR UNITS HISTOGRAM MOVINGRESTRAINT REWEIGHT_METAD FLUSH CONVERT_TO_FES PRINT DUMPGRID METAD | generic setup gridtools bias symfunc |
| 20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Michele Invernizzi | ECV_UMBRELLAS_LINE POSITION ENVIRONMENTSIMILARITY TORSION Q6 CUSTOM ECV_MULTITHERMAL VOLUME MATHEVAL ECV_LINEAR LOAD RMSD ENDPLUMED UPPER_WALLS OPES_EXPANDED WHOLEMOLECULES ECV_MULTITHERMAL_MULTIBARIC ENERGY UNITS MOLINFO PRINT | function generic setup colvar opes envsim bias symfunc |
| 20.014 | amyloid beta small molecule interaction | bio | intrinsically disordered proteins, disordered proteins, IDPs, fuzzy binding, small molecule, drugs, entropy, binding, Alzheimer’s disease, amyloid beta | Gabriella Heller | PBMETAD TORSION GROUP GYRATION FLUSH ANTIBETARMSD ENSEMBLE STATS METAINFERENCE DIHCOR ENDPLUMED COORDINATION INCLUDE PARABETARMSD WHOLEMOLECULES COMBINE ALPHARMSD MOLINFO CS2BACKBONE PRINT | function generic colvar secondarystructure multicolvar isdb core bias |
| 20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Jim Pfaendtner | RESTART CENTER WHOLEMOLECULES DISTANCE COORDINATION GROUP DISTANCES PRINT | generic setup colvar vatom core multicolvar |
| 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 | CUSTOM UNITS COORDINATION DISTANCES PRINT METAD | function generic bias setup colvar multicolvar |
| 20.006 | Class B GPCR activation mechanism | bio | metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | RMSD CENTER WHOLEMOLECULES MATHEVAL LOWER_WALLS UPPER_WALLS ENERGY DISTANCE COMBINE MOLINFO PRINT METAD | function generic colvar vatom bias |
| 19.076 | Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones | bio | molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics | Salvatore Assenza | ENDPLUMED GYRATION UNITS MOVINGRESTRAINT PRINT | setup bias generic colvar |
| 19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Giovanni Bussi | WHOLEMOLECULES ENDPLUMED LOWER_WALLS RESTRAINT DISTANCE COORDINATION | bias generic colvar |
| 19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Matteo Salvalaglio | REWEIGHT_BIAS MATHEVAL BIASVALUE DISTANCE COMMITTOR HISTOGRAM REWEIGHT_METAD TORSION READ EXTERNAL CONVERT_TO_FES PRINT DUMPGRID METAD | function generic gridtools colvar bias |
| 19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Carlo Camilloni | RESTART BIASVALUE LOWER_WALLS WHOLEMOLECULES PBMETAD UPPER_WALLS ENDPLUMED ALPHABETA MOLINFO GROUP FLUSH ANTIBETARMSD CS2BACKBONE PRINT | generic bias setup secondarystructure isdb core multicolvar |
| 25.014 | Atomic resolution ensembles of intrinsically disordered proteins with Alphafold | bio | bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement | Vincent Schnapka | PRINT GROUP BAIES BIASVALUE | bias isdb core generic |
| 25.008 | Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting | methods | metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting | Dhiman Ray | PYTORCH_MODEL ENDPLUMED RMSD PRINT UPPER_WALLS CUSTOM METAD LOWER_WALLS BIASVALUE TORSION GROUP DISTANCE WHOLEMOLECULES UNITS POSITION OPES_METAD MOLINFO ENERGY | colvar function pytorch core bias opes setup generic |
| 24.032 | DeepLNE++ | methods | PATHCV, OPES | Thorben Fröhlking | LOAD COMBINE COORDINATION PRINT CUSTOM TORSION GROUP DISTANCE OPES_METAD ENERGY | colvar function core opes setup generic |
| 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 | OPES_EXPANDED COMBINE ECV_MULTITHERMAL COORDINATION PRINT CUSTOM TORSION GROUP RESTART DISTANCE OPES_METAD_EXPLORE ENERGY | colvar function core opes setup generic |
| 24.012 | Molecular simulations to investigate the impact of N6-methylation in RNA recognition | bio | metadynamics, alchemistry, RNA modification, RNA:protein interactions | Giovanni Bussi | COMBINE COORDINATION CENTER PRINT UPPER_WALLS METAD COM BIASVALUE LOWER_WALLS GROUP DISTANCE GHBFIX DEBUG MOLINFO | colvar function core bias vatom generic |
| 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 | PRINT UPPER_WALLS ZDISTANCES GROUP DISTANCE COORDINATIONNUMBER FIXEDATOM UNITS FLUSH OPES_METAD | colvar symfunc multicolvar core bias opes setup vatom generic |
| 23.044 | Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition | materials | metadynamics, interlocked molecules | Luigi Leanza | ENDPLUMED COORDINATION CONVERT_TO_FES PRINT HISTOGRAM METAD COMMITTOR GROUP READ DUMPGRID | colvar gridtools core bias generic |
| 23.040 | Supramolecular capsules assembly dynamics | chemistry | Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics | Riccardo Capelli | DISTANCES CENTER PRINT CUSTOM METAD COM WHOLEMOLECULES GROUP DISTANCE FLUSH UNITS POSITION | colvar function multicolvar core bias setup vatom generic |
| 23.030 | Data Driven Classification of Ligand Unbinding Pathways | bio | OPES Explore, OPES Flooding, Benzene T4 Lysozyme, Ligand unbinding, Pathway classification, Kinetics, Residence time | Dhiman Ray | PRINT LOWER_WALLS WHOLEMOLECULES DISTANCE OPES_METAD COORDINATION CENTER COM TORSION FLUSH FIT_TO_TEMPLATE WRAPAROUND OPES_METAD_EXPLORE ENDPLUMED UPPER_WALLS BIASVALUE COMMITTOR GROUP UNITS MOLINFO MATHEVAL CUSTOM POSITION ENERGY | colvar function core bias opes setup vatom generic |
| 23.015 | MPCs aggregation | bio | opes_explore, dimerization, MPCs, self-assembly | Vikas Tiwari | COORDINATION CENTER PRINT UPPER_WALLS CUSTOM METAD LOWER_WALLS COM GROUP WHOLEMOLECULES DISTANCE OPES_METAD_EXPLORE | colvar function core bias opes vatom generic |
| 23.007 | Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains | bio | metadynamics, peptoids, parallel-bias metadynamics | Jim Pfaendtner | GYRATION RESTRAINT COORDINATION INCLUDE PRINT PBMETAD COM TORSION WHOLEMOLECULES | bias colvar vatom generic |
| 22.039 | Driving and characterizing nucleation of urea and glycine polymorphs in water | bio | metadynamics, nucleation, amino acids, polymorphism | Eric Beyerle | LOAD MATHEVAL COMBINE Q6 CENTER INCLUDE PRINT METAD GROUP COORDINATIONNUMBER PAIRENTROPY Q4 | symfunc function gridtools core bias setup vatom generic |
| 22.029 | Angiotensin-1-7_Metadynamics | bio | Metadynamics, Angiotensin-(1-7), peptide | L.-América Chi | GYRATION COORDINATION PRINT UPPER_WALLS METAD LOWER_WALLS GROUP WHOLEMOLECULES FLUSH | bias colvar core 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 | OPES_EXPANDED INCLUDE PRINT UPPER_WALLS LOWER_WALLS ECV_UMBRELLAS_LINE ENVIRONMENTSIMILARITY | bias opes envsim generic |
| 21.047 | Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations | materials | pair entropy, metadynamics, ves, solids, crystallization | Pablo Piaggi | LOAD COMBINE OPT_AVERAGED_SGD VOLUME PRINT VES_LINEAR_EXPANSION METAD BF_LEGENDRE RESTART PAIRENTROPY TD_WELLTEMPERED ENERGY | colvar ves function gridtools bias setup generic |
| 21.044 | NaCl nucleation | chemistry | metadynamics, DFS clustering | Aaron Finney | CLUSTER_DISTRIBUTION COMBINE Q6 HISTOGRAM PRINT CLUSTER_NATOMS METAD CONTACT_MATRIX LOCAL_Q6 MFILTER_MORE GROUP DFSCLUSTERING COORDINATIONNUMBER FIXEDATOM INSPHERE DUMPGRID | symfunc function gridtools multicolvar core adjmat volumes bias clusters vatom generic |
| 21.029 | Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs | bio | metadynamics, small peptide, machine learning | Pratyush Tiwary | PRINT TORSION RESTART FLUSH MOLINFO ENERGY EXTERNAL | bias colvar setup generic |
| 21.019 | Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations | materials | Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen | Matteo Salvalaglio | KDE MATHEVAL PRINT COM DISTANCE TORSIONS | colvar gridtools function multicolvar vatom generic |
| 21.016 | MD SAXS GTPase associated center | bio | metadynamics, RNA, folding, SAXS | Giovanni Bussi | GYRATION INCLUDE PRINT UPPER_WALLS CUSTOM METAD LOWER_WALLS ERMSD WHOLEMOLECULES GROUP SAXS MOLINFO | isdb colvar function core bias generic |
| 21.014 | how to determine statistically accurate conformational ensembles | bio | metadynamics, metainference, errors, cv, SAXS, ensemble determination | Cristina Paissoni | GYRATION STATS CENTER PRINT PBMETAD METAD ANTIBETARMSD CONTACTMAP TORSION BIASVALUE ENSEMBLE WHOLEMOLECULES SAXS ALPHABETA MOLINFO | isdb colvar function multicolvar secondarystructure bias vatom generic |
| 21.013 | Role of vibrational excitation in heterogeneous catalysis | chemistry | catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption | Kristof Bal | RESTRAINT CONVERT_TO_FES HISTOGRAM PRINT VES_LINEAR_EXPANSION METAD LOWER_WALLS DISTANCE REWEIGHT_METAD ANGLES EXTERNAL DISTANCES COORDINATION TD_GRID UWALLS FLUSH REWEIGHT_BIAS LOAD OPT_AVERAGED_SGD UPPER_WALLS UNITS DUMPGRID COMBINE COORDINATIONNUMBER BF_CHEBYSHEV | colvar ves symfunc gridtools multicolvar function bias setup generic |
| 20.026 | Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor | bio | Metadynamics, Umbrella sampling | Brandon Peters | RESTRAINT CONVERT_TO_FES MULTI_RMSD HISTOGRAM PRINT METAD REWEIGHT_METAD DUMPGRID | bias gridtools colvar generic |
| 19.075 | PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python | other | Python, automatic differentiation | Toni Giorgino | ENDPLUMED COMBINE RESTRAINT CENTER PRINT CUSTOM TORSION GROUP DISTANCE ANGLE DUMPDERIVATIVES | colvar function core bias vatom generic |
| 19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Matteo Salvalaglio | ENDPLUMED INCLUDE CENTER PRINT GROUP DISTANCE | colvar core vatom generic |
| 19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_LOSS MAZE_OPTIMIZER_BIAS PRINT UNITS POSITION MAZE_SIMULATED_ANNEALING | maze colvar setup generic |
| 19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | GYRATION PRINT UPPER_WALLS METAD COM DISTANCE MOLINFO ENERGY | bias colvar vatom generic |
| 19.056 | maze | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_LOSS MAZE_OPTIMIZER_BIAS PRINT UNITS POSITION MAZE_SIMULATED_ANNEALING | maze colvar setup generic |
| 19.048 | Understanding Ligand Binding Selectivity in a Prototypical GPCR Family | bio | metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | MATHEVAL PRINT UPPER_WALLS METAD COM LOWER_WALLS BIASVALUE WHOLEMOLECULES DISTANCE CONSTANT | colvar function bias vatom generic |
| 19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Pratyush Tiwary | COMBINE PRINT COM TORSION COMMITTOR WHOLEMOLECULES DISTANCE RESTART ALPHABETA EXTERNAL | colvar function multicolvar bias setup vatom generic |
| 19.023 | RECT | methods | metadynamics, replica exchange | Giovanni Bussi | GYRATION PRINT METAD TORSION WHOLEMOLECULES | bias colvar generic |
| 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 | MOVINGRESTRAINT CENTER MOLINFO GROUP UPPER_WALLS GYRATION WHOLEMOLECULES DISTANCE PRINT SAXS INCLUDE METAD | isdb colvar generic vatom core bias |
| 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 | CUSTOM COORDINATIONNUMBER ZDISTANCES OPES_METAD UNITS GROUP UPPER_WALLS DISTANCES FIXEDATOM COMMITTOR DISTANCE PRINT FLUSH | opes setup multicolvar generic colvar vatom core function symfunc bias |
| 25.001 | RNA G-quadruplex folding with ST-metaD protocol | bio | RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | MOLINFO ERMSD WHOLEMOLECULES COMBINE METAD | colvar bias generic function |
| 25.000 | Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer | bio | metadynamics, pathCV | Sahithya Sridharan Iyer | FUNCPATHGENERAL RESTART MOLINFO GROUP UPPER_WALLS COM WHOLEMOLECULES DISTANCE PRINT METAD | setup generic colvar vatom core function bias |
| 24.036 | Leveraging cryptic ligand envelopes through enhanced molecular simulations | bio | HREX, conformational heterogeneity, drug discovery, ligand binding, plitidepsin, aplidin, ligand-target complexes, cryptic ligand envelope | Francesco Colizzi | DUMPGRID COORDINATION ANGLE HISTOGRAM GROUP CONVERT_TO_FES WHOLEMOLECULES TORSION DISTANCE PRINT | generic core colvar gridtools |
| 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 | CUSTOM COORDINATION LOWER_WALLS PYTORCH_MODEL RESTART OPES_METAD CENTER GROUP UPPER_WALLS FIT_TO_TEMPLATE FIXEDATOM WHOLEMOLECULES PATH TORSION DISTANCE PRINT | pytorch opes setup colvar generic vatom mapping core function bias |
| 24.018 | A new route to the prebiotic synthesis of glycine via ab initio-based machine learning calculations | chemistry | prebiotic chemistry, glycine, Strecker synthesis, ab initio calculations, machine learning | Léon HUET | DISTANCE PRINT | generic colvar |
| 24.016 | Cryo-EM guided simulations of ribozyme | bio | metainference, cryo-EM | Giovanni Bussi | EMMIVOX RESTRAINT BIASVALUE MOLINFO GROUP ERMSD WHOLEMOLECULES INCLUDE PRINT | isdb colvar generic core bias |
| 24.005 | Learning Markovian Dynamics with Spectral Maps | methods | spectral map, collective variables, machine learning | Jakub Rydzewski | CUSTOM BIASVALUE UNITS DISTANCE PRINT | setup generic colvar function 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 | FUNCPATHMSD CONTACTMAP LOWER_WALLS ALPHARMSD MOLINFO PATHMSD UPPER_WALLS DISTANCE PRINT INCLUDE METAD | colvar generic secondarystructure function bias |
| 23.037 | Estimating binding free energy of solid binding peptides without extensive sampling | bio | metadynamics, solid binding peptides | Xin Qi | PBMETAD LOWER_WALLS MOLINFO GYRATION UPPER_WALLS COM DISTANCE PRINT | colvar bias generic vatom |
| 23.034 | Urea nucleation in water: do long-range forces matter? | materials | LMF theory, Metadynamics, Nucleation | Ziyue Zou | COORDINATIONNUMBER LOAD CENTER GROUP INCLUDE PRINT METAD | setup generic vatom core symfunc bias |
| 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 | ENSEMBLE BIASVALUE RMSD CENTER MOLINFO GROUP UPPER_WALLS WRAPAROUND STATS DISTANCE PRINT SAXS | isdb generic colvar vatom core function bias |
| 23.027 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, DFS, Q3, Pair Entropy | Aaron Finney | AROUND DUMPGRID RESTRAINT COORDINATIONNUMBER Q3 CONTACT_MATRIX CLUSTER_DISTRIBUTION LOAD UNITS GROUP HISTOGRAM DFSCLUSTERING CLUSTER_NATOMS FIXEDATOM LOCAL_AVERAGE DENSITY LOCAL_Q3 PRINT | adjmat gridtools setup clusters generic vatom volumes core symfunc bias |
| 23.010 | An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G‑Protein-Coupled Receptor Ligands | bio | GPCR, binding free energy, free energy surface | Timothy Clark | LOWER_WALLS BIASVALUE CONSTANT UPPER_WALLS MATHEVAL WHOLEMOLECULES DISTANCE PRINT METAD | colvar bias generic function |
| 22.025 | Bubble nucleation rate predictions in a Lennard-Jones fluid | materials | free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation | Kristof Bal | RESTRAINT CUSTOM DUMPGRID COORDINATIONNUMBER BIASVALUE MOVINGRESTRAINT LOAD REWEIGHT_BIAS VOLUME UNITS UPPER_WALLS ANN HISTOGRAM CONVERT_TO_FES COMMITTOR PRINT FLUSH | gridtools setup colvar annfunc generic function symfunc 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 | TORSION PBMETAD RMSD RESTART BIASVALUE EMMI MOLINFO GROUP UPPER_WALLS COM WHOLEMOLECULES COORDINATION PRINT | isdb setup generic colvar vatom core bias |
| 22.015 | Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome | bio | photodynamics, bacteriophytochrome, variationally enhanced sampling | Jakub Rydzewski | VES_LINEAR_EXPANSION OPT_AVERAGED_SGD BF_FOURIER TORSION PRINT TD_UNIFORM | generic colvar ves |
| 22.003 | Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling | methods | opes, metadynamics, reweighting, alanine, muller | Michele Invernizzi | PBMETAD OPES_EXPANDED CUSTOM LOWER_WALLS BIASVALUE ECV_MULTITHERMAL OPES_METAD_EXPLORE ENERGY OPES_METAD UNITS POSITION UPPER_WALLS ENDPLUMED TORSION PRINT ECV_UMBRELLAS_FILE METAD | opes setup colvar generic function bias |
| 21.050 | N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity | methods | bio | Isabell Louise Grothaus | DISTANCE PRINT CENTER | generic colvar vatom |
| 21.033 | Multiple-path-metadynamics applied to DNA base-pairing transitions | bio | path-CV, metadynamics, multiple-walker, dna | Alberto Pérez-de-Alba-Ortíz | RESTRAINT CONSTANT MOVINGRESTRAINT UPPER_WALLS COMBINE INCLUDE PRINT METAD | bias generic function |
| 21.012 | NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition | bio | funnel metadynamics | Jim Pfaendtner | LOWER_WALLS UPPER_WALLS COM FUNNEL_PS DISTANCE PRINT FUNNEL METAD | generic colvar vatom bias funnel |
| 21.011 | CmuMD simulations of NaCl(aq) at graphite | chemistry | CmuMD, DFS clustering | Aaron Finney | AROUND RESTRAINT DUMPGRID COORDINATIONNUMBER CONTACT_MATRIX CLUSTER_DISTRIBUTION LOAD GROUP DFSCLUSTERING CLUSTER_NATOMS MFILTER_MORE FIXEDATOM DENSITY MULTICOLVARDENS PRINT | adjmat gridtools setup multicolvar clusters generic vatom volumes core symfunc bias |
| 21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Tarak Karmakar | LOWER_WALLS PYTORCH_MODEL LOAD OPES_METAD GROUP UPPER_WALLS MATHEVAL PRINT FLUSH | pytorch opes setup generic core function bias |
| 21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Kresten Lindorff-Larsen | PBMETAD EEFSOLV METAINFERENCE BIASVALUE ALPHARMSD CENTER MOLINFO GROUP GYRATION WHOLEMOLECULES PRINT SAXS FLUSH | isdb colvar generic vatom secondarystructure core bias |
| 20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Max Bonomi | PBMETAD DIHCOR MOLINFO GYRATION ALPHABETA WHOLEMOLECULES COORDINATION INCLUDE PRINT | colvar bias multicolvar generic |
| 20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Luigi Bonati | LOWER_WALLS PYTORCH_MODEL LOAD OPES_METAD UNITS GROUP UPPER_WALLS ENDPLUMED COM MATHEVAL TORSION DISTANCE PRINT FLUSH | pytorch opes setup generic colvar vatom core function bias |
| 19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Jakub Rydzewski | LOWER_WALLS RESTART UNITS PATHMSD UPPER_WALLS PRINT METAD | setup bias generic colvar |
| 19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Jim Pfaendtner | ENERGY GYRATION WHOLEMOLECULES PRINT METAD | bias generic colvar |
| 19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Kim E. Jelfs | LOWER_WALLS RESTART CENTER GROUP UPPER_WALLS COM DISTANCE PRINT METAD | setup colvar generic vatom core bias |
| 19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | RESTART UNITS UPPER_WALLS DISTANCES COMBINE DISTANCE PRINT FLUSH METAD | setup multicolvar colvar generic function bias |
| 19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Elena Papaleo | LOWER_WALLS MOLINFO GROUP ALPHABETA GYRATION UPPER_WALLS WHOLEMOLECULES PRINT METAD | multicolvar colvar generic core bias |
| 19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Haochuan Chen | TORSION PRINT DRR | generic drr colvar |
| 19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Matteo Salvalaglio | LOWER_WALLS CENTER UPPER_WALLS COMMITTOR TORSION DISTANCE PRINT METAD | colvar bias generic vatom |
| 19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Max Bonomi | BIASVALUE EMMI MOLINFO GROUP PRINT | bias generic core isdb |
| 19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Giovanni Bussi | LOWER_WALLS MOLINFO ANGLE UPPER_WALLS RANDOM_EXCHANGES ERMSD DISTANCES COMBINE INCLUDE PRINT DISTANCE FLUSH METAD | multicolvar colvar generic function bias |
| 25.026 | Deciphering the Molecular Mechanisms of Startle Disease - the Role of the Asn46Lys Mutation in the Glycine Receptor | bio | metadynamics, glycine receptors, funnel metadynamics | Jacob Adam Clark | FUNNEL PRINT COM LOWER_WALLS UPPER_WALLS METAD FUNNEL_PS | vatom bias funnel generic |
| 25.024 | Sampling glycan-glycan interactions for B22 calculations | bio | B22, glycan, carbohydrates, distance, REST2, metadynamics, RECT, replica exchange | Isabell Louise Grothaus | COMBINE PRINT POSITION COM DISTANCE RESTRAINT METAD | vatom bias generic colvar function |
| 25.009 | Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water | chemistry | metadynamics, nitrate photolysis | Kam-Tung Chan | REWEIGHT_METAD READ FLUSH HISTOGRAM PRINT COORDINATION CUSTOM DISTANCE UPPER_WALLS RESTART DUMPGRID GROUP METAD | core bias generic setup colvar function gridtools |
| 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 | PRINT UNITS LOWER_WALLS OPES_METAD COORDINATION CUSTOM DISTANCE COMMITTOR UPPER_WALLS RESTART GROUP | opes core bias generic setup colvar function |
| 24.034 | Umbrella sampling of ion in transporter SLC26A7 | bio | umbrella sampling, transporter, ions | Xiaoli Lu | PRINT RESTRAINT UNITS POSITION | bias setup generic colvar |
| 24.029 | Combination of OPES and OPES-Explore | methods | OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin | Dhiman Ray | COMBINE RMSD FLUSH OPES_METAD WHOLEMOLECULES CUSTOM DISTANCE CENTER MOLINFO ENDPLUMED POSITION PRINT UNITS LOWER_WALLS COORDINATION FIT_TO_TEMPLATE UPPER_WALLS METAD CONTACTMAP PYTORCH_MODEL MATHEVAL OPES_METAD_EXPLORE BIASVALUE INCLUDE ENERGY FIXEDATOM GROUP | opes core vatom bias generic pytorch setup colvar function |
| 24.028 | All-atom simulations of RNA-membrane interactions | bio | metadynamics, membrane, RNA | Giovanni Bussi | COMBINE GYRATION PRINT POSITION LOWER_WALLS SORT GHOST WHOLEMOLECULES PUCKERING DISTANCE MATHEVAL CENTER UPPER_WALLS DISTANCES MOLINFO METAD GROUP | core bias vatom generic colvar function multicolvar |
| 24.027 | Proline cis and trans subensembles of a disordered peptide | bio | intrinsically disordered proteins, proline cis trans isomerisation, metadynamics, collective variables | Alice Pettitt | PBMETAD COMBINE PARABETARMSD FLUSH GYRATION DIHCOR ALPHARMSD PRINT TORSION INCLUDE WHOLEMOLECULES COORDINATION DISTANCE MOLINFO ANTIBETARMSD ENDPLUMED GROUP | secondarystructure core bias generic colvar function multicolvar |
| 24.002 | Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes | chemistry | metadynamics, ligand design, solvent extraction | Xiaoyu Wang | PRINT UNITS TORSION METAD RESTART | setup bias generic colvar |
| 23.038 | Determinants of Neutral Antagonism and Inverse Agonism in the β2-adrenergic receptor | bio | protein coupled receptor, beta-adrenergic, receptor activation, antagonism, inverse agonism, metadynamics | Timothy Clark | RMSD PRINT MATHEVAL WHOLEMOLECULES DISTANCE MOLINFO METAD | bias generic colvar function |
| 23.035 | An Extended Metadynamics Protocol for Binding/Unbinding of Peptide Ligands to Class A G-Protein Coupled Receptors | bio | G protein coupled receptor, peptide ligands, metadynamics, multiple-walker | Timothy Clark | PRINT LOWER_WALLS BIASVALUE MATHEVAL WHOLEMOLECULES DISTANCE CENTER UPPER_WALLS CONSTANT METAD | bias vatom generic colvar function |
| 23.022 | A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar | methods | collective variables, machine learning, toy model | Enrico Trizio | PRINT UNITS PYTORCH_MODEL LOWER_WALLS BIASVALUE OPES_METAD CUSTOM UPPER_WALLS ENDPLUMED POSITION | opes bias generic pytorch setup colvar function |
| 23.008 | PBMetaD simulations of Histatin5 | bio | metadynamics, IDP, Rg, PPII | Francesco Pesce | PBMETAD GYRATION PRINT TORSION WHOLEMOLECULES MOLINFO GROUP | bias generic colvar core |
| 23.006 | Transcription factor unbinding | bio | metadynamics, DNA, conformational changes | Malin Lüking | CONTACTMAP ALPHARMSD PRINT DUMPFORCES COM DISTANCE ANGLE MOLINFO METAD | secondarystructure vatom bias generic colvar |
| 23.003 | Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations | methods | metadynamics, alchemical variable, alchemical free energy calculations | Wei-Tse Hsu | READ PRINT TORSION EXTRACV METAD | bias generic colvar |
| 22.040 | From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure | bio | SARS-CoV-2, Spike, Omicron | Miłosz Wieczór | PRINT LOWER_WALLS WHOLEMOLECULES PCAVARS UPPER_WALLS METAD | bias mapping generic |
| 22.035 | Deciphering the alphabet of disorder — Glu and Asp act differently on local but not global properties | bio | intrinsically disordered proteins, parallel bias metadynamics, protein | Kresten Lindorff-Larsen | PBMETAD GYRATION TORSION WHOLEMOLECULES MOLINFO | bias generic colvar |
| 22.031 | Rare Event Kinetics from Adaptive Bias Enhanced Sampling | methods | OPES Flooding, Kinetics, Rate, OPES, Machine Learning | Dhiman Ray | COMBINE RMSD OPES_METAD CUSTOM WHOLEMOLECULES DISTANCE MOLINFO ENDPLUMED POSITION PRINT UNITS CONTACTMAP PYTORCH_MODEL TORSION COMMITTOR CONSTANT BIASVALUE INCLUDE ENERGY GROUP | opes core bias generic pytorch setup colvar function |
| 22.028 | N-glycan conformer distributions in atomistic simulation | bio | REST2, RECT, N-glycan, pucker | Isabell Grothaus | CONVERT_TO_FES READ PRINT HISTOGRAM TORSION DUMPGRID PUCKERING MOLINFO METAD | bias generic colvar gridtools |
| 22.024 | Conformational Entropy as a Potential Liability of Computationally Designed Antibodies | bio | metadynamics, conformational entropy, antibody, nanobody | Thomas Löhr | PBMETAD ALPHABETA ALPHARMSD PRINT COM TORSION WHOLEMOLECULES MOLINFO ANTIBETARMSD RESTART | secondarystructure bias vatom generic setup colvar multicolvar |
| 22.022 | Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir | bio | RMSD, protein-ligand interactions | Isabell Grothaus | PRINT RMSD | generic colvar |
| 22.017 | 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 | RMSD PRINT PYTORCH_MODEL LOWER_WALLS OPES_METAD MATHEVAL WHOLEMOLECULES COORDINATION DISTANCE CUSTOM CENTER FIT_TO_TEMPLATE UPPER_WALLS COMMITTOR FIXEDATOM GROUP | opes core bias vatom pytorch generic colvar function |
| 22.009 | Glycosylation in calixarenes capsule | chemistry | Metadynamics, glycosylation, supramolecular catalysis | GiovanniMaria Piccini | COMBINE RMSD FLUSH PRINT UNITS BRIDGE LOWER_WALLS MATHEVAL WHOLEMOLECULES COORDINATION DISTANCE FIT_TO_TEMPLATE ANGLE UPPER_WALLS DISTANCES GROUP METAD | core bias generic setup colvar multicolvar function adjmat |
| 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 | PRINT UNITS TORSION COM LOWER_WALLS CUSTOM DISTANCE UPPER_WALLS METAD | bias vatom generic setup colvar function |
| 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 | ALPHABETA GYRATION PRINT LOWER_WALLS WHOLEMOLECULES UPPER_WALLS GROUP ENDPLUMED METAD | core bias generic colvar multicolvar |
| 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 | PRINT TORSION FIT_TO_TEMPLATE FIXEDATOM METAD | vatom bias generic colvar |
| 21.032 | Metal-coupled folding mechanism to metallothionein | bio | parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination | Manuel-Peris Diaz | PBMETAD UNITS WHOLEMOLECULES COORDINATION GROUP | core bias generic setup colvar |
| 20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Faidon Brotzakis | RMSD CONVERT_TO_FES READ EMMI PRINT HISTOGRAM BIASVALUE WHOLEMOLECULES DUMPGRID DISTANCES MOLINFO GROUP | core bias generic colvar multicolvar isdb gridtools |
| 20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Cristina Paissoni | SAXS MOLINFO PRINT BIASVALUE INCLUDE WHOLEMOLECULES DISTANCE STATS CENTER GROUP RESTRAINT ENSEMBLE | core bias vatom generic colvar function isdb |
| 20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Valerio Rizzi | PRINT PYTORCH_MODEL OPES_METAD MATHEVAL WHOLEMOLECULES COORDINATION DISTANCE CENTER FIT_TO_TEMPLATE UPPER_WALLS ANGLE ENERGY FIXEDATOM ENDPLUMED GROUP | opes core vatom bias pytorch generic colvar function |
| 20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Vojtech Spiwok | PRINT TORSION METAD | bias generic colvar |
| 20.015 | Rational design of ASCT2 inhibitors using an integrated experimental-computational approach | bio | ASCT2 transporter, small-molecules, cryo-EM, metainference | Max Bonomi | PRINT BIASVALUE DUMPATOMS WHOLEMOLECULES LOAD MOLINFO EMMIVOX GROUP | core bias generic setup isdb |
| 20.012 | Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies | bio | metadynamics, well-tempered ensemble, ligand binding, binding affinity calculations, novel COLVAR, funnel restraints, Hamiltonian replica-exchange, PathCV, COMetPath, SWISH | Francesco Gervasio | MOLINFO CONTACTMAP PRINT COM LOWER_WALLS INCLUDE WHOLEMOLECULES MATHEVAL PROJECTION_ON_AXIS DISTANCE BIASVALUE LOAD FUNCPATHGENERAL UPPER_WALLS GROUP CONSTANT METAD | core vatom bias generic setup colvar function |
| 20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Pratyush Tiwary | COMBINE RMSD PRINT TORSION WHOLEMOLECULES DISTANCE UPPER_WALLS RESTART MOLINFO METAD | bias generic setup colvar function |
| 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 | PRINT WHOLEMOLECULES PATHMSD UPPER_WALLS GROUP MOLINFO METAD RESTART | core bias generic setup colvar |
| 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 | COMBINE CONVERT_TO_FES REWEIGHT_METAD READ PRINT HISTOGRAM COM LOWER_WALLS MATHEVAL DISTANCE UPPER_WALLS DUMPGRID ABMD ENDPLUMED METAD | bias vatom generic colvar function gridtools |
| 19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Giovanni Bussi | MAXENT FLUSH PRINT COM TORSION INCLUDE WHOLEMOLECULES COORDINATION DISTANCE MATHEVAL MOLINFO SORT METAD | bias vatom generic colvar function |
| 19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | GiovanniMaria Piccini | COMBINE FLUSH PRINT UNITS LOWER_WALLS DISTANCE ENERGY UPPER_WALLS METAD | bias generic setup colvar function |
| 19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Gareth Tribello | FCCUBIC FIND_CONTOUR_SURFACE UNITS MORE_THAN CENTER MULTICOLVARDENS DUMPGRID FOURIER_TRANSFORM GROUP | symfunc core vatom function setup fourier contour gridtools |
| 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 MATHEVAL ENDPLUMED METAD | bias generic colvar function |
| 19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Silvio Pipolo | PRINT PIV FUNCPATHMSD LOWER_WALLS CELL UPPER_WALLS METAD | piv bias generic colvar function |
| 19.011 | Automatic Gradient Computation for Collective Variables | other | gradient, differentiation, curvature | Toni Giorgino | ENDPLUMED | generic |
| 19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Max Bonomi | EMMI PRINT BIASVALUE WHOLEMOLECULES MOLINFO GROUP | bias generic isdb core |
| 19.003 | EMMI ClpP | bio | metainference, cryo-EM | Max Bonomi | EMMI PRINT BIASVALUE MOLINFO GROUP | bias generic isdb core |
| 19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Michele Invernizzi | PRINT UNITS POSITION TORSION VES_DELTA_F ENERGY RESTART LOAD ENDPLUMED METAD | bias generic setup ves colvar |
| 25.023 | Molecular simulations of Tau-protein oligomers | bio | metadynamics, proteins, aggregation | Giovanni Bussi | CUSTOM CONTACTMAP METAD RESTART RESTRAINT FLUSH RMSD PRINT | generic colvar function bias setup |
| 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 | BIASVALUE GROUP EMMIVOX MOLINFO WHOLEMOLECULES PRINT | bias generic core isdb |
| 25.016 | Advancing in silico drug design with Bayesian refinement of AlphaFold models | bio | bAIes, AlphaFold, Bayesian refinement, virtual screening, docking, small-molecule, enrichment | Samiran Sen | PRINT GROUP BIASVALUE BAIES | bias isdb core generic |
| 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 | DUMPATOMS DISTANCE BIASVALUE COORDINATION GROUP MOLINFO UPPER_WALLS CENTER DUMPMASSCHARGE EMMI WHOLEMOLECULES RMSD PARABETARMSD PRINT ALPHARMSD PBMETAD COM | vatom generic secondarystructure colvar core bias isdb |
| 24.026 | Constant pH metadynamics of RNA oligomers | bio | metadynamics, pH, RNA | Giovanni Bussi | PUCKERING METAD MOLINFO RESTART TORSION PRINT | bias colvar generic setup |
| 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 | OPES_EXPANDED ECV_MULTITHERMAL DISTANCE FIT_TO_TEMPLATE OPES_METAD_EXPLORE FIXEDATOM GROUP UPPER_WALLS LOWER_WALLS CENTER TORSION ENERGY WHOLEMOLECULES COORDINATION ENDPLUMED ANGLE PRINT MATHEVAL | vatom generic colvar core function bias opes |
| 24.008 | yCD Metadynamics | bio | volume-based MetaD, path CVs, infrequent MetaD, product release | James McCarty | DISTANCE METAD PATH RMSD PRINT COM COMMITTOR GROUP FLUSH ENDPLUMED READ DUMPGRID FIT_TO_TEMPLATE REWEIGHT_METAD UPPER_WALLS WHOLEMOLECULES WRAPAROUND MATHEVAL CONTACTMAP CONVERT_TO_FES FIXEDATOM MOLINFO INCLUDE HISTOGRAM COORDINATION | vatom gridtools generic mapping colvar core function bias |
| 24.007 | SWISH-X | bio | swish-x, SWISH-X, swish, expanded SWISH | Alberto Borsatto | OPES_EXPANDED ECV_MULTITHERMAL CONTACTMAP MOLINFO UPPER_WALLS INCLUDE ENERGY WHOLEMOLECULES PRINT | colvar opes generic bias |
| 24.003 | Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations | chemistry | steered molecular dynamics, foldamers, peptoids, bio-inspired | Kaylyn Torkelson | ALPHABETA DISTANCE COORDINATION INCLUDE MOVINGRESTRAINT TORSION WHOLEMOLECULES GYRATION PRINT COM | vatom generic colvar multicolvar bias |
| 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 | CUSTOM DISTANCE OPES_METAD UNITS UPPER_WALLS COMBINE LOWER_WALLS TORSION FLUSH PRINT COMMITTOR | generic colvar function bias opes setup |
| 23.043 | Modeling the ferroelectric phase transition in barium titanate with DFT accuracy and converged sampling | materials | Barium Titanate, ferroelectric phase transition, Machine Learning, polarization order parameters | Lorenzo Gigli | SELECT_COMPONENTS METAD TRANSPOSE SUM INCLUDE FLUSH PRINT MATHEVAL | valtools generic function bias matrixtools |
| 23.039 | Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation | chemistry | metadynamics, ligand dissociation | Eric Beyerle | DISTANCE METAD FIXEDATOM MOLINFO COMBINE UPPER_WALLS CENTER DUMPMASSCHARGE RESTRAINT PRINT | vatom generic colvar function 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 | CUSTOM DISTANCE OPES_METAD FIXEDATOM UNITS GROUP UPPER_WALLS LOWER_WALLS COORDINATIONNUMBER ZDISTANCES ENERGY FLUSH PRINT DISTANCES COMMITTOR COM MATHEVAL | vatom generic colvar function core symfunc multicolvar bias opes setup |
| 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 | CUSTOM METAD BIASVALUE UNITS UPPER_WALLS LOWER_WALLS PATHMSD FLUSH TIME PRINT DRR | drr generic colvar function bias setup |
| 23.005 | A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs | bio | metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A | Timothy Clark | READ DISTANCE METAD DUMPGRID CONVERT_TO_FES REWEIGHT_METAD MOLINFO HISTOGRAM WHOLEMOLECULES RMSD PRINT MATHEVAL | gridtools generic colvar function bias |
| 22.044 | Colloid Crystallisation Analyses | materials | Q4, Q6, Pair Entropy, DFS | Aaron Finney | Q4 MFILTER_LESS DFSCLUSTERING MFILTER_MORE LOCAL_Q4 GROUP COMBINE LOCAL_AVERAGE CLUSTER_NATOMS COORDINATIONNUMBER CONTACT_MATRIX LOCAL_Q6 PRINT Q6 | generic clusters core function adjmat multicolvar symfunc |
| 22.042 | Metadynamics of NSP10 and variants | bio | metadynamics, NSP10, crystal structure, variants | Shozeb Haider | PRINT TORSION METAD | bias colvar generic |
| 22.041 | Skipping the Replica Exchange Ladder with Normalizing Flows | methods | OPES, alanine, normalizing flows, replica exchange | Michele Invernizzi | OPES_EXPANDED ECV_MULTITHERMAL OPES_METAD UNITS TORSION ENERGY PRINT ENDPLUMED POSITION | colvar opes generic setup |
| 22.037 | Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site | chemistry | metadynamics, DNA, abasic | Mike Jones | PRINT DISTANCES DISTANCE METAD | multicolvar colvar generic bias |
| 22.016 | Homogeneous ice nucleation in an ab initio machine learning model of water | chemistry | ice, water, nucleation, seeding, environment similarity, interfacial free energy, interfaces | Pablo Piaggi | CUSTOM OPES_METAD DUMPGRID UPPER_WALLS ENVIRONMENTSIMILARITY RESTART ENERGY HISTOGRAM PRINT VOLUME AROUND | envsim gridtools volumes generic colvar function bias opes setup |
| 22.013 | Ligand dissociation from PreQ1 riboswitch | bio | ligand, RNA, metadynamics, pRAVE | Yihang Wang | DISTANCE METAD MOLINFO COMBINE COORDINATIONNUMBER WHOLEMOLECULES RMSD PRINT COM COMMITTOR | vatom generic colvar function bias symfunc |
| 22.006 | Peptide framework for screening the effects of amino acids on assembly | bio | metadynamics, peptides | Andrew White | PRINT METAD DUMPGRID CONVERT_TO_FES COMBINE GROUP INCLUDE HISTOGRAM GYRATION REWEIGHT_BIAS DISTANCES COM | vatom gridtools generic colvar function core multicolvar 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 | DISTANCE METAD COMBINE UPPER_WALLS LOWER_WALLS COORDINATIONNUMBER COORDINATION PRINT | generic colvar function bias symfunc |
| 21.037 | Molecular Dynamics simulations of RBD/hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain | Max Bonomi | PRINT DISTANCE RMSD | colvar 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 | |
| 21.004 | 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 UPPER_WALLS LOWER_WALLS PATHMSD RESTART WHOLEMOLECULES PRINT | bias colvar generic setup |
| 20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Adriana Pietropaolo | COORDINATION CENTER WHOLEMOLECULES PRINT PBMETAD | bias vatom colvar generic |
| 20.028 | Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane | bio | metadynamics, KRas-4B, anionic membrane | Huixia Lu | DISTANCE METAD FIT_TO_TEMPLATE RESTART CENTER PRINT | vatom generic colvar bias setup |
| 20.021 | Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins. | bio | phi-values, restrained MD, transition-state, protein folding, disordered proteins, protein evolution | Cristina Paissoni | MOLINFO RESTRAINT WHOLEMOLECULES COORDINATION STATS PRINT | bias colvar function 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 | ALPHABETA BIASVALUE ANTIBETARMSD CS2BACKBONE GROUP MOLINFO LOWER_WALLS UPPER_WALLS FLUSH WHOLEMOLECULES PRINT ENDPLUMED PBMETAD | generic secondarystructure core multicolvar bias isdb |
| 19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Valerio Rizzi | METAD UNITS GROUP COMBINE COORDINATIONNUMBER RESTART FLUSH PRINT ENDPLUMED EXTERNAL | generic function core bias symfunc setup |
| 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 | PRINT VOLUME Q6 TD_WELLTEMPERED OPT_DUMMY COMBINE OPT_AVERAGED_SGD REWEIGHT_BIAS READ DUMPGRID BF_LEGENDRE UPPER_WALLS ENERGY CELL MATHEVAL REWEIGHT_TEMP_PRESS TD_MULTITHERMAL_MULTIBARIC CONVERT_TO_FES LOAD LOWER_WALLS RESTART VES_LINEAR_EXPANSION HISTOGRAM | gridtools ves generic colvar function bias symfunc setup |
| 19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Sandro Bottaro | DISTANCE METAD MOLINFO TORSION WHOLEMOLECULES RMSD PRINT ERMSD | bias colvar generic |
| 19.059 | cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide | bio | bias-exchange metadynamics, cis-trans isomerization | Fabrizio Marinelli | METAD RANDOM_EXCHANGES INCLUDE TORSION PRINT | bias colvar generic |
| 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 UPPER_WALLS ENERGY PRINT COM | bias vatom colvar generic |
| 19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Paolo Raiteri | DISTANCE METAD UNITS UPPER_WALLS RESTART FLUSH PRINT MATHEVAL | generic colvar function bias setup |
| 19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Davide Provasi | CONTACTMAP DISTANCE METAD FUNCPATHMSD WHOLEMOLECULES RMSD PRINT ENDPLUMED COM | vatom generic colvar function bias |
| 19.030 | Coarse-Grained MetaDynamics (CG-MetaD) | bio | Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy | Vittorio Limongelli | DISTANCE METAD UPPER_WALLS LOWER_WALLS WHOLEMOLECULES PRINT COM | bias vatom colvar generic |
| 19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Glen Hocky | DISTANCE COMBINE RESTRAINT TORSION EDS PRINT | eds generic colvar function bias |
| 19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Kresten Lindorff-Larsen | ALPHABETA METAD MOLINFO COMBINE FLUSH PRINT COMMITTOR | multicolvar function generic bias |
| 19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Adriana Pietropaolo | METAD BIASVALUE CONSTANT TORSION WHOLEMOLECULES PRINT MATHEVAL | bias colvar function generic |
| 19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Matteo Salvalaglio | METAD COMBINE UPPER_WALLS LOWER_WALLS TORSION ENERGY PRINT CELL ENDPLUMED VOLUME MATHEVAL | bias colvar function generic |
| 19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Matteo Salvalaglio | METAD COORDINATIONNUMBER RESTART GYRATION PRINT DISTANCES ENDPLUMED | generic colvar multicolvar bias symfunc setup |
| 19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Carlo Camilloni | DISTANCE BIASVALUE MOLINFO GROUP UPPER_WALLS INCLUDE ENDPLUMED CENTER RESTRAINT WHOLEMOLECULES RMSD SAXS STATS PRINT | vatom generic colvar core function bias isdb |
| 19.009 | RNA tetraloops folding | bio | metadynamics, RNA, folding | Giovanni Bussi | METAD MOLINFO WHOLEMOLECULES RMSD PRINT ENDPLUMED ERMSD | bias colvar generic |
| 19.005 | Cmyc small molecule interaction | bio | metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP | Gabriella Heller | ALPHABETA DISTANCE CS2BACKBONE METAINFERENCE MOLINFO GROUP INCLUDE CENTER WHOLEMOLECULES GYRATION COORDINATION PBMETAD PRINT | vatom generic colvar core multicolvar bias isdb |
| 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 | WHOLEMOLECULES DISTANCE UPPER_WALLS FIXEDATOM ANGLE OPES_METAD_EXPLORE PRINT FIT_TO_TEMPLATE GROUP MATHEVAL COORDINATION ENERGY CENTER | colvar bias generic vatom core function opes |
| 25.011 | Chiral perovskite nucleation | chemistry | metadynamics, chiral perovskites, nucleation | Adriana Pietropaolo | MULTI_RMSD DISTANCE UPPER_WALLS UNITS RESTART PBMETAD PRINT MATHEVAL LOWER_WALLS | colvar bias setup generic function |
| 24.030 | NMR guided simulation of dsRBD | bio | Metainference, NMR, protein dynamics | Debadutta Patra | WHOLEMOLECULES FLUSH RDC ENSEMBLE METAINFERENCE STATS DISTANCE MOLINFO PRINT GROUP ALPHABETA | colvar generic core function multicolvar isdb |
| 24.020 | Graph Neural Network-State Predictive Information Bottleneck (GNN-SPIB) approach for learning molecular thermodynamics and kinetics | bio | LJ7, alanine, well-tempered metadynamics, infrequent metadynamics, machine learning | Ziyue Zou, Dedi Wang, Pratyush Tiwary | METAD COMMITTOR LOAD PRINT GROUP TORSION | colvar bias setup generic core |
| 24.014 | Learning Collective Variables with Synthetic Data Augmentation through Physics-inspired Geodesic Interpolation | methods | data augmentation, geodesic interpolation, collective variables, protein folding | Juno Nam | METAD WHOLEMOLECULES FLUSH UPPER_WALLS MOLINFO RMSD PRINT LOWER_WALLS COORDINATION DRR PYTORCH_MODEL | drr colvar bias pytorch generic |
| 24.011 | Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble | methods | committor, machine learning | Peilin Kang | LOWER_WALLS ENDPLUMED POSITION TORSION DISTANCE MOLINFO PRINT CELL MATHEVAL INCLUDE UPPER_WALLS UNITS CUSTOM LOAD RMSD GROUP COORDINATION BIASVALUE WHOLEMOLECULES ENERGY | colvar bias generic setup core function |
| 24.010 | Oxytocin metadynamics simulation | bio | metadynamics, oxytocin, peptide | Jan Beránek | METAD WHOLEMOLECULES FLUSH RESTART PRINT TORSION | setup generic colvar bias |
| 23.032 | Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics | bio | metadynamics, tSNE, neural network, machine learning, trp-cage, folding | Vojtech Spiwok | METAD WHOLEMOLECULES ALPHARMSD MOLINFO COMBINE FIT_TO_TEMPLATE ANN PRINT POSITION | bias colvar generic secondarystructure function annfunc |
| 23.023 | Rational design of novel biomimetic sequence-defined polymers for mineralization applications | methods | metadynamics, surface binding, biomimetic mineralization | Kaylyn Torkelson | DISTANCE GYRATION UPPER_WALLS COM PBMETAD PRINT COORDINATION | generic vatom colvar bias |
| 23.018 | Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention | materials | metadynamics, surface binding, peptide adsorption | Kaylyn Torkelson | DISTANCE GYRATION UPPER_WALLS COM PBMETAD PRINT | generic vatom colvar bias |
| 23.000 | Atomistic simulations of RNA tetraloop folding via PTWTE-WTM | bio | parallel tempering, well-tempered metadynamics, well-tempered ensemble, RNA, Tetraloop, Folding | Gül Zerze | METAD WHOLEMOLECULES CONTACTMAP UPPER_WALLS PRINT ENERGY LOWER_WALLS | colvar generic bias |
| 22.038 | Enhanced Sampling Aided Design of Molecular Photoswitches | chemistry | reaction discovery, OPES explore, graph CV | Umberto Raucci | UNITS OPES_METAD_EXPLORE CUSTOM PRINT COORDINATION PYTORCH_MODEL | colvar pytorch setup generic function opes |
| 22.036 | Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction | bio | Well-tempered MetaDynamics with Hamiltonian Replica Exchange | Miroslav Krepl | METAD GHBFIX FLUSH UPPER_WALLS CUSTOM LOAD MOLINFO COMBINE GROUP PRINT COORDINATION BIASVALUE | colvar bias generic setup core function |
| 22.032 | Reciprocal barrier restraint. Application to path-meta-eABF | methods | restraint, upper wall, lower wall, path colvar, meta-eABF, metadynamics, DRR, protein conformational transition, PROTAC | Istvan Kolossvary | METAD FLUSH CUSTOM PATHMSD PRINT DRR BIASVALUE | drr colvar bias generic function |
| 22.020 | Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix–Junction–Helix RNA | bio | RNA force field, Helix-Junction-Helix RNA, SAXS, Well tempered metadynamics | Weiwei He | METAD WHOLEMOLECULES DISTANCE COM PRINT GROUP TORSION | colvar bias generic vatom core |
| 22.012 | Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT | bio | contact maps, protein-protein interactions | Isabell-Louise Grothaus | PRINT CONTACTMAP DISTANCE CENTER | generic vatom colvar |
| 21.051 | Automatic learning of hydrogen-bond fixes in an AMBER RNA force field | methods | force field, RNA | Giovanni Bussi | METAD WHOLEMOLECULES MOLINFO COMBINE PRINT COORDINATION ERMSD BIASVALUE | colvar generic function bias |
| 21.038 | Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics | materials | metadynamics, SGOOP, nucleation, urea | Ziyue Zou | METAD INCLUDE VOLUME LOAD COMBINE GROUP PRINT ENERGY COORDINATIONNUMBER CENTER | colvar bias generic setup vatom core function symfunc |
| 21.031 | Photo-switchable sulfonulureas in KATP channel | bio | metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels | Katarzyna Walczewska-Szewc | METAD WHOLEMOLECULES DISTANCE UPPER_WALLS UNITS COM PRINT LOWER_WALLS | colvar bias generic setup vatom |
| 21.026 | Probing allosteric regulations with coevolution-driven molecular simulations | bio | metadynamics, coevolution, allostery, adenylate cyclase | Francesco Colizzi | METAD WHOLEMOLECULES DISTANCE UPPER_WALLS UNITS COM PATHMSD PRINT | colvar bias generic setup vatom |
| 21.025 | Computational and biochemical analysis of type IV pilus dynamics and stability | bio | molecular dynamics, calcium binding, Type IV pilus | Yasaman Karami | PRINT LOWER_WALLS DISTANCE UPPER_WALLS | colvar generic 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 | ENVIRONMENTSIMILARITY VOLUME UPPER_WALLS ECV_MULTITHERMAL_MULTIBARIC VES_LINEAR_EXPANSION OPES_EXPANDED TD_UNIFORM RESTART PRINT MATHEVAL ENERGY OPT_AVERAGED_SGD ECV_UMBRELLAS_LINE Q6 BF_LEGENDRE | ves colvar bias setup generic function envsim symfunc opes |
| 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 | ABMD DISTANCE MOLINFO RESTART PRINT TORSION ERMSD CENTER | colvar bias generic setup vatom |
| 19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Gabriele Cesare Sosso | LOCAL_Q6 FLUSH CLUSTER_NATOMS CLUSTER_WITHSURFACE COMMITTOR Q6 MFILTER_MORE DFSCLUSTERING OUTPUT_CLUSTER ENDPLUMED CONTACT_MATRIX | clusters generic adjmat multicolvar symfunc |
| 19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Jim Pfaendtner | METAD EXTERNAL GROUP ENERGY COORDINATION | colvar core bias |
| 19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Mattia Bernetti | METAD WHOLEMOLECULES GYRATION ALPHARMSD MOLINFO PRINT ENERGY ENDPLUMED | colvar generic secondarystructure bias |
| 19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Riccardo Capelli | METAD WHOLEMOLECULES FLUSH UPPER_WALLS HISTOGRAM COM WRAPAROUND CONVERT_TO_FES READ ENDPLUMED PRINT GROUP FIT_TO_TEMPLATE MATHEVAL COORDINATION REWEIGHT_METAD DUMPGRID POSITION | bias colvar generic vatom core function gridtools |
| 19.013 | RNA FF FITTING | methods | force field, RNA | Giovanni Bussi | INCLUDE PUCKERING MOLINFO MATHEVAL CONSTANT TORSION BIASVALUE | generic function colvar bias |