Browse the eggs in PLUMED-NEST

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

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

plumID	Name	Category	Keywords	Contributor	Actions	Modules
25.024	Sampling glycan-glycan interactions for B22 calculations	bio	B22, glycan, carbohydrates, distance, REST2, metadynamics, RECT, replica exchange	Isabell Louise Grothaus	DISTANCE COMBINE METAD PRINT RESTRAINT POSITION COM	generic vatom bias function 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	TORSIONS SMAC PRINT DUMPMULTICOLVAR DISTANCES	generic multicolvar symfunc
25.010	Kinetic rates calculation with Ratchet&Pawl MD	methods	kinetics, ligand binding, ABMD, ratchet&pawl MD	Riccardo Capelli	WHOLEMOLECULES COMMITTOR DISTANCE ABMD GROUP PRINT FLUSH COM	generic core vatom bias colvar
25.009	Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water	chemistry	metadynamics, nitrate photolysis	Kam-Tung Chan	RESTART REWEIGHT_METAD DISTANCE CUSTOM COORDINATION UPPER_WALLS METAD DUMPGRID PRINT GROUP FLUSH HISTOGRAM READ	generic core colvar function bias gridtools setup
25.003	Surrogate Model CV	methods	Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding	Sompriya Chatterjee	TORSION WHOLEMOLECULES COMMITTOR DISTANCE COMBINE OPES_METAD CUSTOM ENERGY PYTORCH_MODEL MOLINFO PRINT MATHEVAL GROUP ENDPLUMED	opes generic core function colvar pytorch
25.000	Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer	bio	metadynamics, pathCV	Sahithya Sridharan Iyer	RESTART WHOLEMOLECULES DISTANCE UPPER_WALLS METAD PRINT MOLINFO GROUP FUNCPATHGENERAL COM	generic core vatom bias colvar function setup
24.030	NMR guided simulation of dsRBD	bio	Metainference, NMR, protein dynamics	Debadutta Patra	METAINFERENCE RDC ALPHABETA WHOLEMOLECULES DISTANCE GROUP PRINT MOLINFO FLUSH STATS ENSEMBLE	generic core isdb colvar function multicolvar
24.009	Weighted Shape Gaussian Mixture Models	bio	metadynamics, clustering	Glen Hocky	TORSION UNITS METAD PRINT GROUP	generic core bias colvar setup
24.006	Water vapor condensation	chemistry	metadynamics, homogeneous condensation, chemical potential	Shenghui Zhong	CLUSTER_PROPERTIES UNITS CONTACT_MATRIX UPPER_WALLS COORDINATIONNUMBER METAD PRINT CLUSTER_NATOMS DFSCLUSTERING	symfunc adjmat generic clusters bias setup
24.005	Learning Markovian Dynamics with Spectral Maps	methods	spectral map, collective variables, machine learning	Jakub Rydzewski	UNITS DISTANCE CUSTOM PRINT BIASVALUE	generic bias function colvar setup
24.003	Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations	chemistry	steered molecular dynamics, foldamers, peptoids, bio-inspired	Kaylyn Torkelson	GYRATION TORSION WHOLEMOLECULES ALPHABETA INCLUDE DISTANCE MOVINGRESTRAINT COORDINATION PRINT COM	generic vatom bias colvar multicolvar
23.046	Lasso Peptides - HLDA CV	bio	metadynamics, protein folding, HLDA, harmonic	Gabriel da Hora	WHOLEMOLECULES UNITS DISTANCE COMBINE METAD PRINT	generic bias setup function colvar
23.038	Determinants of Neutral Antagonism and Inverse Agonism in the β2-adrenergic receptor	bio	protein coupled receptor, beta-adrenergic, receptor activation, antagonism, inverse agonism, metadynamics	Timothy Clark	WHOLEMOLECULES DISTANCE METAD PRINT RMSD MOLINFO MATHEVAL	bias function colvar generic
23.031	Identifying small molecules binding sites in RNA conformational ensembles with SHAMAN	bio	RNA, metadynamics, probes, mixed-solvent MD, small molecules, binding sites	Max Bonomi	WHOLEMOLECULES FIT_TO_TEMPLATE UPPER_WALLS METAD WRAPAROUND PRINT MOLINFO CENTER GROUP POSITION DISTANCES SHADOW	generic core isdb vatom colvar bias multicolvar
23.025	Probing ion binding to G-quadruplexes and related events	chemistry	metadynamics, repulsive potential, nucleic acids, G-quadruplexes	Marcelo Poleto	RESTART WHOLEMOLECULES UNITS FIT_TO_TEMPLATE DISTANCE UPPER_WALLS WRAPAROUND METAD DUMPATOMS PRINT GROUP FLUSH MATHEVAL LOWER_WALLS POSITION DISTANCES COM	generic core vatom bias colvar function multicolvar setup
23.024	Permutationally Invariant Networks for Enhanced Sampling (PINES)	methods	collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent	Nicholas Herringer	PBMETAD LOAD PRINT	generic bias setup
23.022	A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar	methods	collective variables, machine learning, toy model	Enrico Trizio	UNITS OPES_METAD UPPER_WALLS CUSTOM PRINT PYTORCH_MODEL LOWER_WALLS POSITION BIASVALUE ENDPLUMED	pytorch opes generic function bias colvar setup
23.014	Structural basis of dimerization of chemokine receptors CCR5 and CXCR4	bio	metadynamics, oligomerization, chemokine receptors, GPCR, membrane	Vittorio Limongelli	TORSION WHOLEMOLECULES DISTANCE COMBINE METAD UPPER_WALLS PRINT FLUSH COM	generic vatom bias function colvar
22.043	Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES	bio	OPES, RNA, Tetraloop, Folding	Gül Zerze	CONTACTMAP WHOLEMOLECULES PRINT ENERGY ECV_UMBRELLAS_LINE ECV_MULTITHERMAL OPES_EXPANDED	opes colvar generic
22.033	Reciprocal barrier restraint. Application to PROTAC passive permeability prediction	methods	PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR	Istvan Kolossvary	UNITS DISTANCE METAD CUSTOM PRINT FLUSH BIASVALUE DRR COM	drr generic vatom bias function colvar setup
22.026	Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification	materials	Peptoid, silica	Jim Pfaendtner	GYRATION DISTANCE UPPER_WALLS PRINT MOLINFO PBMETAD COM	bias vatom colvar generic
22.008	Ab initio metadynamics determination of temperature-dependent free-energy landscape in ultrasmall silver clusters	materials	Well tempered metadynamics, ab-initio, ase	Daniel Sucerquia	GYRATION UNITS DISTANCE COMBINE UPPER_WALLS COORDINATION METAD LOWER_WALLS COORDINATIONNUMBER FLUSH COM	symfunc generic vatom bias function colvar setup
21.047	Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations	materials	pair entropy, metadynamics, ves, solids, crystallization	Pablo Piaggi	VES_LINEAR_EXPANSION BF_LEGENDRE RESTART PAIRENTROPY COMBINE METAD TD_WELLTEMPERED ENERGY PRINT LOAD OPT_AVERAGED_SGD VOLUME	ves generic bias function colvar gridtools setup
21.040	A structural ensemble of a tau-microtubule complex reveals regulatory tau phosphorylation and acetylation mechanisms	bio	EMMI, CryoEM, tau-microtubules, post-translational modifications, chemical mutagenesis, structural ensemble, Metainference	Faidon Brotzakis	RESTART WHOLEMOLECULES DISTANCE EMMI UPPER_WALLS PRINT MOLINFO GROUP BIASVALUE COM	generic core isdb vatom bias colvar setup
21.032	Metal-coupled folding mechanism to metallothionein	bio	parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination	Manuel-Peris Diaz	WHOLEMOLECULES UNITS COORDINATION GROUP PBMETAD	generic core bias setup colvar
21.029	Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs	bio	metadynamics, small peptide, machine learning	Pratyush Tiwary	RESTART TORSION ENERGY PRINT MOLINFO FLUSH EXTERNAL	bias generic colvar setup
21.027	EGFR activating mutations mechanism	bio	metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA	Francesco Gervasio	CONTACTMAP WHOLEMOLECULES INCLUDE DISTANCE UPPER_WALLS METAD ENERGY PRINT MOLINFO ALPHARMSD MATHEVAL LOWER_WALLS	generic secondarystructure bias function 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	WHOLEMOLECULES DISTANCE PRINT GROUP COM	core 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	WHOLEMOLECULES COMBINE COORDINATION PRINT MOLINFO RESTRAINT STATS	bias colvar function generic
20.029	High Conformational Flexibility of the E2F1/DP1/DNA complex	bio	SAXS, protein-DNA complex, hySAXS, ensemble determination	Cristina Paissoni	WHOLEMOLECULES INCLUDE DISTANCE PRINT MOLINFO CENTER RESTRAINT GROUP BIASVALUE STATS SAXS ENSEMBLE	generic core isdb vatom bias colvar function
20.027	Allosteric Regulation of SARS-CoV-2 Protease. Towards Informed Structure-Based Drug Discovery	bio	SARS-CoV2, MPro, Covid-19, Molecular Dynamics, Metadynamics, Computer-Aided Drug Discovery	Khaled Abdel-Maksoud	DISTANCE METAD TORSION PRINT	bias colvar generic
20.025	The role of water in host-guest interaction	bio	ligand binding, water, opes, SAMPL5	Valerio Rizzi	ANGLE WHOLEMOLECULES FIT_TO_TEMPLATE DISTANCE OPES_METAD COORDINATION UPPER_WALLS ENERGY PYTORCH_MODEL CENTER PRINT FIXEDATOM MATHEVAL GROUP ENDPLUMED	opes generic core vatom bias colvar function pytorch
20.015	Rational design of ASCT2 inhibitors using an integrated experimental-computational approach	bio	ASCT2 transporter, small-molecules, cryo-EM, metainference	Max Bonomi	WHOLEMOLECULES DUMPATOMS PRINT MOLINFO LOAD EMMIVOX GROUP BIASVALUE	generic core isdb bias setup
20.011	Uremic toxin analysis	bio	metadynamics, uremic toxin, serum albumin	Jim Pfaendtner	RESTART WHOLEMOLECULES DISTANCE COORDINATION PRINT CENTER GROUP DISTANCES	generic core vatom colvar setup multicolvar
20.009	The dynamics of linear polyubiquitin	bio	saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics	Carlo Camilloni	GYRATION METAINFERENCE TORSION WHOLEMOLECULES ALPHABETA DISTANCE PRINT CENTER MOLINFO FLUSH PBMETAD STATS SAXS ENSEMBLE	generic isdb vatom colvar bias function multicolvar
20.002	Exploring conformational dynamics of the extracellular Venus flytrap domain of the GABAB receptor, a path-metadynamics study	bio	Metadynamics, path CVs	Riccardo Ocello	RESTART WHOLEMOLECULES PATHMSD UPPER_WALLS METAD PRINT MOLINFO GROUP	generic core bias colvar setup
20.000	Muscarinic M2 receptor-ligand funnel metadynamics	bio	multiple walker metadynamics, well-tempered metadynamics, funnel metadynamics, MC-HLDA, GPCR, receptor, Adiabatic Bias MD	Riccardo Capelli	HISTOGRAM COM REWEIGHT_METAD DISTANCE COMBINE UPPER_WALLS ABMD METAD PRINT DUMPGRID CONVERT_TO_FES MATHEVAL LOWER_WALLS ENDPLUMED READ	generic vatom bias function colvar gridtools
19.059	cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide	bio	bias-exchange metadynamics, cis-trans isomerization	Fabrizio Marinelli	TORSION INCLUDE RANDOM_EXCHANGES METAD PRINT	bias colvar generic
19.052	Gibbs free energy of homogeneous nucleation	materials	nucleation, surface excess free energy	Gareth Tribello	UNITS CELL UPPER_WALLS METAD PRINT FCCUBIC ENDPLUMED	symfunc generic bias colvar setup
19.051	Solid liquid interfacial free energy out of equilibrium	materials	metadynamics, nucleation, surface excess free energy	Gareth Tribello	UNITS CELL AROUND METAD UPPER_WALLS PRINT FCCUBIC LOWER_WALLS ENDPLUMED	symfunc generic volumes bias colvar setup
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	FUNNEL TORSION WHOLEMOLECULES ALPHABETA BRIDGE REWEIGHT_METAD DISTANCE COMBINE UPPER_WALLS METAD LOWER_WALLS RMSD PRINT MOLINFO GROUP DISTANCES COM	adjmat generic core vatom colvar funnel bias function multicolvar
19.039	Funnel Metadynamics	bio	funnel-metadynamics, absolute binding free energy, ligand-receptor complexes	Vittorio Limongelli	FUNNEL COM WHOLEMOLECULES DISTANCE METAD UPPER_WALLS RMSD PRINT LOWER_WALLS FUNNEL_PS	funnel generic vatom bias colvar
19.036	Thermodynamics and kinetics of G protein-coupled receptor activation	bio	metadynamics, allostery, receptor conformation, GPCR, pharmacology	Davide Provasi	CONTACTMAP COM WHOLEMOLECULES DISTANCE METAD RMSD PRINT FUNCPATHMSD ENDPLUMED	generic vatom bias function colvar
19.035	Dimerization of GPCRs from coarse-grained umbrella sampling	bio	Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization	Davide Provasi	TORSION DISTANCE PRINT RESTRAINT GROUP COM	generic core vatom bias colvar
19.005	Cmyc small molecule interaction	bio	metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP	Gabriella Heller	GYRATION METAINFERENCE ALPHABETA WHOLEMOLECULES INCLUDE DISTANCE COORDINATION PRINT MOLINFO CENTER GROUP PBMETAD CS2BACKBONE	generic core isdb vatom colvar bias multicolvar
19.003	EMMI ClpP	bio	metainference, cryo-EM	Max Bonomi	EMMI PRINT MOLINFO GROUP BIASVALUE	core isdb bias generic
25.017	Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity	bio	EMMIVox, cryo-EM, allostery, decamer, filament, ensemble refinement, glutamine synthetase	Samuel Hoff	EMMIVOX GROUP BIASVALUE WHOLEMOLECULES MOLINFO PRINT	isdb core bias generic
25.007	Shaping the glycan landscape. Hidden relationships between linkage and ring distortion induced by carbohydrate-active enzmyes	bio	REST-RECT, REST2, glycan, enzyme, CAZyme, steered	Isabell Grothaus	METAD TORSION PUCKERING DISTANCE RESTART RESTRAINT MOLINFO PRINT MOVINGRESTRAINT	colvar setup bias generic
25.004	Machine Learning-Driven Molecular Dynamics Unveil a Bulk Phase Transformation Driving Ammonia Synthesis on Barium Hydride	chemistry	OPES, OPES flooding, Catalysis, Ammonia Synthesis	Axel Tosello Gardini	COMMITTOR FLUSH OPES_METAD GROUP DISTANCES FIXEDATOM ZDISTANCES UPPER_WALLS COORDINATIONNUMBER DISTANCE UNITS CUSTOM PRINT	function generic symfunc colvar setup bias vatom core multicolvar opes
24.012	Molecular simulations to investigate the impact of N6-methylation in RNA recognition	bio	metadynamics, alchemistry, RNA modification, RNA:protein interactions	Giovanni Bussi	COMBINE METAD GROUP BIASVALUE GHBFIX COM LOWER_WALLS DISTANCE DEBUG UPPER_WALLS COORDINATION CENTER MOLINFO PRINT	function generic colvar bias vatom core
24.004	Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables	materials	metadynamics, nucleation, machine learning	Ziyue Zou	METAD GROUP LOAD RESTART INCLUDE PRINT	core bias setup generic
23.002	Critical comparison of general-purpose collective variables for crystal nucleation	methods	metadynamics, umbrella sampling, commitor, entropy, PIV	Julien Lam	ENERGY METAD LOCAL_AVERAGE Q6 RESTRAINT UNITS VOLUME PAIRENTROPY Q4 UPPER_WALLS CUSTOM FUNCPATHMSD PRINT PIV	function piv generic symfunc colvar setup bias gridtools
22.042	Metadynamics of NSP10 and variants	bio	metadynamics, NSP10, crystal structure, variants	Shozeb Haider	METAD TORSION PRINT	colvar bias generic
22.038	Enhanced Sampling Aided Design of Molecular Photoswitches	chemistry	reaction discovery, OPES explore, graph CV	Umberto Raucci	PYTORCH_MODEL OPES_METAD_EXPLORE UNITS COORDINATION CUSTOM PRINT	function pytorch generic colvar setup opes
22.035	Deciphering the alphabet of disorder — Glu and Asp act differently on local but not global properties	bio	intrinsically disordered proteins, parallel bias metadynamics, protein	Kresten Lindorff-Larsen	TORSION PBMETAD WHOLEMOLECULES MOLINFO GYRATION	colvar bias generic
22.032	Reciprocal barrier restraint. Application to path-meta-eABF	methods	restraint, upper wall, lower wall, path colvar, meta-eABF, metadynamics, DRR, protein conformational transition, PROTAC	Istvan Kolossvary	FLUSH METAD BIASVALUE DRR CUSTOM PATHMSD PRINT	function generic colvar bias drr
22.018	Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations	bio	ligand binding, docking, EMMI, LAT1	Max Bonomi	EMMIVOX GROUP BIASVALUE WHOLEMOLECULES LOAD MOLINFO PRINT	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	COMMITTOR FIT_TO_TEMPLATE PYTORCH_MODEL OPES_METAD GROUP FIXEDATOM CUSTOM RMSD LOWER_WALLS WHOLEMOLECULES DISTANCE UPPER_WALLS COORDINATION CENTER MATHEVAL PRINT	function pytorch generic colvar bias vatom core opes
21.052	On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets	materials	Ibuprofen, unbinding, WTmetaD	Matteo Salvalaglio	COMMITTOR METAD TORSION ENDPLUMED DISTANCE COORDINATIONNUMBER CENTER PRINT	generic symfunc colvar bias vatom
21.051	Automatic learning of hydrogen-bond fixes in an AMBER RNA force field	methods	force field, RNA	Giovanni Bussi	COMBINE METAD BIASVALUE COORDINATION WHOLEMOLECULES ERMSD MOLINFO PRINT	colvar bias function generic
21.048	Enhancing ligand exploration within a channel pore and fenestrations using metadynamics	bio	well-tempered metadynamics, protein-ligand enhanced sampling, sodium channel, Nav, small molecule drug	Elaine Tao	METAD TORSION COM LOWER_WALLS UNITS DISTANCE UPPER_WALLS CUSTOM PRINT	function generic colvar setup bias vatom
21.045	QM/MM metadynamics of thiol-disulfide exchange between methylthiolate and dimethyldisulfide in water with an imposed external electrostatic potential (ESP)	chemistry	metadynamics, QM/MM, electrostatic potential, thiol-disulfide exchange	Denis Maag	COMBINE METAD LOWER_WALLS DISTANCE COORDINATIONNUMBER UPPER_WALLS COORDINATION PRINT	function generic symfunc colvar bias
21.019	Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations	materials	Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen	Matteo Salvalaglio	KDE COM DISTANCE TORSIONS MATHEVAL PRINT	function generic colvar gridtools vatom multicolvar
21.012	NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition	bio	funnel metadynamics	Jim Pfaendtner	METAD COM LOWER_WALLS FUNNEL DISTANCE FUNNEL_PS UPPER_WALLS PRINT	funnel generic colvar bias vatom
21.005	Crystallization Collective Variable	methods	Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA	Tarak Karmakar	FLUSH PYTORCH_MODEL OPES_METAD GROUP LOWER_WALLS LOAD UPPER_WALLS MATHEVAL PRINT	function pytorch generic setup bias core opes
21.004	Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy	bio	machine learning, well-tempered metadynamics, path collective variable, potential of mean force, standard binding free energy calculations, host-guest, protein-ligand unbinding	Dorothea Gobbo	METAD LOWER_WALLS WHOLEMOLECULES UPPER_WALLS RESTART PATHMSD PRINT	colvar setup bias generic
21.001	Substrate recognition and catalysis by glycosaminoglycan sulfotransferases	bio	metadynamics, well-tempered metadynamics, puckering, coordination	Tarsis Ferreira	ENERGY HISTOGRAM RANDOM_EXCHANGES METAD GROUP REWEIGHT_METAD LOWER_WALLS PUCKERING DISTANCE WHOLEMOLECULES DUMPGRID UPPER_WALLS COORDINATION INCLUDE MOLINFO PRINT	generic colvar bias gridtools core
20.031	Soft fluorescent nanoshuttles targeting receptors	chemistry	polymers, receptors, nanoparticles, fluorescent probes	Adriana Pietropaolo	PBMETAD WHOLEMOLECULES COORDINATION CENTER PRINT	colvar bias vatom generic
20.023	metadynminer and metadynminer3d	methods	metadynamics, visualization, R	Vojtech Spiwok	METAD TORSION PRINT	colvar bias generic
20.012	Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies	bio	metadynamics, well-tempered ensemble, ligand binding, binding affinity calculations, novel COLVAR, funnel restraints, Hamiltonian replica-exchange, PathCV, COMetPath, SWISH	Francesco Gervasio	MOLINFO METAD GROUP BIASVALUE MATHEVAL COM LOWER_WALLS WHOLEMOLECULES DISTANCE LOAD CONTACTMAP UPPER_WALLS PROJECTION_ON_AXIS INCLUDE CONSTANT PRINT FUNCPATHGENERAL	function generic colvar setup bias vatom core
19.062	Elucidating molecular design principles for charge-alternating peptides	bio	peptide folding, metadynamics, well-tempered ensemble, parallel tempering	Jim Pfaendtner	ENERGY METAD WHOLEMOLECULES GYRATION PRINT	colvar bias generic
19.060	Neural networks-based variationally enhanced sampling	methods	ves, neural networks	Luigi Bonati	POSITION ENERGY TORSION Q6 ENDPLUMED LOAD UNITS ENVIRONMENTSIMILARITY PRINT	generic symfunc colvar setup envsim
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	POSITION FLUSH METAD GROUP UNITS LOWER_WALLS UPPER_WALLS RESTART COORDINATION PRINT	generic colvar setup bias core
19.042	Harmonic Linear Discriminant Analysis (HLDA)	methods	metadynamics, chemistry, HLDA	GiovanniMaria Piccini	ENERGY FLUSH COMBINE METAD UNITS DISTANCE UPPER_WALLS PRINT	function generic colvar setup bias
19.028	pRAVE	methods	RAVE, reaction coordinate, deep learning, metadynamics, kinetics	Pratyush Tiwary	COMBINE COMMITTOR ALPHABETA TORSION COM WHOLEMOLECULES DISTANCE EXTERNAL RESTART PRINT	function generic colvar setup bias vatom multicolvar
19.020	PTMetaD-WTE simulation of the Ntail IDP	bio	metadynamics, IDPs, protein folding	Mattia Bernetti	ENERGY METAD WHOLEMOLECULES ENDPLUMED ALPHARMSD MOLINFO GYRATION PRINT	colvar bias generic secondarystructure
19.017	Ligand binding pathways exploration	bio	metadynamics, ligand binding	Riccardo Capelli	POSITION FLUSH FIT_TO_TEMPLATE HISTOGRAM GROUP METAD READ CONVERT_TO_FES REWEIGHT_METAD COM WHOLEMOLECULES ENDPLUMED DUMPGRID UPPER_WALLS COORDINATION MATHEVAL WRAPAROUND PRINT	function generic colvar bias gridtools vatom core
19.010	Multi-domain protein dynamics	bio	metainference, NMR, protein dynamics	Carlo Camilloni	DHENERGY ALPHABETA GROUP TORSION PBMETAD METAINFERENCE ENSEMBLE RESTRAINT DIHCOR WHOLEMOLECULES DISTANCE ENDPLUMED UPPER_WALLS STATS CENTER MOLINFO PRINT RDC	function generic isdb colvar bias vatom core multicolvar
19.000	VesDeltaF	methods	VES, convergence, suboptimal CVs	Michele Invernizzi	ENERGY POSITION METAD TORSION UNITS ENDPLUMED LOAD VES_DELTA_F RESTART PRINT	generic colvar setup bias ves
25.020	Revealing Water-Mediated Activation Mechanisms in the Beta 1-Adrenergic Receptor via OneOPES-Enhanced Free Energy Landscapes	bio	OneOPES, GPCR, ADRB1, activation, microswitches, conformational changes, allostery	Valerio Rizzi	LOWER_WALLS ECV_MULTITHERMAL COORDINATION GHOST DISTANCES GROUP PRINT OPES_EXPANDED OPES_METAD_EXPLORE UPPER_WALLS PATHMSD CENTER CUSTOM RMSD DISTANCE ENERGY	vatom colvar multicolvar opes generic function core bias
24.034	Umbrella sampling of ion in transporter SLC26A7	bio	umbrella sampling, transporter, ions	Xiaoli Lu	PRINT RESTRAINT POSITION UNITS	colvar generic bias setup
24.024	Host-Guest binding free energies à la carte, an automated OneOPES protocol	bio	OneOPES, ligand binding, binding free energy,SAMPL challenge, host-guest	Valerio Rizzi	LOWER_WALLS ANGLE ENDPLUMED COORDINATION WHOLEMOLECULES ENERGY TORSION GROUP FIT_TO_TEMPLATE MATHEVAL PRINT OPES_EXPANDED FIXEDATOM OPES_METAD_EXPLORE UPPER_WALLS DISTANCE ECV_MULTITHERMAL CENTER	vatom colvar opes generic function core bias
23.036	Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water?	bio	NaCl, nucleation, metadynamics	Ruiyu Wang	COMBINE Q6 VOLUME MATHEVAL Q4 PRINT METAD COORDINATIONNUMBER ENERGY	colvar symfunc generic function 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	ERMSD MOLINFO COMBINE WHOLEMOLECULES COORDINATION PRINT BIASVALUE METAD GHBFIX	colvar generic bias function
23.028	Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process	chemistry	Ammonia decomposition; Dynamics;OPES; Neural Network potential	Manyi Yang	FLUSH LOWER_WALLS UNITS ENERGY DISTANCES GROUP MATHEVAL PRINT FIXEDATOM UPPER_WALLS CUSTOM COM ZDISTANCES COORDINATIONNUMBER OPES_METAD COMMITTOR DISTANCE	vatom colvar multicolvar symfunc opes generic function core bias setup
23.008	PBMetaD simulations of Histatin5	bio	metadynamics, IDP, Rg, PPII	Francesco Pesce	WHOLEMOLECULES TORSION GROUP GYRATION PRINT MOLINFO PBMETAD	colvar generic bias core
23.003	Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations	methods	metadynamics, alchemical variable, alchemical free energy calculations	Wei-Tse Hsu	READ EXTRACV TORSION PRINT METAD	colvar generic bias
23.000	Atomistic simulations of RNA tetraloop folding via PTWTE-WTM	bio	parallel tempering, well-tempered metadynamics, well-tempered ensemble, RNA, Tetraloop, Folding	Gül Zerze	LOWER_WALLS CONTACTMAP WHOLEMOLECULES PRINT UPPER_WALLS METAD ENERGY	colvar generic bias
22.040	From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure	bio	SARS-CoV-2, Spike, Omicron	Miłosz Wieczór	LOWER_WALLS WHOLEMOLECULES PRINT UPPER_WALLS PCAVARS METAD	mapping generic bias
22.031	Rare Event Kinetics from Adaptive Bias Enhanced Sampling	methods	OPES Flooding, Kinetics, Rate, OPES, Machine Learning	Dhiman Ray	CONTACTMAP POSITION PRINT CUSTOM OPES_METAD ENERGY ENDPLUMED COMBINE BIASVALUE UNITS CONSTANT INCLUDE TORSION GROUP PYTORCH_MODEL WHOLEMOLECULES MOLINFO DISTANCE RMSD COMMITTOR	colvar opes generic function core bias pytorch setup
22.021	Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations	chemistry	Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella	Sigbjørn Løland Bore	LOWER_WALLS ENVIRONMENTSIMILARITY INCLUDE ECV_UMBRELLAS_LINE PRINT OPES_EXPANDED UPPER_WALLS	envsim bias generic opes
22.011	Accelerating all-atom simulations and gaining mechanistic understanding of biophysical systems through State Predictive Information Bottleneck	methods	metadynamics, membrane permeation, protein folding	Shams Mehdi	XANGLES LOWER_WALLS COMBINE WHOLEMOLECULES YANGLES TORSION ZANGLES MATHEVAL PRINT UPPER_WALLS COM METAD MOLINFO CUSTOM ALPHABETA DISTANCE	vatom colvar multicolvar generic function bias
22.004	Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques	chemistry	reaction discovery, OPES, collective variables	Umberto Raucci	LOWER_WALLS COORDINATION COM LOAD GROUP MATHEVAL PRINT OPES_METAD_EXPLORE UPPER_WALLS UNITS PYTORCH_MODEL CUSTOM OPES_METAD DISTANCE	vatom colvar opes generic function core bias pytorch setup
22.000	Amyloid precursor protein processing by human γ-secretase	bio	Bias Exchange Metadynamics, Helix unfolding, coupled binding	Xiaoli Lu	CONTACTMAP RANDOM_EXCHANGES ALPHARMSD COORDINATION INCLUDE PRINT ANTIBETARMSD UNITS METAD MOLINFO DISTANCE CENTER	vatom colvar generic secondarystructure bias setup
21.039	Deep learning the slow modes for rare events sampling	methods	collective variables, machine learning, slow modes, deep-tica, opes	Luigi Bonati	CONTACTMAP ENVIRONMENTSIMILARITY LOAD PRINT OPES_METAD ENERGY ENDPLUMED COMBINE Q6 OPES_EXPANDED UNITS ECV_MULTITHERMAL VOLUME INCLUDE TORSION GROUP PYTORCH_MODEL FLUSH WHOLEMOLECULES MOLINFO DISTANCE RMSD	colvar symfunc opes generic function core envsim pytorch setup
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	LOWER_WALLS RANDOM_EXCHANGES COORDINATION WHOLEMOLECULES DIHCOR ALPHARMSD GROUP GYRATION PRINT ANTIBETARMSD UPPER_WALLS PARABETARMSD METAD MOLINFO ENERGY	colvar multicolvar generic secondarystructure core bias
21.030	Thermodynamic Basis for Stabilization of Helical Peptoids by Chiral Sidechains	bio	parallel bias parallel tempered metadynamics in WTE, synthetic foldamers, self-assembly, peptoid secondary structure	Jim Pfaendtner	COORDINATION INCLUDE TORSION GYRATION PRINT COM METAD DISTANCE ALPHABETA PBMETAD ENERGY	vatom colvar multicolvar generic bias
21.022	Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly	materials	parallel bias metadynamics, adsorption, peptide	Xin Qi	LOWER_WALLS GYRATION PRINT UPPER_WALLS COM MOLINFO DISTANCE PBMETAD ENERGY	vatom colvar generic bias
21.003	aSYN SAXS metainference	bio	metainference, SAXS	Kresten Lindorff-Larsen	FLUSH ALPHARMSD WHOLEMOLECULES SAXS GROUP GYRATION PRINT BIASVALUE MOLINFO METAINFERENCE EEFSOLV PBMETAD CENTER	vatom colvar isdb generic secondarystructure core bias
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	FLUSH LOWER_WALLS ENDPLUMED WHOLEMOLECULES GROUP CS2BACKBONE PRINT BIASVALUE UPPER_WALLS ALPHABETA ANTIBETARMSD MOLINFO PBMETAD	isdb multicolvar generic secondarystructure core bias
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	LOAD TD_WELLTEMPERED PRINT RESTART ENERGY COMBINE Q6 OPT_AVERAGED_SGD VES_LINEAR_EXPANSION LOWER_WALLS VOLUME CONVERT_TO_FES HISTOGRAM MATHEVAL REWEIGHT_TEMP_PRESS UPPER_WALLS CELL REWEIGHT_BIAS OPT_DUMMY READ BF_LEGENDRE DUMPGRID TD_MULTITHERMAL_MULTIBARIC	colvar gridtools symfunc generic ves function bias setup
19.057	SAXS ensembles using Martini-Beads multi-scale SAXS	methods	metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics	Cristina Paissoni	ANGLE ENDPLUMED COMBINE COORDINATION WHOLEMOLECULES ENSEMBLE INCLUDE SAXS GROUP MATHEVAL PRINT BIASVALUE STATS ALPHABETA MOLINFO PBMETAD CENTER	vatom colvar isdb multicolvar generic function core bias
19.040	Optimal Metric for Path Collective Variables	bio	metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path	Francesco Luigi Gervasio	ENDPLUMED TORSION MATHEVAL PRINT METAD	colvar generic bias function
19.031	Ice nucleation using PIV-based path coordinates	materials	phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics	Silvio Pipolo	LOWER_WALLS PIV PRINT UPPER_WALLS FUNCPATHMSD METAD CELL	colvar generic function piv bias
19.030	Coarse-Grained MetaDynamics (CG-MetaD)	bio	Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy	Vittorio Limongelli	LOWER_WALLS WHOLEMOLECULES PRINT UPPER_WALLS COM METAD DISTANCE	vatom colvar generic bias
19.024	PT-MetaD-WTE	methods	metadynamics, WTE, trp cage, PT	Jim Pfaendtner	COORDINATION GROUP EXTERNAL METAD ENERGY	colvar bias core
19.013	RNA FF FITTING	methods	force field, RNA	Giovanni Bussi	PUCKERING INCLUDE TORSION MATHEVAL BIASVALUE CONSTANT MOLINFO	colvar generic bias function
19.009	RNA tetraloops folding	bio	metadynamics, RNA, folding	Giovanni Bussi	ERMSD ENDPLUMED WHOLEMOLECULES PRINT METAD MOLINFO RMSD	colvar generic bias
25.005	Mechanism of Nanocluster Formation from Machine-Learned Potential-based Simulations	chemistry	WT-metadynamics, metal nanoclusters, nucleation, neural network potential, deepMD	Vikas Tiwari, Tarak Karmakar	LOWER_WALLS RESTRAINT ANGLE METAD DISTANCE PRINT FIXEDATOM COORDINATION COMBINE COORDINATIONNUMBER UNITS FLUSH UPPER_WALLS COM GROUP DISTANCES	multicolvar generic setup core symfunc bias colvar function vatom
25.023	Molecular simulations of Tau-protein oligomers	bio	metadynamics, proteins, aggregation	Giovanni Bussi	RMSD RESTART RESTRAINT FLUSH METAD PRINT CUSTOM CONTACTMAP	setup generic colvar function bias
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	RMSD OPES_METAD_EXPLORE CENTER GHOST GROUP MOLINFO DISTANCE PRINT ECV_MULTITHERMAL OPES_EXPANDED COORDINATION CUSTOM COMBINE ENERGY	vatom generic core opes colvar function
25.011	Chiral perovskite nucleation	chemistry	metadynamics, chiral perovskites, nucleation	Adriana Pietropaolo	RESTART DISTANCE UNITS MATHEVAL PRINT MULTI_RMSD PBMETAD UPPER_WALLS LOWER_WALLS	setup generic colvar function bias
24.029	Combination of OPES and OPES-Explore	methods	OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin	Dhiman Ray	GROUP MOLINFO DISTANCE PRINT INCLUDE CONTACTMAP UNITS CENTER OPES_METAD FLUSH FIXEDATOM WHOLEMOLECULES METAD CUSTOM PYTORCH_MODEL MATHEVAL COORDINATION BIASVALUE COMBINE UPPER_WALLS LOWER_WALLS RMSD OPES_METAD_EXPLORE POSITION ENDPLUMED ENERGY FIT_TO_TEMPLATE	vatom setup generic pytorch core opes colvar function bias
24.026	Constant pH metadynamics of RNA oligomers	bio	metadynamics, pH, RNA	Giovanni Bussi	RESTART MOLINFO TORSION PUCKERING METAD PRINT	colvar setup generic bias
24.021	Ab initio machine learning simulation of calcium carbonate from aqueous solutions to the solid state	chemistry	ion pairing, caco3, opes, proton transfer, crystallization	Pablo Piaggi	ENERGY OPES_METAD DISTANCE PRINT COORDINATION UPPER_WALLS	colvar generic opes bias
24.002	Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes	chemistry	metadynamics, ligand design, solvent extraction	Xiaoyu Wang	RESTART TORSION METAD PRINT UNITS	colvar setup generic bias
24.001	A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations	bio	OPES, OPES-Flooding, QM/MM, Kinetics, Enzyme Catalysis	Dhiman Ray	OPES_METAD FLUSH DISTANCE LOWER_WALLS TORSION PRINT CUSTOM COMBINE COMMITTOR UPPER_WALLS UNITS	setup generic opes colvar function bias
23.044	Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition	materials	metadynamics, interlocked molecules	Luigi Leanza	DUMPGRID GROUP ENDPLUMED METAD PRINT CONVERT_TO_FES HISTOGRAM COORDINATION READ COMMITTOR	generic core colvar gridtools bias
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	RMSD MOLINFO DISTANCE WHOLEMOLECULES MATHEVAL METAD PRINT CONVERT_TO_FES HISTOGRAM READ DUMPGRID REWEIGHT_METAD	generic gridtools colvar function bias
23.007	Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains	bio	metadynamics, peptoids, parallel-bias metadynamics	Jim Pfaendtner	RESTRAINT PBMETAD TORSION WHOLEMOLECULES GYRATION PRINT INCLUDE COORDINATION COM	vatom colvar generic bias
23.004	Melting curves of ice polymorphs in the vicinity of the liquid-liquid critical point	chemistry	water, liquid-liquid transition, second critical point, ice, polymorphs, melting curves, environment similarity, opes, density-functional theory, scan, machine learning potential	Pablo Piaggi	RESTART ECV_UMBRELLAS_LINE PRINT OPES_EXPANDED ENVIRONMENTSIMILARITY HISTOGRAM DUMPGRID UPPER_WALLS LOWER_WALLS	setup generic opes envsim gridtools 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 DISTANCE DISTANCES	colvar multicolvar generic bias
22.028	N-glycan conformer distributions in atomistic simulation	bio	REST2, RECT, N-glycan, pucker	Isabell Grothaus	MOLINFO TORSION PUCKERING METAD PRINT CONVERT_TO_FES HISTOGRAM READ DUMPGRID	colvar gridtools generic bias
22.022	Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir	bio	RMSD, protein-ligand interactions	Isabell Grothaus	RMSD PRINT	colvar generic
22.015	Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome	bio	photodynamics, bacteriophytochrome, variationally enhanced sampling	Jakub Rydzewski	TD_UNIFORM OPT_AVERAGED_SGD TORSION PRINT VES_LINEAR_EXPANSION BF_FOURIER	ves colvar generic
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	DISTANCE PRINT CONTACTMAP CENTER	colvar generic vatom
22.005	Collective Variable for Metadynamics Derived from AlphaFold Output	bio	AlphaFold, protein folding, protein structure prediction, metadynamics, deep learning, free energy simulation, collective variable	Vojtech Spiwok	METAD LOAD PRINT WHOLEMOLECULES	setup generic bias
22.001	Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials	methods	enhanced sampling, variationally enhanced sampling, ves, metadynamics, bias representation, wavelets, adam	Benjamin Pampel	VES_OUTPUT_BASISFUNCTIONS DISTANCE PRINT INCLUDE BF_WAVELETS UNITS BF_GAUSSIANS OPT_ADAM FLUSH METAD TD_WELLTEMPERED TD_UNIFORM OPT_AVERAGED_SGD BF_CUBIC_B_SPLINES BF_LEGENDRE BF_CHEBYSHEV COORDINATION VES_LINEAR_EXPANSION UPPER_WALLS POSITION ENERGY	setup generic colvar ves bias
21.049	Multiple-path-metadynamics and PathMaps	methods	path-CV, metadynamics, multiple-walker, multiple paths, pathmap	Alberto Pérez-de-Alba-Ortíz	LOAD LOWER_WALLS RESTRAINT CONSTANT TORSION MOVINGRESTRAINT METAD PRINT ENSEMBLE CUSTOM COMBINE UPPER_WALLS UNITS	setup generic colvar function bias
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	RESTART CENTER POSITION REWEIGHT_BIAS RESTRAINT WHOLEMOLECULES MATHEVAL METAD PRINT COORDINATION	vatom setup generic colvar function bias
21.011	CmuMD simulations of NaCl(aq) at graphite	chemistry	CmuMD, DFS clustering	Aaron Finney	LOAD AROUND MFILTER_MORE CLUSTER_DISTRIBUTION GROUP FIXEDATOM COORDINATIONNUMBER RESTRAINT DFSCLUSTERING PRINT CLUSTER_NATOMS CONTACT_MATRIX DENSITY DUMPGRID MULTICOLVARDENS	vatom setup symfunc multicolvar generic core adjmat gridtools clusters volumes bias
20.019	Systematic finite-temperature reduction of crystal energy landscapes	materials	crystals, organics, structure prediction	Matteo Salvalaglio	LOWER_WALLS CELL METAD PRINT MATHEVAL UPPER_WALLS ENERGY VOLUME	colvar function generic bias
20.008	Simulating solvation and acidity in complex mixtures with first-principles accuracy. The case of CH3SO3H and H2O2 in phenol	chemistry	proton trasfer, metadynamics	Kevin Rossi	METAD PRINT DISTANCES COORDINATION CUSTOM UNITS	setup multicolvar generic colvar function bias
20.007	Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics	bio	metadynamics, loop movement, artificial intelligence	Pratyush Tiwary	RMSD RESTART MOLINFO DISTANCE TORSION WHOLEMOLECULES METAD PRINT COMBINE UPPER_WALLS	setup generic colvar function bias
19.070	Unexpected Dynamics in the UUCG RNA Tetraloop	bio	well-tempered metadynamics, RNA, UUCG, maximum entropy	Sandro Bottaro	RMSD MOLINFO DISTANCE TORSION WHOLEMOLECULES METAD PRINT ERMSD	colvar generic bias
19.066	Finding ligand unbinding reaction pathways	methods	maze, ligand unbinding	Jakub Rydzewski	POSITION MAZE_OPTIMIZER_BIAS PRINT MAZE_LOSS MAZE_SIMULATED_ANNEALING UNITS	colvar setup generic maze
19.065	Molecular Enhanced Sampling with Autoencoders	methods	enhanced sampling, collective variables, deep learning	Wei Chen	POSITION ANN RESTRAINT COMBINE COM	annfunc vatom colvar function bias
19.032	Chemical reaction in solution using path collective variables based on coordination patterns	chemistry	chemical reactions, solutions, metadynamics, coordination patterns	Fabio Pietrucci	RESTART PATH FLUSH METAD PRINT DISTANCES UPPER_WALLS	setup multicolvar generic mapping bias
19.029	WTE-metaD of FF domain of URNF1 C57D variant	bio	metadynamics, mutations, post-translational modification, ff domain	Elena Papaleo	GROUP ALPHABETA MOLINFO WHOLEMOLECULES GYRATION METAD PRINT UPPER_WALLS LOWER_WALLS	multicolvar generic core colvar bias
19.018	Excited state FEP/Metadynamics simulations	chemistry	metadynamics, FEP, excited states, conjugated polymers, torsional potential	Adriana Pietropaolo	CONSTANT TORSION WHOLEMOLECULES MATHEVAL METAD PRINT BIASVALUE	colvar function generic bias
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 GROUP OPES_METAD CENTER COM FUNNEL_PS UPPER_WALLS WRAPAROUND WHOLEMOLECULES TORSION COORDINATION RMSD FUNNEL MATHEVAL COMMITTOR PRINT METAD LOWER_WALLS	bias colvar core function funnel opes generic vatom
25.006	Characterizing the conformational ensemble of PROTAC degraders in solutions via atomistic simulations	methods	Enhanced sampling, Atomistic simulations, Conformational ensemble, PROTACs, Targeted Protein Degradation, Chamelonic molecules	Shikshya Bhusal, Omar Valsson	DISTANCE READ VOLUME DUMPATOMS GYRATION CENTER RESTART UPDATE_IF PBMETAD MOLINFO WHOLEMOLECULES TORSION PRINT INCLUDE ENERGY	bias colvar generic setup vatom
25.001	RNA G-quadruplex folding with ST-metaD protocol	bio	RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD	Pavlína Pokorná	COMBINE ERMSD MOLINFO WHOLEMOLECULES METAD	function 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	DISTANCE GROUP OPES_METAD CUSTOM RESTART UPPER_WALLS COORDINATION UNITS COMMITTOR PRINT LOWER_WALLS	bias colvar core function generic opes setup
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	GROUP TORSION LOAD COMMITTOR PRINT METAD	bias colvar core generic setup
24.016	Cryo-EM guided simulations of ribozyme	bio	metainference, cryo-EM	Giovanni Bussi	GROUP ERMSD RESTRAINT MOLINFO WHOLEMOLECULES EMMIVOX BIASVALUE PRINT INCLUDE	bias colvar core isdb generic
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	FLUSH MOLINFO PYTORCH_MODEL DRR COORDINATION UPPER_WALLS WHOLEMOLECULES RMSD PRINT METAD LOWER_WALLS	bias colvar generic pytorch drr
24.011	Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble	methods	committor, machine learning	Peilin Kang	DISTANCE WHOLEMOLECULES RMSD UNITS CELL MOLINFO LOAD MATHEVAL INCLUDE LOWER_WALLS CUSTOM POSITION ENDPLUMED BIASVALUE GROUP UPPER_WALLS COORDINATION TORSION PRINT ENERGY	bias colvar core function generic setup
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	DISTANCE ALPHARMSD FUNCPATHMSD PATHMSD METAD MOLINFO UPPER_WALLS INCLUDE PRINT CONTACTMAP LOWER_WALLS	bias colvar secondarystructure function generic
23.043	Modeling the ferroelectric phase transition in barium titanate with DFT accuracy and converged sampling	materials	Barium Titanate, ferroelectric phase transition, Machine Learning, polarization order parameters	Lorenzo Gigli	SELECT_COMPONENTS SUM FLUSH TRANSPOSE MATHEVAL PRINT INCLUDE METAD	bias function generic matrixtools valtools
23.039	Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation	chemistry	metadynamics, ligand dissociation	Eric Beyerle	DISTANCE COMBINE FIXEDATOM CENTER RESTRAINT MOLINFO UPPER_WALLS DUMPMASSCHARGE PRINT METAD	bias colvar function generic vatom
23.027	CmuMD simulations of NaCl(aq) at NaCl	chemistry	CmuMD, DFS, Q3, Pair Entropy	Aaron Finney	GROUP HISTOGRAM FIXEDATOM LOCAL_Q3 RESTRAINT DFSCLUSTERING CLUSTER_DISTRIBUTION CLUSTER_NATOMS LOCAL_AVERAGE AROUND LOAD UNITS PRINT COORDINATIONNUMBER CONTACT_MATRIX DUMPGRID Q3 DENSITY	gridtools symfunc bias clusters core adjmat generic volumes setup vatom
23.020	FEP simulations of ATOX1 homodimer	chemistry	parallel bias metadynamics, FEP, free-energy of metal ion dissociation	Adriana Pietropaolo	DISTANCE CONSTANT PBMETAD ANGLE MATHEVAL WHOLEMOLECULES BIASVALUE PRINT	function generic bias colvar
23.012	JAK2 2D meta-eABF PMF with statistical analysis	bio	2D meta-eABF, path CV, PMF	Istvan Kolossvary	CUSTOM PATHMSD FLUSH UPPER_WALLS DRR BIASVALUE PRINT METAD LOWER_WALLS	bias colvar function drr generic
22.034	Rationalising the difference in crystallisability of two Sulflowers using efficient in silico methods	materials	metadynamics, crystallizability, crystal structure prediction, sulflower, persulforated coronene	Matteo Salvalaglio	CUSTOM UPPER_WALLS DRMSD MATHEVAL CELL COMMITTOR PRINT METAD LOWER_WALLS	function generic bias colvar
22.030	Mixing physics across temperatures with generative artificial intelligence	methods	REMD, Generative AI, DDPM	Yihang Wang	WHOLEMOLECULES TORSION PRINT	generic colvar
22.006	Peptide framework for screening the effects of amino acids on assembly	bio	metadynamics, peptides	Andrew White	HISTOGRAM COMBINE GROUP GYRATION COM METAD REWEIGHT_BIAS DISTANCES PRINT DUMPGRID INCLUDE CONVERT_TO_FES	gridtools multicolvar bias colvar core function generic vatom
21.044	NaCl nucleation	chemistry	metadynamics, DFS clustering	Aaron Finney	GROUP COMBINE INSPHERE HISTOGRAM FIXEDATOM DUMPGRID LOCAL_Q6 MFILTER_MORE DFSCLUSTERING CLUSTER_DISTRIBUTION CLUSTER_NATOMS Q6 COORDINATIONNUMBER CONTACT_MATRIX PRINT METAD	gridtools symfunc multicolvar bias clusters core adjmat function generic volumes vatom
21.038	Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics	materials	metadynamics, SGOOP, nucleation, urea	Ziyue Zou	GROUP COMBINE VOLUME ENERGY CENTER LOAD COORDINATIONNUMBER PRINT INCLUDE METAD	symfunc bias colvar core function generic setup vatom
21.034	Efficient sampling of high-dimensional free energy landscapes using adaptive reinforced dynamics	bio	reinforced dynamics, bias-exchange metadynamics, parallel-bias metadynamics	Dongdong Wang	RANDOM_EXCHANGES PBMETAD ENDPLUMED TORSION PRINT INCLUDE METAD	generic bias colvar
21.020	Reweighted Jarzynski sampling	methods	free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions	Kristof Bal	DISTANCE RESTRAINT BF_CHEBYSHEV UNITS METAD ANN LOAD COORDINATIONNUMBER PRINT CUSTOM COMBINE REWEIGHT_METAD MOVINGRESTRAINT REWEIGHT_BIAS FLUSH TD_WELLTEMPERED BIASVALUE CONVERT_TO_FES HISTOGRAM OPES_METAD CONSTANT VES_LINEAR_EXPANSION OPT_AVERAGED_SGD UPPER_WALLS DUMPGRID	gridtools symfunc bias colvar annfunc generic function opes setup ves
21.017	All-atom simulations of the Vav1 AD construct	bio	metadynamics, parallel-bias, well-tempered	Simone Orioli	GROUP ALPHARMSD RESTART PBMETAD REWEIGHT_BIAS MOLINFO WHOLEMOLECULES ALPHABETA PRINT CONTACTMAP METAD	multicolvar bias colvar core secondarystructure generic setup
21.016	MD SAXS GTPase associated center	bio	metadynamics, RNA, folding, SAXS	Giovanni Bussi	CUSTOM GROUP ERMSD GYRATION MOLINFO SAXS WHOLEMOLECULES UPPER_WALLS INCLUDE PRINT METAD LOWER_WALLS	bias colvar core isdb function generic
20.033	COVID-19 Spike protein opening transition mechanism	bio	EMMI, CryoEM, COVID-19, Spike, Metainference	Faidon Brotzakis	READ HISTOGRAM GROUP DISTANCES MOLINFO EMMI WHOLEMOLECULES RMSD PRINT BIASVALUE DUMPGRID CONVERT_TO_FES	gridtools multicolvar bias colvar core isdb generic
20.022	Unified Approach to Enhanced Sampling	methods	OPES, expanded ensembles, importance sampling	Michele Invernizzi	ECV_LINEAR WHOLEMOLECULES ECV_MULTITHERMAL_MULTIBARIC RMSD UNITS OPES_EXPANDED VOLUME MOLINFO LOAD ECV_MULTITHERMAL MATHEVAL CUSTOM POSITION ENDPLUMED UPPER_WALLS ENVIRONMENTSIMILARITY TORSION Q6 PRINT ECV_UMBRELLAS_LINE ENERGY	symfunc bias colvar envsim function generic opes setup
20.021	Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins.	bio	phi-values, restrained MD, transition-state, protein folding, disordered proteins, protein evolution	Cristina Paissoni	RESTRAINT MOLINFO COORDINATION WHOLEMOLECULES PRINT STATS	function generic bias colvar
20.017	FISST	methods	FISST, force, peptide, sampling, tempering	Glen Hocky	DISTANCE GROUP BIASVALUE GYRATION RESTRAINT UNITS MATHEVAL FISST PRINT ENERGY	bias colvar core fisst function generic setup
20.006	Class B GPCR activation mechanism	bio	metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding	Francesco Gervasio	DISTANCE LOWER_WALLS COMBINE CENTER MOLINFO UPPER_WALLS WHOLEMOLECULES RMSD MATHEVAL PRINT METAD ENERGY	bias colvar function generic vatom
19.080	Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium	methods	ves, variationally enhanced sampling, vibrational excitation, chemical reactions	Kristof Bal	DISTANCE EXTERNAL HISTOGRAM COMBINE DUMPGRID TD_GRID VES_LINEAR_EXPANSION LOWER_WALLS OPT_AVERAGED_SGD FLUSH ANGLE UPPER_WALLS COORDINATION BF_CHEBYSHEV UNITS TD_WELLTEMPERED PRINT CONVERT_TO_FES	gridtools bias colvar function generic setup ves
19.077	Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations	materials	metadynamics, peptide-surface binding	Jim Pfaendtner	DISTANCE GYRATION COM MOLINFO UPPER_WALLS PRINT METAD ENERGY	generic vatom bias colvar
19.064	Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations	materials	metadynamics, peptide-surface binding	Jim Pfaendtner	DISTANCE GYRATION COM MOLINFO UPPER_WALLS PRINT METAD ENERGY	generic vatom bias colvar
19.061	Diffusion in porous materials	materials	metadynamics, porous materials, diffusion	Kim E. Jelfs	DISTANCE GROUP CENTER COM RESTART UPPER_WALLS PRINT METAD LOWER_WALLS	bias colvar core generic setup vatom
19.058	Constrained MD for maintaining a cavity in a calculation	chemistry	constrained MD, porous molecules, porosity, cavity	Kim Jelfs	MOVINGRESTRAINT COM RESTART DISTANCES FLUSH INPLANEDISTANCES PRINT	multicolvar bias generic setup vatom
19.056	maze	methods	maze, ligand unbinding	Jakub Rydzewski	POSITION MAZE_LOSS MAZE_SIMULATED_ANNEALING UNITS MAZE_OPTIMIZER_BIAS PRINT	setup generic maze colvar
19.053	Capillary fluctuations with PLUMED	methods	nucleation, surface tension, capillary fluctuations	Gareth Tribello	MORE_THAN GROUP MULTICOLVARDENS CENTER FCCUBIC FIND_CONTOUR_SURFACE UNITS DUMPGRID FOURIER_TRANSFORM	gridtools symfunc fourier core function contour setup vatom
19.037	Scission free energy of organic dyes	chemistry	metadynamics, multiple walkers, matheval/lepton	Paolo Raiteri	DISTANCE RESTART FLUSH UPPER_WALLS UNITS MATHEVAL PRINT METAD	bias colvar function generic setup
19.023	RECT	methods	metadynamics, replica exchange	Giovanni Bussi	GYRATION WHOLEMOLECULES TORSION PRINT METAD	generic bias colvar
19.021	Coarse-Grained Directed Simulation	methods	experiment directed simulation, coarse-grain, bias	Glen Hocky	DISTANCE COMBINE RESTRAINT TORSION EDS PRINT	bias colvar function generic eds
19.019	FA-MetaD-JCP-Wang-et-al	bio	Frequency adaptive metadynamics; peptide	Kresten Lindorff-Larsen	COMBINE MOLINFO FLUSH ALPHABETA COMMITTOR PRINT METAD	function generic bias multicolvar
19.015	Ibuprofen conformational dynamics and thermodynamics surface	materials	Ibuprofen, crystal, surface, solvents, conformers, metadynamics	Matteo Salvalaglio	DISTANCE CENTER UPPER_WALLS TORSION COMMITTOR PRINT METAD LOWER_WALLS	generic vatom bias colvar
19.012	Martini-Beads multi-scale SAXS	methods	metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex	Carlo Camilloni	DISTANCE GROUP CENTER RESTRAINT ENDPLUMED MOLINFO UPPER_WALLS WHOLEMOLECULES SAXS RMSD BIASVALUE PRINT INCLUDE STATS	bias colvar core isdb function generic vatom
19.007	EMMI Microtubules	bio	metainference, cryo-EM	Max Bonomi	GROUP MOLINFO EMMI WHOLEMOLECULES BIASVALUE PRINT	isdb core generic bias
25.022	Imidazole Diffusion in SALEM-2 MOF	materials	OPES, Diffusion, Ring opening, MOFs, Machine Learning Potentials	Sudheesh Kumar Ethirajan	DISTANCE PRINT WHOLEMOLECULES ENDPLUMED OPES_METAD DISTANCES CENTER UNITS MOLINFO PROJECTION_ON_AXIS GROUP	setup vatom generic colvar core multicolvar opes
25.014	Atomic resolution ensembles of intrinsically disordered proteins with Alphafold	bio	bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement	Vincent Schnapka	BIASVALUE PRINT GROUP BAIES	isdb bias generic core
24.031	DeepLNE	methods	PATHCV, OPES, OneOPES	Thorben Fröhlking	PYTORCH_MODEL RESTART ECV_MULTITHERMAL PRINT ERMSD VOLUME ENERGY OPES_METAD_EXPLORE COMBINE MOLINFO COORDINATION OPES_EXPANDED	setup function generic colvar opes pytorch
24.025	Correlating Enzymatic Reactivity for Different Substrates using Transferable Data-Driven Collective Variables	bio	enzymatic reactivity, k_cat, transfer learning, data-driven CVs, catalysis, ligand-binding modes, water, alpha-amylase, sugar, classical MD, OPES, machine learning, Deep TDA CV, path CV	Sudip Das	CUSTOM PYTORCH_MODEL RESTART UPPER_WALLS DISTANCE FIT_TO_TEMPLATE PATH PRINT WHOLEMOLECULES OPES_METAD TORSION LOWER_WALLS CENTER FIXEDATOM COORDINATION GROUP	setup vatom function bias generic colvar core mapping opes pytorch
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	CUSTOM RESTART DISTANCE ECV_MULTITHERMAL PRINT ENERGY OPES_METAD_EXPLORE TORSION COMBINE COORDINATION GROUP OPES_EXPANDED	setup function generic colvar core opes
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	CUSTOM DISTANCE PRINT GYRATION WHOLEMOLECULES OPES_METAD TORSION COMBINE MOLINFO COORDINATION ALPHARMSD	secondarystructure function generic colvar opes
24.007	SWISH-X	bio	swish-x, SWISH-X, swish, expanded SWISH	Alberto Borsatto	CONTACTMAP UPPER_WALLS ECV_MULTITHERMAL INCLUDE PRINT WHOLEMOLECULES ENERGY MOLINFO OPES_EXPANDED	bias generic colvar opes
24.000	Ammonia Decomposition on Non-stoichiometric Lithium Imide	chemistry	ammonia decomposition, non-stoichiometric lithium imide, machine learning interatomic potentials, enhanced sampling, heterogeneous catalysis	Francesco Mambretti	ZDISTANCES UPPER_WALLS DISTANCE FIXEDATOM COORDINATIONNUMBER PRINT FLUSH OPES_METAD UNITS GROUP	setup vatom bias generic colvar core multicolvar symfunc opes
23.040	Supramolecular capsules assembly dynamics	chemistry	Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics	Riccardo Capelli	CUSTOM POSITION DISTANCE PRINT FLUSH WHOLEMOLECULES METAD COM DISTANCES CENTER UNITS GROUP	setup vatom function bias generic colvar core multicolvar
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	DISTANCE UPPER_WALLS CONSTANT PRINT WHOLEMOLECULES METAD BIASVALUE LOWER_WALLS CENTER MATHEVAL	vatom function bias generic colvar
23.034	Urea nucleation in water: do long-range forces matter?	materials	LMF theory, Metadynamics, Nucleation	Ziyue Zou	COORDINATIONNUMBER INCLUDE PRINT METAD CENTER LOAD GROUP	setup vatom bias generic core symfunc
23.026	Machine Learning Nucleation Collective Variables with Graph Neural Networks	chemistry	Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks	Florian Dietrich	Q6 MFILTER_MORE COORDINATIONNUMBER PRINT METAD LOCAL_Q6 LOWER_WALLS COMBINE GROUP MOVINGRESTRAINT	function bias generic core multicolvar symfunc
23.023	Rational design of novel biomimetic sequence-defined polymers for mineralization applications	methods	metadynamics, surface binding, biomimetic mineralization	Kaylyn Torkelson	UPPER_WALLS DISTANCE PRINT GYRATION COM PBMETAD COORDINATION	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	PYTORCH_MODEL CUSTOM DISTANCE UPPER_WALLS FIT_TO_TEMPLATE FIXEDATOM PATH PRINT WHOLEMOLECULES OPES_METAD_EXPLORE OPES_METAD TORSION LOWER_WALLS CENTER UNITS COORDINATION GROUP	setup vatom function bias generic colvar core mapping opes pytorch
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	UPPER_WALLS DISTANCE CONSTANT PRINT WHOLEMOLECULES METAD BIASVALUE LOWER_WALLS MATHEVAL	function bias 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	CONTACTMAP DISTANCE ENDPLUMED LOWER_WALLS RMSD PYTORCH_MODEL ANGLE COMMITTOR INCLUDE MATHEVAL UPPER_WALLS WHOLEMOLECULES ENERGY OPES_METAD CENTER FIXEDATOM MOLINFO COORDINATION GROUP CUSTOM FIT_TO_TEMPLATE PRINT COMBINE	vatom function bias generic colvar core opes pytorch
22.045	Binding mode and mechanism of enzymatic polyethylene terephthalate degradation	bio	metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation	Francesco Colizzi	ANGLE UPPER_WALLS DISTANCE PRINT WHOLEMOLECULES METAD LOWER_WALLS COM MOVINGRESTRAINT	bias vatom generic colvar
22.029	Angiotensin-1-7_Metadynamics	bio	Metadynamics, Angiotensin-(1-7), peptide	L.-América Chi	UPPER_WALLS PRINT FLUSH GYRATION WHOLEMOLECULES METAD LOWER_WALLS COORDINATION GROUP	bias generic colvar core
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	RMSD EMMI RESTART UPPER_WALLS PRINT WHOLEMOLECULES BIASVALUE TORSION COM PBMETAD MOLINFO COORDINATION GROUP	setup vatom bias generic colvar core isdb
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 PATHMSD UPPER_WALLS PRINT FUNNEL WHOLEMOLECULES METAD COM LOWER_WALLS FUNNEL_PS	vatom bias generic colvar funnel
22.009	Glycosylation in calixarenes capsule	chemistry	Metadynamics, glycosylation, supramolecular catalysis	GiovanniMaria Piccini	RMSD ANGLE DISTANCE UPPER_WALLS FIT_TO_TEMPLATE BRIDGE PRINT FLUSH WHOLEMOLECULES METAD LOWER_WALLS COMBINE DISTANCES UNITS COORDINATION GROUP MATHEVAL	setup adjmat function bias generic colvar core multicolvar
22.002	GAMBES_SAMPL5_RATES	other	GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding	Jayashrita Debnath	PYTORCH_MODEL ANGLE COMMITTOR DISTANCE UPPER_WALLS FIT_TO_TEMPLATE PRINT FLUSH WHOLEMOLECULES ENERGY ENDPLUMED CENTER FIXEDATOM LOAD COORDINATION GROUP MATHEVAL	setup vatom function bias generic colvar core pytorch
21.050	N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity	methods	bio	Isabell Louise Grothaus	PRINT DISTANCE CENTER	vatom generic colvar
21.043	Predicting the Conformational Variability of Oncogenic GTP-bound G12D Mutated KRas-4B Proteins at Cell Membranes	chemistry	well-tempered metadynamics, KRas-4B, anionic membrane, conformational variability	Huixia Lu	FIT_TO_TEMPLATE PRINT METAD TORSION FIXEDATOM	bias vatom generic colvar
21.035	CmuMD simulations of NaCl(aq) at NaCl	chemistry	CmuMD, interface	Aaron Finney	DISTANCE PRINT FIXEDATOM LOAD GROUP RESTRAINT	setup vatom bias generic colvar core
21.026	Probing allosteric regulations with coevolution-driven molecular simulations	bio	metadynamics, coevolution, allostery, adenylate cyclase	Francesco Colizzi	DISTANCE PATHMSD UPPER_WALLS PRINT WHOLEMOLECULES METAD COM UNITS	setup vatom bias generic colvar
21.025	Computational and biochemical analysis of type IV pilus dynamics and stability	bio	molecular dynamics, calcium binding, Type IV pilus	Yasaman Karami	PRINT DISTANCE LOWER_WALLS UPPER_WALLS	bias generic colvar
20.028	Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane	bio	metadynamics, KRas-4B, anionic membrane	Huixia Lu	RESTART DISTANCE FIT_TO_TEMPLATE PRINT METAD CENTER	setup vatom bias generic colvar
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	PARABETARMSD METAINFERENCE FLUSH ENDPLUMED STATS INCLUDE ALPHARMSD GYRATION WHOLEMOLECULES DIHCOR TORSION ANTIBETARMSD PBMETAD MOLINFO COORDINATION GROUP ENSEMBLE PRINT COMBINE CS2BACKBONE	secondarystructure function bias generic colvar core isdb multicolvar
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	DUMPGRID CONTACTMAP DISTANCE CONVERT_TO_FES FLUSH READ ENDPLUMED LOWER_WALLS FUNCPATHMSD METAD ABMD HISTOGRAM REWEIGHT_METAD UPPER_WALLS WHOLEMOLECULES COM MOLINFO PRINT COMBINE	vatom function bias gridtools generic colvar
20.004	Data-driven collective variables for enhanced sampling	methods	collective variables, machine learning, deep-lda	Luigi Bonati	PYTORCH_MODEL DISTANCE UPPER_WALLS PRINT FLUSH ENDPLUMED OPES_METAD TORSION COM LOWER_WALLS UNITS LOAD GROUP MATHEVAL	setup vatom function bias generic colvar core opes pytorch
19.074	Asymmetric base pair opening in nucleic acids	bio	double helix, DNA, RNA, unwindability	Giovanni Bussi	DISTANCE WHOLEMOLECULES ENDPLUMED LOWER_WALLS COORDINATION RESTRAINT	bias generic colvar
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	UPPER_WALLS COORDINATIONNUMBER PRINT GYRATION METAD ENERGY ENDPLUMED LOWER_WALLS DISTANCES	bias generic colvar multicolvar symfunc
19.067	Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways	bio	metadynamics, ligand unbinding	Jakub Rydzewski	RESTART UPPER_WALLS PATHMSD PRINT METAD LOWER_WALLS UNITS	setup bias generic colvar
19.048	Understanding Ligand Binding Selectivity in a Prototypical GPCR Family	bio	metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding	Francesco Gervasio	DISTANCE UPPER_WALLS CONSTANT PRINT WHOLEMOLECULES METAD BIASVALUE COM LOWER_WALLS MATHEVAL	vatom function bias generic colvar
19.043	Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA)	methods	metadynamics, chemistry, HLDA	GiovanniMaria Piccini	RESTART UPPER_WALLS DISTANCE PRINT FLUSH METAD DISTANCES COMBINE UNITS	setup function bias generic colvar multicolvar
19.025	Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide	bio	metainference, NMR, protein dynamics, force-fields	Carlo Camilloni	METAINFERENCE PRINT FLUSH RDC GYRATION ENSEMBLE WHOLEMOLECULES ENDPLUMED BIASVALUE JCOUPLING TORSION PBMETAD MOLINFO CS2BACKBONE STATS	function bias generic colvar isdb
19.022	eABF simulation of NANMA (alanine dipeptide)	methods	eABF, DRR, alanine dipeptide	Haochuan Chen	PRINT TORSION DRR	drr generic colvar
19.001	RNA SHAPE	bio	metadynamics, RNA, ligand binding	Giovanni Bussi	ANGLE DISTANCE UPPER_WALLS INCLUDE FLUSH PRINT ERMSD METAD LOWER_WALLS COMBINE DISTANCES MOLINFO RANDOM_EXCHANGES	function bias generic colvar multicolvar
25.018	Metainference simulation for dimerization of RNA binding protein	bio	Metainference, Metadynamics, SAXS, protein dimer	Debadutta Patra	DISTANCE MOLINFO FLUSH WHOLEMOLECULES PBMETAD CENTER ENSEMBLE GYRATION STATS METAINFERENCE UPPER_WALLS TORSION PRINT SAXS	function isdb generic vatom bias colvar
25.012	A Machine Learning-Driven, Probability-Based Approach to Enzyme Catalysis	bio	enzyme catalysis, transition state, structure-activity relationship, free energy surface, reaction mechanism, water, alpha-amylase, sugar, QM/MM MD, OPES, committor function, machine learning	Sudip Das	LOAD COMBINE DISTANCE FLUSH POSITION UNITS ENERGY INCLUDE TORSION CELL OPES_METAD CUSTOM MATHEVAL PRINT COORDINATION BIASVALUE	function setup opes generic bias colvar
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	DISTANCE WHOLEMOLECULES GROUP HISTOGRAM ANGLE TORSION PRINT DUMPGRID COORDINATION CONVERT_TO_FES	generic colvar core gridtools
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	DISTANCE MOLINFO DUMPATOMS WHOLEMOLECULES GROUP ALPHARMSD PBMETAD CENTER DUMPMASSCHARGE COM UPPER_WALLS PARABETARMSD PRINT EMMI RMSD BIASVALUE COORDINATION	secondarystructure isdb core generic vatom bias colvar
24.032	DeepLNE++	methods	PATHCV, OPES	Thorben Fröhlking	LOAD DISTANCE COMBINE GROUP ENERGY TORSION OPES_METAD CUSTOM PRINT COORDINATION	function setup core opes generic colvar
24.028	All-atom simulations of RNA-membrane interactions	bio	metadynamics, membrane, RNA	Giovanni Bussi	DISTANCE MOLINFO COMBINE POSITION SORT GROUP DISTANCES CENTER WHOLEMOLECULES GYRATION GHOST UPPER_WALLS LOWER_WALLS METAD MATHEVAL PRINT PUCKERING	function core generic vatom bias colvar multicolvar
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	FIXEDATOM ENDPLUMED MATHEVAL OPES_METAD UPPER_WALLS COORDINATION COMBINE COMMITTOR FIT_TO_TEMPLATE METAD CONTACTMAP CUSTOM TORSION PRINT RMSD DISTANCE MOLINFO WHOLEMOLECULES GROUP CENTER ANGLE	function core opes generic vatom bias colvar
24.018	A new route to the prebiotic synthesis of glycine via ab initio-based machine learning calculations	chemistry	prebiotic chemistry, glycine, Strecker synthesis, ab initio calculations, machine learning	Léon HUET	DISTANCE PRINT	generic colvar
24.010	Oxytocin metadynamics simulation	bio	metadynamics, oxytocin, peptide	Jan Beránek	FLUSH WHOLEMOLECULES METAD TORSION PRINT RESTART	bias setup generic colvar
23.037	Estimating binding free energy of solid binding peptides without extensive sampling	bio	metadynamics, solid binding peptides	Xin Qi	DISTANCE MOLINFO PBMETAD GYRATION COM UPPER_WALLS LOWER_WALLS PRINT	generic colvar vatom bias
23.032	Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics	bio	metadynamics, tSNE, neural network, machine learning, trp-cage, folding	Vojtech Spiwok	COMBINE MOLINFO POSITION WHOLEMOLECULES FIT_TO_TEMPLATE ALPHARMSD ANN METAD PRINT	function secondarystructure generic bias annfunc colvar
23.015	MPCs aggregation	bio	opes_explore, dimerization, MPCs, self-assembly	Vikas Tiwari	DISTANCE OPES_METAD_EXPLORE WHOLEMOLECULES GROUP CENTER COM UPPER_WALLS LOWER_WALLS METAD CUSTOM PRINT COORDINATION	function core opes generic vatom bias colvar
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	PATHMSD DRR FLUSH TIME UNITS UPPER_WALLS LOWER_WALLS METAD CUSTOM PRINT BIASVALUE	function setup drr generic bias colvar
22.044	Colloid Crystallisation Analyses	materials	Q4, Q6, Pair Entropy, DFS	Aaron Finney	COMBINE MFILTER_MORE LOCAL_Q6 LOCAL_AVERAGE GROUP MFILTER_LESS CLUSTER_NATOMS COORDINATIONNUMBER CONTACT_MATRIX Q4 LOCAL_Q4 Q6 DFSCLUSTERING PRINT	function adjmat core generic symfunc multicolvar clusters
22.041	Skipping the Replica Exchange Ladder with Normalizing Flows	methods	OPES, alanine, normalizing flows, replica exchange	Michele Invernizzi	POSITION ECV_MULTITHERMAL ENDPLUMED PRINT UNITS OPES_METAD ENERGY OPES_EXPANDED TORSION	generic opes colvar setup
22.039	Driving and characterizing nucleation of urea and glycine polymorphs in water	bio	metadynamics, nucleation, amino acids, polymorphism	Eric Beyerle	LOAD COMBINE PAIRENTROPY GROUP CENTER COORDINATIONNUMBER INCLUDE METAD Q4 MATHEVAL Q6 PRINT	function setup gridtools core vatom generic symfunc bias
22.036	Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction	bio	Well-tempered MetaDynamics with Hamiltonian Replica Exchange	Miroslav Krepl	LOAD MOLINFO COMBINE FLUSH GROUP GHBFIX UPPER_WALLS METAD CUSTOM PRINT COORDINATION BIASVALUE	function setup core generic bias colvar
22.027	Molecular Dynamics simulations of BANAL-236 RBD-hACE2 complexes	bio	SARS-CoV-2, COVID-19, MD, human-ACE2, spike, BANAL-236, receptor-binding domain	Max Bonomi	PRINT RMSD	generic colvar
22.016	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 AROUND HISTOGRAM UPPER_WALLS ENVIRONMENTSIMILARITY VOLUME OPES_METAD CUSTOM PRINT DUMPGRID RESTART	function setup gridtools opes generic bias colvar volumes envsim
22.013	Ligand dissociation from PreQ1 riboswitch	bio	ligand, RNA, metadynamics, pRAVE	Yihang Wang	DISTANCE MOLINFO COMBINE WHOLEMOLECULES COMMITTOR COM COORDINATIONNUMBER METAD PRINT RMSD	function generic vatom symfunc bias colvar
22.007	Characterization of a natural variant of human NDP52 and its functional consequences on mitophagy	bio	metadynamics, well-tempered, protein-protein interactions, disordered proteins, mutations autophagy	Elena Papaleo	DISTANCE MOLINFO FLUSH WHOLEMOLECULES ALPHARMSD ANGLE UPPER_WALLS METAD TORSION PRINT COORDINATION ALPHABETA	secondarystructure generic bias colvar multicolvar
22.003	Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling	methods	opes, metadynamics, reweighting, alanine, muller	Michele Invernizzi	OPES_METAD_EXPLORE ECV_UMBRELLAS_FILE ECV_MULTITHERMAL ENDPLUMED ENERGY PBMETAD POSITION UNITS UPPER_WALLS LOWER_WALLS METAD TORSION OPES_METAD CUSTOM OPES_EXPANDED PRINT BIASVALUE	function setup opes generic bias colvar
21.046	Ubiquitin Interacting Motifs, Duality Between Structured and Disordered Motifs	bio	wt metadynamics, ubiquitin, ataxin-3, short linear motifs, ubiquitin binding motif, moonlight functions, intrinsic disorder	Elena Papaleo	WHOLEMOLECULES GROUP ENDPLUMED GYRATION UPPER_WALLS LOWER_WALLS METAD PRINT ALPHABETA	core generic bias colvar multicolvar
21.041	Nucleating a Different Coordination in a Crystal under Pressure. A Study of the B1−B2 Transition in NaCl by Metadynamics	methods	metadynamics, structural phase transitions, pressure-induced phase transition, martensitic transitions	Matej Badin	COMBINE ENDPLUMED METAD CUSTOM PRINT VOLUME COORDINATION	bias function generic colvar
21.033	Multiple-path-metadynamics applied to DNA base-pairing transitions	bio	path-CV, metadynamics, multiple-walker, dna	Alberto Pérez-de-Alba-Ortíz	COMBINE INCLUDE UPPER_WALLS CONSTANT METAD RESTRAINT PRINT MOVINGRESTRAINT	bias function generic
21.031	Photo-switchable sulfonulureas in KATP channel	bio	metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels	Katarzyna Walczewska-Szewc	DISTANCE WHOLEMOLECULES UNITS COM UPPER_WALLS LOWER_WALLS METAD PRINT	setup generic vatom bias colvar
21.006	OPES, On-the-fly Probability Enhanced Sampling Method	methods	opes, alanine dipeptide, well-tempered, multithermal, multiumbrella	Michele Invernizzi	ECV_UMBRELLAS_LINE ECV_MULTITHERMAL ENDPLUMED PRINT OPES_METAD ENERGY OPES_EXPANDED TORSION	opes generic colvar
20.024	Gaussian Mixture Based Enhanced Sampling (GAMBES)	methods	enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias	Jayashrita Debnath	LOAD DISTANCE COMBINE DISTANCES UNITS GROUP UPPER_WALLS LOWER_WALLS TORSION ENERGY PRINT	function setup core generic bias colvar multicolvar
20.020	Parallel Bias Metadynamics	methods	pbmetad, trp-cage, folding	Max Bonomi	DIHCOR MOLINFO WHOLEMOLECULES PBMETAD GYRATION INCLUDE PRINT COORDINATION ALPHABETA	bias generic multicolvar colvar
19.083	Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis	chemistry	metadynamics, chemical reactions, reaction discovery	Valerio Rizzi	COMBINE FLUSH DISTANCES UNITS GROUP ENDPLUMED COORDINATIONNUMBER UPPER_WALLS METAD PRINT RESTART	function setup core generic symfunc bias multicolvar
19.071	Time-independent free energies from metadynamics via Mean Force Integration	methods	metadynamics, mean force integration, MFI, thermodynamic integration	Matteo Salvalaglio	DISTANCE COMMITTOR REWEIGHT_METAD HISTOGRAM EXTERNAL REWEIGHT_BIAS METAD TORSION MATHEVAL READ CONVERT_TO_FES PRINT DUMPGRID BIASVALUE	function gridtools generic bias colvar
19.068	Rethinking Metadynamics	methods	metadynamics, opes, convergence	Michele Invernizzi	POSITION UNITS ENDPLUMED EXTERNAL METAD TORSION OPES_METAD PRINT	setup opes generic bias colvar
19.050	Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes	chemistry	metadynamics, membranes, Willard Chandler surface	Gareth Tribello	COMBINE HISTOGRAM UPPER_WALLS REWEIGHT_BIAS METAD READ DISTANCE_FROM_CONTOUR PRINT DUMPGRID RESTART CONVERT_TO_FES	function contour setup gridtools generic bias
19.049	Determining the sizes of solid/liquid clusters in MD trajectories of nucleation	methods	nucleation, metadynamics, clustering, Steinhardt order parameters	Gareth Tribello	OUTER_PRODUCT LOCAL_Q6 DISTANCES ONES CLUSTER_NATOMS COORDINATIONNUMBER CONTACT_MATRIX MATRIX_VECTOR_PRODUCT MORE_THAN DFSCLUSTERING CLUSTER_DISTRIBUTION Q6 CUSTOM METAD PRINT CLUSTER_PROPERTIES SMAC OUTPUT_CLUSTER	adjmat function generic symfunc bias matrixtools multicolvar clusters
19.041	Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces	bio	metadynamics, collective variables, conformational changes, multiple walkers, Well-Tempered MetaD, peptide, binding, phosphorylation, post-transitional motif, sio2, adsorption	Jim Pfaendtner	DISTANCE COM UPPER_WALLS METAD ENERGY PRINT	bias colvar vatom generic
19.038	native state dynamics of human and mouse b2m	bio	metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation	Carlo Camilloni	MOLINFO CS2BACKBONE FLUSH WHOLEMOLECULES GROUP PBMETAD ENDPLUMED ANTIBETARMSD LOWER_WALLS UPPER_WALLS PRINT RESTART BIASVALUE ALPHABETA	secondarystructure setup isdb core generic bias multicolvar
19.004	MI Ubiquitin	bio	metainference, NMR	Max Bonomi	MOLINFO CS2BACKBONE WHOLEMOLECULES GROUP RDC METAINFERENCE PRINT	core generic isdb
25.021	All You Need Is Water. Converging Ligand Binding Simulations with Hydration Collective Variables	bio	OPES Explore, ligand binding, binding free energy, water, hydration CVs, SAMPL challenge, host-guest	Valerio Rizzi	GROUP FIT_TO_TEMPLATE CENTER OPES_METAD_EXPLORE PRINT ANGLE FIXEDATOM UPPER_WALLS DISTANCE COORDINATION WHOLEMOLECULES MATHEVAL ENERGY	colvar vatom function opes bias generic core
25.016	Advancing in silico drug design with Bayesian refinement of AlphaFold models	bio	bAIes, AlphaFold, Bayesian refinement, virtual screening, docking, small-molecule, enrichment	Samiran Sen	BIASVALUE GROUP PRINT BAIES	isdb generic bias core
25.013	Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices	bio	umbrella sampling, temperature ramping	Alexander Berlaga	RESTRAINT PRINT DISTANCE PYTORCH_MODEL GYRATION	generic pytorch bias colvar
25.008	Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting	methods	metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting	Dhiman Ray	GROUP CUSTOM LOWER_WALLS BIASVALUE TORSION PRINT POSITION UPPER_WALLS DISTANCE RMSD OPES_METAD METAD ENDPLUMED WHOLEMOLECULES UNITS MOLINFO ENERGY PYTORCH_MODEL	colvar setup function bias opes generic core pytorch
25.002	M3_PCV-ABMD	chemistry	Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor	Gian Marco Elisi	ABMD PRINT UPPER_WALLS ENDPLUMED UNITS PATHMSD	generic bias setup colvar
24.027	Proline cis and trans subensembles of a disordered peptide	bio	intrinsically disordered proteins, proline cis trans isomerisation, metadynamics, collective variables	Alice Pettitt	ALPHARMSD GROUP PBMETAD ANTIBETARMSD INCLUDE COMBINE TORSION PRINT DISTANCE DIHCOR PARABETARMSD COORDINATION WHOLEMOLECULES ENDPLUMED FLUSH MOLINFO GYRATION	colvar function bias secondarystructure generic core multicolvar
24.013	Estimating Free Energy Surfaces and their Convergence from multiple, independent static and history-dependent biased molecular-dynamics simulations with Mean Force Integration	methods	Mean Force Integration, Convergence, FES, Umbrella Sampling	Matteo Salvalaglio	RESTRAINT BIASVALUE TORSION PRINT COORDINATIONNUMBER DISTANCE RESTART METAD COMMITTOR MATHEVAL FLUSH MOLINFO ENERGY	setup colvar function bias symfunc generic
24.008	yCD Metadynamics	bio	volume-based MetaD, path CVs, infrequent MetaD, product release	James McCarty	PATH HISTOGRAM PRINT CONTACTMAP REWEIGHT_METAD FIT_TO_TEMPLATE GROUP CONVERT_TO_FES ENDPLUMED DUMPGRID FLUSH COM INCLUDE UPPER_WALLS DISTANCE COORDINATION WHOLEMOLECULES METAD READ WRAPAROUND FIXEDATOM RMSD COMMITTOR MATHEVAL MOLINFO	mapping colvar vatom function bias generic core gridtools
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	CENTER GROUP BIASVALUE PRINT UPPER_WALLS DISTANCE RMSD WRAPAROUND SAXS MOLINFO ENSEMBLE STATS	colvar vatom function bias generic core isdb
23.021	Into the Dynamics of Rotaxanes at Atomistic Resolution	materials	metadynamics, rotaxanes, molecular shuttles, molecular machines	Luigi Leanza	CENTER CUSTOM TORSION PRINT FIXEDATOM UPPER_WALLS DISTANCE METAD MATHEVAL	colvar vatom function bias generic
23.019	Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors	bio	binding pathway, binding energy, sketch-map, drug development	Raitis Bobrovs	COLLECT_FRAMES DISSIMILARITIES LANDMARK_SELECT_FPS CUSTOM SKETCHMAP_PROJECTION COM VSTACK PRINT UPPER_WALLS DISTANCE VORONOI SKETCHMAP METAD WHOLEMOLECULES TRANSPOSE PATHMSD	valtools matrixtools landmarks vatom colvar dimred function bias generic
23.018	Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention	materials	metadynamics, surface binding, peptide adsorption	Kaylyn Torkelson	PBMETAD COM PRINT UPPER_WALLS DISTANCE GYRATION	generic bias colvar vatom
23.006	Transcription factor unbinding	bio	metadynamics, DNA, conformational changes	Malin Lüking	ALPHARMSD COM PRINT ANGLE DISTANCE DUMPFORCES METAD MOLINFO CONTACTMAP	colvar vatom bias secondarystructure generic
22.025	Bubble nucleation rate predictions in a Lennard-Jones fluid	materials	free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation	Kristof Bal	ANN CUSTOM HISTOGRAM REWEIGHT_BIAS CONVERT_TO_FES COMMITTOR VOLUME RESTRAINT BIASVALUE MOVINGRESTRAINT COORDINATIONNUMBER PRINT UPPER_WALLS DUMPGRID UNITS LOAD FLUSH	colvar setup function bias symfunc generic annfunc gridtools
21.037	Molecular Dynamics simulations of RBD/hACE2 complexes	bio	SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain	Max Bonomi	RMSD PRINT DISTANCE	generic colvar
21.018	Localized Volume-based Metadynamics	bio	LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification	Riccardo Capelli	HISTOGRAM PRINT REWEIGHT_METAD GROUP CONVERT_TO_FES ENDPLUMED DUMPGRID FLUSH COM POSITION UPPER_WALLS DISTANCE COORDINATION WHOLEMOLECULES METAD READ FIXEDATOM RMSD MATHEVAL	colvar vatom function bias generic core gridtools
21.014	how to determine statistically accurate conformational ensembles	bio	metadynamics, metainference, errors, cv, SAXS, ensemble determination	Cristina Paissoni	CENTER PBMETAD ANTIBETARMSD BIASVALUE ALPHABETA PRINT TORSION STATS METAD WHOLEMOLECULES SAXS MOLINFO ENSEMBLE CONTACTMAP GYRATION	colvar vatom function bias isdb secondarystructure generic multicolvar
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	CENTER ABMD ERMSD TORSION PRINT DISTANCE RESTART MOLINFO	setup colvar vatom bias generic
20.032	Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil	materials	clustering, conformational isomers	Matteo Salvalaglio	TORSION PRINT ENDPLUMED	generic colvar
20.026	Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor	bio	Metadynamics, Umbrella sampling	Brandon Peters	HISTOGRAM CONVERT_TO_FES RESTRAINT PRINT MULTI_RMSD METAD DUMPGRID REWEIGHT_METAD	generic bias gridtools colvar
20.018	Free energy barriers from biased molecular dynamics simulations	methods	kinetics, free energy barriers, chemical reactions, nucleation, metadynamics	Kristof Bal	HISTOGRAM REWEIGHT_BIAS COMBINE PRINT COORDINATIONNUMBER REWEIGHT_METAD CENTER CONVERT_TO_FES CONTACT_MATRIX SPRINT DUMPGRID FLUSH ENERGY Q6 LOCAL_AVERAGE PAIRENTROPY UPPER_WALLS DISTANCE METAD COORDINATION LOWER_WALLS VOLUME DENSITY UNITS LOAD	colvar vatom adjmat setup function bias symfunc generic volumes sprint gridtools
20.016	Predicting polymorphism in molecular crystals using orientational entropy	materials	metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy	Pablo Piaggi	GROUP CENTER VOLUME INCLUDE PRINT UPPER_WALLS METAD LOAD	colvar vatom setup bias generic core
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	VOLUME OPT_AVERAGED_SGD PRINT BF_LEGENDRE UPPER_WALLS RESTART OPT_DUMMY ENVIRONMENTSIMILARITY MATHEVAL VES_LINEAR_EXPANSION TD_WELLTEMPERED Q6	colvar setup envsim function ves bias symfunc generic
19.082	Ammonia Borane Dehydrogenation	chemistry	metadynamics, reaction discovery, hydrogen production, chemistry	Valerio Rizzi	GROUP COMBINE EXTERNAL COORDINATIONNUMBER PRINT RESTART ENDPLUMED METAD UNITS FLUSH	setup function bias symfunc generic core
19.069	Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen	materials	ibuprofen, crystal, solvent, surface	Matteo Salvalaglio	CENTER GROUP INCLUDE PRINT DISTANCE ENDPLUMED	core generic colvar vatom
19.063	Protein-ligand binding through metadynamics with path CVs	bio	metadynamics, path CVs, ligand binding	Mattia Bernetti	LOWER_WALLS PRINT UPPER_WALLS METAD WHOLEMOLECULES PATHMSD	generic bias colvar
19.054	MetaFEP	methods	metadynamics, chemistry, free energy perturbation	GiovanniMaria Piccini	LOWER_WALLS COMBINE PRINT UPPER_WALLS DISTANCE METAD UNITS FLUSH ENERGY	setup colvar function bias generic
19.016	Succinnic acid gamma polymorph	materials	Succinnic acid, conformers, polymorphs, metadynamics	Matteo Salvalaglio	LOWER_WALLS VOLUME CELL COMBINE TORSION PRINT UPPER_WALLS ENDPLUMED METAD MATHEVAL ENERGY	generic function bias colvar
19.014	MIL101(Cr) SBUs assembly	materials	MOFs, nucleation, self-assembly, metadynamics	Matteo Salvalaglio	COORDINATIONNUMBER PRINT DISTANCES RESTART ENDPLUMED METAD GYRATION	setup colvar bias symfunc generic multicolvar
19.011	Automatic Gradient Computation for Collective Variables	other	gradient, differentiation, curvature	Toni Giorgino	ENDPLUMED	generic
19.002	EMMI STRA6	bio	metainference, cryo-EM	Max Bonomi	GROUP BIASVALUE PRINT EMMI MOLINFO	isdb generic 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	WRAPAROUND GROUP LOWER_WALLS RMSD ENERGY ECV_MULTITHERMAL OPES_METAD_EXPLORE COM CONTACTMAP MATHEVAL PROJECTION_ON_AXIS WHOLEMOLECULES RESTART MOLINFO OPES_EXPANDED METAD CONSTANT UPPER_WALLS TORSION INCLUDE BIASVALUE COORDINATION CUSTOM PRINT	bias colvar setup function core vatom opes generic
23.041	Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference	methods	EMMIVox, cryo-EM, single-structure refinement, ensemble refinement, Bayesian inference, B-factors, structural ensembles	Samuel Hoff	DISTANCE WRAPAROUND UPPER_WALLS EMMIVOX GROUP INCLUDE BIASVALUE MOLINFO PRINT WHOLEMOLECULES	bias colvar core isdb generic
23.030	Data Driven Classification of Ligand Unbinding Pathways	bio	OPES Explore, OPES Flooding, Benzene T4 Lysozyme, Ligand unbinding, Pathway classification, Kinetics, Residence time	Dhiman Ray	CENTER UNITS WRAPAROUND GROUP LOWER_WALLS ENERGY OPES_METAD_EXPLORE COM MATHEVAL WHOLEMOLECULES FLUSH POSITION ENDPLUMED MOLINFO DISTANCE UPPER_WALLS TORSION COMMITTOR FIT_TO_TEMPLATE BIASVALUE COORDINATION CUSTOM OPES_METAD PRINT	bias colvar setup function core vatom opes generic
23.011	OneOPES, a combined enhanced sampling method to rule them all	bio	OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding	Valerio Rizzi	DISTANCE TORSION ENERGY ECV_MULTITHERMAL OPES_METAD_EXPLORE ENDPLUMED MOLINFO OPES_EXPANDED PRINT METAD	opes bias generic colvar
23.005	A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs	bio	metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A	Timothy Clark	PRINT HISTOGRAM REWEIGHT_METAD DUMPGRID RMSD MATHEVAL CONVERT_TO_FES READ MOLINFO DISTANCE METAD WHOLEMOLECULES	bias colvar gridtools function generic
23.001	Quantum phase diagram of water	chemistry	Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella	Sigbjørn-Løland Bore	PRINT LOWER_WALLS ECV_UMBRELLAS_LINE ENVIRONMENTSIMILARITY INCLUDE RESTART OPES_EXPANDED UPPER_WALLS	bias setup opes envsim generic
22.024	Conformational Entropy as a Potential Liability of Computationally Designed Antibodies	bio	metadynamics, conformational entropy, antibody, nanobody	Thomas Löhr	ANTIBETARMSD ALPHARMSD PBMETAD TORSION COM RESTART ALPHABETA MOLINFO PRINT WHOLEMOLECULES	bias colvar setup multicolvar vatom generic secondarystructure
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	DISTANCE GROUP TORSION COM PRINT METAD WHOLEMOLECULES	bias colvar core vatom generic
21.042	Peptoid-mediated Au nanocrystal growth	materials	parallel-bias metadynamics, peptoid, Au	Xin Qi	DISTANCE UPPER_WALLS PBMETAD GYRATION COM MOLINFO PRINT	bias generic colvar vatom
21.028	From Enhanced Sampling to Reaction Profiles	methods	collective variables, multi-state, machine learning, Deep-TDA	Enrico Trizio	CENTER UNITS PRINT PYTORCH_MODEL GROUP LOWER_WALLS MATHEVAL WHOLEMOLECULES LOAD FIXEDATOM ENDPLUMED ANGLE UPPER_WALLS TORSION FIT_TO_TEMPLATE COORDINATION DISTANCES OPES_METAD DISTANCE	bias colvar setup function core pytorch multicolvar vatom opes generic
21.023	Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling	methods	enhanced sampling, collective variables, machine learning	Jakub Rydzewski	UNITS PRINT DISTANCE TORSION ENERGY INCLUDE CUSTOM BIASVALUE REWEIGHT_METAD METAD CONSTANT	bias colvar setup function generic
21.013	Role of vibrational excitation in heterogeneous catalysis	chemistry	catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption	Kristof Bal	UNITS LOWER_WALLS CONVERT_TO_FES BF_CHEBYSHEV OPT_AVERAGED_SGD RESTRAINT UWALLS FLUSH TD_GRID LOAD REWEIGHT_BIAS DUMPGRID REWEIGHT_METAD METAD DISTANCE ANGLES UPPER_WALLS COMBINE EXTERNAL HISTOGRAM VES_LINEAR_EXPANSION COORDINATIONNUMBER COORDINATION DISTANCES PRINT	symfunc bias colvar setup gridtools ves function multicolvar generic
21.010	Step by Step Strecker Amino Acid Synthesis from Ab Initio Prebiotic Chemistry	chemistry	Strecker reaction, free energy landscape, ab initio molecular dynamics, glycine, prebiotic synthesis	Théo Magrino	PRINT	generic
21.009	Nucleation rates from small scale atomistic simulations and transition state theory	materials	kinetics, free energy barriers, nucleation, droplets, metadynamics	Kristof Bal	UNITS UPPER_WALLS HISTOGRAM FLUSH REWEIGHT_METAD LOAD COORDINATIONNUMBER MOVINGRESTRAINT METAD COMMITTOR CONVERT_TO_FES PRINT DUMPGRID	symfunc bias setup gridtools generic
21.008	Multi-replica biased sampling for photoisomerization processes in conjugated polymers	methods	metadynamics, FEP, replica-exchange	Adriana Pietropaolo	CONSTANT PBMETAD TORSION RESTART MATHEVAL BIASVALUE PRINT WHOLEMOLECULES	bias colvar setup function generic
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 UPPER_WALLS VES_LINEAR_EXPANSION ENERGY ECV_UMBRELLAS_LINE ENVIRONMENTSIMILARITY ECV_MULTITHERMAL_MULTIBARIC RESTART MATHEVAL BF_LEGENDRE OPES_EXPANDED PRINT Q6 TD_UNIFORM VOLUME	symfunc bias colvar setup ves function opes envsim generic
19.076	Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones	bio	molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics	Salvatore Assenza	UNITS GYRATION MOVINGRESTRAINT ENDPLUMED PRINT	bias generic colvar setup
19.075	PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python	other	Python, automatic differentiation	Toni Giorgino	CENTER PRINT RESTRAINT DUMPDERIVATIVES GROUP TORSION CUSTOM ENDPLUMED COMBINE DISTANCE ANGLE	bias colvar function core vatom generic
19.072	SINE hairpin MD+NMR	bio	metadynamics, RNA, NMR	Giovanni Bussi	DISTANCE FLUSH TORSION SORT COM INCLUDE COORDINATION MATHEVAL MAXENT MOLINFO PRINT METAD WHOLEMOLECULES	bias colvar function vatom generic
19.026	Ice Nucleation on Cholesterol Crystals	materials	forward flux sampling, crystal nucleation, water, ice, organic crystals	Gabriele Cesare Sosso	OUTPUT_CLUSTER LOCAL_Q6 CLUSTER_NATOMS DFSCLUSTERING FLUSH MFILTER_MORE ENDPLUMED CONTACT_MATRIX COMMITTOR CLUSTER_WITHSURFACE Q6	symfunc clusters multicolvar generic adjmat

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