Browse the eggs in PLUMED-NEST

PLUMED-NEST provides all the data needed to reproduce the results of a PLUMED-enhanced molecular dynamics simulation or analysis contained in a published paper. Furthermore, PLUMED-NEST monitors the compatibility of the provided PLUMED input files with the current and development versions of the code and integrates links from these files to the PLUMED manual.

Here is the list of projects already deposited in PLUMED-NEST, while a complete bibliography can be found here.

plumID	Name	Category	Keywords	Contributor	Actions	Modules
26.011	Lets Stalk About Membranes. Committor-Based Enhanced Sampling of Stalk Formation.	bio	committor, machine learning, enhanced sampling, OPES, membrane fusion, stalk formation, nanoparticles	Giorgia Rossi	COORDINATION GROUP PRINT CENTER LOAD LOWER_WALLS OPES_METAD_EXPLORE CUSTOM BIASVALUE	generic colvar vatom core bias setup opes function
26.008	Ensemble Dynamics	methods	State Exploration, Protein Folding, Drug Binding, Phase Transition	Florian M. Dietrich	TORSION GROUP PRINT DISTANCE UNITS CELL LOAD OPES_METAD_EXPLORE CUSTOM BIASVALUE POSITION	generic colvar core bias setup opes function
26.004	Resolving the ambiguous binding site of quercetin at the calcineurin subunit junction using funnel metadynamics with deep learning collective variables	bio	metadynamics, funnel metadynamics, DeepTICA	Jason Loo	WRAPAROUND COORDINATION GROUP PRINT DISTANCE FUNNEL_PS MATHEVAL ENERGY COM LOWER_WALLS METAD FUNNEL PYTORCH_MODEL UPPER_WALLS WHOLEMOLECULES RMSD	generic colvar funnel vatom pytorch core bias function
25.023	Molecular simulations of Tau-protein oligomers	bio	metadynamics, proteins, aggregation	Giovanni Bussi	PRINT DUMPGRID CONVERT_TO_FES HISTOGRAM CUSTOM METAD REWEIGHT_BIAS CONTACTMAP FLUSH RESTART RESTRAINT RMSD	gridtools generic colvar bias setup function
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	COORDINATION GROUP DISTANCE PRINT MOLINFO ECV_MULTITHERMAL CENTER COMBINE ENERGY OPES_EXPANDED CUSTOM OPES_METAD_EXPLORE GHOST RMSD	generic colvar vatom core opes function
25.013	Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices	bio	umbrella sampling, temperature ramping	Alexander Berlaga	DISTANCE PRINT GYRATION PYTORCH_MODEL RESTRAINT	pytorch generic bias colvar
24.035	Data efficient machine learning potentials for modeling catalytic reactivity via active learning and enhanced sampling	chemistry	opes, catalysis, ammonia, machine learning potentials	Luigi Bonati	GROUP PRINT DISTANCE OPES_METAD UNITS RESTART LOWER_WALLS COMMITTOR COORDINATION UPPER_WALLS CUSTOM	generic colvar core bias setup opes function
24.030	NMR guided simulation of dsRBD	bio	Metainference, NMR, protein dynamics	Debadutta Patra	GROUP PRINT METAINFERENCE MOLINFO DISTANCE ENSEMBLE STATS ALPHABETA FLUSH RDC WHOLEMOLECULES	generic colvar isdb core multicolvar function
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	COORDINATION TORSION GROUP PRINT DISTANCE ECV_MULTITHERMAL COMBINE ENERGY OPES_EXPANDED CUSTOM OPES_METAD_EXPLORE RESTART	generic colvar core setup opes function
23.038	Determinants of Neutral Antagonism and Inverse Agonism in the β2-adrenergic receptor	bio	protein coupled receptor, beta-adrenergic, receptor activation, antagonism, inverse agonism, metadynamics	Timothy Clark	MOLINFO PRINT DISTANCE MATHEVAL METAD WHOLEMOLECULES RMSD	generic function bias colvar
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	UPPER_WALLS FIT_TO_TEMPLATE CENTER OPES_METAD COORDINATION OPES_METAD_EXPLORE ENDPLUMED GROUP PRINT UNITS COMMITTOR LOWER_WALLS BIASVALUE TORSION MOLINFO DISTANCE WRAPAROUND MATHEVAL ENERGY COM FLUSH CUSTOM POSITION WHOLEMOLECULES	generic colvar vatom core bias setup opes function
23.026	Machine Learning Nucleation Collective Variables with Graph Neural Networks	chemistry	Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks	Florian Dietrich	GROUP PRINT COMBINE LOWER_WALLS METAD MOVINGRESTRAINT LOCAL_Q6 COORDINATIONNUMBER Q6 MFILTER_MORE	symfunc generic core bias multicolvar 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 OPES_METAD UNITS LOWER_WALLS PYTORCH_MODEL UPPER_WALLS CUSTOM BIASVALUE POSITION ENDPLUMED	generic colvar pytorch bias setup opes function
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	MOLINFO PRINT DISTANCE DUMPGRID CONVERT_TO_FES MATHEVAL HISTOGRAM METAD REWEIGHT_METAD WHOLEMOLECULES RMSD READ	gridtools generic colvar bias function
23.012	JAK2 2D meta-eABF PMF with statistical analysis	bio	2D meta-eABF, path CV, PMF	Istvan Kolossvary	PRINT UPPER_WALLS DRR LOWER_WALLS METAD PATHMSD FLUSH CUSTOM BIASVALUE	generic colvar drr bias function
23.001	Quantum phase diagram of water	chemistry	Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella	Sigbjørn-Løland Bore	INCLUDE PRINT ENVIRONMENTSIMILARITY OPES_EXPANDED LOWER_WALLS UPPER_WALLS RESTART ECV_UMBRELLAS_LINE	generic envsim bias setup opes
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	PRINT ENERGY LOWER_WALLS METAD CONTACTMAP UPPER_WALLS WHOLEMOLECULES	generic bias colvar
22.041	Skipping the Replica Exchange Ladder with Normalizing Flows	methods	OPES, alanine, normalizing flows, replica exchange	Michele Invernizzi	TORSION PRINT ECV_MULTITHERMAL OPES_METAD UNITS ENERGY OPES_EXPANDED POSITION ENDPLUMED	generic opes colvar setup
22.020	Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix–Junction–Helix RNA	bio	RNA force field, Helix-Junction-Helix RNA, SAXS, Well tempered metadynamics	Weiwei He	TORSION GROUP PRINT DISTANCE COM METAD WHOLEMOLECULES	generic colvar vatom core bias
22.019	Exploring aspartic protease inhibitor binding to design selective antimalarials	bio	ligand binding, loop opening, path CV, funnel metadynamics, drug development	Raitis Bobrovs	DISTANCE PRINT FUNNEL_PS COM LOWER_WALLS METAD FUNNEL PATHMSD UPPER_WALLS WHOLEMOLECULES	generic colvar funnel vatom bias
22.013	Ligand dissociation from PreQ1 riboswitch	bio	ligand, RNA, metadynamics, pRAVE	Yihang Wang	MOLINFO PRINT DISTANCE COMBINE COM COMMITTOR METAD COORDINATIONNUMBER WHOLEMOLECULES RMSD	generic symfunc colvar vatom bias function
22.009	Glycosylation in calixarenes capsule	chemistry	Metadynamics, glycosylation, supramolecular catalysis	GiovanniMaria Piccini	ANGLE GROUP PRINT DISTANCE FIT_TO_TEMPLATE BRIDGE UPPER_WALLS UNITS MATHEVAL COMBINE LOWER_WALLS METAD DISTANCES COORDINATION FLUSH WHOLEMOLECULES RMSD	generic colvar core bias multicolvar setup adjmat function
22.005	Collective Variable for Metadynamics Derived from AlphaFold Output	bio	AlphaFold, protein folding, protein structure prediction, metadynamics, deep learning, free energy simulation, collective variable	Vojtech Spiwok	METAD WHOLEMOLECULES LOAD PRINT	generic bias setup
22.004	Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques	chemistry	reaction discovery, OPES, collective variables	Umberto Raucci	DISTANCE PRINT GROUP OPES_METAD UNITS PYTORCH_MODEL MATHEVAL LOAD COM LOWER_WALLS OPES_METAD_EXPLORE COORDINATION UPPER_WALLS CUSTOM	generic colvar vatom pytorch core bias setup opes function
21.042	Peptoid-mediated Au nanocrystal growth	materials	parallel-bias metadynamics, peptoid, Au	Xin Qi	MOLINFO PRINT DISTANCE GYRATION PBMETAD COM UPPER_WALLS	generic vatom bias colvar
21.031	Photo-switchable sulfonulureas in KATP channel	bio	metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels	Katarzyna Walczewska-Szewc	DISTANCE PRINT UNITS COM LOWER_WALLS METAD UPPER_WALLS WHOLEMOLECULES	generic colvar vatom bias setup
21.023	Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling	methods	enhanced sampling, collective variables, machine learning	Jakub Rydzewski	CONSTANT INCLUDE DISTANCE PRINT TORSION UNITS ENERGY METAD REWEIGHT_METAD CUSTOM BIASVALUE	generic colvar bias setup function
20.029	High Conformational Flexibility of the E2F1/DP1/DNA complex	bio	SAXS, protein-DNA complex, hySAXS, ensemble determination	Cristina Paissoni	INCLUDE GROUP PRINT DISTANCE MOLINFO CENTER SAXS ENSEMBLE STATS BIASVALUE RESTRAINT WHOLEMOLECULES	generic colvar vatom isdb core bias function
20.006	Class B GPCR activation mechanism	bio	metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding	Francesco Gervasio	MOLINFO PRINT DISTANCE CENTER MATHEVAL ENERGY COMBINE LOWER_WALLS METAD UPPER_WALLS WHOLEMOLECULES RMSD	generic colvar vatom bias function
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	GROUP PRINT MOLINFO UPPER_WALLS ANTIBETARMSD PBMETAD CS2BACKBONE LOWER_WALLS ALPHABETA FLUSH BIASVALUE WHOLEMOLECULES ENDPLUMED	generic isdb core bias multicolvar secondarystructure
19.074	Asymmetric base pair opening in nucleic acids	bio	double helix, DNA, RNA, unwindability	Giovanni Bussi	DISTANCE LOWER_WALLS COORDINATION RESTRAINT WHOLEMOLECULES ENDPLUMED	generic bias colvar
19.070	Unexpected Dynamics in the UUCG RNA Tetraloop	bio	well-tempered metadynamics, RNA, UUCG, maximum entropy	Sandro Bottaro	ERMSD TORSION MOLINFO PRINT DISTANCE METAD WHOLEMOLECULES RMSD	generic bias colvar
19.067	Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways	bio	metadynamics, ligand unbinding	Jakub Rydzewski	PRINT UNITS LOWER_WALLS METAD PATHMSD UPPER_WALLS RESTART	generic bias colvar setup
19.026	Ice Nucleation on Cholesterol Crystals	materials	forward flux sampling, crystal nucleation, water, ice, organic crystals	Gabriele Cesare Sosso	CLUSTER_WITHSURFACE CONTACT_MATRIX COMMITTOR LOCAL_Q6 DFSCLUSTERING FLUSH Q6 CLUSTER_NATOMS OUTPUT_CLUSTER ENDPLUMED MFILTER_MORE	symfunc generic multicolvar clusters adjmat
19.024	PT-MetaD-WTE	methods	metadynamics, WTE, trp cage, PT	Jim Pfaendtner	EXTERNAL GROUP ENERGY METAD COORDINATION	core bias colvar
19.019	FA-MetaD-JCP-Wang-et-al	bio	Frequency adaptive metadynamics; peptide	Kresten Lindorff-Larsen	MOLINFO PRINT COMBINE COMMITTOR METAD ALPHABETA FLUSH	generic function bias multicolvar
19.018	Excited state FEP/Metadynamics simulations	chemistry	metadynamics, FEP, excited states, conjugated polymers, torsional potential	Adriana Pietropaolo	CONSTANT TORSION PRINT MATHEVAL METAD BIASVALUE WHOLEMOLECULES	generic function bias colvar
26.006	Metadynamics simulations of buried phosphorylation sites and proline isomerisation	bio	metadynamics	Julian Streit	METAD PRINT WHOLEMOLECULES TORSION COORDINATION MOLINFO	generic colvar bias
26.005	Cryptic pocket discovery in Alzheimer disease risk proteins BIN1, PICALM, and CD2AP via well-tempered metadynamics	methods	cryptic pockets, Alzheimer disease, BIN1, PICALM, CD2AP, well-tempered metadynamics, endocytosis, clathrin-mediated trafficking, virtual screening	Cagrı Ozkurt	METAD PRINT DISTANCE WHOLEMOLECULES ANGLE	generic colvar 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	METAD UPPER_WALLS PRINT COM FUNNEL FUNNEL_PS LOWER_WALLS	generic vatom bias funnel
25.018	Metainference simulation for dimerization of RNA binding protein	bio	Metainference, Metadynamics, SAXS, protein dimer	Debadutta Patra	UPPER_WALLS PRINT STATS DISTANCE CENTER WHOLEMOLECULES SAXS TORSION GYRATION PBMETAD MOLINFO ENSEMBLE METAINFERENCE FLUSH	function generic vatom isdb colvar 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	UNITS COMMITTOR CUSTOM PRINT UPPER_WALLS ZDISTANCES COORDINATIONNUMBER DISTANCE OPES_METAD GROUP FIXEDATOM DISTANCES FLUSH	function generic core vatom setup opes multicolvar colvar bias symfunc
24.006	Water vapor condensation	chemistry	metadynamics, homogeneous condensation, chemical potential	Shenghui Zhong	UNITS METAD UPPER_WALLS PRINT COORDINATIONNUMBER CONTACT_MATRIX DFSCLUSTERING CLUSTER_NATOMS CLUSTER_PROPERTIES	generic adjmat setup clusters bias symfunc
24.003	Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations	chemistry	steered molecular dynamics, foldamers, peptoids, bio-inspired	Kaylyn Torkelson	PRINT COM DISTANCE WHOLEMOLECULES MOVINGRESTRAINT GYRATION TORSION COORDINATION INCLUDE ALPHABETA	generic vatom multicolvar colvar bias
24.000	Ammonia Decomposition on Non-stoichiometric Lithium Imide	chemistry	ammonia decomposition, non-stoichiometric lithium imide, machine learning interatomic potentials, enhanced sampling, heterogeneous catalysis	Francesco Mambretti	UNITS UPPER_WALLS PRINT COORDINATIONNUMBER DISTANCE ZDISTANCES OPES_METAD GROUP FIXEDATOM FLUSH	generic core vatom setup opes multicolvar colvar bias symfunc
23.043	Modeling the ferroelectric phase transition in barium titanate with DFT accuracy and converged sampling	materials	Barium Titanate, ferroelectric phase transition, Machine Learning, polarization order parameters	Lorenzo Gigli	METAD PRINT MATHEVAL TRANSPOSE SUM SELECT_COMPONENTS INCLUDE FLUSH	function generic matrixtools valtools bias
23.040	Supramolecular capsules assembly dynamics	chemistry	Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics	Riccardo Capelli	CUSTOM UNITS METAD PRINT COM DISTANCE WHOLEMOLECULES CENTER POSITION GROUP DISTANCES FLUSH	function generic core vatom setup multicolvar colvar bias
23.039	Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation	chemistry	metadynamics, ligand dissociation	Eric Beyerle	METAD UPPER_WALLS PRINT DISTANCE CENTER DUMPMASSCHARGE MOLINFO RESTRAINT COMBINE FIXEDATOM	function generic vatom colvar 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	METAD PRINT WHOLEMOLECULES ERMSD COORDINATION MOLINFO GHBFIX COMBINE BIASVALUE	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	UNITS CUSTOM UPPER_WALLS PRINT COM COORDINATIONNUMBER DISTANCE ZDISTANCES COMMITTOR MATHEVAL OPES_METAD ENERGY GROUP FIXEDATOM LOWER_WALLS DISTANCES FLUSH	function generic core vatom setup opes multicolvar colvar bias symfunc
23.027	CmuMD simulations of NaCl(aq) at NaCl	chemistry	CmuMD, DFS, Q3, Pair Entropy	Aaron Finney	UNITS AROUND PRINT LOAD COORDINATIONNUMBER CONTACT_MATRIX LOCAL_AVERAGE Q3 DUMPGRID DFSCLUSTERING DENSITY CLUSTER_NATOMS HISTOGRAM GROUP CLUSTER_DISTRIBUTION RESTRAINT LOCAL_Q3 FIXEDATOM	generic core gridtools vatom adjmat setup clusters volumes bias symfunc
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	UNITS CUSTOM UPPER_WALLS PRINT METAD TIME DRR LOWER_WALLS PATHMSD BIASVALUE FLUSH	function drr generic setup colvar bias
22.037	Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site	chemistry	metadynamics, DNA, abasic	Mike Jones	METAD PRINT DISTANCES DISTANCE	generic multicolvar colvar bias
22.028	N-glycan conformer distributions in atomistic simulation	bio	REST2, RECT, N-glycan, pucker	Isabell Grothaus	METAD PRINT READ DUMPGRID TORSION HISTOGRAM MOLINFO PUCKERING CONVERT_TO_FES	generic gridtools colvar bias
22.023	Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy	bio	CryoEM, MEMMI,EMMI, Metadynamics, Metainference, IAPP, structural ensemble	Faidon Brotzakis	UPPER_WALLS PRINT COM WHOLEMOLECULES RMSD TORSION COORDINATION GROUP MOLINFO PBMETAD BIASVALUE EMMI RESTART	generic core vatom setup isdb colvar bias
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 METAD UPPER_WALLS COM COORDINATIONNUMBER DISTANCE GYRATION COORDINATION LOWER_WALLS COMBINE FLUSH	function generic vatom setup colvar bias symfunc
21.033	Multiple-path-metadynamics applied to DNA base-pairing transitions	bio	path-CV, metadynamics, multiple-walker, dna	Alberto Pérez-de-Alba-Ortíz	METAD UPPER_WALLS PRINT MOVINGRESTRAINT INCLUDE RESTRAINT CONSTANT COMBINE	generic function bias
21.030	Thermodynamic Basis for Stabilization of Helical Peptoids by Chiral Sidechains	bio	parallel bias parallel tempered metadynamics in WTE, synthetic foldamers, self-assembly, peptoid secondary structure	Jim Pfaendtner	METAD PRINT COM DISTANCE TORSION GYRATION ENERGY COORDINATION PBMETAD ALPHABETA INCLUDE	generic vatom multicolvar colvar bias
21.026	Probing allosteric regulations with coevolution-driven molecular simulations	bio	metadynamics, coevolution, allostery, adenylate cyclase	Francesco Colizzi	UNITS METAD UPPER_WALLS PRINT COM DISTANCE WHOLEMOLECULES PATHMSD	generic vatom setup colvar bias
20.031	Soft fluorescent nanoshuttles targeting receptors	chemistry	polymers, receptors, nanoparticles, fluorescent probes	Adriana Pietropaolo	PRINT WHOLEMOLECULES CENTER COORDINATION PBMETAD	bias vatom 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 PRINT WHOLEMOLECULES COORDINATION MOLINFO RESTRAINT COMBINE	bias function colvar generic
20.017	FISST	methods	FISST, force, peptide, sampling, tempering	Glen Hocky	UNITS PRINT FISST DISTANCE MATHEVAL GYRATION ENERGY GROUP RESTRAINT BIASVALUE	function fisst generic core setup colvar bias
19.073	On the role of enthalpic and entropic contributions on the conformational free energy landscape of MIL-101(Cr) building units	materials	metadynamics, MOF, MIL101Cr, conformational	Matteo Salvalaglio	METAD UPPER_WALLS PRINT COORDINATIONNUMBER ENDPLUMED GYRATION ENERGY LOWER_WALLS DISTANCES	generic multicolvar colvar bias symfunc
19.068	Rethinking Metadynamics	methods	metadynamics, opes, convergence	Michele Invernizzi	METAD UNITS PRINT OPES_METAD ENDPLUMED TORSION POSITION EXTERNAL	generic setup colvar bias opes
19.065	Molecular Enhanced Sampling with Autoencoders	methods	enhanced sampling, collective variables, deep learning	Wei Chen	COM POSITION ANN RESTRAINT COMBINE	annfunc function vatom colvar bias
19.062	Elucidating molecular design principles for charge-alternating peptides	bio	peptide folding, metadynamics, well-tempered ensemble, parallel tempering	Jim Pfaendtner	METAD PRINT WHOLEMOLECULES GYRATION ENERGY	generic colvar bias
19.049	Determining the sizes of solid/liquid clusters in MD trajectories of nucleation	methods	nucleation, metadynamics, clustering, Steinhardt order parameters	Gareth Tribello	CUSTOM LOCAL_Q6 METAD PRINT CONTACT_MATRIX DFSCLUSTERING COORDINATIONNUMBER CLUSTER_NATOMS OUTER_PRODUCT Q6 CLUSTER_PROPERTIES DISTANCES MORE_THAN OUTPUT_CLUSTER CLUSTER_DISTRIBUTION SMAC MATRIX_VECTOR_PRODUCT ONES	function generic matrixtools adjmat clusters multicolvar bias symfunc
19.045	Adsorption free energy of Ca/CO3 ions on calcite steps in contact with water	materials	metadynamics, well-tempered, multiple walkers, LAMMPS	Marco De La Pierre	UNITS METAD UPPER_WALLS PRINT POSITION GROUP COORDINATION LOWER_WALLS RESTART FLUSH	generic core setup colvar bias
19.043	Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA)	methods	metadynamics, chemistry, HLDA	GiovanniMaria Piccini	UNITS METAD UPPER_WALLS PRINT DISTANCE DISTANCES COMBINE RESTART FLUSH	function generic setup multicolvar colvar bias
19.020	PTMetaD-WTE simulation of the Ntail IDP	bio	metadynamics, IDPs, protein folding	Mattia Bernetti	METAD PRINT WHOLEMOLECULES ENDPLUMED ALPHARMSD GYRATION ENERGY MOLINFO	generic colvar bias secondarystructure
19.017	Ligand binding pathways exploration	bio	metadynamics, ligand binding	Riccardo Capelli	METAD UPPER_WALLS PRINT COM READ WRAPAROUND WHOLEMOLECULES MATHEVAL DUMPGRID ENDPLUMED POSITION GROUP COORDINATION HISTOGRAM CONVERT_TO_FES REWEIGHT_METAD FIT_TO_TEMPLATE FLUSH	function generic core gridtools vatom colvar bias
26.015	Ensemble Dynamics	methods	State Exploration, Protein Folding, Drug Binding, Phase Transition	Florian M. Dietrich	OPES_METAD_EXPLORE DISTANCE PRINT GROUP LOAD BIASVALUE CELL UNITS TORSION POSITION CUSTOM	colvar core function opes bias setup generic
26.014	Dissociation free energy (DFE) calculationsfor GPR15L–polySia	bio	metadynamics, protein-carbohydrate interaction	Davide Luciano and Gaston Courtade	METAD UPPER_WALLS DISTANCE PRINT GROUP COM	colvar core bias vatom generic
26.007	Metadynamics Simulations Reveal the Protonation-Dependent Conformational Landscape of GSK-3β Dual Inhibitors	chemistry	metadynamics, ligand unbinding, path CVs, funnel metadynamics	Gian Marco Elisi	METAD UPPER_WALLS DISTANCE FUNNEL_PS PRINT FUNNEL MOLINFO COMBINE RMSD PATHMSD ANGLE LOWER_WALLS ENDPLUMED UNITS MATHEVAL COM WHOLEMOLECULES	colvar function bias vatom funnel setup generic
25.017	Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity	bio	EMMIVox, cryo-EM, allostery, decamer, filament, ensemble refinement, glutamine synthetase	Samuel Hoff	PRINT MOLINFO EMMIVOX BIASVALUE GROUP WHOLEMOLECULES	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	BAIES GROUP BIASVALUE PRINT	bias isdb generic core
25.002	M3_PCV-ABMD	chemistry	Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor	Gian Marco Elisi	UPPER_WALLS PRINT ABMD PATHMSD ENDPLUMED UNITS	bias generic colvar setup
24.016	Cryo-EM guided simulations of ribozyme	bio	metainference, cryo-EM	Giovanni Bussi	PRINT MOLINFO EMMIVOX RESTRAINT BIASVALUE ERMSD INCLUDE GROUP WHOLEMOLECULES	colvar core isdb bias generic
24.004	Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables	materials	metadynamics, nucleation, machine learning	Ziyue Zou	METAD PRINT LOAD RESTART INCLUDE GROUP	bias generic setup core
24.001	A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations	bio	OPES, OPES-Flooding, QM/MM, Kinetics, Enzyme Catalysis	Dhiman Ray	UPPER_WALLS DISTANCE FLUSH PRINT COMBINE COMMITTOR OPES_METAD LOWER_WALLS UNITS TORSION CUSTOM	colvar function opes bias setup generic
23.044	Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition	materials	metadynamics, interlocked molecules	Luigi Leanza	METAD PRINT COORDINATION COMMITTOR HISTOGRAM DUMPGRID ENDPLUMED GROUP CONVERT_TO_FES READ	colvar core bias generic gridtools
23.037	Estimating binding free energy of solid binding peptides without extensive sampling	bio	metadynamics, solid binding peptides	Xin Qi	UPPER_WALLS DISTANCE PRINT MOLINFO GYRATION PBMETAD LOWER_WALLS COM	bias colvar generic vatom
23.036	Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water?	bio	NaCl, nucleation, metadynamics	Ruiyu Wang	VOLUME METAD Q6 PRINT Q4 COMBINE ENERGY COORDINATIONNUMBER MATHEVAL	colvar function bias generic symfunc
23.021	Into the Dynamics of Rotaxanes at Atomistic Resolution	materials	metadynamics, rotaxanes, molecular shuttles, molecular machines	Luigi Leanza	METAD UPPER_WALLS DISTANCE PRINT CENTER MATHEVAL FIXEDATOM TORSION CUSTOM	colvar function bias vatom generic
23.020	FEP simulations of ATOX1 homodimer	chemistry	parallel bias metadynamics, FEP, free-energy of metal ion dissociation	Adriana Pietropaolo	DISTANCE PRINT CONSTANT BIASVALUE PBMETAD MATHEVAL ANGLE WHOLEMOLECULES	bias colvar generic function
23.005	A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs	bio	metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A	Timothy Clark	METAD REWEIGHT_METAD DISTANCE PRINT MOLINFO RMSD HISTOGRAM DUMPGRID MATHEVAL CONVERT_TO_FES READ WHOLEMOLECULES	colvar function bias generic gridtools
23.003	Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations	methods	metadynamics, alchemical variable, alchemical free energy calculations	Wei-Tse Hsu	EXTRACV METAD PRINT TORSION READ	bias colvar generic
22.042	Metadynamics of NSP10 and variants	bio	metadynamics, NSP10, crystal structure, variants	Shozeb Haider	METAD TORSION PRINT	bias colvar generic
22.039	Driving and characterizing nucleation of urea and glycine polymorphs in water	bio	metadynamics, nucleation, amino acids, polymorphism	Eric Beyerle	METAD Q6 PRINT Q4 CENTER COMBINE LOAD COORDINATIONNUMBER INCLUDE GROUP MATHEVAL PAIRENTROPY	function core bias vatom setup generic symfunc gridtools
22.038	Enhanced Sampling Aided Design of Molecular Photoswitches	chemistry	reaction discovery, OPES explore, graph CV	Umberto Raucci	PYTORCH_MODEL OPES_METAD_EXPLORE PRINT COORDINATION UNITS CUSTOM	colvar function opes pytorch setup 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	MOLINFO GYRATION PBMETAD TORSION WHOLEMOLECULES	bias generic colvar
22.033	Reciprocal barrier restraint. Application to PROTAC passive permeability prediction	methods	PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR	Istvan Kolossvary	METAD DISTANCE FLUSH PRINT BIASVALUE UNITS DRR COM CUSTOM	drr colvar function bias vatom setup generic
22.030	Mixing physics across temperatures with generative artificial intelligence	methods	REMD, Generative AI, DDPM	Yihang Wang	TORSION PRINT WHOLEMOLECULES	colvar generic
22.025	Bubble nucleation rate predictions in a Lennard-Jones fluid	materials	free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation	Kristof Bal	VOLUME UPPER_WALLS REWEIGHT_BIAS FLUSH PRINT LOAD COORDINATIONNUMBER RESTRAINT BIASVALUE HISTOGRAM ANN DUMPGRID COMMITTOR MOVINGRESTRAINT UNITS CONVERT_TO_FES CUSTOM	colvar function annfunc bias setup generic symfunc gridtools
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	METAD UPPER_WALLS PRINT GYRATION LOWER_WALLS ENDPLUMED GROUP ALPHABETA WHOLEMOLECULES	colvar core bias multicolvar 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	METAD PRINT FIT_TO_TEMPLATE FIXEDATOM TORSION	bias generic colvar vatom
21.041	Nucleating a Different Coordination in a Crystal under Pressure. A Study of the B1−B2 Transition in NaCl by Metadynamics	methods	metadynamics, structural phase transitions, pressure-induced phase transition, martensitic transitions	Matej Badin	VOLUME METAD PRINT COMBINE COORDINATION ENDPLUMED CUSTOM	bias colvar generic function
21.038	Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics	materials	metadynamics, SGOOP, nucleation, urea	Ziyue Zou	METAD VOLUME PRINT CENTER COMBINE ENERGY LOAD COORDINATIONNUMBER INCLUDE GROUP	colvar function core bias vatom setup generic symfunc
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	METAD UPPER_WALLS PARABETARMSD RANDOM_EXCHANGES PRINT ANTIBETARMSD MOLINFO ENERGY COORDINATION GYRATION LOWER_WALLS DIHCOR GROUP ALPHARMSD WHOLEMOLECULES	colvar core bias multicolvar generic secondarystructure
21.035	CmuMD simulations of NaCl(aq) at NaCl	chemistry	CmuMD, interface	Aaron Finney	DISTANCE PRINT LOAD RESTRAINT GROUP FIXEDATOM	colvar core bias vatom setup generic
21.027	EGFR activating mutations mechanism	bio	metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA	Francesco Gervasio	METAD UPPER_WALLS DISTANCE PRINT MOLINFO ENERGY CONTACTMAP INCLUDE LOWER_WALLS MATHEVAL ALPHARMSD WHOLEMOLECULES	colvar function bias generic secondarystructure
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
20.025	The role of water in host-guest interaction	bio	ligand binding, water, opes, SAMPL5	Valerio Rizzi	PYTORCH_MODEL UPPER_WALLS DISTANCE PRINT WHOLEMOLECULES CENTER FIT_TO_TEMPLATE COORDINATION ENERGY OPES_METAD ENDPLUMED GROUP ANGLE FIXEDATOM MATHEVAL	colvar core function opes bias pytorch vatom generic
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	PRINT MOLINFO COORDINATION RESTRAINT STATS WHOLEMOLECULES	bias generic colvar function
20.018	Free energy barriers from biased molecular dynamics simulations	methods	kinetics, free energy barriers, chemical reactions, nucleation, metadynamics	Kristof Bal	UPPER_WALLS REWEIGHT_BIAS Q6 COORDINATION PAIRENTROPY VOLUME COMBINE LOAD COORDINATIONNUMBER CONTACT_MATRIX HISTOGRAM LOWER_WALLS LOCAL_AVERAGE DENSITY CONVERT_TO_FES METAD REWEIGHT_METAD FLUSH SPRINT DUMPGRID DISTANCE PRINT CENTER ENERGY UNITS	colvar function sprint bias volumes adjmat vatom setup generic symfunc gridtools
20.010	Phase equilibrium of liquid water and hexagonal ice from enhanced sampling molecular dynamics simulations	materials	water, ice, TIP4P, crystallization, EnvironmentSimilarity, RefCV, kernel, VES, variationally enhanced sampling	Pablo Piaggi	OPT_AVERAGED_SGD VOLUME UPPER_WALLS OPT_DUMMY Q6 BF_LEGENDRE PRINT RESTART ENVIRONMENTSIMILARITY VES_LINEAR_EXPANSION MATHEVAL TD_WELLTEMPERED	colvar function ves envsim bias setup generic symfunc
19.082	Ammonia Borane Dehydrogenation	chemistry	metadynamics, reaction discovery, hydrogen production, chemistry	Valerio Rizzi	METAD FLUSH PRINT GROUP COMBINE COORDINATIONNUMBER RESTART ENDPLUMED UNITS EXTERNAL	function core bias setup generic symfunc
19.071	Time-independent free energies from metadynamics via Mean Force Integration	methods	metadynamics, mean force integration, MFI, thermodynamic integration	Matteo Salvalaglio	METAD REWEIGHT_METAD DISTANCE REWEIGHT_BIAS PRINT COMMITTOR BIASVALUE HISTOGRAM DUMPGRID MATHEVAL CONVERT_TO_FES TORSION READ EXTERNAL	colvar function bias generic gridtools
19.066	Finding ligand unbinding reaction pathways	methods	maze, ligand unbinding	Jakub Rydzewski	PRINT MAZE_OPTIMIZER_BIAS MAZE_LOSS UNITS POSITION MAZE_SIMULATED_ANNEALING	setup generic colvar maze
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 PRINT INCLUDE TORSION	bias generic colvar
19.051	Solid liquid interfacial free energy out of equilibrium	materials	metadynamics, nucleation, surface excess free energy	Gareth Tribello	AROUND METAD UPPER_WALLS PRINT LOWER_WALLS CELL UNITS ENDPLUMED FCCUBIC	colvar volumes bias setup 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	METAD UPPER_WALLS REWEIGHT_BIAS PRINT COMBINE HISTOGRAM DUMPGRID DISTANCE_FROM_CONTOUR RESTART CONVERT_TO_FES READ	function contour bias setup generic gridtools
19.042	Harmonic Linear Discriminant Analysis (HLDA)	methods	metadynamics, chemistry, HLDA	GiovanniMaria Piccini	METAD UPPER_WALLS DISTANCE FLUSH PRINT COMBINE ENERGY UNITS	colvar function bias setup generic
19.037	Scission free energy of organic dyes	chemistry	metadynamics, multiple walkers, matheval/lepton	Paolo Raiteri	METAD UPPER_WALLS DISTANCE PRINT FLUSH RESTART UNITS MATHEVAL	colvar function bias setup generic
19.031	Ice nucleation using PIV-based path coordinates	materials	phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics	Silvio Pipolo	METAD UPPER_WALLS PRINT FUNCPATHMSD LOWER_WALLS CELL PIV	colvar piv function bias generic
19.025	Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide	bio	metainference, NMR, protein dynamics, force-fields	Carlo Camilloni	ENSEMBLE CS2BACKBONE FLUSH PRINT RDC MOLINFO BIASVALUE GYRATION PBMETAD ENDPLUMED JCOUPLING STATS TORSION METAINFERENCE WHOLEMOLECULES	colvar function bias isdb generic
19.016	Succinnic acid gamma polymorph	materials	Succinnic acid, conformers, polymorphs, metadynamics	Matteo Salvalaglio	METAD VOLUME UPPER_WALLS PRINT COMBINE ENERGY ENDPLUMED LOWER_WALLS CELL MATHEVAL TORSION	bias colvar generic function
19.010	Multi-domain protein dynamics	bio	metainference, NMR, protein dynamics	Carlo Camilloni	UPPER_WALLS DISTANCE ENSEMBLE PRINT RDC CENTER MOLINFO RESTRAINT ALPHABETA PBMETAD ENDPLUMED DIHCOR GROUP STATS DHENERGY TORSION METAINFERENCE WHOLEMOLECULES	colvar function core isdb bias multicolvar vatom generic
19.007	EMMI Microtubules	bio	metainference, cryo-EM	Max Bonomi	PRINT MOLINFO BIASVALUE EMMI GROUP WHOLEMOLECULES	bias generic core isdb
25.028	Designing transferable transition state guided collective variable via interpretable machine learning model for enhanced sampling. A case study on polymer collapse transition	bio	metadynamics, polymer collapse transition, transferable CV,interpretable ML-model	Saikat Dhibar and Biman Jana	WHOLEMOLECULES COORDINATION COMBINE CENTER LOWER_WALLS UPPER_WALLS MATHEVAL DISTANCE PRINT GROUP GYRATION METAD	vatom colvar generic bias core function
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	CUSTOM COMMITTOR FUNNEL MATHEVAL FUNNEL_PS ENDPLUMED CENTER WRAPAROUND METAD COM OPES_METAD WHOLEMOLECULES LOWER_WALLS RMSD PRINT COORDINATION UPPER_WALLS DISTANCE GROUP TORSION	vatom colvar opes generic funnel bias core function
25.011	Chiral perovskite nucleation	chemistry	metadynamics, chiral perovskites, nucleation	Adriana Pietropaolo	PBMETAD LOWER_WALLS MULTI_RMSD UPPER_WALLS MATHEVAL DISTANCE PRINT RESTART UNITS	colvar generic setup bias function
25.010	Kinetic rates calculation with Ratchet&Pawl MD	methods	kinetics, ligand binding, ABMD, ratchet&pawl MD	Riccardo Capelli	WHOLEMOLECULES FLUSH COMMITTOR DISTANCE ABMD PRINT GROUP COM	vatom colvar generic bias core
25.000	Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer	bio	metadynamics, pathCV	Sahithya Sridharan Iyer	WHOLEMOLECULES COM UPPER_WALLS MOLINFO PRINT DISTANCE GROUP METAD RESTART FUNCPATHGENERAL	vatom colvar generic setup bias core function
24.032	DeepLNE++	methods	PATHCV, OPES	Thorben Fröhlking	OPES_METAD CUSTOM COORDINATION COMBINE ENERGY LOAD DISTANCE PRINT GROUP TORSION	colvar opes generic setup core function
24.029	Combination of OPES and OPES-Explore	methods	OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin	Dhiman Ray	CUSTOM FIXEDATOM INCLUDE MATHEVAL UNITS FLUSH ENDPLUMED CENTER FIT_TO_TEMPLATE POSITION ENERGY PYTORCH_MODEL CONTACTMAP METAD OPES_METAD WHOLEMOLECULES OPES_METAD_EXPLORE LOWER_WALLS RMSD PRINT BIASVALUE COORDINATION COMBINE UPPER_WALLS MOLINFO DISTANCE GROUP	vatom colvar opes generic setup bias pytorch core function
24.027	Proline cis and trans subensembles of a disordered peptide	bio	intrinsically disordered proteins, proline cis trans isomerisation, metadynamics, collective variables	Alice Pettitt	WHOLEMOLECULES COORDINATION FLUSH COMBINE PBMETAD ENDPLUMED ALPHARMSD ANTIBETARMSD MOLINFO INCLUDE DISTANCE PRINT GROUP PARABETARMSD GYRATION TORSION DIHCOR	colvar secondarystructure multicolvar generic bias core function
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 COORDINATION ENERGY UPPER_WALLS DISTANCE PRINT	bias colvar generic opes
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 LOAD PRINT METAD GROUP TORSION	colvar generic setup bias core
24.017	Absolute Binding Free Energies with OneOPES	methods	protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy	Francesco Gervasio	CUSTOM OPES_EXPANDED INCLUDE MATHEVAL ECV_MULTITHERMAL WRAPAROUND ENERGY PROJECTION_ON_AXIS CONTACTMAP METAD COM WHOLEMOLECULES OPES_METAD_EXPLORE LOWER_WALLS RMSD CONSTANT PRINT BIASVALUE RESTART COORDINATION UPPER_WALLS MOLINFO GROUP TORSION	vatom colvar opes generic setup bias core function
24.007	SWISH-X	bio	swish-x, SWISH-X, swish, expanded SWISH	Alberto Borsatto	WHOLEMOLECULES ENERGY OPES_EXPANDED UPPER_WALLS MOLINFO INCLUDE PRINT CONTACTMAP ECV_MULTITHERMAL	bias generic colvar 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	WHOLEMOLECULES CENTER LOWER_WALLS CONSTANT UPPER_WALLS MATHEVAL DISTANCE PRINT BIASVALUE METAD	vatom colvar generic bias function
23.034	Urea nucleation in water: do long-range forces matter?	materials	LMF theory, Metadynamics, Nucleation	Ziyue Zou	CENTER COORDINATIONNUMBER INCLUDE LOAD PRINT GROUP METAD	vatom generic setup bias symfunc core
23.032	Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics	bio	metadynamics, tSNE, neural network, machine learning, trp-cage, folding	Vojtech Spiwok	WHOLEMOLECULES COMBINE FIT_TO_TEMPLATE POSITION ALPHARMSD ANN MOLINFO PRINT METAD	colvar generic bias annfunc function secondarystructure
23.023	Rational design of novel biomimetic sequence-defined polymers for mineralization applications	methods	metadynamics, surface binding, biomimetic mineralization	Kaylyn Torkelson	COORDINATION PBMETAD UPPER_WALLS PRINT DISTANCE GYRATION COM	bias vatom generic colvar
23.018	Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention	materials	metadynamics, surface binding, peptide adsorption	Kaylyn Torkelson	PBMETAD UPPER_WALLS PRINT DISTANCE GYRATION COM	bias vatom generic colvar
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	OPES_METAD CUSTOM COORDINATION WHOLEMOLECULES FIXEDATOM OPES_METAD_EXPLORE CENTER FIT_TO_TEMPLATE LOWER_WALLS PATH UPPER_WALLS PRINT PYTORCH_MODEL DISTANCE GROUP UNITS TORSION	vatom colvar opes generic setup bias pytorch core function mapping
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	WHOLEMOLECULES LOWER_WALLS CONSTANT UPPER_WALLS MATHEVAL DISTANCE PRINT BIASVALUE METAD	bias colvar generic function
23.007	Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains	bio	metadynamics, peptoids, parallel-bias metadynamics	Jim Pfaendtner	WHOLEMOLECULES COORDINATION RESTRAINT PBMETAD INCLUDE PRINT GYRATION TORSION COM	bias vatom generic colvar
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 MOVINGRESTRAINT UPPER_WALLS PRINT DISTANCE ANGLE METAD COM	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	generic colvar
22.018	Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations	bio	ligand binding, docking, EMMI, LAT1	Max Bonomi	WHOLEMOLECULES EMMIVOX MOLINFO LOAD PRINT BIASVALUE GROUP	generic isdb setup bias core
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	OPES_METAD WHOLEMOLECULES COORDINATION CUSTOM COMMITTOR FIXEDATOM CENTER FIT_TO_TEMPLATE LOWER_WALLS RMSD UPPER_WALLS MATHEVAL DISTANCE PYTORCH_MODEL PRINT GROUP	vatom colvar opes generic bias pytorch core function
21.052	On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets	materials	Ibuprofen, unbinding, WTmetaD	Matteo Salvalaglio	COMMITTOR ENDPLUMED COORDINATIONNUMBER CENTER DISTANCE PRINT TORSION METAD	vatom colvar generic bias symfunc
21.032	Metal-coupled folding mechanism to metallothionein	bio	parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination	Manuel-Peris Diaz	WHOLEMOLECULES COORDINATION PBMETAD GROUP UNITS	colvar generic setup bias core
21.025	Computational and biochemical analysis of type IV pilus dynamics and stability	bio	molecular dynamics, calcium binding, Type IV pilus	Yasaman Karami	UPPER_WALLS DISTANCE LOWER_WALLS PRINT	bias generic colvar
21.012	NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition	bio	funnel metadynamics	Jim Pfaendtner	LOWER_WALLS FUNNEL UPPER_WALLS PRINT DISTANCE FUNNEL_PS METAD COM	vatom colvar generic funnel bias
20.032	Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil	materials	clustering, conformational isomers	Matteo Salvalaglio	ENDPLUMED PRINT TORSION	generic colvar
20.024	Gaussian Mixture Based Enhanced Sampling (GAMBES)	methods	enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias	Jayashrita Debnath	COMBINE LOWER_WALLS ENERGY UPPER_WALLS LOAD PRINT DISTANCE GROUP UNITS DISTANCES TORSION	colvar multicolvar generic setup bias core function
20.014	amyloid beta small molecule interaction	bio	intrinsically disordered proteins, disordered proteins, IDPs, fuzzy binding, small molecule, drugs, entropy, binding, Alzheimer’s disease, amyloid beta	Gabriella Heller	METAINFERENCE INCLUDE FLUSH PBMETAD ENDPLUMED WHOLEMOLECULES ALPHARMSD PRINT PARABETARMSD DIHCOR ENSEMBLE COORDINATION COMBINE CS2BACKBONE ANTIBETARMSD MOLINFO GROUP GYRATION TORSION STATS	colvar multicolvar generic isdb bias core function secondarystructure
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 COORDINATION PRINT UNITS DISTANCES METAD	colvar multicolvar generic setup bias function
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	Q6 OPT_DUMMY TD_WELLTEMPERED MATHEVAL LOAD TD_MULTITHERMAL_MULTIBARIC REWEIGHT_BIAS DUMPGRID OPT_AVERAGED_SGD ENERGY VES_LINEAR_EXPANSION BF_LEGENDRE LOWER_WALLS CONVERT_TO_FES HISTOGRAM PRINT RESTART COMBINE VOLUME UPPER_WALLS READ REWEIGHT_TEMP_PRESS CELL	colvar ves generic setup bias symfunc gridtools function
19.064	Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations	materials	metadynamics, peptide-surface binding	Jim Pfaendtner	ENERGY UPPER_WALLS MOLINFO PRINT DISTANCE GYRATION METAD COM	bias vatom generic colvar
19.060	Neural networks-based variationally enhanced sampling	methods	ves, neural networks	Luigi Bonati	ENVIRONMENTSIMILARITY Q6 ENDPLUMED POSITION ENERGY LOAD PRINT UNITS TORSION	colvar envsim generic setup symfunc
19.052	Gibbs free energy of homogeneous nucleation	materials	nucleation, surface excess free energy	Gareth Tribello	ENDPLUMED FCCUBIC UPPER_WALLS PRINT CELL UNITS METAD	colvar generic setup bias symfunc
19.041	Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces	bio	metadynamics, collective variables, conformational changes, multiple walkers, Well-Tempered MetaD, peptide, binding, phosphorylation, post-transitional motif, sio2, adsorption	Jim Pfaendtner	ENERGY UPPER_WALLS PRINT DISTANCE METAD COM	bias vatom generic colvar
19.038	native state dynamics of human and mouse b2m	bio	metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation	Carlo Camilloni	WHOLEMOLECULES FLUSH PBMETAD ENDPLUMED LOWER_WALLS ALPHABETA CS2BACKBONE ANTIBETARMSD UPPER_WALLS MOLINFO PRINT BIASVALUE GROUP RESTART	multicolvar generic isdb setup bias core secondarystructure
19.035	Dimerization of GPCRs from coarse-grained umbrella sampling	bio	Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization	Davide Provasi	RESTRAINT DISTANCE PRINT GROUP TORSION COM	vatom colvar generic bias core
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 COORDINATION PBMETAD METAINFERENCE CENTER ALPHABETA CS2BACKBONE MOLINFO INCLUDE PRINT DISTANCE GROUP GYRATION	vatom colvar multicolvar generic isdb bias core
26.012	Buprenorphine Restricts the Conformational Landscape of the μ-Opioid Receptor	bio	OneOPES, GPCR, MOR, activation, euclidean path, conformational changes, allostery	Simone Aureli	OPES_METAD_EXPLORE ECV_MULTITHERMAL VOLUME OPES_EXPANDED PRINT CUSTOM GROUP CENTER PATH ENERGY UPPER_WALLS DISTANCE COORDINATION RMSD	vatom bias function generic core opes mapping colvar
26.002	A Transferable and Robust Computational Framework for Class A GPCR Activation Free Energies	bio	OneOPES, GPCR, ADRB1, activation, euclidean path, microswitches, conformational changes, allostery	Valerio Rizzi	OPES_METAD_EXPLORE ECV_MULTITHERMAL VOLUME OPES_EXPANDED PRINT LOWER_WALLS CUSTOM GROUP CENTER PATH PATHMSD ENERGY UPPER_WALLS DISTANCE COORDINATION RMSD	vatom bias function generic core opes mapping colvar
25.024	Sampling glycan-glycan interactions for B22 calculations	bio	B22, glycan, carbohydrates, distance, REST2, metadynamics, RECT, replica exchange	Isabell Louise Grothaus	METAD POSITION PRINT RESTRAINT COM DISTANCE COMBINE	vatom bias function generic colvar
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	DUMPMULTICOLVAR DISTANCES PRINT TORSIONS SMAC	multicolvar symfunc generic
25.001	RNA G-quadruplex folding with ST-metaD protocol	bio	RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD	Pavlína Pokorná	METAD MOLINFO ERMSD WHOLEMOLECULES COMBINE	colvar bias function generic
24.036	Leveraging cryptic ligand envelopes through enhanced molecular simulations	bio	HREX, conformational heterogeneity, drug discovery, ligand binding, plitidepsin, aplidin, ligand-target complexes, cryptic ligand envelope	Francesco Colizzi	TORSION COORDINATION ANGLE PRINT CONVERT_TO_FES WHOLEMOLECULES GROUP HISTOGRAM DUMPGRID DISTANCE	gridtools core colvar generic
24.034	Umbrella sampling of ion in transporter SLC26A7	bio	umbrella sampling, transporter, ions	Xiaoli Lu	POSITION PRINT UNITS RESTRAINT	setup colvar bias generic
24.026	Constant pH metadynamics of RNA oligomers	bio	metadynamics, pH, RNA	Giovanni Bussi	TORSION METAD RESTART MOLINFO PRINT PUCKERING	setup colvar bias 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	TORSION PYTORCH_MODEL RESTART FIXEDATOM PRINT LOWER_WALLS FIT_TO_TEMPLATE CUSTOM OPES_METAD GROUP CENTER PATH UPPER_WALLS WHOLEMOLECULES COORDINATION DISTANCE	setup vatom bias function generic core opes pytorch mapping colvar
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	TORSION OPES_METAD_EXPLORE ECV_MULTITHERMAL FIXEDATOM OPES_EXPANDED ANGLE PRINT ENDPLUMED LOWER_WALLS FIT_TO_TEMPLATE GROUP CENTER ENERGY UPPER_WALLS WHOLEMOLECULES COORDINATION DISTANCE MATHEVAL	vatom bias function generic core opes colvar
23.025	Probing ion binding to G-quadruplexes and related events	chemistry	metadynamics, repulsive potential, nucleic acids, G-quadruplexes	Marcelo Poleto	WRAPAROUND METAD RESTART UNITS POSITION DISTANCES PRINT LOWER_WALLS DUMPATOMS FIT_TO_TEMPLATE COM GROUP UPPER_WALLS WHOLEMOLECULES FLUSH DISTANCE MATHEVAL	setup vatom bias function generic core multicolvar colvar
23.015	MPCs aggregation	bio	opes_explore, dimerization, MPCs, self-assembly	Vikas Tiwari	OPES_METAD_EXPLORE METAD PRINT LOWER_WALLS CUSTOM COM GROUP CENTER UPPER_WALLS WHOLEMOLECULES COORDINATION DISTANCE	vatom bias function generic core opes colvar
23.014	Structural basis of dimerization of chemokine receptors CCR5 and CXCR4	bio	metadynamics, oligomerization, chemokine receptors, GPCR, membrane	Vittorio Limongelli	TORSION METAD FLUSH PRINT COM UPPER_WALLS WHOLEMOLECULES COMBINE DISTANCE	vatom bias function generic colvar
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	PYTORCH_MODEL MOLINFO CONTACTMAP OPES_METAD WHOLEMOLECULES DISTANCE INCLUDE RMSD FIXEDATOM ANGLE FIT_TO_TEMPLATE GROUP PRINT LOWER_WALLS CENTER MATHEVAL COMBINE ENDPLUMED CUSTOM ENERGY UPPER_WALLS COORDINATION COMMITTOR	vatom bias function generic core opes pytorch colvar
23.008	PBMetaD simulations of Histatin5	bio	metadynamics, IDP, Rg, PPII	Francesco Pesce	TORSION MOLINFO GYRATION PRINT GROUP PBMETAD WHOLEMOLECULES	core colvar bias generic
23.002	Critical comparison of general-purpose collective variables for crystal nucleation	methods	metadynamics, umbrella sampling, commitor, entropy, PIV	Julien Lam	METAD VOLUME Q4 PRINT RESTRAINT CUSTOM ENERGY PIV PAIRENTROPY UPPER_WALLS LOCAL_AVERAGE Q6 UNITS FUNCPATHMSD	gridtools symfunc setup bias function generic piv colvar
22.032	Reciprocal barrier restraint. Application to path-meta-eABF	methods	restraint, upper wall, lower wall, path colvar, meta-eABF, metadynamics, DRR, protein conformational transition, PROTAC	Istvan Kolossvary	METAD PRINT CUSTOM DRR PATHMSD BIASVALUE FLUSH	drr bias function generic colvar
22.031	Rare Event Kinetics from Adaptive Bias Enhanced Sampling	methods	OPES Flooding, Kinetics, Rate, OPES, Machine Learning	Dhiman Ray	PYTORCH_MODEL MOLINFO CONTACTMAP OPES_METAD WHOLEMOLECULES UNITS INCLUDE CONSTANT DISTANCE RMSD GROUP BIASVALUE TORSION POSITION PRINT COMBINE ENDPLUMED CUSTOM ENERGY COMMITTOR	setup bias function generic core opes pytorch colvar
22.024	Conformational Entropy as a Potential Liability of Computationally Designed Antibodies	bio	metadynamics, conformational entropy, antibody, nanobody	Thomas Löhr	TORSION RESTART MOLINFO PRINT ANTIBETARMSD ALPHABETA COM PBMETAD ALPHARMSD WHOLEMOLECULES	setup vatom bias generic secondarystructure multicolvar colvar
22.015	Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome	bio	photodynamics, bacteriophytochrome, variationally enhanced sampling	Jakub Rydzewski	TORSION OPT_AVERAGED_SGD PRINT VES_LINEAR_EXPANSION TD_UNIFORM BF_FOURIER	ves colvar generic
22.002	GAMBES_SAMPL5_RATES	other	GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding	Jayashrita Debnath	PYTORCH_MODEL COMMITTOR LOAD COORDINATION FIXEDATOM ANGLE PRINT ENDPLUMED FIT_TO_TEMPLATE GROUP CENTER ENERGY UPPER_WALLS WHOLEMOLECULES FLUSH DISTANCE MATHEVAL	setup vatom bias function generic core pytorch colvar
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	TD_WELLTEMPERED DISTANCE COORDINATION UNITS INCLUDE VES_OUTPUT_BASISFUNCTIONS OPT_ADAM VES_LINEAR_EXPANSION BF_GAUSSIANS POSITION PRINT FLUSH OPT_AVERAGED_SGD BF_CHEBYSHEV METAD BF_LEGENDRE BF_WAVELETS TD_UNIFORM ENERGY UPPER_WALLS BF_CUBIC_B_SPLINES	setup bias generic ves colvar
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
21.029	Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs	bio	metadynamics, small peptide, machine learning	Pratyush Tiwary	TORSION RESTART EXTERNAL MOLINFO PRINT ENERGY FLUSH	setup colvar bias generic
21.016	MD SAXS GTPase associated center	bio	metadynamics, RNA, folding, SAXS	Giovanni Bussi	METAD GYRATION MOLINFO PRINT LOWER_WALLS CUSTOM GROUP SAXS UPPER_WALLS ERMSD WHOLEMOLECULES INCLUDE	bias function generic core colvar isdb
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 RESTART VOLUME BF_LEGENDRE ECV_UMBRELLAS_LINE ENVIRONMENTSIMILARITY OPES_EXPANDED PRINT VES_LINEAR_EXPANSION TD_UNIFORM ENERGY ECV_MULTITHERMAL_MULTIBARIC UPPER_WALLS Q6 MATHEVAL	symfunc setup bias function generic envsim opes ves colvar
21.000	Uremic toxin time scale dynamics	bio	uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs)	Jim Pfaendtner	PRINT COM GROUP WHOLEMOLECULES DISTANCE	core vatom colvar generic
20.020	Parallel Bias Metadynamics	methods	pbmetad, trp-cage, folding	Max Bonomi	INCLUDE GYRATION MOLINFO PRINT ALPHABETA PBMETAD WHOLEMOLECULES COORDINATION DIHCOR	multicolvar colvar bias generic
19.077	Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations	materials	metadynamics, peptide-surface binding	Jim Pfaendtner	METAD GYRATION MOLINFO PRINT COM ENERGY UPPER_WALLS DISTANCE	vatom colvar bias generic
19.058	Constrained MD for maintaining a cavity in a calculation	chemistry	constrained MD, porous molecules, porosity, cavity	Kim Jelfs	RESTART MOVINGRESTRAINT FLUSH PRINT DISTANCES COM INPLANEDISTANCES	setup vatom bias generic multicolvar
19.056	maze	methods	maze, ligand unbinding	Jakub Rydzewski	MAZE_SIMULATED_ANNEALING POSITION MAZE_LOSS PRINT UNITS MAZE_OPTIMIZER_BIAS	setup colvar generic maze
19.048	Understanding Ligand Binding Selectivity in a Prototypical GPCR Family	bio	metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding	Francesco Gervasio	METAD PRINT LOWER_WALLS WHOLEMOLECULES COM CONSTANT UPPER_WALLS BIASVALUE DISTANCE MATHEVAL	vatom bias function generic colvar
19.015	Ibuprofen conformational dynamics and thermodynamics surface	materials	Ibuprofen, crystal, surface, solvents, conformers, metadynamics	Matteo Salvalaglio	TORSION METAD PRINT LOWER_WALLS CENTER UPPER_WALLS DISTANCE COMMITTOR	vatom colvar bias generic
19.014	MIL101(Cr) SBUs assembly	materials	MOFs, nucleation, self-assembly, metadynamics	Matteo Salvalaglio	METAD RESTART GYRATION ENDPLUMED PRINT DISTANCES COORDINATIONNUMBER	symfunc setup bias generic multicolvar colvar
19.013	RNA FF FITTING	methods	force field, RNA	Giovanni Bussi	TORSION MOLINFO CONSTANT PUCKERING BIASVALUE INCLUDE MATHEVAL	colvar bias function generic
19.002	EMMI STRA6	bio	metainference, cryo-EM	Max Bonomi	MOLINFO PRINT EMMI GROUP BIASVALUE	core bias isdb generic
26.013	Characterizing Partially Unfolded States of the C-Terminal Domain in WT and 3PA Mouse Prion Protein	bio	parallel-bias metadynamics, PBMetaD, metadynamics, mouse prion protein, prion protein, protein folding, partially unfolded states, molecular dynamics	Sonali M. Jadhav	GYRATION DISTANCE INCLUDE MOLINFO CONTACTMAP GROUP PRINT PBMETAD DUMPMASSCHARGE COORDINATION WHOLEMOLECULES ALPHARMSD COM	vatom generic core colvar secondarystructure bias
26.000	OPES simulations of disordered proteins	bio	OPES, IDPs	Julian Streit	RESTART OPES_EXPANDED ENERGY PRINT ECV_MULTITHERMAL	opes colvar generic setup
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	CUSTOM CELL MATHEVAL DISTANCE ENERGY INCLUDE POSITION PRINT BIASVALUE COMBINE COORDINATION OPES_METAD LOAD UNITS FLUSH TORSION	opes generic colvar function setup bias
25.009	Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water	chemistry	metadynamics, nitrate photolysis	Kam-Tung Chan	METAD READ CUSTOM DISTANCE RESTART GROUP PRINT REWEIGHT_METAD COORDINATION DUMPGRID HISTOGRAM UPPER_WALLS FLUSH	generic core gridtools colvar function setup bias
25.008	Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting	methods	metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting	Dhiman Ray	METAD PYTORCH_MODEL CUSTOM DISTANCE ENERGY LOWER_WALLS MOLINFO POSITION GROUP PRINT BIASVALUE WHOLEMOLECULES UNITS RMSD UPPER_WALLS OPES_METAD ENDPLUMED TORSION	opes pytorch generic core colvar function setup bias
25.005	Mechanism of Nanocluster Formation from Machine-Learned Potential-based Simulations	chemistry	WT-metadynamics, metal nanoclusters, nucleation, neural network potential, deepMD	Vikas Tiwari, Tarak Karmakar	METAD DISTANCE RESTRAINT FIXEDATOM LOWER_WALLS DISTANCES GROUP PRINT FLUSH ANGLE COMBINE COORDINATION UNITS COM UPPER_WALLS COORDINATIONNUMBER	vatom generic symfunc core multicolvar colvar function setup bias
24.028	All-atom simulations of RNA-membrane interactions	bio	metadynamics, membrane, RNA	Giovanni Bussi	METAD GYRATION MATHEVAL DISTANCE LOWER_WALLS MOLINFO POSITION GROUP PRINT DISTANCES GHOST COMBINE SORT WHOLEMOLECULES UPPER_WALLS CENTER PUCKERING	vatom generic core colvar multicolvar function bias
22.036	Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction	bio	Well-tempered MetaDynamics with Hamiltonian Replica Exchange	Miroslav Krepl	METAD CUSTOM MOLINFO GROUP PRINT BIASVALUE COMBINE COORDINATION GHBFIX LOAD UPPER_WALLS FLUSH	generic core colvar function setup bias
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	COMMITTOR METAD CUSTOM CELL MATHEVAL LOWER_WALLS DRMSD PRINT UPPER_WALLS	function bias colvar generic
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	METAD ALPHABETA DISTANCE MOLINFO PRINT ANGLE COORDINATION WHOLEMOLECULES ALPHARMSD UPPER_WALLS FLUSH TORSION	generic colvar multicolvar secondarystructure bias
21.044	NaCl nucleation	chemistry	metadynamics, DFS clustering	Aaron Finney	CLUSTER_DISTRIBUTION METAD CONTACT_MATRIX FIXEDATOM GROUP PRINT LOCAL_Q6 INSPHERE COMBINE DUMPGRID Q6 HISTOGRAM DFSCLUSTERING CLUSTER_NATOMS MFILTER_MORE COORDINATIONNUMBER	adjmat vatom generic symfunc core gridtools multicolvar function volumes clusters bias
21.009	Nucleation rates from small scale atomistic simulations and transition state theory	materials	kinetics, free energy barriers, nucleation, droplets, metadynamics	Kristof Bal	COMMITTOR METAD CONVERT_TO_FES MOVINGRESTRAINT FLUSH PRINT REWEIGHT_METAD DUMPGRID LOAD HISTOGRAM UNITS UPPER_WALLS COORDINATIONNUMBER	generic symfunc gridtools setup bias
20.016	Predicting polymorphism in molecular crystals using orientational entropy	materials	metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy	Pablo Piaggi	METAD INCLUDE GROUP PRINT VOLUME LOAD UPPER_WALLS CENTER	vatom generic core colvar setup bias
20.011	Uremic toxin analysis	bio	metadynamics, uremic toxin, serum albumin	Jim Pfaendtner	DISTANCE RESTART DISTANCES GROUP PRINT COORDINATION WHOLEMOLECULES CENTER	vatom generic core multicolvar colvar setup
19.075	PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python	other	Python, automatic differentiation	Toni Giorgino	CUSTOM DISTANCE RESTRAINT GROUP PRINT ANGLE COMBINE CENTER ENDPLUMED TORSION DUMPDERIVATIVES	vatom generic core colvar function bias
19.012	Martini-Beads multi-scale SAXS	methods	metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex	Carlo Camilloni	DISTANCE RESTRAINT INCLUDE MOLINFO SAXS GROUP PRINT BIASVALUE WHOLEMOLECULES STATS RMSD UPPER_WALLS CENTER ENDPLUMED	vatom generic core colvar function isdb bias
19.003	EMMI ClpP	bio	metainference, cryo-EM	Max Bonomi	EMMI MOLINFO GROUP PRINT BIASVALUE	core bias isdb generic
25.030	Committor Regularization	methods	metadynamics, enhanced sampling, mlcvs, committor, machine learning	Florian Dietrich	PRINT UNITS METAD MOVINGRESTRAINT	setup generic bias
25.022	Imidazole Diffusion in SALEM-2 MOF	materials	OPES, Diffusion, Ring opening, MOFs, Machine Learning Potentials	Sudheesh Kumar Ethirajan	CENTER DISTANCES PRINT UNITS GROUP ENDPLUMED PROJECTION_ON_AXIS OPES_METAD WHOLEMOLECULES MOLINFO DISTANCE	setup core colvar generic opes multicolvar vatom
25.014	Atomic resolution ensembles of intrinsically disordered proteins with Alphafold	bio	bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement	Vincent Schnapka	BIASVALUE PRINT BAIES GROUP	isdb generic core bias
25.006	Characterizing the conformational ensemble of PROTAC degraders in solutions via atomistic simulations	methods	Enhanced sampling, Atomistic simulations, Conformational ensemble, PROTACs, Targeted Protein Degradation, Chamelonic molecules	Shikshya Bhusal, Omar Valsson	VOLUME CENTER TORSION READ PRINT GYRATION ENERGY PBMETAD INCLUDE UPDATE_IF RESTART WHOLEMOLECULES DUMPATOMS MOLINFO DISTANCE	setup colvar generic vatom bias
25.003	Surrogate Model CV	methods	Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding	Sompriya Chatterjee	TORSION COMBINE PRINT CUSTOM GROUP ENDPLUMED ENERGY COMMITTOR OPES_METAD MATHEVAL WHOLEMOLECULES MOLINFO PYTORCH_MODEL DISTANCE	pytorch core function colvar generic opes
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	RMSD CENTER DUMPATOMS UPPER_WALLS PRINT GROUP PARABETARMSD ALPHARMSD PBMETAD COM DUMPMASSCHARGE EMMI WHOLEMOLECULES BIASVALUE COORDINATION MOLINFO DISTANCE	core isdb colvar generic secondarystructure vatom 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	DRR RMSD UPPER_WALLS PRINT METAD LOWER_WALLS FLUSH WHOLEMOLECULES COORDINATION MOLINFO PYTORCH_MODEL	pytorch colvar generic drr bias
24.011	Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble	methods	committor, machine learning	Peilin Kang	RMSD LOWER_WALLS DISTANCE TORSION PRINT CUSTOM CELL INCLUDE BIASVALUE UNITS GROUP LOAD MATHEVAL WHOLEMOLECULES POSITION UPPER_WALLS ENDPLUMED ENERGY COORDINATION MOLINFO	setup core function colvar generic bias
24.005	Learning Markovian Dynamics with Spectral Maps	methods	spectral map, collective variables, machine learning	Jakub Rydzewski	PRINT UNITS CUSTOM BIASVALUE DISTANCE	setup function colvar generic bias
23.046	Lasso Peptides - HLDA CV	bio	metadynamics, protein folding, HLDA, harmonic	Gabriel da Hora	COMBINE PRINT METAD UNITS WHOLEMOLECULES DISTANCE	setup function colvar generic bias
23.019	Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors	bio	binding pathway, binding energy, sketch-map, drug development	Raitis Bobrovs	VSTACK LANDMARK_SELECT_FPS UPPER_WALLS COLLECT_FRAMES PRINT METAD CUSTOM PATHMSD SKETCHMAP VORONOI SKETCHMAP_PROJECTION COM WHOLEMOLECULES TRANSPOSE DISSIMILARITIES DISTANCE	valtools function colvar generic landmarks matrixtools dimred vatom bias
23.006	Transcription factor unbinding	bio	metadynamics, DNA, conformational changes	Malin Lüking	CONTACTMAP PRINT ANGLE METAD ALPHARMSD COM DUMPFORCES MOLINFO DISTANCE	colvar generic secondarystructure vatom bias
22.040	From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure	bio	SARS-CoV-2, Spike, Omicron	Miłosz Wieczór	UPPER_WALLS PRINT METAD LOWER_WALLS PCAVARS WHOLEMOLECULES	mapping generic bias
21.051	Automatic learning of hydrogen-bond fixes in an AMBER RNA force field	methods	force field, RNA	Giovanni Bussi	COMBINE PRINT METAD ERMSD WHOLEMOLECULES BIASVALUE COORDINATION MOLINFO	function colvar generic bias
21.049	Multiple-path-metadynamics and PathMaps	methods	path-CV, metadynamics, multiple-walker, multiple paths, pathmap	Alberto Pérez-de-Alba-Ortíz	RESTRAINT TORSION COMBINE CONSTANT UPPER_WALLS PRINT UNITS METAD CUSTOM LOWER_WALLS LOAD ENSEMBLE MOVINGRESTRAINT	setup 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	UPPER_WALLS PRINT GROUP COM RESTART EMMI WHOLEMOLECULES BIASVALUE MOLINFO DISTANCE	setup core isdb colvar generic vatom bias
21.039	Deep learning the slow modes for rare events sampling	methods	collective variables, machine learning, slow modes, deep-tica, opes	Luigi Bonati	RMSD COMBINE Q6 ENVIRONMENTSIMILARITY DISTANCE TORSION PRINT INCLUDE OPES_EXPANDED ECV_MULTITHERMAL PYTORCH_MODEL VOLUME CONTACTMAP UNITS GROUP FLUSH LOAD OPES_METAD WHOLEMOLECULES ENDPLUMED ENERGY MOLINFO	setup pytorch envsim core function colvar symfunc generic opes
21.020	Reweighted Jarzynski sampling	methods	free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions	Kristof Bal	RESTRAINT COMBINE CONSTANT METAD ANN TD_WELLTEMPERED DUMPGRID DISTANCE MOVINGRESTRAINT PRINT CUSTOM CONVERT_TO_FES REWEIGHT_BIAS VES_LINEAR_EXPANSION BIASVALUE UNITS COORDINATIONNUMBER FLUSH BF_CHEBYSHEV LOAD OPES_METAD HISTOGRAM OPT_AVERAGED_SGD REWEIGHT_METAD UPPER_WALLS	setup ves annfunc gridtools function colvar symfunc generic opes bias
21.018	Localized Volume-based Metadynamics	bio	LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification	Riccardo Capelli	RMSD METAD FIXEDATOM DUMPGRID DISTANCE PRINT COM CONVERT_TO_FES READ GROUP FLUSH HISTOGRAM MATHEVAL WHOLEMOLECULES REWEIGHT_METAD POSITION UPPER_WALLS ENDPLUMED COORDINATION	core gridtools function colvar generic vatom bias
21.011	CmuMD simulations of NaCl(aq) at graphite	chemistry	CmuMD, DFS clustering	Aaron Finney	RESTRAINT DENSITY AROUND MULTICOLVARDENS PRINT GROUP COORDINATIONNUMBER CLUSTER_DISTRIBUTION MFILTER_MORE DFSCLUSTERING FIXEDATOM LOAD CLUSTER_NATOMS CONTACT_MATRIX DUMPGRID	setup clusters core gridtools volumes symfunc generic adjmat multicolvar vatom bias
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 METAD PATHMSD LOWER_WALLS RESTART WHOLEMOLECULES	setup colvar generic bias
20.033	COVID-19 Spike protein opening transition mechanism	bio	EMMI, CryoEM, COVID-19, Spike, Metainference	Faidon Brotzakis	RMSD DISTANCES PRINT GROUP CONVERT_TO_FES HISTOGRAM EMMI WHOLEMOLECULES READ MOLINFO DUMPGRID BIASVALUE	core gridtools isdb colvar generic multicolvar bias
20.012	Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies	bio	metadynamics, well-tempered ensemble, ligand binding, binding affinity calculations, novel COLVAR, funnel restraints, Hamiltonian replica-exchange, PathCV, COMetPath, SWISH	Francesco Gervasio	CONTACTMAP FUNCPATHGENERAL UPPER_WALLS CONSTANT PRINT METAD GROUP LOWER_WALLS INCLUDE COM LOAD PROJECTION_ON_AXIS MATHEVAL WHOLEMOLECULES BIASVALUE MOLINFO DISTANCE	setup core function colvar generic vatom bias
19.061	Diffusion in porous materials	materials	metadynamics, porous materials, diffusion	Kim E. Jelfs	CENTER UPPER_WALLS PRINT METAD GROUP LOWER_WALLS COM RESTART DISTANCE	setup core colvar generic vatom bias
19.057	SAXS ensembles using Martini-Beads multi-scale SAXS	methods	metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics	Cristina Paissoni	CENTER COMBINE PRINT ANGLE GROUP ENDPLUMED ALPHABETA INCLUDE PBMETAD ENSEMBLE MATHEVAL WHOLEMOLECULES BIASVALUE STATS SAXS MOLINFO COORDINATION	core isdb function colvar generic multicolvar vatom bias
19.053	Capillary fluctuations with PLUMED	methods	nucleation, surface tension, capillary fluctuations	Gareth Tribello	FCCUBIC CENTER FIND_CONTOUR_SURFACE FOURIER_TRANSFORM MULTICOLVARDENS UNITS GROUP DUMPGRID MORE_THAN	setup core gridtools fourier contour symfunc function vatom
19.029	WTE-metaD of FF domain of URNF1 C57D variant	bio	metadynamics, mutations, post-translational modification, ff domain	Elena Papaleo	UPPER_WALLS PRINT METAD GROUP LOWER_WALLS ALPHABETA WHOLEMOLECULES GYRATION MOLINFO	core colvar generic multicolvar bias
19.023	RECT	methods	metadynamics, replica exchange	Giovanni Bussi	TORSION PRINT METAD WHOLEMOLECULES GYRATION	colvar generic bias
19.001	RNA SHAPE	bio	metadynamics, RNA, ligand binding	Giovanni Bussi	COMBINE DISTANCES UPPER_WALLS ANGLE METAD PRINT LOWER_WALLS FLUSH INCLUDE ERMSD RANDOM_EXCHANGES MOLINFO DISTANCE	function colvar generic multicolvar bias
26.001	Molecular simulations Alx riboswitch	bio	RNA, riboswitch	Giovanni Bussi	DISTANCE MATHEVAL MOVINGRESTRAINT PRINT RESTRAINT MOLINFO ERMSD	function generic colvar bias
25.027	Enhanced-sampling MD simulations of a protein-peptide complex integrating SAXS and XL-MS experimental information	bio	steered MD, metadynamics, SAXS, XL-MS, ensemble reconstruction	Mattia Bernetti	CENTER DISTANCE GYRATION METAD WHOLEMOLECULES GROUP UPPER_WALLS PRINT MOVINGRESTRAINT INCLUDE SAXS MOLINFO	core colvar bias isdb generic vatom
24.031	DeepLNE	methods	PATHCV, OPES, OneOPES	Thorben Fröhlking	OPES_METAD_EXPLORE ENERGY COORDINATION VOLUME OPES_EXPANDED PYTORCH_MODEL PRINT COMBINE ECV_MULTITHERMAL RESTART MOLINFO ERMSD	opes colvar generic function setup 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	ENDPLUMED COORDINATION MATHEVAL UPPER_WALLS TORSION COMMITTOR DISTANCE FIT_TO_TEMPLATE METAD OPES_METAD COMBINE CONTACTMAP CENTER ANGLE FIXEDATOM WHOLEMOLECULES GROUP PRINT CUSTOM RMSD MOLINFO	core opes colvar bias generic function vatom
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	PRINT DISTANCE	colvar generic
24.010	Oxytocin metadynamics simulation	bio	metadynamics, oxytocin, peptide	Jan Beránek	METAD WHOLEMOLECULES PRINT FLUSH TORSION RESTART	bias colvar setup generic
24.009	Weighted Shape Gaussian Mixture Models	bio	metadynamics, clustering	Glen Hocky	UNITS METAD GROUP PRINT TORSION	core colvar bias generic setup
24.008	yCD Metadynamics	bio	volume-based MetaD, path CVs, infrequent MetaD, product release	James McCarty	ENDPLUMED COORDINATION REWEIGHT_METAD MATHEVAL UPPER_WALLS INCLUDE FLUSH PATH COMMITTOR HISTOGRAM DUMPGRID WRAPAROUND DISTANCE FIT_TO_TEMPLATE METAD READ CONVERT_TO_FES CONTACTMAP COM FIXEDATOM WHOLEMOLECULES GROUP PRINT RMSD MOLINFO	mapping core colvar gridtools bias generic function vatom
23.029	An accurate and efficient SAXS/SANS implementation including solvation layer effects suitable for restrained Molecular Dynamics simulations	bio	SAXS, SANS, SAS, metainference, proteins, nucleic-acid	Federico Ballabio	BIASVALUE CENTER DISTANCE STATS UPPER_WALLS GROUP PRINT WRAPAROUND SAXS RMSD MOLINFO ENSEMBLE	core generic colvar bias isdb vatom function
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 PINES PBMETAD	bias pines setup generic
22.029	Angiotensin-1-7_Metadynamics	bio	Metadynamics, Angiotensin-(1-7), peptide	L.-América Chi	LOWER_WALLS COORDINATION GYRATION METAD UPPER_WALLS GROUP WHOLEMOLECULES PRINT FLUSH	core bias colvar 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	PRINT RMSD	colvar generic
22.026	Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification	materials	Peptoid, silica	Jim Pfaendtner	DISTANCE GYRATION PBMETAD COM UPPER_WALLS PRINT MOLINFO	bias generic colvar vatom
22.016	Homogeneous ice nucleation in an ab initio machine learning model of water	chemistry	ice, water, nucleation, seeding, environment similarity, interfacial free energy, interfaces	Pablo Piaggi	ENERGY VOLUME HISTOGRAM UPPER_WALLS DUMPGRID PRINT AROUND OPES_METAD CUSTOM RESTART ENVIRONMENTSIMILARITY	envsim opes colvar gridtools bias generic function setup volumes
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	CENTER PRINT DISTANCE CONTACTMAP	generic colvar vatom
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 LOWER_WALLS ZANGLES METAD COM UPPER_WALLS WHOLEMOLECULES MATHEVAL XANGLES COMBINE CUSTOM PRINT ALPHABETA TORSION MOLINFO	function colvar bias generic multicolvar vatom
21.050	N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity	methods	bio	Isabell Louise Grothaus	CENTER PRINT DISTANCE	generic colvar vatom
21.047	Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations	materials	pair entropy, metadynamics, ves, solids, crystallization	Pablo Piaggi	TD_WELLTEMPERED BF_LEGENDRE ENERGY VES_LINEAR_EXPANSION VOLUME METAD PAIRENTROPY OPT_AVERAGED_SGD PRINT COMBINE RESTART LOAD	colvar gridtools bias generic function setup ves
21.034	Efficient sampling of high-dimensional free energy landscapes using adaptive reinforced dynamics	bio	reinforced dynamics, bias-exchange metadynamics, parallel-bias metadynamics	Dongdong Wang	RANDOM_EXCHANGES ENDPLUMED METAD PBMETAD PRINT INCLUDE TORSION	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	DISTANCE KDE MATHEVAL PRINT COM TORSIONS	multicolvar generic colvar gridtools vatom function
21.014	how to determine statistically accurate conformational ensembles	bio	metadynamics, metainference, errors, cv, SAXS, ensemble determination	Cristina Paissoni	CENTER BIASVALUE STATS ANTIBETARMSD GYRATION METAD PBMETAD WHOLEMOLECULES PRINT ALPHABETA CONTACTMAP SAXS TORSION MOLINFO ENSEMBLE	multicolvar generic colvar secondarystructure bias isdb vatom function
21.006	OPES, On-the-fly Probability Enhanced Sampling Method	methods	opes, alanine dipeptide, well-tempered, multithermal, multiumbrella	Michele Invernizzi	ENDPLUMED ENERGY ECV_UMBRELLAS_LINE OPES_EXPANDED PRINT OPES_METAD TORSION ECV_MULTITHERMAL	opes colvar generic
21.005	Crystallization Collective Variable	methods	Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA	Tarak Karmakar	LOWER_WALLS UPPER_WALLS GROUP PYTORCH_MODEL MATHEVAL OPES_METAD PRINT FLUSH LOAD	core opes bias generic function setup pytorch
20.027	Allosteric Regulation of SARS-CoV-2 Protease. Towards Informed Structure-Based Drug Discovery	bio	SARS-CoV2, MPro, Covid-19, Molecular Dynamics, Metadynamics, Computer-Aided Drug Discovery	Khaled Abdel-Maksoud	TORSION PRINT DISTANCE METAD	bias colvar 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	REWEIGHT_METAD HISTOGRAM MULTI_RMSD METAD DUMPGRID PRINT CONVERT_TO_FES RESTRAINT	colvar bias gridtools generic
20.023	metadynminer and metadynminer3d	methods	metadynamics, visualization, R	Vojtech Spiwok	TORSION PRINT METAD	bias colvar generic
20.022	Unified Approach to Enhanced Sampling	methods	OPES, expanded ensembles, importance sampling	Michele Invernizzi	ECV_LINEAR POSITION ENDPLUMED ENERGY ECV_UMBRELLAS_LINE MATHEVAL UPPER_WALLS TORSION LOAD ECV_MULTITHERMAL ENVIRONMENTSIMILARITY OPES_EXPANDED ECV_MULTITHERMAL_MULTIBARIC VOLUME UNITS WHOLEMOLECULES PRINT CUSTOM RMSD Q6 MOLINFO	envsim opes symfunc colvar bias generic function setup
20.015	Rational design of ASCT2 inhibitors using an integrated experimental-computational approach	bio	ASCT2 transporter, small-molecules, cryo-EM, metainference	Max Bonomi	BIASVALUE WHOLEMOLECULES GROUP PRINT EMMIVOX DUMPATOMS LOAD MOLINFO	core isdb bias generic setup
20.002	Exploring conformational dynamics of the extracellular Venus flytrap domain of the GABAB receptor, a path-metadynamics study	bio	Metadynamics, path CVs	Riccardo Ocello	METAD UPPER_WALLS GROUP WHOLEMOLECULES PRINT RESTART MOLINFO PATHMSD	core colvar bias generic setup
19.069	Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen	materials	ibuprofen, crystal, solvent, surface	Matteo Salvalaglio	CENTER DISTANCE ENDPLUMED GROUP PRINT INCLUDE	core generic colvar vatom
19.039	Funnel Metadynamics	bio	funnel-metadynamics, absolute binding free energy, ligand-receptor complexes	Vittorio Limongelli	FUNNEL DISTANCE LOWER_WALLS FUNNEL_PS METAD WHOLEMOLECULES UPPER_WALLS PRINT RMSD COM	funnel colvar generic bias vatom
26.010	Solvation-Mediated Ammonia Synthesis in a Nanoheterogeneous Liquid Alloy	materials	OPES, Catalysis, Ammonia Synthesis	Axel Tosello Gardini	COORDINATIONNUMBER OPES_METAD_EXPLORE CUSTOM UNITS COORDINATION INCLUDE FLUSH GROUP PRINT DISTANCES OPES_METAD DISTANCE UPPER_WALLS	core generic colvar symfunc bias multicolvar setup function opes
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	CUSTOM OPES_METAD_EXPLORE COORDINATION GHOST GROUP CENTER LOWER_WALLS RMSD PRINT ENERGY DISTANCES DISTANCE OPES_EXPANDED ECV_MULTITHERMAL PATHMSD UPPER_WALLS	core colvar function bias multicolvar generic vatom opes
24.002	Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes	chemistry	metadynamics, ligand design, solvent extraction	Xiaoyu Wang	UNITS RESTART METAD TORSION PRINT	setup generic bias colvar
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	ALPHARMSD INCLUDE METAD MOLINFO LOWER_WALLS PRINT CONTACTMAP DISTANCE PATHMSD FUNCPATHMSD UPPER_WALLS	colvar secondarystructure bias generic 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	EMMIVOX INCLUDE WRAPAROUND MOLINFO GROUP PRINT BIASVALUE WHOLEMOLECULES DISTANCE UPPER_WALLS	core generic colvar bias isdb
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	SHADOW POSITION WRAPAROUND MOLINFO GROUP CENTER METAD FIT_TO_TEMPLATE PRINT WHOLEMOLECULES DISTANCES UPPER_WALLS	core generic colvar bias multicolvar isdb vatom
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	DUMPGRID OPES_EXPANDED RESTART LOWER_WALLS HISTOGRAM PRINT ENVIRONMENTSIMILARITY ECV_UMBRELLAS_LINE UPPER_WALLS	gridtools bias envsim generic setup opes
22.003	Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling	methods	opes, metadynamics, reweighting, alanine, muller	Michele Invernizzi	OPES_METAD_EXPLORE CUSTOM UNITS POSITION ENDPLUMED PBMETAD ECV_UMBRELLAS_FILE METAD LOWER_WALLS TORSION PRINT ENERGY BIASVALUE OPES_METAD OPES_EXPANDED ECV_MULTITHERMAL UPPER_WALLS	colvar bias generic function setup opes
22.000	Amyloid precursor protein processing by human γ-secretase	bio	Bias Exchange Metadynamics, Helix unfolding, coupled binding	Xiaoli Lu	UNITS COORDINATION ANTIBETARMSD INCLUDE ALPHARMSD METAD MOLINFO RANDOM_EXCHANGES CENTER PRINT CONTACTMAP DISTANCE	generic colvar secondarystructure bias setup vatom
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 UNITS METAD LOWER_WALLS TORSION PRINT COM DISTANCE UPPER_WALLS	generic colvar bias setup function vatom
21.022	Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly	materials	parallel bias metadynamics, adsorption, peptide	Xin Qi	UPPER_WALLS PBMETAD MOLINFO LOWER_WALLS PRINT ENERGY COM DISTANCE GYRATION	bias generic colvar vatom
21.017	All-atom simulations of the Vav1 AD construct	bio	metadynamics, parallel-bias, well-tempered	Simone Orioli	PBMETAD ALPHARMSD RESTART MOLINFO GROUP ALPHABETA METAD REWEIGHT_BIAS CONTACTMAP WHOLEMOLECULES PRINT	core colvar secondarystructure bias multicolvar generic setup
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	MATHEVAL RESTRAINT POSITION COORDINATION RESTART METAD CENTER PRINT WHOLEMOLECULES REWEIGHT_BIAS	generic colvar bias setup function vatom
21.013	Role of vibrational excitation in heterogeneous catalysis	chemistry	catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption	Kristof Bal	COORDINATIONNUMBER UNITS RESTRAINT COORDINATION METAD BF_CHEBYSHEV UPPER_WALLS CONVERT_TO_FES EXTERNAL LOAD FLUSH DISTANCES REWEIGHT_BIAS DISTANCE LOWER_WALLS ANGLES UWALLS TD_GRID VES_LINEAR_EXPANSION OPT_AVERAGED_SGD DUMPGRID REWEIGHT_METAD HISTOGRAM PRINT COMBINE	generic colvar symfunc bias gridtools multicolvar setup function ves
21.008	Multi-replica biased sampling for photoisomerization processes in conjugated polymers	methods	metadynamics, FEP, replica-exchange	Adriana Pietropaolo	MATHEVAL PBMETAD RESTART TORSION PRINT WHOLEMOLECULES BIASVALUE CONSTANT	generic colvar bias setup function
21.003	aSYN SAXS metainference	bio	metainference, SAXS	Kresten Lindorff-Larsen	PBMETAD ALPHARMSD FLUSH MOLINFO GROUP CENTER PRINT BIASVALUE WHOLEMOLECULES EEFSOLV SAXS GYRATION METAINFERENCE	core colvar secondarystructure bias isdb generic vatom
21.001	Substrate recognition and catalysis by glycosaminoglycan sulfotransferases	bio	metadynamics, well-tempered metadynamics, puckering, coordination	Tarsis Ferreira	COORDINATION REWEIGHT_METAD DUMPGRID INCLUDE METAD GROUP MOLINFO LOWER_WALLS RANDOM_EXCHANGES PUCKERING HISTOGRAM PRINT ENERGY WHOLEMOLECULES DISTANCE UPPER_WALLS	core colvar bias gridtools generic
20.028	Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane	bio	metadynamics, KRas-4B, anionic membrane	Huixia Lu	RESTART CENTER METAD FIT_TO_TEMPLATE PRINT DISTANCE	generic colvar bias setup vatom
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	METAD WHOLEMOLECULES UPPER_WALLS ABMD CONVERT_TO_FES FLUSH COM DISTANCE ENDPLUMED LOWER_WALLS CONTACTMAP FUNCPATHMSD DUMPGRID REWEIGHT_METAD READ MOLINFO HISTOGRAM PRINT COMBINE	colvar function bias gridtools generic vatom
19.054	MetaFEP	methods	metadynamics, chemistry, free energy perturbation	GiovanniMaria Piccini	UPPER_WALLS UNITS METAD FLUSH LOWER_WALLS PRINT ENERGY DISTANCE COMBINE	colvar bias generic function setup
19.021	Coarse-Grained Directed Simulation	methods	experiment directed simulation, coarse-grain, bias	Glen Hocky	EDS RESTRAINT TORSION PRINT DISTANCE COMBINE	colvar bias eds generic function
19.000	VesDeltaF	methods	VES, convergence, suboptimal CVs	Michele Invernizzi	UNITS POSITION ENDPLUMED LOAD METAD RESTART TORSION PRINT ENERGY VES_DELTA_F	generic colvar bias setup ves
26.009	Exploring the Conformational Landscape of HIV-1 TAR RNA by PT-WTE	bio	RNA, PT-WTE, HIV-1 TAR	Stefano Bosio	ENERGY GROUP MOLINFO PRINT METAD WHOLEMOLECULES	generic bias core colvar
25.029	Energetic Constraints in the Enzymatic Depolymerization of Crystalline PET from enhanced molecular simulations	bio	HREX-Metadynamics, PETase, crystalline PET, amorphous PET, conformational ensembles, substrate binding, chain detachment	Ania Di Pede-Mattatelli and Francesco Colizzi	DISTANCE LOWER_WALLS REWEIGHT_BIAS MOLINFO FIXEDATOM UPPER_WALLS PRINT DUMPGRID CONVERT_TO_FES METAD HISTOGRAM COM WHOLEMOLECULES	bias colvar vatom generic gridtools
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	ENERGY GROUP DISTANCE FIT_TO_TEMPLATE CENTER FIXEDATOM UPPER_WALLS PRINT MATHEVAL OPES_METAD_EXPLORE COORDINATION ANGLE WHOLEMOLECULES	bias core colvar function vatom generic opes
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 DISTANCE MOVINGRESTRAINT RESTART MOLINFO PRINT METAD RESTRAINT PUCKERING	generic setup bias colvar
24.019	Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning	bio	OPES, machine learning, protein folding, adaptive sampling	Mingyuan Zhang	TORSION DISTANCE COMBINE MOLINFO PRINT OPES_METAD GYRATION CUSTOM ALPHARMSD COORDINATION WHOLEMOLECULES	secondarystructure colvar function generic opes
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	BIASVALUE ENERGY COMMITTOR TORSION DISTANCE RESTART MOLINFO PRINT COORDINATIONNUMBER MATHEVAL METAD FLUSH RESTRAINT	bias setup colvar symfunc function 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	BIASVALUE GROUP DISTANCE LOWER_WALLS COMBINE MOLINFO CENTER UPPER_WALLS DEBUG PRINT METAD COM COORDINATION GHBFIX	bias core colvar function vatom generic
23.011	OneOPES, a combined enhanced sampling method to rule them all	bio	OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding	Valerio Rizzi	ENERGY TORSION ENDPLUMED DISTANCE MOLINFO PRINT OPES_METAD_EXPLORE METAD ECV_MULTITHERMAL OPES_EXPANDED	generic bias opes colvar
22.044	Colloid Crystallisation Analyses	materials	Q4, Q6, Pair Entropy, DFS	Aaron Finney	MFILTER_LESS DFSCLUSTERING Q6 GROUP LOCAL_Q6 MFILTER_MORE PRINT COORDINATIONNUMBER CONTACT_MATRIX CLUSTER_NATOMS LOCAL_Q4 COMBINE LOCAL_AVERAGE Q4	core multicolvar adjmat clusters symfunc function generic
22.043	Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES	bio	OPES, RNA, Tetraloop, Folding	Gül Zerze	ENERGY ECV_UMBRELLAS_LINE CONTACTMAP PRINT ECV_MULTITHERMAL OPES_EXPANDED WHOLEMOLECULES	generic opes colvar
22.021	Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations	chemistry	Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella	Sigbjørn Løland Bore	ECV_UMBRELLAS_LINE INCLUDE LOWER_WALLS UPPER_WALLS PRINT ENVIRONMENTSIMILARITY OPES_EXPANDED	generic bias envsim opes
22.006	Peptide framework for screening the effects of amino acids on assembly	bio	metadynamics, peptides	Andrew White	COM REWEIGHT_BIAS INCLUDE GROUP PRINT DUMPGRID CONVERT_TO_FES DISTANCES METAD GYRATION HISTOGRAM COMBINE	bias core multicolvar colvar function vatom generic gridtools
21.028	From Enhanced Sampling to Reaction Profiles	methods	collective variables, multi-state, machine learning, Deep-TDA	Enrico Trizio	TORSION DISTANCE CENTER FIXEDATOM PRINT COORDINATION WHOLEMOLECULES LOWER_WALLS LOAD PYTORCH_MODEL FIT_TO_TEMPLATE MATHEVAL OPES_METAD DISTANCES UNITS ENDPLUMED GROUP UPPER_WALLS ANGLE	bias core multicolvar setup pytorch colvar function vatom generic 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	TORSION ABMD DISTANCE RESTART MOLINFO CENTER PRINT ERMSD	bias setup colvar vatom generic
20.019	Systematic finite-temperature reduction of crystal energy landscapes	materials	crystals, organics, structure prediction	Matteo Salvalaglio	ENERGY LOWER_WALLS UPPER_WALLS PRINT MATHEVAL CELL METAD VOLUME	generic bias function colvar
20.009	The dynamics of linear polyubiquitin	bio	saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics	Carlo Camilloni	ALPHABETA TORSION DISTANCE SAXS MOLINFO CENTER METAINFERENCE ENSEMBLE PRINT PBMETAD WHOLEMOLECULES FLUSH GYRATION STATS	bias multicolvar colvar isdb function vatom generic
20.007	Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics	bio	metadynamics, loop movement, artificial intelligence	Pratyush Tiwary	TORSION DISTANCE RESTART MOLINFO UPPER_WALLS PRINT METAD RMSD COMBINE WHOLEMOLECULES	bias setup colvar function generic
20.004	Data-driven collective variables for enhanced sampling	methods	collective variables, machine learning, deep-lda	Luigi Bonati	TORSION ENDPLUMED PYTORCH_MODEL DISTANCE GROUP LOWER_WALLS LOAD UPPER_WALLS PRINT OPES_METAD MATHEVAL FLUSH COM UNITS	bias core setup pytorch colvar function vatom generic opes
20.000	Muscarinic M2 receptor-ligand funnel metadynamics	bio	multiple walker metadynamics, well-tempered metadynamics, funnel metadynamics, MC-HLDA, GPCR, receptor, Adiabatic Bias MD	Riccardo Capelli	READ ENDPLUMED ABMD DISTANCE COM LOWER_WALLS UPPER_WALLS PRINT DUMPGRID REWEIGHT_METAD CONVERT_TO_FES MATHEVAL METAD HISTOGRAM COMBINE	bias colvar function vatom generic gridtools
19.083	Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis	chemistry	metadynamics, chemical reactions, reaction discovery	Valerio Rizzi	ENDPLUMED GROUP RESTART UPPER_WALLS PRINT COORDINATIONNUMBER DISTANCES METAD FLUSH COMBINE UNITS	bias core multicolvar setup symfunc function generic
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 VES_LINEAR_EXPANSION DISTANCE COMBINE LOWER_WALLS UPPER_WALLS PRINT EXTERNAL DUMPGRID CONVERT_TO_FES BF_CHEBYSHEV FLUSH TD_WELLTEMPERED OPT_AVERAGED_SGD COORDINATION HISTOGRAM UNITS ANGLE	bias ves setup colvar function generic gridtools
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 MOVINGRESTRAINT PRINT GYRATION UNITS	generic bias setup colvar
19.072	SINE hairpin MD+NMR	bio	metadynamics, RNA, NMR	Giovanni Bussi	TORSION MAXENT DISTANCE INCLUDE MOLINFO SORT PRINT MATHEVAL METAD FLUSH COM COORDINATION WHOLEMOLECULES	bias colvar function vatom generic
19.063	Protein-ligand binding through metadynamics with path CVs	bio	metadynamics, path CVs, ligand binding	Mattia Bernetti	LOWER_WALLS UPPER_WALLS PRINT PATHMSD METAD WHOLEMOLECULES	generic bias 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	ALPHABETA FUNNEL TORSION GROUP DISTANCE LOWER_WALLS COM MOLINFO UPPER_WALLS PRINT REWEIGHT_METAD DISTANCES METAD RMSD COMBINE BRIDGE WHOLEMOLECULES	bias core multicolvar colvar adjmat function vatom generic funnel
19.040	Optimal Metric for Path Collective Variables	bio	metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path	Francesco Luigi Gervasio	TORSION ENDPLUMED PRINT MATHEVAL METAD	generic bias function colvar
19.036	Thermodynamics and kinetics of G protein-coupled receptor activation	bio	metadynamics, allostery, receptor conformation, GPCR, pharmacology	Davide Provasi	FUNCPATHMSD ENDPLUMED DISTANCE CONTACTMAP PRINT METAD RMSD COM WHOLEMOLECULES	bias colvar function vatom generic
19.032	Chemical reaction in solution using path collective variables based on coordination patterns	chemistry	chemical reactions, solutions, metadynamics, coordination patterns	Fabio Pietrucci	RESTART UPPER_WALLS PRINT DISTANCES METAD FLUSH PATH	bias mapping multicolvar setup generic
19.030	Coarse-Grained MetaDynamics (CG-MetaD)	bio	Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy	Vittorio Limongelli	DISTANCE LOWER_WALLS UPPER_WALLS PRINT METAD COM WHOLEMOLECULES	vatom generic bias colvar
19.028	pRAVE	methods	RAVE, reaction coordinate, deep learning, metadynamics, kinetics	Pratyush Tiwary	ALPHABETA COMMITTOR COM DISTANCE TORSION RESTART PRINT EXTERNAL COMBINE WHOLEMOLECULES	bias multicolvar setup colvar function vatom generic
19.022	eABF simulation of NANMA (alanine dipeptide)	methods	eABF, DRR, alanine dipeptide	Haochuan Chen	TORSION DRR PRINT	generic drr colvar
19.009	RNA tetraloops folding	bio	metadynamics, RNA, folding	Giovanni Bussi	ENDPLUMED MOLINFO PRINT METAD RMSD ERMSD WHOLEMOLECULES	generic bias colvar
19.004	MI Ubiquitin	bio	metainference, NMR	Max Bonomi	GROUP MOLINFO METAINFERENCE PRINT CS2BACKBONE RDC WHOLEMOLECULES	generic core isdb

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