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
25.006	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	PBMETAD READ TORSION PRINT VOLUME GYRATION INCLUDE RESTART ENERGY CENTER DISTANCE	bias setup generic vatom colvar
25.001	RNA G-quadruplex folding with ST-metaD protocol	bio	RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD	Pavlína Pokorná	METAD ERMSD MOLINFO COMBINE WHOLEMOLECULES	bias function generic colvar
24.034	Umbrella sampling of ion in transporter SLC26A7	bio	umbrella sampling, transporter, ions	Xiaoli Lu	POSITION PRINT UNITS RESTRAINT	setup bias generic colvar
24.033	Transient interactions between the fuzzy coat and the cross-b core of brain-derived Ab42 filaments	bio	CryoEM, MEMMI, Metadynamics, Metainference, Ab42 Fibrils, structural ensemble	Maria Milanesi	PBMETAD UPPER_WALLS DISTANCE PARABETARMSD GROUP ALPHARMSD RMSD COM EMMI PRINT BIASVALUE CENTER DUMPATOMS COORDINATION MOLINFO DUMPMASSCHARGE WHOLEMOLECULES	bias isdb generic core secondarystructure vatom 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	METAD DISTANCE PRINT RMSD MATHEVAL MOLINFO WHOLEMOLECULES	bias function generic colvar
23.034	Urea nucleation in water: do long-range forces matter?	materials	LMF theory, Metadynamics, Nucleation	Ziyue Zou	LOAD GROUP PRINT INCLUDE CENTER COORDINATIONNUMBER METAD	symfunc setup bias generic core vatom
23.020	FEP simulations of ATOX1 homodimer	chemistry	parallel bias metadynamics, FEP, free-energy of metal ion dissociation	Adriana Pietropaolo	PBMETAD PRINT MATHEVAL CONSTANT ANGLE BIASVALUE DISTANCE WHOLEMOLECULES	bias function generic colvar
23.014	Structural basis of dimerization of chemokine receptors CCR5 and CXCR4	bio	metadynamics, oligomerization, chemokine receptors, GPCR, membrane	Vittorio Limongelli	METAD UPPER_WALLS TORSION PRINT FLUSH COM DISTANCE COMBINE WHOLEMOLECULES	bias function generic vatom colvar
22.043	Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES	bio	OPES, RNA, Tetraloop, Folding	Gül Zerze	ECV_UMBRELLAS_LINE OPES_EXPANDED CONTACTMAP PRINT ENERGY ECV_MULTITHERMAL WHOLEMOLECULES	opes generic colvar
22.025	Bubble nucleation rate predictions in a Lennard-Jones fluid	materials	free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation	Kristof Bal	LOAD CUSTOM UNITS UPPER_WALLS CONVERT_TO_FES REWEIGHT_BIAS RESTRAINT PRINT VOLUME FLUSH COMMITTOR COORDINATIONNUMBER BIASVALUE DUMPGRID MOVINGRESTRAINT HISTOGRAM ANN	symfunc annfunc setup function bias generic gridtools colvar
22.020	Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix–Junction–Helix RNA	bio	RNA force field, Helix-Junction-Helix RNA, SAXS, Well tempered metadynamics	Weiwei He	METAD TORSION GROUP PRINT COM DISTANCE WHOLEMOLECULES	bias generic core vatom colvar
22.008	Ab initio metadynamics determination of temperature-dependent free-energy landscape in ultrasmall silver clusters	materials	Well tempered metadynamics, ab-initio, ase	Daniel Sucerquia	UNITS UPPER_WALLS METAD DISTANCE GYRATION FLUSH COM COORDINATIONNUMBER COORDINATION LOWER_WALLS COMBINE	symfunc setup bias function generic vatom colvar
22.006	Peptide framework for screening the effects of amino acids on assembly	bio	metadynamics, peptides	Andrew White	DISTANCES CONVERT_TO_FES REWEIGHT_BIAS GROUP GYRATION COM PRINT INCLUDE DUMPGRID METAD HISTOGRAM COMBINE	gridtools bias function generic core multicolvar vatom colvar
21.047	Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations	materials	pair entropy, metadynamics, ves, solids, crystallization	Pablo Piaggi	LOAD VES_LINEAR_EXPANSION PRINT VOLUME PAIRENTROPY BF_LEGENDRE RESTART TD_WELLTEMPERED ENERGY OPT_AVERAGED_SGD METAD COMBINE	setup ves bias function generic gridtools colvar
21.046	Ubiquitin Interacting Motifs, Duality Between Structured and Disordered Motifs	bio	wt metadynamics, ubiquitin, ataxin-3, short linear motifs, ubiquitin binding motif, moonlight functions, intrinsic disorder	Elena Papaleo	ALPHABETA UPPER_WALLS METAD GROUP GYRATION PRINT ENDPLUMED LOWER_WALLS WHOLEMOLECULES	bias generic core multicolvar colvar
21.028	From Enhanced Sampling to Reaction Profiles	methods	collective variables, multi-state, machine learning, Deep-TDA	Enrico Trizio	UNITS PRINT ANGLE PYTORCH_MODEL DISTANCES LOWER_WALLS WHOLEMOLECULES FIXEDATOM FIT_TO_TEMPLATE GROUP ENDPLUMED TORSION COORDINATION DISTANCE LOAD UPPER_WALLS MATHEVAL CENTER OPES_METAD	setup bias function generic core opes pytorch multicolvar vatom colvar
21.025	Computational and biochemical analysis of type IV pilus dynamics and stability	bio	molecular dynamics, calcium binding, Type IV pilus	Yasaman Karami	DISTANCE PRINT LOWER_WALLS UPPER_WALLS	bias generic colvar
21.023	Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling	methods	enhanced sampling, collective variables, machine learning	Jakub Rydzewski	CUSTOM UNITS METAD REWEIGHT_METAD TORSION PRINT CONSTANT INCLUDE BIASVALUE ENERGY DISTANCE	function setup bias generic colvar
21.006	OPES, On-the-fly Probability Enhanced Sampling Method	methods	opes, alanine dipeptide, well-tempered, multithermal, multiumbrella	Michele Invernizzi	ECV_UMBRELLAS_LINE OPES_EXPANDED TORSION PRINT ENDPLUMED ENERGY OPES_METAD ECV_MULTITHERMAL	opes generic colvar
21.004	Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy	bio	machine learning, well-tempered metadynamics, path collective variable, potential of mean force, standard binding free energy calculations, host-guest, protein-ligand unbinding	Dorothea Gobbo	UPPER_WALLS PRINT RESTART METAD PATHMSD LOWER_WALLS WHOLEMOLECULES	bias setup generic colvar
20.033	COVID-19 Spike protein opening transition mechanism	bio	EMMI, CryoEM, COVID-19, Spike, Metainference	Faidon Brotzakis	DISTANCES CONVERT_TO_FES READ PRINT GROUP RMSD EMMI BIASVALUE DUMPGRID MOLINFO HISTOGRAM WHOLEMOLECULES	gridtools bias isdb generic core multicolvar colvar
20.026	Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor	bio	Metadynamics, Umbrella sampling	Brandon Peters	CONVERT_TO_FES RESTRAINT REWEIGHT_METAD PRINT DUMPGRID METAD HISTOGRAM MULTI_RMSD	bias gridtools generic colvar
20.011	Uremic toxin analysis	bio	metadynamics, uremic toxin, serum albumin	Jim Pfaendtner	DISTANCES GROUP PRINT RESTART CENTER COORDINATION DISTANCE WHOLEMOLECULES	setup generic core multicolvar vatom colvar
20.001	Conformational stability and dynamics in solution and in crystals report similarly on unfolding and aggregation propensity of amyloidogenic proteins	bio	metainference, metadynamics, NMR, protein dynamics, b2m, protein crystals	Carlo Camilloni	ALPHABETA PBMETAD UPPER_WALLS CS2BACKBONE GROUP PRINT FLUSH ENDPLUMED BIASVALUE MOLINFO ANTIBETARMSD LOWER_WALLS WHOLEMOLECULES	bias isdb generic core secondarystructure multicolvar
19.079	Impact of Glutamate Carboxylation in the Adsorption of the alpha-1 Domain of Osteocalcin to Hydroxyapatite and Titania	bio	metadynamics, peptide adsorption, parallel tempering, well-tempered ensemble	Sarah Alamdari	METAD DISTANCE UPPER_WALLS GROUP GYRATION COM PRINT ENERGY MOLINFO	bias generic core vatom colvar
19.068	Rethinking Metadynamics	methods	metadynamics, opes, convergence	Michele Invernizzi	UNITS TORSION PRINT ENDPLUMED EXTERNAL OPES_METAD METAD POSITION	setup bias generic opes colvar
19.066	Finding ligand unbinding reaction pathways	methods	maze, ligand unbinding	Jakub Rydzewski	UNITS MAZE_SIMULATED_ANNEALING MAZE_OPTIMIZER_BIAS PRINT MAZE_LOSS POSITION	setup maze generic colvar
19.060	Neural networks-based variationally enhanced sampling	methods	ves, neural networks	Luigi Bonati	LOAD UNITS TORSION PRINT ENDPLUMED ENERGY ENVIRONMENTSIMILARITY Q6 POSITION	symfunc setup generic envsim colvar
19.055	Flying Gaussian method	methods	flying Gaussians, alanine dipeptide, peptide bond, Met-enkephalin	Vojtech Spiwok	DISTANCE TORSION PRINT MATHEVAL METAD COMBINE	function bias generic colvar
19.044	Multithermal-multibaric simulations using VES	methods	ves, Wang Landau, multicanonical, water, density anomaly	Pablo Piaggi	VES_LINEAR_EXPANSION READ CONVERT_TO_FES REWEIGHT_BIAS PRINT VOLUME BF_LEGENDRE RESTART ENERGY OPT_DUMMY OPT_AVERAGED_SGD REWEIGHT_TEMP_PRESS AVERAGE DUMPGRID HISTOGRAM COMBINE TD_MULTITHERMAL_MULTIBARIC	bias ves setup function generic gridtools colvar
19.039	Funnel Metadynamics	bio	funnel-metadynamics, absolute binding free energy, ligand-receptor complexes	Vittorio Limongelli	FUNNEL_PS FUNNEL METAD UPPER_WALLS PRINT RMSD COM DISTANCE LOWER_WALLS WHOLEMOLECULES	bias generic funnel vatom colvar
19.030	Coarse-Grained MetaDynamics (CG-MetaD)	bio	Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy	Vittorio Limongelli	UPPER_WALLS METAD PRINT COM DISTANCE LOWER_WALLS WHOLEMOLECULES	bias vatom generic colvar
19.015	Ibuprofen conformational dynamics and thermodynamics surface	materials	Ibuprofen, crystal, surface, solvents, conformers, metadynamics	Matteo Salvalaglio	UPPER_WALLS METAD COMMITTOR TORSION PRINT CENTER DISTANCE LOWER_WALLS	bias vatom generic colvar
19.013	RNA FF FITTING	methods	force field, RNA	Giovanni Bussi	PUCKERING TORSION MATHEVAL CONSTANT INCLUDE BIASVALUE MOLINFO	function bias generic colvar
19.002	EMMI STRA6	bio	metainference, cryo-EM	Max Bonomi	GROUP PRINT EMMI BIASVALUE MOLINFO	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	UNITS ENDPLUMED CUSTOM BIASVALUE MOLINFO RMSD METAD WHOLEMOLECULES POSITION DISTANCE TORSION PYTORCH_MODEL UPPER_WALLS GROUP PRINT LOWER_WALLS OPES_METAD ENERGY	function colvar pytorch bias core generic opes setup
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	WHOLEMOLECULES HISTOGRAM DISTANCE TORSION ANGLE COORDINATION GROUP PRINT DUMPGRID CONVERT_TO_FES	generic gridtools colvar core
24.032	DeepLNE++	methods	PATHCV, OPES	Thorben Fröhlking	DISTANCE GROUP TORSION COORDINATION OPES_METAD COMBINE CUSTOM PRINT ENERGY LOAD	function colvar core generic opes setup
24.030	NMR guided simulation of dsRBD	bio	Metainference, NMR, protein dynamics	Debadutta Patra	FLUSH PRINT MOLINFO RDC WHOLEMOLECULES STATS DISTANCE METAINFERENCE ALPHABETA GROUP ENSEMBLE	function colvar isdb core generic 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	DIHCOR FLUSH ENDPLUMED MOLINFO WHOLEMOLECULES ANTIBETARMSD GYRATION DISTANCE PBMETAD TORSION PARABETARMSD COORDINATION ALPHARMSD COMBINE GROUP PRINT INCLUDE	function colvar secondarystructure bias core generic multicolvar
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	FLUSH COORDINATIONNUMBER BIASVALUE RESTART MOLINFO MATHEVAL METAD DISTANCE RESTRAINT TORSION PRINT COMMITTOR ENERGY	function colvar bias generic symfunc setup
24.012	Molecular simulations to investigate the impact of N6-methylation in RNA recognition	bio	metadynamics, alchemistry, RNA modification, RNA:protein interactions	Giovanni Bussi	DEBUG CENTER BIASVALUE MOLINFO METAD DISTANCE COORDINATION GHBFIX COMBINE GROUP PRINT COM LOWER_WALLS UPPER_WALLS	function colvar bias core generic vatom
24.010	Oxytocin metadynamics simulation	bio	metadynamics, oxytocin, peptide	Jan Beránek	FLUSH RESTART WHOLEMOLECULES METAD TORSION PRINT	generic colvar setup bias
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	BIASVALUE MOLINFO ERMSD WHOLEMOLECULES METAD COORDINATION GHBFIX COMBINE PRINT	generic colvar function bias
23.030	Data Driven Classification of Ligand Unbinding Pathways	bio	OPES Explore, OPES Flooding, Benzene T4 Lysozyme, Ligand unbinding, Pathway classification, Kinetics, Residence time	Dhiman Ray	CENTER TORSION CUSTOM UPPER_WALLS ENDPLUMED BIASVALUE WHOLEMOLECULES DISTANCE COORDINATION COMMITTOR OPES_METAD_EXPLORE FLUSH MOLINFO MATHEVAL PRINT ENERGY UNITS POSITION FIT_TO_TEMPLATE GROUP COM LOWER_WALLS OPES_METAD WRAPAROUND	function colvar bias core generic opes setup vatom
23.026	Machine Learning Nucleation Collective Variables with Graph Neural Networks	chemistry	Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks	Florian Dietrich	MFILTER_MORE COORDINATIONNUMBER MOVINGRESTRAINT Q6 LOCAL_Q6 METAD COMBINE GROUP PRINT LOWER_WALLS	function bias core generic multicolvar symfunc
23.019	Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors	bio	binding pathway, binding energy, sketch-map, drug development	Raitis Bobrovs	PATHMSD CUSTOM VSTACK DISSIMILARITIES WHOLEMOLECULES METAD DISTANCE COLLECT_FRAMES SKETCHMAP_PROJECTION LANDMARK_SELECT_FPS TRANSPOSE PRINT VORONOI COM SKETCHMAP UPPER_WALLS	function valtools colvar landmarks bias generic matrixtools dimred vatom
23.001	Quantum phase diagram of water	chemistry	Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella	Sigbjørn-Løland Bore	RESTART OPES_EXPANDED ENVIRONMENTSIMILARITY ECV_UMBRELLAS_LINE PRINT LOWER_WALLS INCLUDE UPPER_WALLS	bias envsim generic opes setup
22.045	Binding mode and mechanism of enzymatic polyethylene terephthalate degradation	bio	metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation	Francesco Colizzi	MOVINGRESTRAINT WHOLEMOLECULES METAD DISTANCE ANGLE PRINT COM LOWER_WALLS UPPER_WALLS	generic colvar vatom bias
22.041	Skipping the Replica Exchange Ladder with Normalizing Flows	methods	OPES, alanine, normalizing flows, replica exchange	Michele Invernizzi	UNITS ENDPLUMED ECV_MULTITHERMAL OPES_EXPANDED POSITION TORSION PRINT OPES_METAD ENERGY	generic opes setup colvar
22.031	Rare Event Kinetics from Adaptive Bias Enhanced Sampling	methods	OPES Flooding, Kinetics, Rate, OPES, Machine Learning	Dhiman Ray	TORSION COMBINE CUSTOM ENDPLUMED BIASVALUE WHOLEMOLECULES DISTANCE CONTACTMAP COMMITTOR INCLUDE MOLINFO RMSD CONSTANT PRINT ENERGY UNITS POSITION PYTORCH_MODEL GROUP OPES_METAD	function colvar pytorch bias core generic opes setup
22.013	Ligand dissociation from PreQ1 riboswitch	bio	ligand, RNA, metadynamics, pRAVE	Yihang Wang	COORDINATIONNUMBER MOLINFO RMSD WHOLEMOLECULES METAD DISTANCE COMBINE PRINT COMMITTOR COM	function colvar bias generic symfunc vatom
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 CENTER DISTANCE	generic vatom colvar
22.009	Glycosylation in calixarenes capsule	chemistry	Metadynamics, glycosylation, supramolecular catalysis	GiovanniMaria Piccini	UNITS FLUSH RMSD MATHEVAL WHOLEMOLECULES METAD DISTANCE ANGLE COORDINATION BRIDGE FIT_TO_TEMPLATE COMBINE GROUP PRINT DISTANCES LOWER_WALLS UPPER_WALLS	function colvar bias core generic adjmat multicolvar setup
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	PRINT WHOLEMOLECULES LOAD METAD	generic setup bias
21.052	On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets	materials	Ibuprofen, unbinding, WTmetaD	Matteo Salvalaglio	CENTER COORDINATIONNUMBER ENDPLUMED METAD DISTANCE TORSION PRINT COMMITTOR	colvar bias generic symfunc vatom
21.044	NaCl nucleation	chemistry	metadynamics, DFS clustering	Aaron Finney	CONTACT_MATRIX MFILTER_MORE COORDINATIONNUMBER CLUSTER_DISTRIBUTION Q6 LOCAL_Q6 METAD INSPHERE DFSCLUSTERING HISTOGRAM FIXEDATOM CLUSTER_NATOMS COMBINE GROUP PRINT DUMPGRID	function bias core generic adjmat multicolvar vatom volumes symfunc gridtools clusters
21.029	Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs	bio	metadynamics, small peptide, machine learning	Pratyush Tiwary	FLUSH RESTART MOLINFO TORSION EXTERNAL PRINT ENERGY	generic bias setup colvar
21.018	Localized Volume-based Metadynamics	bio	LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification	Riccardo Capelli	HISTOGRAM UPPER_WALLS ENDPLUMED WHOLEMOLECULES DISTANCE FIXEDATOM COORDINATION FLUSH RMSD MATHEVAL METAD READ PRINT DUMPGRID REWEIGHT_METAD POSITION GROUP CONVERT_TO_FES COM	function colvar bias core generic gridtools vatom
21.017	All-atom simulations of the Vav1 AD construct	bio	metadynamics, parallel-bias, well-tempered	Simone Orioli	RESTART MOLINFO WHOLEMOLECULES METAD PBMETAD CONTACTMAP ALPHABETA ALPHARMSD REWEIGHT_BIAS GROUP PRINT	colvar secondarystructure bias core generic multicolvar setup
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	OPT_AVERAGED_SGD BF_LEGENDRE Q6 RESTART OPES_EXPANDED VOLUME MATHEVAL TD_UNIFORM VES_LINEAR_EXPANSION ENVIRONMENTSIMILARITY ECV_UMBRELLAS_LINE UPPER_WALLS ECV_MULTITHERMAL_MULTIBARIC PRINT ENERGY	function colvar bias envsim generic ves opes symfunc setup
20.031	Soft fluorescent nanoshuttles targeting receptors	chemistry	polymers, receptors, nanoparticles, fluorescent probes	Adriana Pietropaolo	CENTER WHOLEMOLECULES PBMETAD COORDINATION PRINT	generic colvar bias vatom
20.022	Unified Approach to Enhanced Sampling	methods	OPES, expanded ensembles, importance sampling	Michele Invernizzi	TORSION ENVIRONMENTSIMILARITY CUSTOM LOAD UPPER_WALLS ENDPLUMED OPES_EXPANDED WHOLEMOLECULES VOLUME MOLINFO RMSD MATHEVAL ECV_UMBRELLAS_LINE ECV_MULTITHERMAL_MULTIBARIC PRINT ENERGY UNITS ECV_MULTITHERMAL Q6 POSITION ECV_LINEAR	function colvar bias envsim generic opes symfunc setup
20.019	Systematic finite-temperature reduction of crystal energy landscapes	materials	crystals, organics, structure prediction	Matteo Salvalaglio	MATHEVAL VOLUME METAD CELL PRINT LOWER_WALLS ENERGY UPPER_WALLS	generic function bias colvar
20.009	The dynamics of linear polyubiquitin	bio	saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics	Carlo Camilloni	CENTER FLUSH MOLINFO SAXS WHOLEMOLECULES GYRATION DISTANCE STATS PBMETAD TORSION METAINFERENCE ALPHABETA PRINT ENSEMBLE	function colvar isdb bias generic multicolvar vatom
20.007	Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics	bio	metadynamics, loop movement, artificial intelligence	Pratyush Tiwary	RESTART MOLINFO RMSD WHOLEMOLECULES METAD DISTANCE TORSION COMBINE PRINT UPPER_WALLS	function colvar bias generic setup
20.004	Data-driven collective variables for enhanced sampling	methods	collective variables, machine learning, deep-lda	Luigi Bonati	UNITS FLUSH ENDPLUMED MATHEVAL DISTANCE PYTORCH_MODEL TORSION UPPER_WALLS GROUP PRINT COM LOWER_WALLS OPES_METAD LOAD	function colvar pytorch bias core generic opes setup vatom
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	PATHMSD RESTART MOLINFO WHOLEMOLECULES METAD GROUP PRINT UPPER_WALLS	colvar bias core generic 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	OPT_AVERAGED_SGD HISTOGRAM TD_MULTITHERMAL_MULTIBARIC COMBINE LOAD UPPER_WALLS BF_LEGENDRE RESTART VOLUME CELL REWEIGHT_TEMP_PRESS MATHEVAL READ OPT_DUMMY VES_LINEAR_EXPANSION TD_WELLTEMPERED PRINT DUMPGRID ENERGY Q6 REWEIGHT_BIAS CONVERT_TO_FES LOWER_WALLS	function colvar bias generic symfunc gridtools ves setup
19.077	Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations	materials	metadynamics, peptide-surface binding	Jim Pfaendtner	MOLINFO METAD GYRATION DISTANCE UPPER_WALLS PRINT COM ENERGY	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	UNITS MOVINGRESTRAINT ENDPLUMED GYRATION PRINT	generic colvar setup bias
19.072	SINE hairpin MD+NMR	bio	metadynamics, RNA, NMR	Giovanni Bussi	FLUSH MOLINFO MATHEVAL WHOLEMOLECULES METAD DISTANCE MAXENT TORSION COORDINATION PRINT COM SORT INCLUDE	function colvar bias generic vatom
19.061	Diffusion in porous materials	materials	metadynamics, porous materials, diffusion	Kim E. Jelfs	CENTER RESTART METAD DISTANCE GROUP PRINT COM LOWER_WALLS UPPER_WALLS	colvar bias core generic setup vatom
19.052	Gibbs free energy of homogeneous nucleation	materials	nucleation, surface excess free energy	Gareth Tribello	UNITS ENDPLUMED FCCUBIC METAD CELL PRINT UPPER_WALLS	colvar bias generic symfunc setup
19.040	Optimal Metric for Path Collective Variables	bio	metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path	Francesco Luigi Gervasio	ENDPLUMED MATHEVAL METAD TORSION PRINT	generic colvar function bias
19.031	Ice nucleation using PIV-based path coordinates	materials	phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics	Silvio Pipolo	FUNCPATHMSD METAD CELL PRINT LOWER_WALLS PIV UPPER_WALLS	function piv colvar bias generic
19.007	EMMI Microtubules	bio	metainference, cryo-EM	Max Bonomi	EMMI BIASVALUE MOLINFO WHOLEMOLECULES GROUP PRINT	generic isdb bias core
19.003	EMMI ClpP	bio	metainference, cryo-EM	Max Bonomi	EMMI BIASVALUE MOLINFO GROUP PRINT	generic isdb bias core
24.005	Learning Markovian Dynamics with Spectral Maps	methods	spectral map, collective variables, machine learning	Jakub Rydzewski	DISTANCE CUSTOM PRINT UNITS BIASVALUE	colvar function bias generic setup
24.001	A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations	bio	OPES, OPES-Flooding, QM/MM, Kinetics, Enzyme Catalysis	Dhiman Ray	DISTANCE FLUSH OPES_METAD UPPER_WALLS CUSTOM COMBINE TORSION COMMITTOR PRINT UNITS LOWER_WALLS	colvar function bias opes generic setup
23.032	Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics	bio	metadynamics, tSNE, neural network, machine learning, trp-cage, folding	Vojtech Spiwok	COMBINE ALPHARMSD WHOLEMOLECULES MOLINFO PRINT METAD POSITION FIT_TO_TEMPLATE ANN	colvar function annfunc bias secondarystructure generic
23.029	An accurate and efficient SAXS/SANS implementation including solvation layer effects suitable for restrained Molecular Dynamics simulations	bio	SAXS, SANS, SAS, metainference, proteins, nucleic-acid	Federico Ballabio	STATS DISTANCE SAXS RMSD UPPER_WALLS MOLINFO GROUP PRINT WRAPAROUND ENSEMBLE BIASVALUE CENTER	colvar function bias vatom core generic isdb
23.028	Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process	chemistry	Ammonia decomposition; Dynamics;OPES; Neural Network potential	Manyi Yang	DISTANCE FLUSH OPES_METAD UPPER_WALLS CUSTOM GROUP COMMITTOR ENERGY COM PRINT FIXEDATOM DISTANCES UNITS ZDISTANCES COORDINATIONNUMBER LOWER_WALLS MATHEVAL	colvar function bias vatom core opes symfunc generic setup multicolvar
23.021	Into the Dynamics of Rotaxanes at Atomistic Resolution	materials	metadynamics, rotaxanes, molecular shuttles, molecular machines	Luigi Leanza	DISTANCE UPPER_WALLS CUSTOM TORSION PRINT FIXEDATOM METAD CENTER MATHEVAL	colvar function bias vatom generic
23.015	MPCs aggregation	bio	opes_explore, dimerization, MPCs, self-assembly	Vikas Tiwari	DISTANCE UPPER_WALLS CUSTOM GROUP WHOLEMOLECULES COORDINATION PRINT COM OPES_METAD_EXPLORE METAD CENTER LOWER_WALLS	colvar function bias vatom core opes generic
23.010	An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G‑Protein-Coupled Receptor Ligands	bio	GPCR, binding free energy, free energy surface	Timothy Clark	DISTANCE UPPER_WALLS CONSTANT WHOLEMOLECULES PRINT METAD BIASVALUE LOWER_WALLS MATHEVAL	colvar function bias generic
23.008	PBMetaD simulations of Histatin5	bio	metadynamics, IDP, Rg, PPII	Francesco Pesce	GYRATION TORSION WHOLEMOLECULES MOLINFO GROUP PRINT PBMETAD	colvar core bias generic
22.033	Reciprocal barrier restraint. Application to PROTAC passive permeability prediction	methods	PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR	Istvan Kolossvary	DISTANCE FLUSH DRR CUSTOM PRINT COM METAD UNITS BIASVALUE	colvar function bias vatom generic setup drr
22.004	Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques	chemistry	reaction discovery, OPES, collective variables	Umberto Raucci	DISTANCE PYTORCH_MODEL OPES_METAD UPPER_WALLS CUSTOM COORDINATION OPES_METAD_EXPLORE GROUP PRINT COM UNITS LOAD LOWER_WALLS MATHEVAL	colvar function pytorch bias vatom core opes generic setup
22.001	Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials	methods	enhanced sampling, variationally enhanced sampling, ves, metadynamics, bias representation, wavelets, adam	Benjamin Pampel	BF_WAVELETS BF_CUBIC_B_SPLINES BF_LEGENDRE OPT_AVERAGED_SGD PRINT INCLUDE UPPER_WALLS TD_WELLTEMPERED POSITION UNITS VES_OUTPUT_BASISFUNCTIONS FLUSH TD_UNIFORM VES_LINEAR_EXPANSION OPT_ADAM DISTANCE BF_GAUSSIANS COORDINATION ENERGY METAD BF_CHEBYSHEV	colvar bias generic setup ves
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 COMBINE UPPER_WALLS COORDINATION PRINT METAD COORDINATIONNUMBER LOWER_WALLS	colvar function bias symfunc generic
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	ANTIBETARMSD GYRATION PARABETARMSD UPPER_WALLS ALPHARMSD COORDINATION WHOLEMOLECULES GROUP MOLINFO PRINT ENERGY METAD DIHCOR LOWER_WALLS RANDOM_EXCHANGES	colvar bias secondarystructure core generic multicolvar
21.013	Role of vibrational excitation in heterogeneous catalysis	chemistry	catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption	Kristof Bal	EXTERNAL OPT_AVERAGED_SGD REWEIGHT_BIAS PRINT LOAD COORDINATIONNUMBER UPPER_WALLS REWEIGHT_METAD ANGLES DISTANCES UNITS TD_GRID CONVERT_TO_FES FLUSH COMBINE UWALLS HISTOGRAM VES_LINEAR_EXPANSION DISTANCE DUMPGRID COORDINATION RESTRAINT METAD BF_CHEBYSHEV LOWER_WALLS	colvar function gridtools bias symfunc generic setup ves multicolvar
21.007	Sampling enhancement by metadynamics driven by machine learning and de novo protein modelling	bio	metadynamics, machine learning, protein folding	Vojtech Spiwok	COMBINE ALPHARMSD WHOLEMOLECULES MOLINFO POSITION FIT_TO_TEMPLATE MATHEVAL	colvar function generic secondarystructure
20.023	metadynminer and metadynminer3d	methods	metadynamics, visualization, R	Vojtech Spiwok	TORSION METAD PRINT	colvar bias 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	GYRATION UPPER_WALLS ENERGY PRINT DISTANCES METAD COORDINATIONNUMBER LOWER_WALLS ENDPLUMED	colvar bias symfunc generic multicolvar
19.058	Constrained MD for maintaining a cavity in a calculation	chemistry	constrained MD, porous molecules, porosity, cavity	Kim Jelfs	FLUSH INPLANEDISTANCES PRINT COM DISTANCES MOVINGRESTRAINT RESTART	bias vatom generic setup multicolvar
19.056	maze	methods	maze, ligand unbinding	Jakub Rydzewski	PRINT MAZE_OPTIMIZER_BIAS POSITION UNITS MAZE_SIMULATED_ANNEALING MAZE_LOSS	colvar maze generic setup
19.038	native state dynamics of human and mouse b2m	bio	metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation	Carlo Camilloni	FLUSH ANTIBETARMSD ALPHABETA UPPER_WALLS WHOLEMOLECULES GROUP MOLINFO PRINT CS2BACKBONE BIASVALUE LOWER_WALLS RESTART PBMETAD ENDPLUMED	bias isdb secondarystructure core generic setup multicolvar
19.037	Scission free energy of organic dyes	chemistry	metadynamics, multiple walkers, matheval/lepton	Paolo Raiteri	DISTANCE FLUSH UPPER_WALLS PRINT METAD UNITS RESTART MATHEVAL	colvar function bias generic setup
19.027	Multithermal-multibaric simulations using VES	methods	ves, Wang Landau, multicanonical, liquid sodium, density anomaly	Pablo Piaggi	AVERAGE VES_LINEAR_EXPANSION DUMPGRID BF_LEGENDRE COMBINE TD_MULTICANONICAL REWEIGHT_BIAS REWEIGHT_TEMP_PRESS OPT_AVERAGED_SGD PRINT ENERGY OPT_DUMMY UNITS CONVERT_TO_FES HISTOGRAM RESTART READ	colvar function gridtools bias generic setup ves
19.025	Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide	bio	metainference, NMR, protein dynamics, force-fields	Carlo Camilloni	JCOUPLING FLUSH STATS GYRATION METAINFERENCE TORSION WHOLEMOLECULES MOLINFO PRINT ENSEMBLE BIASVALUE RDC CS2BACKBONE PBMETAD ENDPLUMED	colvar function bias generic isdb
19.021	Coarse-Grained Directed Simulation	methods	experiment directed simulation, coarse-grain, bias	Glen Hocky	DISTANCE COMBINE TORSION RESTRAINT PRINT EDS	colvar function bias generic eds
25.002	M3_PCV-ABMD	chemistry	Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor	Gian Marco Elisi	UNITS PATHMSD PRINT ABMD UPPER_WALLS ENDPLUMED	generic bias setup colvar
25.000	Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer	bio	metadynamics, pathCV	Sahithya Sridharan Iyer	FUNCPATHGENERAL WHOLEMOLECULES COM DISTANCE PRINT GROUP RESTART METAD UPPER_WALLS MOLINFO	vatom core setup colvar generic function bias
24.031	DeepLNE	methods	PATHCV, OPES, OneOPES	Thorben Fröhlking	ENERGY COORDINATION PRINT ECV_MULTITHERMAL OPES_EXPANDED RESTART ERMSD OPES_METAD_EXPLORE VOLUME MOLINFO PYTORCH_MODEL COMBINE	opes setup colvar generic function pytorch
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	RMSD GROUP UPPER_WALLS ANGLE CONTACTMAP WHOLEMOLECULES PRINT FIT_TO_TEMPLATE COMMITTOR CUSTOM METAD COORDINATION FIXEDATOM MATHEVAL ENDPLUMED MOLINFO OPES_METAD DISTANCE CENTER TORSION COMBINE	vatom core opes colvar generic function bias
24.011	Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble	methods	committor, machine learning	Peilin Kang	ENERGY RMSD GROUP UPPER_WALLS WHOLEMOLECULES PRINT CUSTOM LOWER_WALLS INCLUDE COORDINATION UNITS MATHEVAL ENDPLUMED MOLINFO BIASVALUE POSITION DISTANCE CELL TORSION LOAD	core setup colvar generic function bias
23.040	Supramolecular capsules assembly dynamics	chemistry	Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics	Riccardo Capelli	FLUSH WHOLEMOLECULES UNITS DISTANCES DISTANCE CENTER PRINT COM CUSTOM GROUP METAD POSITION	vatom core setup colvar generic multicolvar function bias
23.025	Probing ion binding to G-quadruplexes and related events	chemistry	metadynamics, repulsive potential, nucleic acids, G-quadruplexes	Marcelo Poleto	FLUSH UNITS WHOLEMOLECULES DISTANCES COM DISTANCE FIT_TO_TEMPLATE MATHEVAL PRINT LOWER_WALLS GROUP WRAPAROUND METAD DUMPATOMS RESTART UPPER_WALLS POSITION	vatom core setup colvar generic multicolvar function bias
23.023	Rational design of novel biomimetic sequence-defined polymers for mineralization applications	methods	metadynamics, surface binding, biomimetic mineralization	Kaylyn Torkelson	GYRATION COORDINATION COM DISTANCE PRINT PBMETAD UPPER_WALLS	vatom bias generic colvar
23.011	OneOPES, a combined enhanced sampling method to rule them all	bio	OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding	Valerio Rizzi	ENERGY DISTANCE PRINT ECV_MULTITHERMAL OPES_EXPANDED METAD TORSION OPES_METAD_EXPLORE MOLINFO ENDPLUMED	bias opes generic colvar
23.006	Transcription factor unbinding	bio	metadynamics, DNA, conformational changes	Malin Lüking	CONTACTMAP COM DISTANCE PRINT ALPHARMSD METAD DUMPFORCES ANGLE MOLINFO	vatom secondarystructure colvar generic bias
23.005	A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs	bio	metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A	Timothy Clark	HISTOGRAM READ CONVERT_TO_FES WHOLEMOLECULES DISTANCE PRINT MATHEVAL RMSD METAD REWEIGHT_METAD MOLINFO DUMPGRID	gridtools colvar generic function bias
23.004	Melting curves of ice polymorphs in the vicinity of the liquid-liquid critical point	chemistry	water, liquid-liquid transition, second critical point, ice, polymorphs, melting curves, environment similarity, opes, density-functional theory, scan, machine learning potential	Pablo Piaggi	HISTOGRAM PRINT LOWER_WALLS OPES_EXPANDED RESTART ENVIRONMENTSIMILARITY UPPER_WALLS ECV_UMBRELLAS_LINE DUMPGRID	opes gridtools setup generic envsim bias
23.003	Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations	methods	metadynamics, alchemical variable, alchemical free energy calculations	Wei-Tse Hsu	READ EXTRACV PRINT METAD TORSION	bias generic colvar
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	CONTACTMAP ENERGY WHOLEMOLECULES PRINT LOWER_WALLS METAD UPPER_WALLS	bias generic colvar
22.042	Metadynamics of NSP10 and variants	bio	metadynamics, NSP10, crystal structure, variants	Shozeb Haider	METAD PRINT TORSION	bias generic colvar
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	GYRATION WHOLEMOLECULES PBMETAD TORSION MOLINFO	bias generic colvar
22.029	Angiotensin-1-7_Metadynamics	bio	Metadynamics, Angiotensin-(1-7), peptide	L.-América Chi	FLUSH GYRATION COORDINATION WHOLEMOLECULES PRINT LOWER_WALLS GROUP METAD UPPER_WALLS	core bias generic colvar
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	FLUSH COORDINATION WHOLEMOLECULES DISTANCE PRINT ALPHARMSD METAD ALPHABETA TORSION UPPER_WALLS ANGLE MOLINFO	secondarystructure colvar generic multicolvar bias
22.000	Amyloid precursor protein processing by human γ-secretase	bio	Bias Exchange Metadynamics, Helix unfolding, coupled binding	Xiaoli Lu	CONTACTMAP ANTIBETARMSD UNITS COORDINATION DISTANCE CENTER PRINT ALPHARMSD METAD RANDOM_EXCHANGES INCLUDE MOLINFO	vatom secondarystructure setup colvar generic bias
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	COORDINATION PRINT CUSTOM METAD ENDPLUMED VOLUME COMBINE	function bias generic colvar
21.039	Deep learning the slow modes for rare events sampling	methods	collective variables, machine learning, slow modes, deep-tica, opes	Luigi Bonati	ENERGY ECV_MULTITHERMAL RMSD GROUP VOLUME CONTACTMAP WHOLEMOLECULES PRINT INCLUDE PYTORCH_MODEL Q6 UNITS ENDPLUMED MOLINFO FLUSH OPES_METAD DISTANCE OPES_EXPANDED ENVIRONMENTSIMILARITY TORSION LOAD COMBINE	core opes setup colvar generic function symfunc envsim pytorch
21.037	Molecular Dynamics simulations of RBD/hACE2 complexes	bio	SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain	Max Bonomi	RMSD DISTANCE PRINT	generic colvar
19.083	Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis	chemistry	metadynamics, chemical reactions, reaction discovery	Valerio Rizzi	FLUSH UNITS DISTANCES PRINT GROUP RESTART METAD UPPER_WALLS ENDPLUMED COORDINATIONNUMBER COMBINE	core setup generic multicolvar function symfunc bias
19.069	Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen	materials	ibuprofen, crystal, solvent, surface	Matteo Salvalaglio	DISTANCE CENTER PRINT GROUP INCLUDE ENDPLUMED	vatom core generic colvar
19.059	cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide	bio	bias-exchange metadynamics, cis-trans isomerization	Fabrizio Marinelli	PRINT METAD RANDOM_EXCHANGES TORSION INCLUDE	bias generic colvar
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	BRIDGE WHOLEMOLECULES DISTANCES COM DISTANCE PRINT LOWER_WALLS FUNNEL RMSD GROUP METAD ALPHABETA TORSION UPPER_WALLS REWEIGHT_METAD MOLINFO COMBINE	vatom core colvar funnel generic multicolvar function bias adjmat
19.036	Thermodynamics and kinetics of G protein-coupled receptor activation	bio	metadynamics, allostery, receptor conformation, GPCR, pharmacology	Davide Provasi	CONTACTMAP WHOLEMOLECULES COM DISTANCE PRINT RMSD METAD FUNCPATHMSD ENDPLUMED	vatom colvar generic function bias
19.026	Ice Nucleation on Cholesterol Crystals	materials	forward flux sampling, crystal nucleation, water, ice, organic crystals	Gabriele Cesare Sosso	FLUSH MFILTER_MORE OUTPUT_CLUSTER CONTACT_MATRIX CLUSTER_NATOMS DFSCLUSTERING CLUSTER_WITHSURFACE COMMITTOR ENDPLUMED LOCAL_Q6 Q6	generic multicolvar symfunc clusters adjmat
19.017	Ligand binding pathways exploration	bio	metadynamics, ligand binding	Riccardo Capelli	DUMPGRID FLUSH HISTOGRAM READ COORDINATION WHOLEMOLECULES CONVERT_TO_FES COM PRINT FIT_TO_TEMPLATE MATHEVAL GROUP WRAPAROUND METAD REWEIGHT_METAD UPPER_WALLS ENDPLUMED POSITION	vatom core gridtools colvar generic function bias
19.012	Martini-Beads multi-scale SAXS	methods	metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex	Carlo Camilloni	WHOLEMOLECULES SAXS STATS DISTANCE CENTER PRINT RESTRAINT RMSD GROUP UPPER_WALLS INCLUDE MOLINFO BIASVALUE ENDPLUMED	vatom core colvar generic function isdb bias
25.003	Surrogate Model CV	methods	Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding	Sompriya Chatterjee	PYTORCH_MODEL MATHEVAL CUSTOM DISTANCE TORSION PRINT ENDPLUMED COMBINE WHOLEMOLECULES GROUP ENERGY OPES_METAD MOLINFO COMMITTOR	function colvar core opes generic pytorch
24.035	Data efficient machine learning potentials for modeling catalytic reactivity via active learning and enhanced sampling	chemistry	opes, catalysis, ammonia, machine learning potentials	Luigi Bonati	CUSTOM DISTANCE UNITS PRINT LOWER_WALLS GROUP UPPER_WALLS OPES_METAD COORDINATION RESTART COMMITTOR	function setup bias colvar core opes generic
24.008	yCD Metadynamics	bio	volume-based MetaD, path CVs, infrequent MetaD, product release	James McCarty	DISTANCE PRINT GROUP WHOLEMOLECULES FIT_TO_TEMPLATE CONTACTMAP READ FLUSH WRAPAROUND FIXEDATOM ENDPLUMED CONVERT_TO_FES HISTOGRAM MOLINFO INCLUDE COM MATHEVAL UPPER_WALLS METAD COORDINATION RMSD DUMPGRID REWEIGHT_METAD PATH COMMITTOR	vatom function colvar bias core generic gridtools mapping
23.044	Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition	materials	metadynamics, interlocked molecules	Luigi Leanza	DUMPGRID PRINT CONVERT_TO_FES ENDPLUMED HISTOGRAM METAD GROUP COORDINATION READ COMMITTOR	bias colvar core generic gridtools
23.037	Estimating binding free energy of solid binding peptides without extensive sampling	bio	metadynamics, solid binding peptides	Xin Qi	COM DISTANCE PRINT LOWER_WALLS UPPER_WALLS PBMETAD GYRATION MOLINFO	bias vatom generic colvar
23.016	Activation/deactivation free-energy profiles for the β2-adrenergic receptor: Ligand modes of action	bio	G protein coupled receptor, beta-adrenergic, receptor activation, partial agonism, metadynamics	Timothy Clark	DUMPGRID MATHEVAL DISTANCE REWEIGHT_METAD PRINT CONVERT_TO_FES HISTOGRAM METAD WHOLEMOLECULES MOLINFO RMSD READ	function bias colvar generic gridtools
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 FLUSH UNITS PRINT LOWER_WALLS DRR METAD UPPER_WALLS PATHMSD TIME BIASVALUE	drr function setup bias colvar generic
23.012	JAK2 2D meta-eABF PMF with statistical analysis	bio	2D meta-eABF, path CV, PMF	Istvan Kolossvary	CUSTOM FLUSH PRINT LOWER_WALLS METAD DRR UPPER_WALLS PATHMSD BIASVALUE	drr function bias colvar generic
23.002	Critical comparison of general-purpose collective variables for crystal nucleation	methods	metadynamics, umbrella sampling, commitor, entropy, PIV	Julien Lam	Q4 FUNCPATHMSD CUSTOM Q6 UNITS PRINT LOCAL_AVERAGE PAIRENTROPY METAD UPPER_WALLS ENERGY VOLUME RESTRAINT PIV	function setup bias colvar generic symfunc piv gridtools
22.039	Driving and characterizing nucleation of urea and glycine polymorphs in water	bio	metadynamics, nucleation, amino acids, polymorphism	Eric Beyerle	INCLUDE Q6 MATHEVAL CENTER Q4 PRINT PAIRENTROPY COORDINATIONNUMBER GROUP LOAD COMBINE METAD	function vatom setup bias core generic symfunc gridtools
22.036	Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction	bio	Well-tempered MetaDynamics with Hamiltonian Replica Exchange	Miroslav Krepl	CUSTOM FLUSH GHBFIX PRINT COMBINE GROUP LOAD UPPER_WALLS METAD COORDINATION BIASVALUE MOLINFO	function setup colvar bias core generic
22.026	Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification	materials	Peptoid, silica	Jim Pfaendtner	COM DISTANCE PRINT UPPER_WALLS GYRATION PBMETAD MOLINFO	bias vatom generic colvar
22.022	Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir	bio	RMSD, protein-ligand interactions	Isabell Grothaus	PRINT RMSD	colvar generic
22.021	Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations	chemistry	Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella	Sigbjørn Løland Bore	INCLUDE PRINT LOWER_WALLS UPPER_WALLS ENVIRONMENTSIMILARITY ECV_UMBRELLAS_LINE OPES_EXPANDED	bias opes envsim 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	COM DISTANCE FUNNEL PRINT LOWER_WALLS METAD WHOLEMOLECULES UPPER_WALLS PATHMSD FUNNEL_PS	funnel vatom bias colvar generic
22.018	Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations	bio	ligand binding, docking, EMMI, LAT1	Max Bonomi	EMMIVOX PRINT GROUP WHOLEMOLECULES LOAD BIASVALUE MOLINFO	setup bias core isdb generic
21.043	Predicting the Conformational Variability of Oncogenic GTP-bound G12D Mutated KRas-4B Proteins at Cell Membranes	chemistry	well-tempered metadynamics, KRas-4B, anionic membrane, conformational variability	Huixia Lu	FIXEDATOM TORSION PRINT METAD FIT_TO_TEMPLATE	bias vatom generic colvar
21.038	Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics	materials	metadynamics, SGOOP, nucleation, urea	Ziyue Zou	INCLUDE CENTER PRINT COMBINE GROUP LOAD METAD ENERGY COORDINATIONNUMBER VOLUME	vatom function setup bias colvar core generic symfunc
21.035	CmuMD simulations of NaCl(aq) at NaCl	chemistry	CmuMD, interface	Aaron Finney	DISTANCE FIXEDATOM PRINT GROUP LOAD RESTRAINT	vatom setup colvar bias core generic
21.032	Metal-coupled folding mechanism to metallothionein	bio	parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination	Manuel-Peris Diaz	UNITS GROUP WHOLEMOLECULES PBMETAD COORDINATION	setup bias colvar core generic
21.030	Thermodynamic Basis for Stabilization of Helical Peptoids by Chiral Sidechains	bio	parallel bias parallel tempered metadynamics in WTE, synthetic foldamers, self-assembly, peptoid secondary structure	Jim Pfaendtner	INCLUDE COM DISTANCE TORSION PRINT METAD ALPHABETA GYRATION PBMETAD ENERGY COORDINATION	vatom bias colvar generic multicolvar
21.024	Property map collective variable as a useful tool for force field correction	chemistry	molecular mechanics	Vojtech Spiwok	PROPERTYMAP TORSION PRINT METAD WHOLEMOLECULES BIASVALUE	bias generic colvar
21.020	Reweighted Jarzynski sampling	methods	free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions	Kristof Bal	CONSTANT CUSTOM DISTANCE UNITS PRINT COORDINATIONNUMBER MOVINGRESTRAINT FLUSH VES_LINEAR_EXPANSION REWEIGHT_BIAS CONVERT_TO_FES HISTOGRAM OPT_AVERAGED_SGD COMBINE TD_WELLTEMPERED LOAD ANN BF_CHEBYSHEV OPES_METAD UPPER_WALLS METAD BIASVALUE DUMPGRID REWEIGHT_METAD RESTRAINT	annfunc function setup colvar bias opes ves generic symfunc gridtools
21.016	MD SAXS GTPase associated center	bio	metadynamics, RNA, folding, SAXS	Giovanni Bussi	INCLUDE CUSTOM PRINT LOWER_WALLS ERMSD WHOLEMOLECULES GYRATION GROUP SAXS UPPER_WALLS METAD MOLINFO	function bias colvar core isdb 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	PRINT	generic
21.008	Multi-replica biased sampling for photoisomerization processes in conjugated polymers	methods	metadynamics, FEP, replica-exchange	Adriana Pietropaolo	CONSTANT MATHEVAL TORSION PRINT WHOLEMOLECULES PBMETAD BIASVALUE RESTART	function setup bias colvar generic
20.032	Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil	materials	clustering, conformational isomers	Matteo Salvalaglio	TORSION ENDPLUMED PRINT	generic colvar
20.030	Converging experimental and computational views of the knotting mechanism of the smallest knotted protein	bio	phi-values, transition state, knotted proteins	Cristina Paissoni	STATS PRINT COMBINE WHOLEMOLECULES COORDINATION MOLINFO RESTRAINT	bias function colvar generic
20.024	Gaussian Mixture Based Enhanced Sampling (GAMBES)	methods	enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias	Jayashrita Debnath	DISTANCE UNITS TORSION PRINT LOWER_WALLS COMBINE UPPER_WALLS LOAD GROUP ENERGY DISTANCES	function setup bias colvar core generic multicolvar
20.014	amyloid beta small molecule interaction	bio	intrinsically disordered proteins, disordered proteins, IDPs, fuzzy binding, small molecule, drugs, entropy, binding, Alzheimer’s disease, amyloid beta	Gabriella Heller	PRINT GROUP WHOLEMOLECULES GYRATION METAINFERENCE ENSEMBLE FLUSH ENDPLUMED COMBINE CS2BACKBONE MOLINFO INCLUDE STATS ALPHARMSD PBMETAD COORDINATION DIHCOR TORSION ANTIBETARMSD PARABETARMSD	function colvar bias core isdb generic secondarystructure multicolvar
20.006	Class B GPCR activation mechanism	bio	metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding	Francesco Gervasio	MATHEVAL CENTER DISTANCE PRINT LOWER_WALLS COMBINE WHOLEMOLECULES METAD UPPER_WALLS ENERGY MOLINFO RMSD	function vatom bias colvar generic
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	DUMPGRID COM MATHEVAL DISTANCE REWEIGHT_METAD PRINT ENDPLUMED CONVERT_TO_FES HISTOGRAM LOWER_WALLS ABMD COMBINE UPPER_WALLS METAD READ	vatom function bias colvar generic gridtools
19.080	Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium	methods	ves, variationally enhanced sampling, vibrational excitation, chemical reactions	Kristof Bal	TD_GRID DUMPGRID FLUSH DISTANCE VES_LINEAR_EXPANSION UNITS PRINT CONVERT_TO_FES HISTOGRAM OPT_AVERAGED_SGD EXTERNAL UPPER_WALLS TD_WELLTEMPERED COMBINE LOWER_WALLS BF_CHEBYSHEV COORDINATION ANGLE	function setup colvar bias ves generic gridtools
19.070	Unexpected Dynamics in the UUCG RNA Tetraloop	bio	well-tempered metadynamics, RNA, UUCG, maximum entropy	Sandro Bottaro	DISTANCE TORSION PRINT ERMSD WHOLEMOLECULES METAD MOLINFO RMSD	bias generic colvar
19.062	Elucidating molecular design principles for charge-alternating peptides	bio	peptide folding, metadynamics, well-tempered ensemble, parallel tempering	Jim Pfaendtner	PRINT METAD WHOLEMOLECULES GYRATION ENERGY	bias colvar generic
19.051	Solid liquid interfacial free energy out of equilibrium	materials	metadynamics, nucleation, surface excess free energy	Gareth Tribello	FCCUBIC UNITS PRINT ENDPLUMED CELL LOWER_WALLS METAD UPPER_WALLS AROUND	volumes setup bias colvar generic symfunc
19.050	Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes	chemistry	metadynamics, membranes, Willard Chandler surface	Gareth Tribello	DUMPGRID REWEIGHT_BIAS PRINT CONVERT_TO_FES HISTOGRAM METAD UPPER_WALLS COMBINE RESTART READ DISTANCE_FROM_CONTOUR	function setup bias generic contour gridtools
19.047	Close Structure	methods	metadynamics, RMSD, path collective variables, property map	Vojtech Spiwok	WHOLEMOLECULES PRINT PROPERTYMAP METAD	bias colvar generic
19.042	Harmonic Linear Discriminant Analysis (HLDA)	methods	metadynamics, chemistry, HLDA	GiovanniMaria Piccini	FLUSH DISTANCE UNITS PRINT UPPER_WALLS COMBINE METAD ENERGY	function setup 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	COM DISTANCE PRINT METAD UPPER_WALLS ENERGY	bias vatom generic colvar
19.022	eABF simulation of NANMA (alanine dipeptide)	methods	eABF, DRR, alanine dipeptide	Haochuan Chen	TORSION PRINT DRR	drr generic colvar
19.020	PTMetaD-WTE simulation of the Ntail IDP	bio	metadynamics, IDPs, protein folding	Mattia Bernetti	PRINT ENDPLUMED ALPHARMSD METAD WHOLEMOLECULES GYRATION ENERGY MOLINFO	secondarystructure colvar bias generic
19.001	RNA SHAPE	bio	metadynamics, RNA, ligand binding	Giovanni Bussi	INCLUDE FLUSH DISTANCE PRINT LOWER_WALLS COMBINE ERMSD UPPER_WALLS METAD ANGLE MOLINFO RANDOM_EXCHANGES DISTANCES	function bias colvar generic multicolvar
25.009	Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water	chemistry	metadynamics, nitrate photolysis	Kam-Tung Chan	COORDINATION DISTANCE REWEIGHT_METAD READ GROUP DUMPGRID PRINT HISTOGRAM RESTART UPPER_WALLS FLUSH METAD CUSTOM	colvar core setup generic bias gridtools function
25.004	Machine Learning-Driven Molecular Dynamics Unveil a Bulk Phase Transformation Driving Ammonia Synthesis on Barium Hydride	chemistry	OPES, OPES flooding, Catalysis, Ammonia Synthesis	Axel Tosello Gardini	ZDISTANCES DISTANCE GROUP COORDINATIONNUMBER DISTANCES PRINT COMMITTOR OPES_METAD UNITS FLUSH UPPER_WALLS FIXEDATOM CUSTOM	core colvar vatom setup symfunc generic bias function multicolvar opes
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
24.017	Absolute Binding Free Energies with OneOPES	methods	protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy	Francesco Gervasio	ECV_MULTITHERMAL ENERGY WHOLEMOLECULES MATHEVAL MOLINFO COORDINATION INCLUDE BIASVALUE PROJECTION_ON_AXIS CUSTOM WRAPAROUND PRINT CONSTANT UPPER_WALLS CONTACTMAP OPES_METAD_EXPLORE METAD LOWER_WALLS RMSD TORSION GROUP COM RESTART OPES_EXPANDED	colvar core vatom setup generic bias function opes
24.016	Cryo-EM guided simulations of ribozyme	bio	metainference, cryo-EM	Giovanni Bussi	MOLINFO ERMSD GROUP PRINT RESTRAINT BIASVALUE INCLUDE WHOLEMOLECULES EMMIVOX	isdb colvar core generic bias
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	COORDINATION LOWER_WALLS MOLINFO RMSD PYTORCH_MODEL PRINT WHOLEMOLECULES UPPER_WALLS FLUSH DRR METAD	colvar pytorch drr generic bias
24.002	Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes	chemistry	metadynamics, ligand design, solvent extraction	Xiaoyu Wang	TORSION PRINT RESTART UNITS METAD	generic bias setup colvar
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	ZDISTANCES DISTANCE GROUP COORDINATIONNUMBER PRINT OPES_METAD UNITS FLUSH UPPER_WALLS FIXEDATOM	core colvar vatom setup symfunc generic bias multicolvar opes
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	MATHEVAL LOWER_WALLS CENTER DISTANCE PRINT BIASVALUE WHOLEMOLECULES CONSTANT UPPER_WALLS METAD	colvar vatom function bias generic
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	MOLINFO CENTER GROUP WRAPAROUND PRINT FIT_TO_TEMPLATE POSITION DISTANCES WHOLEMOLECULES SHADOW UPPER_WALLS METAD	isdb core colvar vatom generic bias multicolvar
23.018	Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention	materials	metadynamics, surface binding, peptide adsorption	Kaylyn Torkelson	PBMETAD GYRATION DISTANCE COM PRINT UPPER_WALLS	vatom 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	COORDINATION CENTER LOWER_WALLS TORSION PATH PYTORCH_MODEL DISTANCE GROUP PRINT FIT_TO_TEMPLATE WHOLEMOLECULES OPES_METAD UNITS OPES_METAD_EXPLORE UPPER_WALLS FIXEDATOM CUSTOM	mapping colvar core vatom pytorch setup generic bias function opes
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	MATHEVAL LOWER_WALLS DRMSD CELL PRINT COMMITTOR UPPER_WALLS METAD CUSTOM	function bias colvar generic
22.024	Conformational Entropy as a Potential Liability of Computationally Designed Antibodies	bio	metadynamics, conformational entropy, antibody, nanobody	Thomas Löhr	PBMETAD MOLINFO TORSION COM ANTIBETARMSD ALPHARMSD PRINT WHOLEMOLECULES ALPHABETA RESTART	colvar vatom setup generic bias multicolvar secondarystructure
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	PBMETAD MOLINFO RMSD COORDINATION TORSION GROUP COM PRINT BIASVALUE WHOLEMOLECULES RESTART UPPER_WALLS EMMI	isdb colvar core vatom setup generic bias
21.050	N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity	methods	bio	Isabell Louise Grothaus	DISTANCE CENTER PRINT	vatom colvar generic
21.042	Peptoid-mediated Au nanocrystal growth	materials	parallel-bias metadynamics, peptoid, Au	Xin Qi	PBMETAD MOLINFO GYRATION DISTANCE COM PRINT UPPER_WALLS	generic bias colvar vatom
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 PRINT INCLUDE RANDOM_EXCHANGES METAD	generic bias colvar
21.031	Photo-switchable sulfonulureas in KATP channel	bio	metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels	Katarzyna Walczewska-Szewc	LOWER_WALLS DISTANCE COM PRINT WHOLEMOLECULES UNITS UPPER_WALLS METAD	colvar vatom setup generic bias
21.026	Probing allosteric regulations with coevolution-driven molecular simulations	bio	metadynamics, coevolution, allostery, adenylate cyclase	Francesco Colizzi	DISTANCE COM PRINT WHOLEMOLECULES UNITS UPPER_WALLS METAD PATHMSD	colvar vatom setup generic bias
21.022	Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly	materials	parallel bias metadynamics, adsorption, peptide	Xin Qi	PBMETAD MOLINFO LOWER_WALLS GYRATION DISTANCE COM PRINT ENERGY UPPER_WALLS	generic bias colvar vatom
21.021	ATLAS	methods	Machine Learning, Metadynamics	Federico Giberti	MATHEVAL COORDINATION TORSION GYRATION DISTANCE GROUP PRINT COORDINATIONNUMBER BIASVALUE DUMPATOMS WHOLEMOLECULES UNITS METAD	colvar core setup symfunc function generic bias
21.014	how to determine statistically accurate conformational ensembles	bio	metadynamics, metainference, errors, cv, SAXS, ensemble determination	Cristina Paissoni	PBMETAD MOLINFO CENTER GYRATION TORSION ANTIBETARMSD SAXS PRINT BIASVALUE ENSEMBLE WHOLEMOLECULES ALPHABETA STATS CONTACTMAP METAD	isdb colvar vatom generic bias function multicolvar secondarystructure
21.012	NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition	bio	funnel metadynamics	Jim Pfaendtner	LOWER_WALLS FUNNEL_PS DISTANCE COM PRINT UPPER_WALLS FUNNEL METAD	colvar vatom generic bias funnel
21.011	CmuMD simulations of NaCl(aq) at graphite	chemistry	CmuMD, DFS clustering	Aaron Finney	GROUP CONTACT_MATRIX LOAD AROUND CLUSTER_DISTRIBUTION COORDINATIONNUMBER DENSITY PRINT RESTRAINT MFILTER_MORE MULTICOLVARDENS DFSCLUSTERING DUMPGRID CLUSTER_NATOMS FIXEDATOM	volumes core vatom adjmat setup symfunc generic bias clusters gridtools multicolvar
21.005	Crystallization Collective Variable	methods	Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA	Tarak Karmakar	MATHEVAL LOWER_WALLS PYTORCH_MODEL GROUP PRINT OPES_METAD UPPER_WALLS LOAD FLUSH	core pytorch setup function bias generic opes
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 COORDINATION RESTRAINT PRINT WHOLEMOLECULES STATS	generic bias function colvar
20.020	Parallel Bias Metadynamics	methods	pbmetad, trp-cage, folding	Max Bonomi	PBMETAD MOLINFO COORDINATION GYRATION DIHCOR INCLUDE PRINT WHOLEMOLECULES ALPHABETA	generic bias colvar multicolvar
20.018	Free energy barriers from biased molecular dynamics simulations	methods	kinetics, free energy barriers, chemical reactions, nucleation, metadynamics	Kristof Bal	VOLUME DENSITY ENERGY COORDINATION CONTACT_MATRIX REWEIGHT_BIAS CONVERT_TO_FES UNITS LOAD SPRINT COMBINE CENTER PAIRENTROPY DISTANCE REWEIGHT_METAD DUMPGRID PRINT HISTOGRAM UPPER_WALLS METAD Q6 LOWER_WALLS LOCAL_AVERAGE COORDINATIONNUMBER FLUSH	volumes colvar vatom adjmat setup symfunc function bias gridtools generic sprint
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	WHOLEMOLECULES MOLINFO CONVERT_TO_FES ENDPLUMED COMBINE DISTANCE REWEIGHT_METAD READ PRINT DUMPGRID HISTOGRAM UPPER_WALLS CONTACTMAP FUNCPATHMSD METAD LOWER_WALLS COM ABMD FLUSH	colvar vatom generic bias gridtools function
19.065	Molecular Enhanced Sampling with Autoencoders	methods	enhanced sampling, collective variables, deep learning	Wei Chen	COMBINE COM RESTRAINT POSITION ANN	colvar annfunc vatom function bias
19.063	Protein-ligand binding through metadynamics with path CVs	bio	metadynamics, path CVs, ligand binding	Mattia Bernetti	LOWER_WALLS PRINT WHOLEMOLECULES PATHMSD UPPER_WALLS METAD	generic bias colvar
19.032	Chemical reaction in solution using path collective variables based on coordination patterns	chemistry	chemical reactions, solutions, metadynamics, coordination patterns	Fabio Pietrucci	PATH PRINT DISTANCES RESTART UPPER_WALLS FLUSH METAD	mapping setup generic bias multicolvar
19.029	WTE-metaD of FF domain of URNF1 C57D variant	bio	metadynamics, mutations, post-translational modification, ff domain	Elena Papaleo	MOLINFO LOWER_WALLS GYRATION GROUP PRINT WHOLEMOLECULES ALPHABETA UPPER_WALLS METAD	colvar core generic bias multicolvar
19.008	anncolvar	methods	neural network, dimensionality reduction	Vojtech Spiwok	MATHEVAL MOLINFO COMBINE FIT_TO_TEMPLATE POSITION PRINT ALPHARMSD WHOLEMOLECULES METAD	colvar function bias generic secondarystructure
19.004	MI Ubiquitin	bio	metainference, NMR	Max Bonomi	MOLINFO CS2BACKBONE METAINFERENCE GROUP PRINT RDC WHOLEMOLECULES	generic isdb core
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	RESTART MOLINFO MOVINGRESTRAINT PUCKERING PRINT RESTRAINT TORSION DISTANCE METAD	bias setup colvar 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	RESTART COMBINE ENERGY COORDINATION ECV_MULTITHERMAL PRINT CUSTOM OPES_EXPANDED TORSION DISTANCE GROUP OPES_METAD_EXPLORE	opes core colvar setup function generic
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	OPES_METAD ENERGY COORDINATION PRINT UPPER_WALLS DISTANCE	bias colvar opes generic
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	COMMITTOR GROUP PRINT LOAD TORSION METAD	core colvar bias setup generic
24.019	Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning	bio	OPES, machine learning, protein folding, adaptive sampling	Mingyuan Zhang	OPES_METAD MOLINFO WHOLEMOLECULES COMBINE GYRATION COORDINATION PRINT CUSTOM ALPHARMSD TORSION DISTANCE	opes colvar secondarystructure function generic
24.007	SWISH-X	bio	swish-x, SWISH-X, swish, expanded SWISH	Alberto Borsatto	INCLUDE MOLINFO WHOLEMOLECULES ENERGY ECV_MULTITHERMAL PRINT UPPER_WALLS OPES_EXPANDED CONTACTMAP	bias colvar opes generic
24.006	Water vapor condensation	chemistry	metadynamics, homogeneous condensation, chemical potential	Shenghui Zhong	CLUSTER_NATOMS PRINT UPPER_WALLS DFSCLUSTERING COORDINATIONNUMBER CONTACT_MATRIX METAD UNITS CLUSTER_PROPERTIES	bias setup clusters symfunc adjmat generic
23.046	Lasso Peptides - HLDA CV	bio	metadynamics, protein folding, HLDA, harmonic	Gabriel da Hora	WHOLEMOLECULES COMBINE PRINT DISTANCE METAD UNITS	colvar bias setup function generic
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	INCLUDE LOWER_WALLS MOLINFO METAD PATHMSD PRINT FUNCPATHMSD UPPER_WALLS ALPHARMSD DISTANCE CONTACTMAP	colvar secondarystructure bias function generic
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	MATHEVAL COORDINATION DISTANCE CONTACTMAP WHOLEMOLECULES ENERGY PYTORCH_MODEL UPPER_WALLS GROUP FIXEDATOM ANGLE OPES_METAD LOWER_WALLS MOLINFO INCLUDE COMBINE FIT_TO_TEMPLATE RMSD COMMITTOR CENTER ENDPLUMED PRINT CUSTOM	opes core colvar pytorch bias vatom function 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	INCLUDE WHOLEMOLECULES PBMETAD GYRATION COORDINATION COM RESTRAINT PRINT TORSION	bias colvar vatom generic
22.040	From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure	bio	SARS-CoV-2, Spike, Omicron	Miłosz Wieczór	LOWER_WALLS WHOLEMOLECULES PCAVARS PRINT UPPER_WALLS METAD	bias mapping generic
22.032	Reciprocal barrier restraint. Application to path-meta-eABF	methods	restraint, upper wall, lower wall, path colvar, meta-eABF, metadynamics, DRR, protein conformational transition, PROTAC	Istvan Kolossvary	DRR FLUSH PATHMSD PRINT CUSTOM BIASVALUE METAD	colvar drr bias function generic
22.028	N-glycan conformer distributions in atomistic simulation	bio	REST2, RECT, N-glycan, pucker	Isabell Grothaus	MOLINFO HISTOGRAM PUCKERING PRINT READ CONVERT_TO_FES TORSION METAD DUMPGRID	bias gridtools colvar generic
21.051	Automatic learning of hydrogen-bond fixes in an AMBER RNA force field	methods	force field, RNA	Giovanni Bussi	MOLINFO WHOLEMOLECULES COMBINE COORDINATION PRINT BIASVALUE ERMSD METAD	function bias colvar generic
21.019	Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations	materials	Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen	Matteo Salvalaglio	MATHEVAL COM PRINT KDE DISTANCE TORSIONS	multicolvar colvar vatom function gridtools generic
21.015	Coarse-grained metadynamics and umbrella sampling simulations to investigate interactions of carbohydrate-binding modules with chitin	bio	metadynamics, umbrella sampling, coarse-grained, MARTINI, chitin, carbohydrate-binding module	Gaston Courtade	REWEIGHT_BIAS RESTART WHOLEMOLECULES MATHEVAL COORDINATION CENTER PRINT RESTRAINT POSITION METAD	colvar bias setup vatom function 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 COM PRINT DISTANCE GROUP	core colvar vatom 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 TORSION DISTANCE METAD	bias colvar generic
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	INCLUDE LOWER_WALLS MOLINFO WHOLEMOLECULES MATHEVAL FUNCPATHGENERAL METAD COM PROJECTION_ON_AXIS PRINT UPPER_WALLS CONSTANT BIASVALUE LOAD DISTANCE GROUP CONTACTMAP	core colvar bias setup vatom function 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	VES_LINEAR_EXPANSION OPT_AVERAGED_SGD RESTART MATHEVAL BF_LEGENDRE ENVIRONMENTSIMILARITY OPT_DUMMY Q6 PRINT UPPER_WALLS VOLUME TD_WELLTEMPERED	envsim colvar bias setup function symfunc ves generic
20.003	Enhanced sampling of transition states	methods	Variationally Enhanced Sampling, Target distribution, Transition state, Enhanced Sampling, Nucleation, chemical reaction	Jayashrita Debnath	VES_LINEAR_EXPANSION OPT_AVERAGED_SGD ENERGY BF_LEGENDRE PRINT POSITION LOAD UNITS	setup ves colvar generic
19.082	Ammonia Borane Dehydrogenation	chemistry	metadynamics, reaction discovery, hydrogen production, chemistry	Valerio Rizzi	RESTART COMBINE ENDPLUMED METAD FLUSH EXTERNAL PRINT COORDINATIONNUMBER GROUP UNITS	core bias setup function symfunc generic
19.075	PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python	other	Python, automatic differentiation	Toni Giorgino	COMBINE CENTER ENDPLUMED PRINT RESTRAINT CUSTOM TORSION DISTANCE GROUP DUMPDERIVATIVES ANGLE	core colvar bias vatom function generic
19.067	Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways	bio	metadynamics, ligand unbinding	Jakub Rydzewski	LOWER_WALLS RESTART PATHMSD PRINT UPPER_WALLS METAD UNITS	bias setup colvar generic
19.048	Understanding Ligand Binding Selectivity in a Prototypical GPCR Family	bio	metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding	Francesco Gervasio	LOWER_WALLS WHOLEMOLECULES MATHEVAL COM PRINT UPPER_WALLS CONSTANT BIASVALUE DISTANCE METAD	colvar bias vatom function generic
19.028	pRAVE	methods	RAVE, reaction coordinate, deep learning, metadynamics, kinetics	Pratyush Tiwary	COMMITTOR RESTART WHOLEMOLECULES COMBINE ALPHABETA EXTERNAL COM PRINT TORSION DISTANCE	multicolvar colvar bias setup vatom function generic
19.023	RECT	methods	metadynamics, replica exchange	Giovanni Bussi	WHOLEMOLECULES GYRATION PRINT TORSION METAD	bias colvar generic
19.018	Excited state FEP/Metadynamics simulations	chemistry	metadynamics, FEP, excited states, conjugated polymers, torsional potential	Adriana Pietropaolo	WHOLEMOLECULES MATHEVAL PRINT BIASVALUE CONSTANT TORSION METAD	function bias colvar generic
19.016	Succinnic acid gamma polymorph	materials	Succinnic acid, conformers, polymorphs, metadynamics	Matteo Salvalaglio	LOWER_WALLS COMBINE MATHEVAL ENERGY ENDPLUMED PRINT UPPER_WALLS VOLUME TORSION METAD CELL	bias colvar function generic
19.010	Multi-domain protein dynamics	bio	metainference, NMR, protein dynamics	Carlo Camilloni	DIHCOR MOLINFO WHOLEMOLECULES PBMETAD STATS ALPHABETA DHENERGY CENTER METAINFERENCE ENDPLUMED PRINT UPPER_WALLS RESTRAINT RDC TORSION DISTANCE GROUP ENSEMBLE	multicolvar core colvar bias vatom function isdb 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	ANGLE COM PRINT UNITS GROUP COORDINATIONNUMBER UPPER_WALLS COMBINE COORDINATION RESTRAINT FIXEDATOM DISTANCE FLUSH METAD DISTANCES LOWER_WALLS	generic symfunc bias colvar setup vatom function core multicolvar
24.029	Combination of OPES and OPES-Explore	methods	OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin	Dhiman Ray	FIT_TO_TEMPLATE WHOLEMOLECULES CONTACTMAP UPPER_WALLS METAD INCLUDE CENTER OPES_METAD PRINT UNITS PYTORCH_MODEL ENDPLUMED FLUSH MATHEVAL LOWER_WALLS OPES_METAD_EXPLORE BIASVALUE COORDINATION COMBINE CUSTOM RMSD ENERGY GROUP MOLINFO FIXEDATOM DISTANCE POSITION	generic colvar vatom bias core opes function setup pytorch
24.028	All-atom simulations of RNA-membrane interactions	bio	metadynamics, membrane, RNA	Giovanni Bussi	COMBINE SORT WHOLEMOLECULES MOLINFO DISTANCES METAD MATHEVAL UPPER_WALLS LOWER_WALLS DISTANCE GHOST PUCKERING CENTER GYRATION GROUP PRINT POSITION	generic colvar multicolvar vatom bias core function
24.026	Constant pH metadynamics of RNA oligomers	bio	metadynamics, pH, RNA	Giovanni Bussi	MOLINFO METAD RESTART TORSION PUCKERING PRINT	setup colvar generic bias
24.004	Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables	materials	metadynamics, nucleation, machine learning	Ziyue Zou	LOAD METAD RESTART INCLUDE GROUP PRINT	setup generic bias core
24.003	Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations	chemistry	steered molecular dynamics, foldamers, peptoids, bio-inspired	Kaylyn Torkelson	WHOLEMOLECULES MOVINGRESTRAINT DISTANCE TORSION INCLUDE GYRATION ALPHABETA PRINT COM COORDINATION	generic colvar vatom bias multicolvar
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	FLUSH METAD MATHEVAL TRANSPOSE INCLUDE SELECT_COMPONENTS SUM PRINT	generic valtools matrixtools bias function
23.041	Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference	methods	EMMIVox, cryo-EM, single-structure refinement, ensemble refinement, Bayesian inference, B-factors, structural ensembles	Samuel Hoff	WHOLEMOLECULES MOLINFO EMMIVOX UPPER_WALLS DISTANCE INCLUDE GROUP PRINT BIASVALUE WRAPAROUND	generic colvar core bias isdb
23.039	Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation	chemistry	metadynamics, ligand dissociation	Eric Beyerle	COMBINE MOLINFO FIXEDATOM UPPER_WALLS METAD DUMPMASSCHARGE DISTANCE CENTER RESTRAINT PRINT	generic colvar vatom bias function
23.036	Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water?	bio	NaCl, nucleation, metadynamics	Ruiyu Wang	COMBINE METAD MATHEVAL COORDINATIONNUMBER Q4 Q6 ENERGY PRINT VOLUME	generic symfunc colvar bias 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	PYTORCH_MODEL ENDPLUMED CUSTOM UPPER_WALLS LOWER_WALLS OPES_METAD PRINT BIASVALUE UNITS POSITION	generic colvar bias opes function setup pytorch
22.044	Colloid Crystallisation Analyses	materials	Q4, Q6, Pair Entropy, DFS	Aaron Finney	COMBINE DFSCLUSTERING CLUSTER_NATOMS PRINT COORDINATIONNUMBER Q4 LOCAL_Q4 LOCAL_Q6 CONTACT_MATRIX Q6 GROUP MFILTER_LESS MFILTER_MORE LOCAL_AVERAGE	generic symfunc clusters multicolvar core function adjmat
22.038	Enhanced Sampling Aided Design of Molecular Photoswitches	chemistry	reaction discovery, OPES explore, graph CV	Umberto Raucci	PYTORCH_MODEL CUSTOM OPES_METAD_EXPLORE PRINT UNITS COORDINATION	generic colvar opes function setup pytorch
22.037	Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site	chemistry	metadynamics, DNA, abasic	Mike Jones	DISTANCE DISTANCES PRINT METAD	multicolvar colvar generic bias
22.015	Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome	bio	photodynamics, bacteriophytochrome, variationally enhanced sampling	Jakub Rydzewski	TD_UNIFORM VES_LINEAR_EXPANSION TORSION OPT_AVERAGED_SGD PRINT BF_FOURIER	colvar generic ves
22.002	GAMBES_SAMPL5_RATES	other	GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding	Jayashrita Debnath	PYTORCH_MODEL LOAD WHOLEMOLECULES FIT_TO_TEMPLATE FIXEDATOM ANGLE ENDPLUMED COMMITTOR FLUSH UPPER_WALLS MATHEVAL ENERGY DISTANCE CENTER GROUP PRINT COORDINATION	generic colvar vatom bias core function setup pytorch
21.048	Enhancing ligand exploration within a channel pore and fenestrations using metadynamics	bio	well-tempered metadynamics, protein-ligand enhanced sampling, sodium channel, Nav, small molecule drug	Elaine Tao	CUSTOM UPPER_WALLS METAD LOWER_WALLS DISTANCE TORSION PRINT UNITS COM	generic colvar vatom bias function setup
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 MOLINFO EMMI UPPER_WALLS RESTART DISTANCE GROUP PRINT BIASVALUE COM	generic colvar core bias vatom setup isdb
21.027	EGFR activating mutations mechanism	bio	metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA	Francesco Gervasio	WHOLEMOLECULES MOLINFO CONTACTMAP UPPER_WALLS MATHEVAL METAD LOWER_WALLS DISTANCE ALPHARMSD INCLUDE ENERGY PRINT	generic colvar bias secondarystructure function
21.009	Nucleation rates from small scale atomistic simulations and transition state theory	materials	kinetics, free energy barriers, nucleation, droplets, metadynamics	Kristof Bal	LOAD REWEIGHT_METAD HISTOGRAM DUMPGRID MOVINGRESTRAINT CONVERT_TO_FES COMMITTOR FLUSH UPPER_WALLS METAD COORDINATIONNUMBER PRINT UNITS	generic symfunc gridtools bias setup
21.003	aSYN SAXS metainference	bio	metainference, SAXS	Kresten Lindorff-Larsen	WHOLEMOLECULES MOLINFO METAINFERENCE FLUSH PBMETAD SAXS ALPHARMSD CENTER GYRATION GROUP PRINT BIASVALUE EEFSOLV	generic colvar vatom bias secondarystructure core isdb
20.034	Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations	bio	RNA, SARS-CoV-2, partial tempering	Sandro Bottaro	MOLINFO DISTANCE RESTART TORSION CENTER ERMSD PRINT ABMD	generic colvar vatom bias setup
20.029	High Conformational Flexibility of the E2F1/DP1/DNA complex	bio	SAXS, protein-DNA complex, hySAXS, ensemble determination	Cristina Paissoni	WHOLEMOLECULES MOLINFO DISTANCE SAXS STATS INCLUDE CENTER RESTRAINT GROUP PRINT BIASVALUE ENSEMBLE	generic colvar vatom bias core function isdb
20.025	The role of water in host-guest interaction	bio	ligand binding, water, opes, SAMPL5	Valerio Rizzi	PYTORCH_MODEL FIT_TO_TEMPLATE WHOLEMOLECULES FIXEDATOM OPES_METAD ANGLE ENDPLUMED UPPER_WALLS MATHEVAL ENERGY DISTANCE CENTER GROUP PRINT COORDINATION	generic colvar vatom bias core opes function pytorch
20.017	FISST	methods	FISST, force, peptide, sampling, tempering	Glen Hocky	FISST ENERGY MATHEVAL DISTANCE GYRATION RESTRAINT GROUP PRINT BIASVALUE UNITS	generic colvar fisst core bias function setup
20.016	Predicting polymorphism in molecular crystals using orientational entropy	materials	metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy	Pablo Piaggi	LOAD METAD UPPER_WALLS INCLUDE CENTER GROUP PRINT VOLUME	generic colvar vatom bias core setup
20.013	Improving accuracy of biased Alchemistic simulations	methods	flying Gaussian method, Alchemistic simulations, thermodynamic integration, reweighting	Vojtech Spiwok	TORSION METAD PRINT	colvar generic bias
19.078	Iterative unbiasing of quasi-equilibrium sampling	methods	metadynamics, reweighting	Federico Giberti	METAD MATHEVAL COLLECT_FRAMES COORDINATIONNUMBER DISTANCE DUMPATOMS REWEIGHT_BIAS PRINT BIASVALUE UNITS	generic symfunc colvar landmarks bias function setup
19.074	Asymmetric base pair opening in nucleic acids	bio	double helix, DNA, RNA, unwindability	Giovanni Bussi	WHOLEMOLECULES ENDPLUMED LOWER_WALLS DISTANCE RESTRAINT COORDINATION	colvar generic bias
19.064	Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations	materials	metadynamics, peptide-surface binding	Jim Pfaendtner	MOLINFO METAD UPPER_WALLS DISTANCE GYRATION ENERGY PRINT COM	colvar generic bias vatom
19.057	SAXS ensembles using Martini-Beads multi-scale SAXS	methods	metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics	Cristina Paissoni	ALPHABETA COMBINE WHOLEMOLECULES MOLINFO PRINT ANGLE ENDPLUMED MATHEVAL PBMETAD STATS INCLUDE CENTER GROUP SAXS BIASVALUE COORDINATION ENSEMBLE	generic colvar multicolvar vatom bias core function isdb
19.054	MetaFEP	methods	metadynamics, chemistry, free energy perturbation	GiovanniMaria Piccini	COMBINE FLUSH UPPER_WALLS METAD LOWER_WALLS DISTANCE ENERGY PRINT UNITS	generic colvar bias function setup
19.049	Determining the sizes of solid/liquid clusters in MD trajectories of nucleation	methods	nucleation, metadynamics, clustering, Steinhardt order parameters	Gareth Tribello	DFSCLUSTERING CLUSTER_PROPERTIES CLUSTER_NATOMS ONES CLUSTER_DISTRIBUTION PRINT DISTANCES CUSTOM METAD MORE_THAN COORDINATIONNUMBER OUTER_PRODUCT CONTACT_MATRIX LOCAL_Q6 SMAC Q6 MATRIX_VECTOR_PRODUCT OUTPUT_CLUSTER	generic function symfunc clusters matrixtools bias multicolvar adjmat
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	FLUSH UPPER_WALLS METAD LOWER_WALLS RESTART GROUP PRINT UNITS COORDINATION POSITION	generic colvar core bias setup
19.019	FA-MetaD-JCP-Wang-et-al	bio	Frequency adaptive metadynamics; peptide	Kresten Lindorff-Larsen	COMBINE MOLINFO COMMITTOR FLUSH METAD ALPHABETA PRINT	function multicolvar generic bias
19.011	Automatic Gradient Computation for Collective Variables	other	gradient, differentiation, curvature	Toni Giorgino	ENDPLUMED	generic
19.005	Cmyc small molecule interaction	bio	metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP	Gabriella Heller	WHOLEMOLECULES MOLINFO METAINFERENCE PBMETAD DISTANCE INCLUDE CENTER GYRATION CS2BACKBONE ALPHABETA PRINT GROUP COORDINATION	generic colvar vatom bias core multicolvar isdb
25.010	Kinetic rates calculation with Ratchet&Pawl MD	methods	kinetics, ligand binding, ABMD, ratchet&pawl MD	Riccardo Capelli	DISTANCE GROUP PRINT WHOLEMOLECULES ABMD COMMITTOR FLUSH COM	bias core vatom colvar generic
24.025	Correlating Enzymatic Reactivity for Different Substrates using Transferable Data-Driven Collective Variables	bio	enzymatic reactivity, k_cat, transfer learning, data-driven CVs, catalysis, ligand-binding modes, water, alpha-amylase, sugar, classical MD, OPES, machine learning, Deep TDA CV, path CV	Sudip Das	DISTANCE PYTORCH_MODEL FIXEDATOM LOWER_WALLS GROUP TORSION PATH UPPER_WALLS PRINT WHOLEMOLECULES RESTART COORDINATION CENTER FIT_TO_TEMPLATE CUSTOM OPES_METAD	bias function core mapping pytorch vatom setup colvar generic opes
24.024	Host-Guest binding free energies à la carte, an automated OneOPES protocol	bio	OneOPES, ligand binding, binding free energy,SAMPL challenge, host-guest	Valerio Rizzi	DISTANCE FIXEDATOM ENERGY LOWER_WALLS OPES_METAD_EXPLORE GROUP MATHEVAL TORSION ENDPLUMED UPPER_WALLS PRINT WHOLEMOLECULES COORDINATION CENTER ANGLE FIT_TO_TEMPLATE ECV_MULTITHERMAL OPES_EXPANDED	bias function core vatom colvar generic opes
24.009	Weighted Shape Gaussian Mixture Models	bio	metadynamics, clustering	Glen Hocky	GROUP TORSION PRINT METAD UNITS	bias core setup colvar generic
23.027	CmuMD simulations of NaCl(aq) at NaCl	chemistry	CmuMD, DFS, Q3, Pair Entropy	Aaron Finney	CLUSTER_DISTRIBUTION LOAD LOCAL_Q3 FIXEDATOM COORDINATIONNUMBER GROUP DENSITY CLUSTER_NATOMS DUMPGRID DFSCLUSTERING AROUND PRINT RESTRAINT CONTACT_MATRIX UNITS Q3 LOCAL_AVERAGE HISTOGRAM	bias adjmat core volumes clusters symfunc gridtools setup vatom generic
23.024	Permutationally Invariant Networks for Enhanced Sampling (PINES)	methods	collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent	Nicholas Herringer	LOAD PBMETAD PRINT	bias setup generic
22.030	Mixing physics across temperatures with generative artificial intelligence	methods	REMD, Generative AI, DDPM	Yihang Wang	PRINT WHOLEMOLECULES TORSION	generic colvar
22.027	Molecular Dynamics simulations of BANAL-236 RBD-hACE2 complexes	bio	SARS-CoV-2, COVID-19, MD, human-ACE2, spike, BANAL-236, receptor-binding domain	Max Bonomi	PRINT RMSD	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	DISTANCE PYTORCH_MODEL FIXEDATOM COMMITTOR LOWER_WALLS GROUP MATHEVAL UPPER_WALLS PRINT WHOLEMOLECULES COORDINATION CENTER FIT_TO_TEMPLATE RMSD CUSTOM OPES_METAD	bias function core pytorch vatom colvar generic opes
22.016	Homogeneous ice nucleation in an ab initio machine learning model of water	chemistry	ice, water, nucleation, seeding, environment similarity, interfacial free energy, interfaces	Pablo Piaggi	VOLUME ENERGY DUMPGRID AROUND UPPER_WALLS PRINT RESTART CUSTOM ENVIRONMENTSIMILARITY HISTOGRAM OPES_METAD	bias function volumes gridtools setup colvar envsim generic opes
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	DISTANCE YANGLES ALPHABETA LOWER_WALLS ZANGLES COMBINE MATHEVAL TORSION UPPER_WALLS PRINT WHOLEMOLECULES METAD CUSTOM XANGLES MOLINFO COM	bias function multicolvar vatom colvar generic
22.003	Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling	methods	opes, metadynamics, reweighting, alanine, muller	Michele Invernizzi	BIASVALUE PBMETAD ENERGY LOWER_WALLS OPES_METAD_EXPLORE ECV_UMBRELLAS_FILE POSITION TORSION ENDPLUMED UPPER_WALLS PRINT METAD CUSTOM UNITS ECV_MULTITHERMAL OPES_EXPANDED OPES_METAD	bias function setup colvar generic opes
21.049	Multiple-path-metadynamics and PathMaps	methods	path-CV, metadynamics, multiple-walker, multiple paths, pathmap	Alberto Pérez-de-Alba-Ortíz	LOAD MOVINGRESTRAINT CONSTANT LOWER_WALLS COMBINE ENSEMBLE TORSION UPPER_WALLS PRINT RESTRAINT METAD CUSTOM UNITS	bias function setup colvar generic
21.033	Multiple-path-metadynamics applied to DNA base-pairing transitions	bio	path-CV, metadynamics, multiple-walker, dna	Alberto Pérez-de-Alba-Ortíz	MOVINGRESTRAINT CONSTANT COMBINE UPPER_WALLS PRINT RESTRAINT METAD INCLUDE	bias generic function
21.001	Substrate recognition and catalysis by glycosaminoglycan sulfotransferases	bio	metadynamics, well-tempered metadynamics, puckering, coordination	Tarsis Ferreira	DISTANCE RANDOM_EXCHANGES ENERGY PUCKERING LOWER_WALLS GROUP REWEIGHT_METAD DUMPGRID UPPER_WALLS PRINT WHOLEMOLECULES COORDINATION METAD HISTOGRAM INCLUDE MOLINFO	bias core gridtools 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 PRINT RESTART CENTER METAD FIT_TO_TEMPLATE	bias setup vatom colvar generic
20.015	Rational design of ASCT2 inhibitors using an integrated experimental-computational approach	bio	ASCT2 transporter, small-molecules, cryo-EM, metainference	Max Bonomi	LOAD BIASVALUE GROUP PRINT WHOLEMOLECULES MOLINFO DUMPATOMS EMMIVOX	bias core isdb setup generic
20.008	Simulating solvation and acidity in complex mixtures with first-principles accuracy. The case of CH3SO3H and H2O2 in phenol	chemistry	proton trasfer, metadynamics	Kevin Rossi	DISTANCES PRINT COORDINATION METAD CUSTOM UNITS	bias function multicolvar setup colvar generic
19.071	Time-independent free energies from metadynamics via Mean Force Integration	methods	metadynamics, mean force integration, MFI, thermodynamic integration	Matteo Salvalaglio	DISTANCE BIASVALUE MATHEVAL TORSION DUMPGRID REWEIGHT_METAD PRINT READ METAD CONVERT_TO_FES COMMITTOR REWEIGHT_BIAS HISTOGRAM EXTERNAL	bias function gridtools colvar generic
19.053	Capillary fluctuations with PLUMED	methods	nucleation, surface tension, capillary fluctuations	Gareth Tribello	FOURIER_TRANSFORM GROUP MULTICOLVARDENS DUMPGRID FCCUBIC CENTER MORE_THAN UNITS FIND_CONTOUR_SURFACE	contour fourier function core symfunc gridtools vatom setup
19.043	Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA)	methods	metadynamics, chemistry, HLDA	GiovanniMaria Piccini	DISTANCE DISTANCES COMBINE UPPER_WALLS PRINT RESTART METAD FLUSH UNITS	bias function multicolvar setup colvar generic
19.035	Dimerization of GPCRs from coarse-grained umbrella sampling	bio	Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization	Davide Provasi	DISTANCE GROUP TORSION RESTRAINT PRINT COM	bias core vatom colvar generic
19.024	PT-MetaD-WTE	methods	metadynamics, WTE, trp cage, PT	Jim Pfaendtner	ENERGY GROUP COORDINATION METAD EXTERNAL	core bias colvar
19.014	MIL101(Cr) SBUs assembly	materials	MOFs, nucleation, self-assembly, metadynamics	Matteo Salvalaglio	DISTANCES COORDINATIONNUMBER ENDPLUMED PRINT RESTART METAD GYRATION	bias multicolvar symfunc setup colvar generic
19.009	RNA tetraloops folding	bio	metadynamics, RNA, folding	Giovanni Bussi	ERMSD ENDPLUMED PRINT WHOLEMOLECULES METAD RMSD MOLINFO	generic bias colvar
19.006	Flying Gaussian proof	methods	flying Gaussians, alanine dipeptide	Vojtech Spiwok	PRINT TORSION METAD	generic bias colvar
19.000	VesDeltaF	methods	VES, convergence, suboptimal CVs	Michele Invernizzi	LOAD ENERGY VES_DELTA_F POSITION TORSION ENDPLUMED PRINT RESTART METAD UNITS	bias ves setup colvar generic

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