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
26.007	Metadynamics Simulations Reveal the Protonation-Dependent Conformational Landscape of GSK-3β Dual Inhibitors	chemistry	metadynamics, ligand unbinding, path CVs, funnel metadynamics	Gian Marco Elisi	ANGLE COMBINE MOLINFO METAD RMSD WHOLEMOLECULES DISTANCE MATHEVAL ENDPLUMED COM UNITS UPPER_WALLS FUNNEL_PS PATHMSD LOWER_WALLS FUNNEL PRINT	generic funnel colvar function setup vatom bias
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	PATH RMSD CENTER DISTANCE CUSTOM ECV_MULTITHERMAL OPES_EXPANDED PATHMSD OPES_METAD_EXPLORE ENERGY UPPER_WALLS GROUP VOLUME COORDINATION LOWER_WALLS PRINT	generic mapping colvar function opes core vatom 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	MOVINGRESTRAINT SAXS MOLINFO METAD WHOLEMOLECULES DISTANCE INCLUDE CENTER GYRATION UPPER_WALLS GROUP PRINT	generic colvar core vatom bias isdb
25.014	Atomic resolution ensembles of intrinsically disordered proteins with Alphafold	bio	bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement	Vincent Schnapka	GROUP BIASVALUE BAIES PRINT	generic bias core isdb
24.030	NMR guided simulation of dsRBD	bio	Metainference, NMR, protein dynamics	Debadutta Patra	MOLINFO WHOLEMOLECULES DISTANCE ENSEMBLE STATS FLUSH RDC ALPHABETA METAINFERENCE GROUP PRINT	generic colvar function core multicolvar isdb
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	DISTANCE OPES_METAD ENERGY UPPER_WALLS COORDINATION PRINT	colvar bias opes generic
24.012	Molecular simulations to investigate the impact of N6-methylation in RNA recognition	bio	metadynamics, alchemistry, RNA modification, RNA:protein interactions	Giovanni Bussi	COMBINE MOLINFO METAD GHBFIX CENTER BIASVALUE DISTANCE UPPER_WALLS GROUP COM COORDINATION LOWER_WALLS DEBUG PRINT	generic colvar function core vatom 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	DISTANCE OPES_METAD FIXEDATOM COORDINATIONNUMBER UNITS FLUSH ZDISTANCES UPPER_WALLS GROUP PRINT	symfunc generic colvar opes setup core vatom bias multicolvar
23.043	Modeling the ferroelectric phase transition in barium titanate with DFT accuracy and converged sampling	materials	Barium Titanate, ferroelectric phase transition, Machine Learning, polarization order parameters	Lorenzo Gigli	SELECT_COMPONENTS TRANSPOSE METAD INCLUDE MATHEVAL FLUSH SUM PRINT	generic valtools function matrixtools 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 METAD MATHEVAL Q4 COORDINATIONNUMBER ENERGY Q6 VOLUME PRINT	symfunc generic colvar function bias
23.034	Urea nucleation in water: do long-range forces matter?	materials	LMF theory, Metadynamics, Nucleation	Ziyue Zou	METAD INCLUDE CENTER LOAD COORDINATIONNUMBER GROUP PRINT	symfunc generic setup core vatom bias
23.015	MPCs aggregation	bio	opes_explore, dimerization, MPCs, self-assembly	Vikas Tiwari	METAD WHOLEMOLECULES CENTER DISTANCE CUSTOM OPES_METAD_EXPLORE COM UPPER_WALLS GROUP LOWER_WALLS COORDINATION PRINT	generic colvar function opes core vatom bias
23.012	JAK2 2D meta-eABF PMF with statistical analysis	bio	2D meta-eABF, path CV, PMF	Istvan Kolossvary	DRR METAD BIASVALUE CUSTOM UPPER_WALLS FLUSH LOWER_WALLS PATHMSD PRINT	generic drr 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	TORSION WHOLEMOLECULES INCLUDE PBMETAD GYRATION COM COORDINATION RESTRAINT PRINT	colvar bias generic vatom
22.025	Bubble nucleation rate predictions in a Lennard-Jones fluid	materials	free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation	Kristof Bal	MOVINGRESTRAINT ANN VOLUME DUMPGRID BIASVALUE LOAD HISTOGRAM CUSTOM RESTRAINT COMMITTOR REWEIGHT_BIAS COORDINATIONNUMBER UNITS FLUSH CONVERT_TO_FES UPPER_WALLS PRINT	generic symfunc gridtools colvar function setup bias annfunc
21.042	Peptoid-mediated Au nanocrystal growth	materials	parallel-bias metadynamics, peptoid, Au	Xin Qi	MOLINFO DISTANCE PBMETAD GYRATION UPPER_WALLS COM PRINT	generic bias 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	COMBINE METAD ENDPLUMED CUSTOM VOLUME COORDINATION PRINT	generic function bias colvar
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	MOLINFO EMMI WHOLEMOLECULES DISTANCE BIASVALUE RESTART UPPER_WALLS GROUP COM PRINT	generic colvar setup core vatom bias isdb
21.039	Deep learning the slow modes for rare events sampling	methods	collective variables, machine learning, slow modes, deep-tica, opes	Luigi Bonati	TORSION MOLINFO RMSD INCLUDE OPES_METAD OPES_EXPANDED PRINT ECV_MULTITHERMAL COMBINE ENDPLUMED LOAD ENVIRONMENTSIMILARITY UNITS CONTACTMAP FLUSH GROUP Q6 DISTANCE ENERGY WHOLEMOLECULES PYTORCH_MODEL VOLUME	generic symfunc colvar function opes setup core pytorch envsim
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	TORSION METAD ENDPLUMED INCLUDE PBMETAD RANDOM_EXCHANGES PRINT	colvar bias generic
21.032	Metal-coupled folding mechanism to metallothionein	bio	parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination	Manuel-Peris Diaz	WHOLEMOLECULES PBMETAD UNITS GROUP COORDINATION	generic colvar setup core bias
21.009	Nucleation rates from small scale atomistic simulations and transition state theory	materials	kinetics, free energy barriers, nucleation, droplets, metadynamics	Kristof Bal	MOVINGRESTRAINT METAD REWEIGHT_METAD DUMPGRID LOAD HISTOGRAM COMMITTOR CONVERT_TO_FES UNITS COORDINATIONNUMBER FLUSH UPPER_WALLS PRINT	symfunc generic gridtools setup bias
21.008	Multi-replica biased sampling for photoisomerization processes in conjugated polymers	methods	metadynamics, FEP, replica-exchange	Adriana Pietropaolo	TORSION WHOLEMOLECULES MATHEVAL BIASVALUE RESTART PBMETAD CONSTANT PRINT	generic colvar function setup bias
21.005	Crystallization Collective Variable	methods	Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA	Tarak Karmakar	MATHEVAL PYTORCH_MODEL LOAD OPES_METAD UPPER_WALLS FLUSH LOWER_WALLS GROUP PRINT	generic function opes setup core pytorch bias
20.025	The role of water in host-guest interaction	bio	ligand binding, water, opes, SAMPL5	Valerio Rizzi	ANGLE ENDPLUMED WHOLEMOLECULES CENTER DISTANCE MATHEVAL PYTORCH_MODEL OPES_METAD FIT_TO_TEMPLATE FIXEDATOM ENERGY UPPER_WALLS GROUP COORDINATION PRINT	generic colvar function opes core pytorch vatom bias
20.022	Unified Approach to Enhanced Sampling	methods	OPES, expanded ensembles, importance sampling	Michele Invernizzi	TORSION MOLINFO RMSD MATHEVAL OPES_EXPANDED UPPER_WALLS ECV_LINEAR PRINT ECV_MULTITHERMAL ENDPLUMED LOAD CUSTOM ENVIRONMENTSIMILARITY UNITS POSITION Q6 ECV_UMBRELLAS_LINE ECV_MULTITHERMAL_MULTIBARIC ENERGY WHOLEMOLECULES VOLUME	generic symfunc colvar function opes setup envsim bias
20.017	FISST	methods	FISST, force, peptide, sampling, tempering	Glen Hocky	MATHEVAL DISTANCE BIASVALUE GYRATION UNITS ENERGY GROUP RESTRAINT FISST PRINT	generic colvar function fisst setup core 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	MOLINFO METAD INCLUDE DISTANCE LOAD WHOLEMOLECULES MATHEVAL FUNCPATHGENERAL BIASVALUE CONTACTMAP CONSTANT COM UPPER_WALLS GROUP LOWER_WALLS PROJECTION_ON_AXIS PRINT	generic colvar function setup core vatom 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	CS2BACKBONE MOLINFO ENDPLUMED WHOLEMOLECULES BIASVALUE FLUSH PBMETAD UPPER_WALLS ANTIBETARMSD LOWER_WALLS ALPHABETA GROUP PRINT	generic secondarystructure core bias multicolvar isdb
19.062	Elucidating molecular design principles for charge-alternating peptides	bio	peptide folding, metadynamics, well-tempered ensemble, parallel tempering	Jim Pfaendtner	METAD WHOLEMOLECULES GYRATION ENERGY PRINT	generic bias colvar
19.061	Diffusion in porous materials	materials	metadynamics, porous materials, diffusion	Kim E. Jelfs	METAD DISTANCE CENTER RESTART UPPER_WALLS GROUP COM LOWER_WALLS PRINT	generic colvar setup core vatom bias
19.058	Constrained MD for maintaining a cavity in a calculation	chemistry	constrained MD, porous molecules, porosity, cavity	Kim Jelfs	MOVINGRESTRAINT DISTANCES RESTART INPLANEDISTANCES FLUSH COM PRINT	generic setup vatom bias multicolvar
19.057	SAXS ensembles using Martini-Beads multi-scale SAXS	methods	metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics	Cristina Paissoni	ANGLE COMBINE SAXS MOLINFO ENDPLUMED WHOLEMOLECULES CENTER INCLUDE MATHEVAL BIASVALUE PBMETAD ENSEMBLE STATS GROUP COORDINATION ALPHABETA PRINT	generic colvar function core vatom bias multicolvar isdb
19.056	maze	methods	maze, ligand unbinding	Jakub Rydzewski	MAZE_LOSS MAZE_SIMULATED_ANNEALING UNITS POSITION MAZE_OPTIMIZER_BIAS PRINT	maze colvar setup generic
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 READ METAD DUMPGRID HISTOGRAM RESTART REWEIGHT_BIAS CONVERT_TO_FES UPPER_WALLS DISTANCE_FROM_CONTOUR PRINT	generic gridtools function setup contour bias
19.037	Scission free energy of organic dyes	chemistry	metadynamics, multiple walkers, matheval/lepton	Paolo Raiteri	METAD MATHEVAL DISTANCE RESTART UNITS UPPER_WALLS FLUSH PRINT	generic colvar function setup bias
19.030	Coarse-Grained MetaDynamics (CG-MetaD)	bio	Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy	Vittorio Limongelli	METAD WHOLEMOLECULES DISTANCE UPPER_WALLS COM LOWER_WALLS PRINT	generic bias colvar vatom
19.016	Succinnic acid gamma polymorph	materials	Succinnic acid, conformers, polymorphs, metadynamics	Matteo Salvalaglio	COMBINE TORSION METAD ENDPLUMED MATHEVAL ENERGY UPPER_WALLS VOLUME LOWER_WALLS CELL PRINT	colvar function bias generic
19.013	RNA FF FITTING	methods	force field, RNA	Giovanni Bussi	MOLINFO TORSION INCLUDE MATHEVAL BIASVALUE PUCKERING CONSTANT	generic function bias colvar
26.009	Exploring the Conformational Landscape of HIV-1 TAR RNA by PT-WTE	bio	RNA, PT-WTE, HIV-1 TAR	Stefano Bosio	PRINT ENERGY GROUP WHOLEMOLECULES METAD MOLINFO	colvar generic bias 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	GROUP BAIES PRINT BIASVALUE	generic core isdb 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	DISTANCE COORDINATION COMBINE RESTRAINT PRINT UPPER_WALLS COM ANGLE COORDINATIONNUMBER FIXEDATOM UNITS GROUP METAD FLUSH DISTANCES LOWER_WALLS	core symfunc colvar bias vatom setup multicolvar generic function
24.008	yCD Metadynamics	bio	volume-based MetaD, path CVs, infrequent MetaD, product release	James McCarty	ENDPLUMED UPPER_WALLS CONTACTMAP FLUSH HISTOGRAM PRINT FIT_TO_TEMPLATE WRAPAROUND DUMPGRID COORDINATION COM INCLUDE FIXEDATOM GROUP MATHEVAL READ WHOLEMOLECULES MOLINFO METAD DISTANCE PATH REWEIGHT_METAD RMSD COMMITTOR CONVERT_TO_FES	core colvar gridtools bias mapping vatom generic function
23.027	CmuMD simulations of NaCl(aq) at NaCl	chemistry	CmuMD, DFS, Q3, Pair Entropy	Aaron Finney	AROUND LOCAL_AVERAGE CLUSTER_NATOMS RESTRAINT PRINT DFSCLUSTERING Q3 CONTACT_MATRIX CLUSTER_DISTRIBUTION LOAD COORDINATIONNUMBER FIXEDATOM UNITS LOCAL_Q3 GROUP DENSITY DUMPGRID HISTOGRAM	core clusters symfunc gridtools adjmat bias vatom setup generic volumes
23.025	Probing ion binding to G-quadruplexes and related events	chemistry	metadynamics, repulsive potential, nucleic acids, G-quadruplexes	Marcelo Poleto	DISTANCE RESTART POSITION PRINT UPPER_WALLS COM WRAPAROUND UNITS GROUP LOWER_WALLS MATHEVAL FIT_TO_TEMPLATE WHOLEMOLECULES FLUSH DISTANCES DUMPATOMS METAD	core colvar bias vatom setup multicolvar generic function
22.045	Binding mode and mechanism of enzymatic polyethylene terephthalate degradation	bio	metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation	Francesco Colizzi	DISTANCE PRINT UPPER_WALLS MOVINGRESTRAINT COM ANGLE LOWER_WALLS WHOLEMOLECULES METAD	colvar generic bias vatom
22.015	Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome	bio	photodynamics, bacteriophytochrome, variationally enhanced sampling	Jakub Rydzewski	VES_LINEAR_EXPANSION PRINT TORSION BF_FOURIER TD_UNIFORM OPT_AVERAGED_SGD	colvar generic ves
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	COORDINATION GYRATION DISTANCE COMBINE UPPER_WALLS COM COORDINATIONNUMBER UNITS LOWER_WALLS FLUSH METAD	symfunc colvar bias vatom setup generic function
21.050	N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity	methods	bio	Isabell Louise Grothaus	DISTANCE CENTER PRINT	colvar generic vatom
21.016	MD SAXS GTPase associated center	bio	metadynamics, RNA, folding, SAXS	Giovanni Bussi	GYRATION PRINT UPPER_WALLS ERMSD MOLINFO CUSTOM INCLUDE SAXS GROUP WHOLEMOLECULES METAD LOWER_WALLS	core colvar bias generic isdb function
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
20.030	Converging experimental and computational views of the knotting mechanism of the smallest knotted protein	bio	phi-values, transition state, knotted proteins	Cristina Paissoni	STATS COORDINATION COMBINE RESTRAINT PRINT WHOLEMOLECULES MOLINFO	colvar generic bias function
19.054	MetaFEP	methods	metadynamics, chemistry, free energy perturbation	GiovanniMaria Piccini	DISTANCE COMBINE PRINT UPPER_WALLS ENERGY UNITS LOWER_WALLS FLUSH METAD	colvar bias setup generic function
19.026	Ice Nucleation on Cholesterol Crystals	materials	forward flux sampling, crystal nucleation, water, ice, organic crystals	Gabriele Cesare Sosso	ENDPLUMED CLUSTER_NATOMS DFSCLUSTERING COMMITTOR CONTACT_MATRIX LOCAL_Q6 CLUSTER_WITHSURFACE MFILTER_MORE Q6 OUTPUT_CLUSTER FLUSH	clusters symfunc adjmat multicolvar generic
19.024	PT-MetaD-WTE	methods	metadynamics, WTE, trp cage, PT	Jim Pfaendtner	COORDINATION EXTERNAL ENERGY GROUP METAD	colvar core bias
19.017	Ligand binding pathways exploration	bio	metadynamics, ligand binding	Riccardo Capelli	HISTOGRAM COORDINATION ENDPLUMED POSITION PRINT UPPER_WALLS COM REWEIGHT_METAD WRAPAROUND GROUP CONVERT_TO_FES MATHEVAL FIT_TO_TEMPLATE WHOLEMOLECULES READ FLUSH DUMPGRID METAD	core colvar gridtools bias vatom generic function
25.030	Committor Regularization	methods	metadynamics, enhanced sampling, mlcvs, committor, machine learning	Florian Dietrich	UNITS PRINT METAD MOVINGRESTRAINT	bias setup generic
25.029	Energetic Constraints in the Enzymatic Depolymerization of Crystalline PET from enhanced molecular simulations	bio	HREX-Metadynamics, PETase, crystalline PET, amorphous PET, conformational ensembles, substrate binding, chain detachment	Ania Di Pede-Mattatelli and Francesco Colizzi	HISTOGRAM COM WHOLEMOLECULES CONVERT_TO_FES LOWER_WALLS MOLINFO UPPER_WALLS FIXEDATOM DUMPGRID DISTANCE METAD REWEIGHT_BIAS PRINT	gridtools vatom generic bias colvar
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	COM FUNNEL_PS LOWER_WALLS FUNNEL UPPER_WALLS METAD PRINT	vatom bias funnel 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	WHOLEMOLECULES EMMIVOX MOLINFO GROUP BIASVALUE PRINT	core isdb bias generic
25.012	A Machine Learning-Driven, Probability-Based Approach to Enzyme Catalysis	bio	enzyme catalysis, transition state, structure-activity relationship, free energy surface, reaction mechanism, water, alpha-amylase, sugar, QM/MM MD, OPES, committor function, machine learning	Sudip Das	UNITS COMBINE CELL COORDINATION OPES_METAD MATHEVAL INCLUDE POSITION ENERGY CUSTOM TORSION FLUSH DISTANCE BIASVALUE PRINT LOAD	function opes setup generic bias colvar
25.009	Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water	chemistry	metadynamics, nitrate photolysis	Kam-Tung Chan	HISTOGRAM REWEIGHT_METAD COORDINATION READ UPPER_WALLS CUSTOM DUMPGRID GROUP FLUSH DISTANCE METAD PRINT RESTART	function gridtools setup generic bias core colvar
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	MOVINGRESTRAINT MOLINFO TORSION PUCKERING RESTRAINT DISTANCE METAD PRINT RESTART	colvar bias setup generic
24.034	Umbrella sampling of ion in transporter SLC26A7	bio	umbrella sampling, transporter, ions	Xiaoli Lu	UNITS POSITION RESTRAINT PRINT	colvar bias setup generic
24.022	Integrating Path Sampling with Enhanced Sampling for Rare-event Kinetics	methods	OPES Flooding, Weighted Ensemble, Metadynamics, Kinetics, Infrequent Metadynamics, Integrated Sampling	Dhiman Ray	COMBINE ENDPLUMED MATHEVAL GROUP PRINT WHOLEMOLECULES CUSTOM CONTACTMAP FIXEDATOM RMSD METAD COMMITTOR COORDINATION OPES_METAD CENTER MOLINFO FIT_TO_TEMPLATE UPPER_WALLS TORSION DISTANCE ANGLE	function opes vatom generic bias core colvar
24.004	Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables	materials	metadynamics, nucleation, machine learning	Ziyue Zou	INCLUDE GROUP LOAD METAD PRINT RESTART	core bias setup generic
23.046	Lasso Peptides - HLDA CV	bio	metadynamics, protein folding, HLDA, harmonic	Gabriel da Hora	UNITS WHOLEMOLECULES COMBINE DISTANCE METAD PRINT	function setup generic bias colvar
23.044	Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition	materials	metadynamics, interlocked molecules	Luigi Leanza	HISTOGRAM ENDPLUMED CONVERT_TO_FES COORDINATION READ DUMPGRID GROUP METAD PRINT COMMITTOR	gridtools generic bias core colvar
23.040	Supramolecular capsules assembly dynamics	chemistry	Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics	Riccardo Capelli	UNITS WHOLEMOLECULES COM CENTER DISTANCES POSITION CUSTOM GROUP FLUSH DISTANCE METAD PRINT	function vatom setup generic multicolvar bias core colvar
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 CONSTANT LOWER_WALLS CENTER UPPER_WALLS MATHEVAL DISTANCE METAD BIASVALUE PRINT	function vatom generic bias colvar
23.033	DNA G-quadruplex and G-hairpin folding with ST-metaD protocol	bio	DNA, G4, GQ, quadruplex, hairpin, folding, metadynamics, REST2, ST-metaD	Pavlína Pokorná	COMBINE WHOLEMOLECULES GHBFIX COORDINATION MOLINFO BIASVALUE METAD ERMSD PRINT	colvar function bias generic
23.023	Rational design of novel biomimetic sequence-defined polymers for mineralization applications	methods	metadynamics, surface binding, biomimetic mineralization	Kaylyn Torkelson	COM COORDINATION UPPER_WALLS GYRATION DISTANCE PBMETAD PRINT	colvar vatom bias generic
23.017	How and When Does an Enzyme React? Unraveling α-Amylase Catalytic Activity with Enhanced Sampling Techniques	bio	enzymatic reaction discovery, reaction mechanism, catalysis, ligand-binding modes, water, alpha-amylase, sugar, QM/MM MD, OPES, OPES explore, graph CV, machine learning, Deep TDA CV, path CV	Sudip Das	PYTORCH_MODEL UNITS WHOLEMOLECULES PATH COORDINATION OPES_METAD LOWER_WALLS CENTER OPES_METAD_EXPLORE FIT_TO_TEMPLATE UPPER_WALLS FIXEDATOM CUSTOM TORSION GROUP DISTANCE PRINT	pytorch function mapping opes vatom setup generic bias core colvar
23.001	Quantum phase diagram of water	chemistry	Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella	Sigbjørn-Løland Bore	ECV_UMBRELLAS_LINE LOWER_WALLS UPPER_WALLS ENVIRONMENTSIMILARITY INCLUDE OPES_EXPANDED PRINT RESTART	opes setup generic envsim bias
22.038	Enhanced Sampling Aided Design of Molecular Photoswitches	chemistry	reaction discovery, OPES explore, graph CV	Umberto Raucci	PYTORCH_MODEL UNITS COORDINATION OPES_METAD_EXPLORE CUSTOM PRINT	pytorch function opes setup generic colvar
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	CELL LOWER_WALLS DRMSD UPPER_WALLS MATHEVAL CUSTOM METAD PRINT COMMITTOR	colvar function bias generic
22.031	Rare Event Kinetics from Adaptive Bias Enhanced Sampling	methods	OPES Flooding, Kinetics, Rate, OPES, Machine Learning	Dhiman Ray	PYTORCH_MODEL COMBINE ENDPLUMED CONSTANT POSITION ENERGY GROUP PRINT UNITS WHOLEMOLECULES CUSTOM BIASVALUE CONTACTMAP RMSD COMMITTOR OPES_METAD MOLINFO INCLUDE TORSION DISTANCE	pytorch function opes setup generic bias core colvar
22.030	Mixing physics across temperatures with generative artificial intelligence	methods	REMD, Generative AI, DDPM	Yihang Wang	WHOLEMOLECULES TORSION PRINT	colvar generic
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
22.019	Exploring aspartic protease inhibitor binding to design selective antimalarials	bio	ligand binding, loop opening, path CV, funnel metadynamics, drug development	Raitis Bobrovs	COM WHOLEMOLECULES FUNNEL_PS LOWER_WALLS FUNNEL UPPER_WALLS PATHMSD DISTANCE METAD PRINT	funnel vatom generic bias colvar
21.051	Automatic learning of hydrogen-bond fixes in an AMBER RNA force field	methods	force field, RNA	Giovanni Bussi	COMBINE WHOLEMOLECULES COORDINATION MOLINFO BIASVALUE METAD ERMSD PRINT	colvar function bias generic
21.049	Multiple-path-metadynamics and PathMaps	methods	path-CV, metadynamics, multiple-walker, multiple paths, pathmap	Alberto Pérez-de-Alba-Ortíz	UNITS COMBINE ENSEMBLE CONSTANT MOVINGRESTRAINT LOWER_WALLS UPPER_WALLS TORSION CUSTOM RESTRAINT LOAD METAD PRINT	function setup generic bias 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 FIXEDATOM TORSION METAD PRINT	colvar vatom bias generic
21.028	From Enhanced Sampling to Reaction Profiles	methods	collective variables, multi-state, machine learning, Deep-TDA	Enrico Trizio	PYTORCH_MODEL ENDPLUMED MATHEVAL GROUP PRINT UNITS WHOLEMOLECULES LOWER_WALLS DISTANCES FIXEDATOM COORDINATION OPES_METAD CENTER FIT_TO_TEMPLATE UPPER_WALLS TORSION LOAD DISTANCE ANGLE	pytorch function opes vatom setup generic multicolvar bias core colvar
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 ALPHARMSD LOWER_WALLS MOLINFO UPPER_WALLS MATHEVAL INCLUDE ENERGY DISTANCE METAD PRINT	function generic bias colvar secondarystructure
21.026	Probing allosteric regulations with coevolution-driven molecular simulations	bio	metadynamics, coevolution, allostery, adenylate cyclase	Francesco Colizzi	UNITS WHOLEMOLECULES COM UPPER_WALLS PATHMSD DISTANCE METAD PRINT	vatom setup generic bias colvar
21.023	Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling	methods	enhanced sampling, collective variables, machine learning	Jakub Rydzewski	UNITS REWEIGHT_METAD CONSTANT INCLUDE CUSTOM ENERGY TORSION DISTANCE METAD BIASVALUE PRINT	function setup generic bias colvar
21.014	how to determine statistically accurate conformational ensembles	bio	metadynamics, metainference, errors, cv, SAXS, ensemble determination	Cristina Paissoni	WHOLEMOLECULES CONTACTMAP ENSEMBLE MOLINFO CENTER ALPHABETA ANTIBETARMSD SAXS BIASVALUE STATS TORSION GYRATION METAD PBMETAD PRINT	function isdb vatom generic multicolvar bias colvar secondarystructure
20.028	Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane	bio	metadynamics, KRas-4B, anionic membrane	Huixia Lu	CENTER FIT_TO_TEMPLATE DISTANCE METAD PRINT RESTART	vatom setup generic bias colvar
20.019	Systematic finite-temperature reduction of crystal energy landscapes	materials	crystals, organics, structure prediction	Matteo Salvalaglio	CELL LOWER_WALLS UPPER_WALLS MATHEVAL ENERGY VOLUME METAD PRINT	colvar function bias generic
20.008	Simulating solvation and acidity in complex mixtures with first-principles accuracy. The case of CH3SO3H and H2O2 in phenol	chemistry	proton trasfer, metadynamics	Kevin Rossi	UNITS COORDINATION DISTANCES CUSTOM METAD PRINT	function setup generic multicolvar bias colvar
19.074	Asymmetric base pair opening in nucleic acids	bio	double helix, DNA, RNA, unwindability	Giovanni Bussi	WHOLEMOLECULES ENDPLUMED COORDINATION LOWER_WALLS RESTRAINT DISTANCE	colvar bias generic
19.065	Molecular Enhanced Sampling with Autoencoders	methods	enhanced sampling, collective variables, deep learning	Wei Chen	COM COMBINE POSITION RESTRAINT ANN	function vatom annfunc bias colvar
19.053	Capillary fluctuations with PLUMED	methods	nucleation, surface tension, capillary fluctuations	Gareth Tribello	UNITS MORE_THAN FIND_CONTOUR_SURFACE FOURIER_TRANSFORM FCCUBIC CENTER MULTICOLVARDENS DUMPGRID GROUP	contour function gridtools vatom setup symfunc core fourier
19.051	Solid liquid interfacial free energy out of equilibrium	materials	metadynamics, nucleation, surface excess free energy	Gareth Tribello	UNITS ENDPLUMED CELL AROUND FCCUBIC LOWER_WALLS UPPER_WALLS METAD PRINT	setup generic symfunc bias colvar volumes
19.048	Understanding Ligand Binding Selectivity in a Prototypical GPCR Family	bio	metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding	Francesco Gervasio	COM WHOLEMOLECULES CONSTANT LOWER_WALLS UPPER_WALLS MATHEVAL DISTANCE METAD BIASVALUE PRINT	function vatom generic bias colvar
19.043	Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA)	methods	metadynamics, chemistry, HLDA	GiovanniMaria Piccini	UNITS COMBINE DISTANCES UPPER_WALLS FLUSH DISTANCE METAD PRINT RESTART	function setup generic multicolvar bias colvar
19.039	Funnel Metadynamics	bio	funnel-metadynamics, absolute binding free energy, ligand-receptor complexes	Vittorio Limongelli	COM WHOLEMOLECULES RMSD FUNNEL_PS LOWER_WALLS FUNNEL UPPER_WALLS DISTANCE METAD PRINT	funnel vatom generic bias colvar
19.025	Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide	bio	metainference, NMR, protein dynamics, force-fields	Carlo Camilloni	RDC WHOLEMOLECULES ENDPLUMED ENSEMBLE CS2BACKBONE MOLINFO METAINFERENCE PBMETAD STATS TORSION FLUSH BIASVALUE PRINT JCOUPLING GYRATION	function isdb generic bias colvar
19.023	RECT	methods	metadynamics, replica exchange	Giovanni Bussi	WHOLEMOLECULES TORSION GYRATION METAD PRINT	colvar bias generic
19.022	eABF simulation of NANMA (alanine dipeptide)	methods	eABF, DRR, alanine dipeptide	Haochuan Chen	DRR PRINT TORSION	drr colvar generic
19.018	Excited state FEP/Metadynamics simulations	chemistry	metadynamics, FEP, excited states, conjugated polymers, torsional potential	Adriana Pietropaolo	WHOLEMOLECULES CONSTANT MATHEVAL TORSION METAD BIASVALUE PRINT	colvar function bias generic
19.011	Automatic Gradient Computation for Collective Variables	other	gradient, differentiation, curvature	Toni Giorgino	ENDPLUMED	generic
26.010	Solvation-Mediated Ammonia Synthesis in a Nanoheterogeneous Liquid Alloy	materials	OPES, Catalysis, Ammonia Synthesis	Axel Tosello Gardini	GROUP INCLUDE OPES_METAD_EXPLORE OPES_METAD CUSTOM UNITS COORDINATIONNUMBER PRINT FLUSH COORDINATION UPPER_WALLS DISTANCES DISTANCE	opes symfunc core colvar multicolvar function generic setup bias
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	FIXEDATOM GROUP OPES_METAD_EXPLORE CENTER WHOLEMOLECULES FIT_TO_TEMPLATE MATHEVAL COORDINATION ANGLE PRINT UPPER_WALLS ENERGY DISTANCE	opes vatom core colvar function generic bias
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	ECV_MULTITHERMAL GROUP OPES_METAD_EXPLORE CENTER CUSTOM DISTANCES GHOST PRINT COORDINATION LOWER_WALLS RMSD PATHMSD ENERGY UPPER_WALLS OPES_EXPANDED DISTANCE	opes vatom core multicolvar colvar function generic bias
24.029	Combination of OPES and OPES-Explore	methods	OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin	Dhiman Ray	FIXEDATOM GROUP FLUSH RMSD ENERGY COMBINE METAD PYTORCH_MODEL CENTER LOWER_WALLS DISTANCE ENDPLUMED INCLUDE MOLINFO CONTACTMAP PRINT COORDINATION POSITION UPPER_WALLS BIASVALUE OPES_METAD_EXPLORE OPES_METAD CUSTOM WHOLEMOLECULES UNITS FIT_TO_TEMPLATE MATHEVAL	opes pytorch vatom core colvar function generic setup bias
24.006	Water vapor condensation	chemistry	metadynamics, homogeneous condensation, chemical potential	Shenghui Zhong	DFSCLUSTERING CLUSTER_NATOMS UNITS COORDINATIONNUMBER PRINT CONTACT_MATRIX UPPER_WALLS METAD CLUSTER_PROPERTIES	symfunc adjmat clusters generic setup bias
24.003	Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations	chemistry	steered molecular dynamics, foldamers, peptoids, bio-inspired	Kaylyn Torkelson	MOVINGRESTRAINT INCLUDE COM WHOLEMOLECULES PRINT COORDINATION ALPHABETA GYRATION DISTANCE TORSION	vatom colvar multicolvar generic bias
24.002	Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes	chemistry	metadynamics, ligand design, solvent extraction	Xiaoyu Wang	UNITS PRINT METAD RESTART TORSION	setup bias generic colvar
23.020	FEP simulations of ATOX1 homodimer	chemistry	parallel bias metadynamics, FEP, free-energy of metal ion dissociation	Adriana Pietropaolo	PBMETAD BIASVALUE WHOLEMOLECULES PRINT MATHEVAL ANGLE CONSTANT DISTANCE	function bias generic colvar
23.008	PBMetaD simulations of Histatin5	bio	metadynamics, IDP, Rg, PPII	Francesco Pesce	PBMETAD GROUP MOLINFO WHOLEMOLECULES PRINT GYRATION TORSION	core bias generic colvar
23.004	Melting curves of ice polymorphs in the vicinity of the liquid-liquid critical point	chemistry	water, liquid-liquid transition, second critical point, ice, polymorphs, melting curves, environment similarity, opes, density-functional theory, scan, machine learning potential	Pablo Piaggi	ECV_UMBRELLAS_LINE HISTOGRAM PRINT LOWER_WALLS OPES_EXPANDED ENVIRONMENTSIMILARITY UPPER_WALLS DUMPGRID RESTART	opes envsim generic setup bias gridtools
22.043	Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES	bio	OPES, RNA, Tetraloop, Folding	Gül Zerze	ECV_MULTITHERMAL WHOLEMOLECULES ECV_UMBRELLAS_LINE PRINT CONTACTMAP ENERGY OPES_EXPANDED	opes generic colvar
22.035	Deciphering the alphabet of disorder — Glu and Asp act differently on local but not global properties	bio	intrinsically disordered proteins, parallel bias metadynamics, protein	Kresten Lindorff-Larsen	PBMETAD MOLINFO WHOLEMOLECULES GYRATION TORSION	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	BIASVALUE COM CUSTOM UNITS PRINT FLUSH DRR METAD DISTANCE	drr vatom colvar function generic setup bias
21.047	Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations	materials	pair entropy, metadynamics, ves, solids, crystallization	Pablo Piaggi	PAIRENTROPY BF_LEGENDRE VOLUME VES_LINEAR_EXPANSION PRINT TD_WELLTEMPERED OPT_AVERAGED_SGD ENERGY METAD RESTART COMBINE LOAD	ves colvar function generic setup bias gridtools
21.031	Photo-switchable sulfonulureas in KATP channel	bio	metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels	Katarzyna Walczewska-Szewc	COM WHOLEMOLECULES UNITS PRINT LOWER_WALLS UPPER_WALLS METAD DISTANCE	vatom colvar generic setup bias
21.025	Computational and biochemical analysis of type IV pilus dynamics and stability	bio	molecular dynamics, calcium binding, Type IV pilus	Yasaman Karami	LOWER_WALLS DISTANCE UPPER_WALLS PRINT	bias generic colvar
21.006	OPES, On-the-fly Probability Enhanced Sampling Method	methods	opes, alanine dipeptide, well-tempered, multithermal, multiumbrella	Michele Invernizzi	ECV_MULTITHERMAL ENDPLUMED OPES_METAD ECV_UMBRELLAS_LINE PRINT ENERGY OPES_EXPANDED TORSION	opes generic colvar
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	BF_LEGENDRE ECV_MULTITHERMAL_MULTIBARIC TD_UNIFORM VOLUME VES_LINEAR_EXPANSION ECV_UMBRELLAS_LINE PRINT MATHEVAL OPT_AVERAGED_SGD ENVIRONMENTSIMILARITY UPPER_WALLS ENERGY OPES_EXPANDED RESTART Q6	opes symfunc ves colvar envsim function generic setup bias
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	CONVERT_TO_FES REWEIGHT_METAD ENDPLUMED COM ABMD HISTOGRAM PRINT MATHEVAL LOWER_WALLS UPPER_WALLS COMBINE METAD DUMPGRID READ DISTANCE	vatom colvar function generic bias gridtools
19.083	Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis	chemistry	metadynamics, chemical reactions, reaction discovery	Valerio Rizzi	GROUP ENDPLUMED RESTART UNITS COORDINATIONNUMBER PRINT FLUSH UPPER_WALLS METAD DISTANCES COMBINE	symfunc core multicolvar function generic setup 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	HISTOGRAM OPT_AVERAGED_SGD ENERGY COMBINE VES_LINEAR_EXPANSION REWEIGHT_BIAS LOWER_WALLS DUMPGRID BF_LEGENDRE OPT_DUMMY VOLUME PRINT TD_WELLTEMPERED UPPER_WALLS READ Q6 TD_MULTITHERMAL_MULTIBARIC CONVERT_TO_FES CELL MATHEVAL REWEIGHT_TEMP_PRESS RESTART LOAD	symfunc ves colvar function generic setup bias gridtools
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	ENDPLUMED COORDINATIONNUMBER PRINT LOWER_WALLS UPPER_WALLS ENERGY METAD GYRATION DISTANCES	symfunc multicolvar colvar generic bias
19.072	SINE hairpin MD+NMR	bio	metadynamics, RNA, NMR	Giovanni Bussi	TORSION INCLUDE COM MAXENT MOLINFO WHOLEMOLECULES PRINT MATHEVAL COORDINATION FLUSH SORT METAD DISTANCE	vatom colvar function generic bias
19.068	Rethinking Metadynamics	methods	metadynamics, opes, convergence	Michele Invernizzi	ENDPLUMED OPES_METAD UNITS PRINT POSITION METAD EXTERNAL TORSION	opes colvar generic setup bias
19.010	Multi-domain protein dynamics	bio	metainference, NMR, protein dynamics	Carlo Camilloni	DHENERGY PBMETAD ENSEMBLE GROUP RDC ENDPLUMED DISTANCE CENTER METAINFERENCE MOLINFO WHOLEMOLECULES RESTRAINT PRINT STATS UPPER_WALLS ALPHABETA DIHCOR TORSION	vatom core isdb colvar function multicolvar generic bias
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	GROUP MATHEVAL COORDINATION LOWER_WALLS COMBINE CENTER WHOLEMOLECULES DISTANCE METAD UPPER_WALLS GYRATION PRINT	colvar core vatom bias generic function
25.024	Sampling glycan-glycan interactions for B22 calculations	bio	B22, glycan, carbohydrates, distance, REST2, metadynamics, RECT, replica exchange	Isabell Louise Grothaus	RESTRAINT COM COMBINE METAD DISTANCE POSITION PRINT	colvar bias vatom generic 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	ENERGY OPES_EXPANDED GROUP ECV_MULTITHERMAL COORDINATION RMSD MOLINFO COMBINE CENTER GHOST OPES_METAD_EXPLORE DISTANCE CUSTOM PRINT	colvar core opes vatom generic function
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	DISTANCES TORSIONS DUMPMULTICOLVAR SMAC PRINT	generic symfunc multicolvar
25.004	Machine Learning-Driven Molecular Dynamics Unveil a Bulk Phase Transformation Driving Ammonia Synthesis on Barium Hydride	chemistry	OPES, OPES flooding, Catalysis, Ammonia Synthesis	Axel Tosello Gardini	GROUP UNITS COMMITTOR DISTANCES FIXEDATOM ZDISTANCES DISTANCE UPPER_WALLS OPES_METAD COORDINATIONNUMBER CUSTOM FLUSH PRINT	colvar symfunc opes setup multicolvar vatom bias generic function core
25.001	RNA G-quadruplex folding with ST-metaD protocol	bio	RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD	Pavlína Pokorná	MOLINFO COMBINE WHOLEMOLECULES METAD ERMSD	bias generic colvar function
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 GROUP PATH PYTORCH_MODEL COORDINATION FIT_TO_TEMPLATE LOWER_WALLS CENTER WHOLEMOLECULES FIXEDATOM RESTART DISTANCE UPPER_WALLS OPES_METAD CUSTOM PRINT	colvar core opes setup pytorch bias vatom generic function mapping
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	generic colvar
23.041	Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference	methods	EMMIVox, cryo-EM, single-structure refinement, ensemble refinement, Bayesian inference, B-factors, structural ensembles	Samuel Hoff	GROUP MOLINFO WRAPAROUND WHOLEMOLECULES DISTANCE EMMIVOX UPPER_WALLS BIASVALUE PRINT INCLUDE	colvar core bias generic isdb
23.037	Estimating binding free energy of solid binding peptides without extensive sampling	bio	metadynamics, solid binding peptides	Xin Qi	PBMETAD COM LOWER_WALLS MOLINFO DISTANCE UPPER_WALLS GYRATION PRINT	bias vatom generic colvar
23.032	Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics	bio	metadynamics, tSNE, neural network, machine learning, trp-cage, folding	Vojtech Spiwok	FIT_TO_TEMPLATE COMBINE ANN WHOLEMOLECULES MOLINFO ALPHARMSD METAD POSITION PRINT	colvar bias secondarystructure generic annfunc 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	ENERGY GROUP MATHEVAL COM LOWER_WALLS UNITS DISTANCES COMMITTOR FIXEDATOM DISTANCE UPPER_WALLS ZDISTANCES OPES_METAD COORDINATIONNUMBER CUSTOM FLUSH PRINT	colvar core symfunc opes setup multicolvar vatom bias generic function
23.022	A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar	methods	collective variables, machine learning, toy model	Enrico Trizio	PYTORCH_MODEL LOWER_WALLS UNITS UPPER_WALLS BIASVALUE OPES_METAD CUSTOM POSITION PRINT ENDPLUMED	colvar opes setup pytorch bias generic function
23.019	Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors	bio	binding pathway, binding energy, sketch-map, drug development	Raitis Bobrovs	SKETCHMAP VORONOI DISSIMILARITIES LANDMARK_SELECT_FPS COM WHOLEMOLECULES PATHMSD VSTACK METAD UPPER_WALLS DISTANCE COLLECT_FRAMES CUSTOM SKETCHMAP_PROJECTION TRANSPOSE PRINT	landmarks matrixtools valtools colvar vatom bias generic dimred function
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	DRR LOWER_WALLS UNITS PATHMSD METAD TIME UPPER_WALLS BIASVALUE CUSTOM FLUSH PRINT	drr colvar setup bias generic function
23.000	Atomistic simulations of RNA tetraloop folding via PTWTE-WTM	bio	parallel tempering, well-tempered metadynamics, well-tempered ensemble, RNA, Tetraloop, Folding	Gül Zerze	ENERGY LOWER_WALLS WHOLEMOLECULES CONTACTMAP METAD UPPER_WALLS PRINT	bias generic colvar
22.041	Skipping the Replica Exchange Ladder with Normalizing Flows	methods	OPES, alanine, normalizing flows, replica exchange	Michele Invernizzi	ENERGY TORSION OPES_EXPANDED ECV_MULTITHERMAL UNITS OPES_METAD POSITION PRINT ENDPLUMED	generic opes setup colvar
22.026	Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification	materials	Peptoid, silica	Jim Pfaendtner	PBMETAD COM MOLINFO DISTANCE UPPER_WALLS GYRATION PRINT	bias vatom generic colvar
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	vatom generic colvar
22.007	Characterization of a natural variant of human NDP52 and its functional consequences on mitophagy	bio	metadynamics, well-tempered, protein-protein interactions, disordered proteins, mutations autophagy	Elena Papaleo	ALPHABETA TORSION COORDINATION MOLINFO ALPHARMSD WHOLEMOLECULES DISTANCE UPPER_WALLS METAD FLUSH PRINT ANGLE	colvar multicolvar bias secondarystructure generic
22.004	Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques	chemistry	reaction discovery, OPES, collective variables	Umberto Raucci	PYTORCH_MODEL GROUP MATHEVAL COORDINATION COM LOWER_WALLS UNITS OPES_METAD_EXPLORE DISTANCE UPPER_WALLS LOAD OPES_METAD CUSTOM PRINT	colvar core opes setup pytorch vatom bias generic function
21.017	All-atom simulations of the Vav1 AD construct	bio	metadynamics, parallel-bias, well-tempered	Simone Orioli	PBMETAD ALPHABETA GROUP REWEIGHT_BIAS MOLINFO ALPHARMSD WHOLEMOLECULES CONTACTMAP RESTART METAD PRINT	colvar setup multicolvar bias secondarystructure generic core
20.033	COVID-19 Spike protein opening transition mechanism	bio	EMMI, CryoEM, COVID-19, Spike, Metainference	Faidon Brotzakis	CONVERT_TO_FES GROUP EMMI RMSD MOLINFO DISTANCES WHOLEMOLECULES READ BIASVALUE HISTOGRAM PRINT DUMPGRID	colvar core multicolvar bias generic gridtools isdb
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 generic colvar
20.018	Free energy barriers from biased molecular dynamics simulations	methods	kinetics, free energy barriers, chemical reactions, nucleation, metadynamics	Kristof Bal	ENERGY UNITS COMBINE CENTER DISTANCE PAIRENTROPY COORDINATION SPRINT PRINT DUMPGRID VOLUME CONVERT_TO_FES REWEIGHT_BIAS UPPER_WALLS FLUSH DENSITY LOWER_WALLS LOCAL_AVERAGE METAD CONTACT_MATRIX LOAD REWEIGHT_METAD HISTOGRAM COORDINATIONNUMBER Q6	adjmat colvar symfunc setup vatom bias generic sprint volumes gridtools function
20.004	Data-driven collective variables for enhanced sampling	methods	collective variables, machine learning, deep-lda	Luigi Bonati	PYTORCH_MODEL TORSION GROUP MATHEVAL COM LOWER_WALLS UNITS DISTANCE UPPER_WALLS OPES_METAD LOAD FLUSH PRINT ENDPLUMED	colvar core opes setup pytorch vatom bias generic function
20.002	Exploring conformational dynamics of the extracellular Venus flytrap domain of the GABAB receptor, a path-metadynamics study	bio	Metadynamics, path CVs	Riccardo Ocello	GROUP MOLINFO WHOLEMOLECULES PATHMSD METAD RESTART UPPER_WALLS PRINT	colvar setup bias generic core
19.082	Ammonia Borane Dehydrogenation	chemistry	metadynamics, reaction discovery, hydrogen production, chemistry	Valerio Rizzi	GROUP UNITS COMBINE RESTART METAD COORDINATIONNUMBER EXTERNAL FLUSH PRINT ENDPLUMED	symfunc core setup bias generic function
19.067	Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways	bio	metadynamics, ligand unbinding	Jakub Rydzewski	LOWER_WALLS UNITS PATHMSD UPPER_WALLS METAD RESTART PRINT	bias generic setup colvar
19.060	Neural networks-based variationally enhanced sampling	methods	ves, neural networks	Luigi Bonati	ENERGY TORSION Q6 ENVIRONMENTSIMILARITY UNITS LOAD POSITION PRINT ENDPLUMED	symfunc colvar setup generic envsim
19.032	Chemical reaction in solution using path collective variables based on coordination patterns	chemistry	chemical reactions, solutions, metadynamics, coordination patterns	Fabio Pietrucci	PATH DISTANCES RESTART METAD UPPER_WALLS FLUSH PRINT	setup multicolvar bias generic mapping
19.031	Ice nucleation using PIV-based path coordinates	materials	phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics	Silvio Pipolo	CELL LOWER_WALLS FUNCPATHMSD PIV UPPER_WALLS METAD PRINT	colvar bias generic piv function
19.012	Martini-Beads multi-scale SAXS	methods	metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex	Carlo Camilloni	RESTRAINT GROUP RMSD MOLINFO CENTER WHOLEMOLECULES DISTANCE UPPER_WALLS SAXS BIASVALUE STATS PRINT ENDPLUMED INCLUDE	colvar bias vatom isdb generic function core
19.003	EMMI ClpP	bio	metainference, cryo-EM	Max Bonomi	GROUP EMMI MOLINFO BIASVALUE PRINT	bias isdb generic core
19.001	RNA SHAPE	bio	metadynamics, RNA, ligand binding	Giovanni Bussi	LOWER_WALLS MOLINFO COMBINE DISTANCES DISTANCE UPPER_WALLS METAD RANDOM_EXCHANGES ERMSD FLUSH PRINT INCLUDE ANGLE	colvar multicolvar bias generic 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	MATHEVAL COM ENERGY FUNNEL WHOLEMOLECULES GROUP DISTANCE COORDINATION METAD WRAPAROUND PYTORCH_MODEL UPPER_WALLS FUNNEL_PS LOWER_WALLS PRINT RMSD	function pytorch vatom core bias generic colvar funnel
26.000	OPES simulations of disordered proteins	bio	OPES, IDPs	Julian Streit	RESTART OPES_EXPANDED ECV_MULTITHERMAL PRINT ENERGY	generic colvar opes setup
25.022	Imidazole Diffusion in SALEM-2 MOF	materials	OPES, Diffusion, Ring opening, MOFs, Machine Learning Potentials	Sudheesh Kumar Ethirajan	DISTANCES WHOLEMOLECULES GROUP PROJECTION_ON_AXIS DISTANCE UNITS MOLINFO CENTER OPES_METAD ENDPLUMED PRINT	vatom core multicolvar generic colvar opes setup
24.036	Leveraging cryptic ligand envelopes through enhanced molecular simulations	bio	HREX, conformational heterogeneity, drug discovery, ligand binding, plitidepsin, aplidin, ligand-target complexes, cryptic ligand envelope	Francesco Colizzi	HISTOGRAM WHOLEMOLECULES GROUP DISTANCE COORDINATION CONVERT_TO_FES TORSION DUMPGRID ANGLE PRINT	generic gridtools colvar core
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	BIASVALUE RMSD WHOLEMOLECULES GROUP UPPER_WALLS DISTANCE COORDINATION MOLINFO PBMETAD EMMI DUMPATOMS PARABETARMSD CENTER DUMPMASSCHARGE COM PRINT ALPHARMSD	vatom isdb core bias generic colvar secondarystructure
24.026	Constant pH metadynamics of RNA oligomers	bio	metadynamics, pH, RNA	Giovanni Bussi	PUCKERING MOLINFO METAD RESTART TORSION PRINT	bias generic colvar 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	MATHEVAL ECV_MULTITHERMAL WHOLEMOLECULES GROUP DISTANCE COORDINATION OPES_METAD_EXPLORE CENTER FIT_TO_TEMPLATE TORSION ENDPLUMED UPPER_WALLS OPES_EXPANDED FIXEDATOM ANGLE LOWER_WALLS PRINT ENERGY	function vatom core bias generic colvar opes
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 GROUP DISTANCE COMBINE COORDINATION OPES_METAD_EXPLORE RESTART TORSION OPES_EXPANDED ECV_MULTITHERMAL PRINT ENERGY	function core generic colvar opes setup
24.005	Learning Markovian Dynamics with Spectral Maps	methods	spectral map, collective variables, machine learning	Jakub Rydzewski	BIASVALUE CUSTOM DISTANCE UNITS PRINT	function bias generic colvar setup
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	MATHEVAL CUSTOM MOLINFO FLUSH COORDINATION CENTER POSITION WRAPAROUND COM COMMITTOR UPPER_WALLS WHOLEMOLECULES ENDPLUMED LOWER_WALLS OPES_METAD_EXPLORE PRINT BIASVALUE GROUP DISTANCE UNITS OPES_METAD FIT_TO_TEMPLATE TORSION ENERGY	function vatom core bias generic colvar opes setup
23.009	Deep Learning Collective Variables from Transition Path Ensemble	methods	TPI-Deep-TDA, Deep-TDA, Transition Path, OPES, OPES Flooding, Machine Learning, Protein folding, Ligand binding	Dhiman Ray	MATHEVAL CUSTOM MOLINFO PYTORCH_MODEL ANGLE CONTACTMAP COMBINE COORDINATION CENTER UPPER_WALLS COMMITTOR RMSD WHOLEMOLECULES ENDPLUMED INCLUDE LOWER_WALLS PRINT GROUP DISTANCE OPES_METAD FIT_TO_TEMPLATE FIXEDATOM ENERGY	function pytorch vatom core bias generic colvar opes
23.002	Critical comparison of general-purpose collective variables for crystal nucleation	methods	metadynamics, umbrella sampling, commitor, entropy, PIV	Julien Lam	LOCAL_AVERAGE CUSTOM Q6 PAIRENTROPY RESTRAINT UNITS METAD PIV Q4 UPPER_WALLS VOLUME FUNCPATHMSD PRINT ENERGY	function symfunc gridtools bias generic colvar piv setup
22.044	Colloid Crystallisation Analyses	materials	Q4, Q6, Pair Entropy, DFS	Aaron Finney	LOCAL_AVERAGE MFILTER_MORE Q6 GROUP COORDINATIONNUMBER COMBINE LOCAL_Q6 CONTACT_MATRIX Q4 CLUSTER_NATOMS MFILTER_LESS DFSCLUSTERING LOCAL_Q4 PRINT	function symfunc core multicolvar generic clusters adjmat
22.042	Metadynamics of NSP10 and variants	bio	metadynamics, NSP10, crystal structure, variants	Shozeb Haider	TORSION PRINT METAD	bias generic 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	BIASVALUE CUSTOM FLUSH METAD DRR PATHMSD PRINT	function drr bias generic colvar
22.020	Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix–Junction–Helix RNA	bio	RNA force field, Helix-Junction-Helix RNA, SAXS, Well tempered metadynamics	Weiwei He	WHOLEMOLECULES GROUP DISTANCE METAD TORSION COM PRINT	vatom core bias generic colvar
22.017	Water regulates the residence time of Benzamidine in Trypsin	bio	ligand binding, water, opes, benzamidine trypsin, unbinding rates, machine learning, Deep-LDA, Deep-TICA	Narjes Ansari	MATHEVAL CUSTOM COMMITTOR WHOLEMOLECULES GROUP DISTANCE COORDINATION CENTER OPES_METAD FIT_TO_TEMPLATE PYTORCH_MODEL UPPER_WALLS FIXEDATOM LOWER_WALLS PRINT RMSD	function pytorch vatom core bias generic colvar 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	MATHEVAL ZANGLES CUSTOM YANGLES WHOLEMOLECULES UPPER_WALLS ALPHABETA DISTANCE COMBINE MOLINFO METAD TORSION COM XANGLES LOWER_WALLS PRINT	function vatom multicolvar bias generic colvar
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	COM CUSTOM DISTANCE UNITS METAD TORSION UPPER_WALLS LOWER_WALLS PRINT	function vatom bias generic colvar setup
21.033	Multiple-path-metadynamics applied to DNA base-pairing transitions	bio	path-CV, metadynamics, multiple-walker, dna	Alberto Pérez-de-Alba-Ortíz	RESTRAINT CONSTANT COMBINE METAD UPPER_WALLS INCLUDE MOVINGRESTRAINT PRINT	bias generic function
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	ALPHABETA GYRATION DISTANCE COORDINATION METAD PBMETAD TORSION COM INCLUDE PRINT ENERGY	vatom multicolvar generic colvar bias
20.029	High Conformational Flexibility of the E2F1/DP1/DNA complex	bio	SAXS, protein-DNA complex, hySAXS, ensemble determination	Cristina Paissoni	BIASVALUE WHOLEMOLECULES GROUP RESTRAINT DISTANCE ENSEMBLE MOLINFO CENTER STATS SAXS INCLUDE PRINT	function vatom core isdb bias generic colvar
20.023	metadynminer and metadynminer3d	methods	metadynamics, visualization, R	Vojtech Spiwok	TORSION PRINT METAD	bias generic colvar
20.020	Parallel Bias Metadynamics	methods	pbmetad, trp-cage, folding	Max Bonomi	ALPHABETA DIHCOR WHOLEMOLECULES GYRATION COORDINATION MOLINFO PBMETAD INCLUDE PRINT	multicolvar generic colvar bias
20.016	Predicting polymorphism in molecular crystals using orientational entropy	materials	metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy	Pablo Piaggi	GROUP LOAD METAD CENTER UPPER_WALLS VOLUME INCLUDE PRINT	vatom core bias generic colvar setup
20.007	Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics	bio	metadynamics, loop movement, artificial intelligence	Pratyush Tiwary	WHOLEMOLECULES DISTANCE COMBINE METAD MOLINFO RESTART TORSION UPPER_WALLS PRINT RMSD	function bias generic colvar setup
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	MOLINFO CONVERT_TO_FES DUMPGRID REWEIGHT_METAD CONTACTMAP FLUSH COMBINE UPPER_WALLS COM HISTOGRAM READ WHOLEMOLECULES ENDPLUMED FUNCPATHMSD LOWER_WALLS PRINT ABMD DISTANCE METAD	function gridtools vatom bias generic colvar
19.063	Protein-ligand binding through metadynamics with path CVs	bio	metadynamics, path CVs, ligand binding	Mattia Bernetti	WHOLEMOLECULES METAD UPPER_WALLS PATHMSD LOWER_WALLS PRINT	bias generic colvar
19.000	VesDeltaF	methods	VES, convergence, suboptimal CVs	Michele Invernizzi	UNITS LOAD METAD RESTART VES_DELTA_F TORSION ENDPLUMED POSITION PRINT ENERGY	bias generic colvar setup ves
26.008	Ensemble Dynamics	methods	State Exploration, Protein Folding, Drug Binding, Phase Transition	Florian M. Dietrich	CELL DISTANCE BIASVALUE POSITION LOAD OPES_METAD_EXPLORE CUSTOM GROUP TORSION PRINT UNITS	function core setup bias generic opes colvar
25.023	Molecular simulations of Tau-protein oligomers	bio	metadynamics, proteins, aggregation	Giovanni Bussi	RESTRAINT CONTACTMAP REWEIGHT_BIAS METAD RMSD CONVERT_TO_FES FLUSH HISTOGRAM CUSTOM PRINT RESTART DUMPGRID	function setup bias generic gridtools colvar
25.011	Chiral perovskite nucleation	chemistry	metadynamics, chiral perovskites, nucleation	Adriana Pietropaolo	MULTI_RMSD LOWER_WALLS DISTANCE UPPER_WALLS PBMETAD MATHEVAL PRINT RESTART UNITS	function setup bias generic colvar
25.010	Kinetic rates calculation with Ratchet&Pawl MD	methods	kinetics, ligand binding, ABMD, ratchet&pawl MD	Riccardo Capelli	COMMITTOR WHOLEMOLECULES DISTANCE FLUSH ABMD GROUP COM PRINT	core bias vatom generic colvar
25.008	Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting	methods	metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting	Dhiman Ray	MOLINFO WHOLEMOLECULES LOWER_WALLS DISTANCE BIASVALUE CUSTOM METAD OPES_METAD RMSD POSITION UPPER_WALLS ENDPLUMED PYTORCH_MODEL PRINT TORSION GROUP ENERGY UNITS	function core setup bias generic opes pytorch colvar
25.002	M3_PCV-ABMD	chemistry	Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor	Gian Marco Elisi	UPPER_WALLS ENDPLUMED ABMD PRINT UNITS PATHMSD	setup generic bias colvar
24.031	DeepLNE	methods	PATHCV, OPES, OneOPES	Thorben Fröhlking	MOLINFO COORDINATION OPES_EXPANDED ERMSD COMBINE OPES_METAD_EXPLORE VOLUME ECV_MULTITHERMAL PYTORCH_MODEL PRINT RESTART ENERGY	function setup generic opes pytorch colvar
24.028	All-atom simulations of RNA-membrane interactions	bio	metadynamics, membrane, RNA	Giovanni Bussi	MOLINFO SORT LOWER_WALLS WHOLEMOLECULES DISTANCE GYRATION GHOST METAD POSITION UPPER_WALLS COMBINE CENTER DISTANCES MATHEVAL PUCKERING GROUP PRINT	function core bias vatom generic multicolvar 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	MOLINFO COORDINATION WHOLEMOLECULES ANTIBETARMSD GYRATION DISTANCE DIHCOR INCLUDE ALPHARMSD PARABETARMSD COMBINE PBMETAD ENDPLUMED FLUSH GROUP TORSION PRINT	function core bias generic multicolvar secondarystructure colvar
24.017	Absolute Binding Free Energies with OneOPES	methods	protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy	Francesco Gervasio	WHOLEMOLECULES CONTACTMAP LOWER_WALLS UPPER_WALLS INCLUDE METAD ECV_MULTITHERMAL COORDINATION OPES_EXPANDED BIASVALUE PROJECTION_ON_AXIS RMSD ENERGY MOLINFO WRAPAROUND OPES_METAD_EXPLORE MATHEVAL CUSTOM GROUP COM PRINT RESTART TORSION CONSTANT	function core setup bias vatom generic opes colvar
24.016	Cryo-EM guided simulations of ribozyme	bio	metainference, cryo-EM	Giovanni Bussi	MOLINFO WHOLEMOLECULES RESTRAINT BIASVALUE INCLUDE ERMSD EMMIVOX GROUP PRINT	isdb core bias generic colvar
24.009	Weighted Shape Gaussian Mixture Models	bio	metadynamics, clustering	Glen Hocky	TORSION METAD GROUP UNITS PRINT	core setup bias generic 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	MOLINFO CONTACTMAP LOWER_WALLS DISTANCE INCLUDE METAD ALPHARMSD UPPER_WALLS PRINT FUNCPATHMSD PATHMSD	function bias generic secondarystructure colvar
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 DISTANCE BIASVALUE UPPER_WALLS METAD MATHEVAL PRINT CONSTANT	generic function bias colvar
22.040	From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure	bio	SARS-CoV-2, Spike, Omicron	Miłosz Wieczór	WHOLEMOLECULES LOWER_WALLS METAD UPPER_WALLS PCAVARS PRINT	generic bias mapping
22.036	Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction	bio	Well-tempered MetaDynamics with Hamiltonian Replica Exchange	Miroslav Krepl	MOLINFO COORDINATION BIASVALUE UPPER_WALLS METAD COMBINE GHBFIX LOAD FLUSH CUSTOM GROUP PRINT	function core setup bias generic colvar
22.024	Conformational Entropy as a Potential Liability of Computationally Designed Antibodies	bio	metadynamics, conformational entropy, antibody, nanobody	Thomas Löhr	MOLINFO WHOLEMOLECULES ANTIBETARMSD COM ALPHARMSD PBMETAD PRINT ALPHABETA TORSION RESTART	setup bias vatom generic multicolvar secondarystructure colvar
22.023	Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy	bio	CryoEM, MEMMI,EMMI, Metadynamics, Metainference, IAPP, structural ensemble	Faidon Brotzakis	MOLINFO COORDINATION WHOLEMOLECULES TORSION EMMI BIASVALUE UPPER_WALLS RMSD PBMETAD GROUP RESTART COM PRINT	isdb core setup bias vatom 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	UPPER_WALLS OPES_METAD ENVIRONMENTSIMILARITY VOLUME HISTOGRAM CUSTOM PRINT RESTART AROUND DUMPGRID ENERGY	volumes function envsim setup bias generic opes gridtools colvar
22.013	Ligand dissociation from PreQ1 riboswitch	bio	ligand, RNA, metadynamics, pRAVE	Yihang Wang	COMMITTOR MOLINFO WHOLEMOLECULES DISTANCE METAD RMSD COMBINE COORDINATIONNUMBER PRINT COM	function colvar bias vatom generic symfunc
22.006	Peptide framework for screening the effects of amino acids on assembly	bio	metadynamics, peptides	Andrew White	REWEIGHT_BIAS GYRATION INCLUDE METAD COMBINE CONVERT_TO_FES DISTANCES HISTOGRAM GROUP COM DUMPGRID PRINT	function core bias vatom generic gridtools multicolvar colvar
22.003	Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling	methods	opes, metadynamics, reweighting, alanine, muller	Michele Invernizzi	ECV_UMBRELLAS_FILE LOWER_WALLS OPES_EXPANDED BIASVALUE METAD OPES_METAD POSITION UPPER_WALLS PBMETAD OPES_METAD_EXPLORE ENDPLUMED ECV_MULTITHERMAL CUSTOM PRINT TORSION ENERGY UNITS	function setup bias generic opes 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 LOWER_WALLS GYRATION UPPER_WALLS METAD ENDPLUMED GROUP ALPHABETA PRINT	core bias generic multicolvar 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 RMSD DISTANCE	generic colvar
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	MOLINFO COORDINATION LOWER_WALLS WHOLEMOLECULES DIHCOR ANTIBETARMSD GYRATION UPPER_WALLS METAD ALPHARMSD PARABETARMSD GROUP RANDOM_EXCHANGES PRINT ENERGY	core bias generic multicolvar secondarystructure colvar
21.020	Reweighted Jarzynski sampling	methods	free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions	Kristof Bal	UPPER_WALLS ANN METAD OPES_METAD CONVERT_TO_FES REWEIGHT_METAD DUMPGRID RESTRAINT BIASVALUE MOVINGRESTRAINT BF_CHEBYSHEV VES_LINEAR_EXPANSION UNITS COMBINE LOAD COORDINATIONNUMBER CUSTOM OPT_AVERAGED_SGD TD_WELLTEMPERED REWEIGHT_BIAS DISTANCE FLUSH HISTOGRAM PRINT CONSTANT	function annfunc setup colvar bias generic opes gridtools ves symfunc
21.018	Localized Volume-based Metadynamics	bio	LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification	Riccardo Capelli	WHOLEMOLECULES FIXEDATOM READ UPPER_WALLS METAD CONVERT_TO_FES ENDPLUMED REWEIGHT_METAD DUMPGRID COORDINATION RMSD MATHEVAL GROUP COM DISTANCE POSITION FLUSH HISTOGRAM PRINT	function core bias vatom generic gridtools colvar
21.015	Coarse-grained metadynamics and umbrella sampling simulations to investigate interactions of carbohydrate-binding modules with chitin	bio	metadynamics, umbrella sampling, coarse-grained, MARTINI, chitin, carbohydrate-binding module	Gaston Courtade	WHOLEMOLECULES COORDINATION RESTRAINT REWEIGHT_BIAS POSITION METAD CENTER MATHEVAL PRINT RESTART	function setup bias vatom generic colvar
21.001	Substrate recognition and catalysis by glycosaminoglycan sulfotransferases	bio	metadynamics, well-tempered metadynamics, puckering, coordination	Tarsis Ferreira	MOLINFO WHOLEMOLECULES LOWER_WALLS COORDINATION DISTANCE METAD UPPER_WALLS INCLUDE HISTOGRAM REWEIGHT_METAD PUCKERING GROUP RANDOM_EXCHANGES DUMPGRID PRINT ENERGY	core bias generic gridtools colvar
20.024	Gaussian Mixture Based Enhanced Sampling (GAMBES)	methods	enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias	Jayashrita Debnath	LOWER_WALLS DISTANCE UPPER_WALLS COMBINE LOAD DISTANCES PRINT TORSION GROUP ENERGY UNITS	function core setup bias generic multicolvar colvar
20.006	Class B GPCR activation mechanism	bio	metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding	Francesco Gervasio	MOLINFO WHOLEMOLECULES LOWER_WALLS DISTANCE UPPER_WALLS METAD RMSD COMBINE CENTER MATHEVAL PRINT ENERGY	function bias vatom generic colvar
19.077	Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations	materials	metadynamics, peptide-surface binding	Jim Pfaendtner	MOLINFO GYRATION DISTANCE UPPER_WALLS METAD PRINT COM ENERGY	vatom generic bias colvar
19.064	Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations	materials	metadynamics, peptide-surface binding	Jim Pfaendtner	MOLINFO GYRATION DISTANCE METAD UPPER_WALLS PRINT COM ENERGY	vatom 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	BRIDGE MOLINFO WHOLEMOLECULES LOWER_WALLS DISTANCE COM UPPER_WALLS METAD RMSD COMBINE FUNNEL DISTANCES REWEIGHT_METAD GROUP ALPHABETA TORSION PRINT	function core bias vatom generic multicolvar funnel adjmat colvar
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 UPPER_WALLS METAD PRINT COM ENERGY	vatom generic bias 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	RESTRAINT DISTANCE COM GROUP TORSION PRINT	core bias vatom generic colvar
19.014	MIL101(Cr) SBUs assembly	materials	MOFs, nucleation, self-assembly, metadynamics	Matteo Salvalaglio	GYRATION METAD ENDPLUMED DISTANCES COORDINATIONNUMBER PRINT RESTART	setup colvar bias generic multicolvar symfunc
26.006	Metadynamics simulations of buried phosphorylation sites and proline isomerisation	bio	metadynamics	Julian Streit	METAD COORDINATION TORSION WHOLEMOLECULES MOLINFO PRINT	bias generic colvar
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	FUNNEL RMSD LOWER_WALLS COMMITTOR CUSTOM FUNNEL_PS PRINT COORDINATION METAD WRAPAROUND COM GROUP TORSION ENDPLUMED WHOLEMOLECULES MATHEVAL OPES_METAD UPPER_WALLS DISTANCE CENTER	generic funnel function vatom opes core colvar bias
25.013	Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices	bio	umbrella sampling, temperature ramping	Alexander Berlaga	RESTRAINT PYTORCH_MODEL DISTANCE GYRATION PRINT	pytorch bias generic colvar
24.032	DeepLNE++	methods	PATHCV, OPES	Thorben Fröhlking	ENERGY GROUP DISTANCE TORSION LOAD COMBINE CUSTOM COORDINATION OPES_METAD PRINT	generic setup function opes core colvar
24.020	Graph Neural Network-State Predictive Information Bottleneck (GNN-SPIB) approach for learning molecular thermodynamics and kinetics	bio	LJ7, alanine, well-tempered metadynamics, infrequent metadynamics, machine learning	Ziyue Zou, Dedi Wang, Pratyush Tiwary	METAD GROUP TORSION COMMITTOR LOAD PRINT	generic setup core colvar bias
24.010	Oxytocin metadynamics simulation	bio	metadynamics, oxytocin, peptide	Jan Beránek	METAD FLUSH TORSION RESTART WHOLEMOLECULES PRINT	bias setup generic colvar
23.038	Determinants of Neutral Antagonism and Inverse Agonism in the β2-adrenergic receptor	bio	protein coupled receptor, beta-adrenergic, receptor activation, antagonism, inverse agonism, metadynamics	Timothy Clark	METAD RMSD WHOLEMOLECULES DISTANCE MATHEVAL MOLINFO PRINT	function bias generic colvar
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 METAD DISTANCES WRAPAROUND POSITION GROUP UPPER_WALLS CENTER WHOLEMOLECULES MOLINFO FIT_TO_TEMPLATE PRINT	generic vatom core colvar multicolvar bias isdb
23.024	Permutationally Invariant Networks for Enhanced Sampling (PINES)	methods	collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent	Nicholas Herringer	LOAD PRINT PBMETAD	bias generic setup
23.018	Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention	materials	metadynamics, surface binding, peptide adsorption	Kaylyn Torkelson	COM UPPER_WALLS DISTANCE PBMETAD GYRATION PRINT	bias vatom generic colvar
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	bias generic setup
22.000	Amyloid precursor protein processing by human γ-secretase	bio	Bias Exchange Metadynamics, Helix unfolding, coupled binding	Xiaoli Lu	ALPHARMSD METAD ANTIBETARMSD COORDINATION RANDOM_EXCHANGES DISTANCE CENTER MOLINFO UNITS CONTACTMAP INCLUDE PRINT	generic setup vatom colvar bias secondarystructure
21.044	NaCl nucleation	chemistry	metadynamics, DFS clustering	Aaron Finney	METAD DUMPGRID COORDINATIONNUMBER CLUSTER_NATOMS GROUP CONTACT_MATRIX INSPHERE HISTOGRAM COMBINE LOCAL_Q6 DFSCLUSTERING MFILTER_MORE FIXEDATOM CLUSTER_DISTRIBUTION PRINT Q6	gridtools generic function vatom volumes adjmat core symfunc multicolvar bias clusters
21.029	Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs	bio	metadynamics, small peptide, machine learning	Pratyush Tiwary	ENERGY FLUSH EXTERNAL TORSION RESTART MOLINFO PRINT	generic colvar bias setup
21.013	Role of vibrational excitation in heterogeneous catalysis	chemistry	catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption	Kristof Bal	FLUSH CONVERT_TO_FES REWEIGHT_METAD REWEIGHT_BIAS HISTOGRAM LOAD BF_CHEBYSHEV DUMPGRID RESTRAINT LOWER_WALLS UNITS COORDINATION PRINT OPT_AVERAGED_SGD METAD COORDINATIONNUMBER UWALLS COMBINE VES_LINEAR_EXPANSION DISTANCES EXTERNAL UPPER_WALLS DISTANCE ANGLES TD_GRID	ves gridtools generic setup function colvar symfunc multicolvar bias
21.012	NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition	bio	funnel metadynamics	Jim Pfaendtner	FUNNEL METAD LOWER_WALLS COM UPPER_WALLS DISTANCE FUNNEL_PS PRINT	generic funnel vatom colvar 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	PATHMSD METAD LOWER_WALLS UPPER_WALLS RESTART WHOLEMOLECULES PRINT	bias generic colvar setup
20.034	Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations	bio	RNA, SARS-CoV-2, partial tempering	Sandro Bottaro	ABMD ERMSD DISTANCE CENTER RESTART TORSION MOLINFO PRINT	generic setup vatom colvar bias
19.080	Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium	methods	ves, variationally enhanced sampling, vibrational excitation, chemical reactions	Kristof Bal	OPT_AVERAGED_SGD DUMPGRID LOWER_WALLS VES_LINEAR_EXPANSION FLUSH CONVERT_TO_FES EXTERNAL UPPER_WALLS DISTANCE HISTOGRAM COMBINE BF_CHEBYSHEV COORDINATION UNITS TD_WELLTEMPERED TD_GRID ANGLE PRINT	ves generic gridtools setup function colvar bias
19.071	Time-independent free energies from metadynamics via Mean Force Integration	methods	metadynamics, mean force integration, MFI, thermodynamic integration	Matteo Salvalaglio	METAD BIASVALUE READ DUMPGRID CONVERT_TO_FES REWEIGHT_METAD EXTERNAL DISTANCE TORSION COMMITTOR REWEIGHT_BIAS HISTOGRAM MATHEVAL PRINT	gridtools generic function colvar bias
19.069	Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen	materials	ibuprofen, crystal, solvent, surface	Matteo Salvalaglio	GROUP DISTANCE CENTER ENDPLUMED INCLUDE PRINT	core generic vatom colvar
19.059	cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide	bio	bias-exchange metadynamics, cis-trans isomerization	Fabrizio Marinelli	METAD RANDOM_EXCHANGES TORSION INCLUDE PRINT	bias generic colvar
19.021	Coarse-Grained Directed Simulation	methods	experiment directed simulation, coarse-grain, bias	Glen Hocky	RESTRAINT EDS DISTANCE TORSION COMBINE PRINT	generic function colvar bias eds
19.015	Ibuprofen conformational dynamics and thermodynamics surface	materials	Ibuprofen, crystal, surface, solvents, conformers, metadynamics	Matteo Salvalaglio	METAD LOWER_WALLS UPPER_WALLS DISTANCE TORSION CENTER COMMITTOR PRINT	bias vatom generic colvar
19.009	RNA tetraloops folding	bio	metadynamics, RNA, folding	Giovanni Bussi	METAD ERMSD RMSD ENDPLUMED WHOLEMOLECULES MOLINFO PRINT	bias generic colvar
19.004	MI Ubiquitin	bio	metainference, NMR	Max Bonomi	CS2BACKBONE RDC GROUP METAINFERENCE WHOLEMOLECULES MOLINFO PRINT	core generic isdb
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	WHOLEMOLECULES DISTANCE PRINT METAD ANGLE	colvar bias generic
26.001	Molecular simulations Alx riboswitch	bio	RNA, riboswitch	Giovanni Bussi	RESTRAINT MOLINFO MOVINGRESTRAINT DISTANCE ERMSD PRINT MATHEVAL	function bias colvar generic
25.003	Surrogate Model CV	methods	Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding	Sompriya Chatterjee	ENDPLUMED MOLINFO WHOLEMOLECULES DISTANCE COMBINE TORSION CUSTOM COMMITTOR GROUP PRINT ENERGY OPES_METAD MATHEVAL PYTORCH_MODEL	function colvar core opes pytorch generic
25.000	Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer	bio	metadynamics, pathCV	Sahithya Sridharan Iyer	RESTART MOLINFO WHOLEMOLECULES UPPER_WALLS DISTANCE COM PRINT METAD GROUP FUNCPATHGENERAL	function colvar setup core bias vatom generic
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	RESTART LOWER_WALLS COORDINATION UPPER_WALLS DISTANCE CUSTOM COMMITTOR UNITS PRINT GROUP OPES_METAD	function colvar setup core opes bias generic
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	LOWER_WALLS UPPER_WALLS DISTANCE CUSTOM COMBINE COMMITTOR TORSION UNITS PRINT FLUSH OPES_METAD	function colvar setup opes bias generic
23.039	Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation	chemistry	metadynamics, ligand dissociation	Eric Beyerle	RESTRAINT DUMPMASSCHARGE MOLINFO UPPER_WALLS DISTANCE COMBINE FIXEDATOM PRINT METAD CENTER	function colvar bias vatom generic
23.021	Into the Dynamics of Rotaxanes at Atomistic Resolution	materials	metadynamics, rotaxanes, molecular shuttles, molecular machines	Luigi Leanza	UPPER_WALLS DISTANCE TORSION FIXEDATOM PRINT METAD CENTER MATHEVAL CUSTOM	function colvar bias vatom generic
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	READ MOLINFO REWEIGHT_METAD HISTOGRAM WHOLEMOLECULES DISTANCE RMSD PRINT METAD CONVERT_TO_FES DUMPGRID MATHEVAL	function colvar gridtools bias generic
23.014	Structural basis of dimerization of chemokine receptors CCR5 and CXCR4	bio	metadynamics, oligomerization, chemokine receptors, GPCR, membrane	Vittorio Limongelli	WHOLEMOLECULES UPPER_WALLS DISTANCE COMBINE TORSION COM PRINT METAD FLUSH	function colvar bias 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	ENDPLUMED MOLINFO ECV_MULTITHERMAL DISTANCE TORSION OPES_EXPANDED PRINT METAD ENERGY OPES_METAD_EXPLORE	opes colvar bias generic
23.006	Transcription factor unbinding	bio	metadynamics, DNA, conformational changes	Malin Lüking	MOLINFO CONTACTMAP DISTANCE COM ALPHARMSD DUMPFORCES PRINT METAD ANGLE	colvar secondarystructure bias vatom generic
22.039	Driving and characterizing nucleation of urea and glycine polymorphs in water	bio	metadynamics, nucleation, amino acids, polymorphism	Eric Beyerle	PAIRENTROPY INCLUDE Q6 COMBINE COORDINATIONNUMBER LOAD Q4 PRINT METAD CENTER GROUP MATHEVAL	function setup core symfunc gridtools bias vatom generic
22.037	Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site	chemistry	metadynamics, DNA, abasic	Mike Jones	METAD DISTANCES DISTANCE PRINT	multicolvar bias colvar generic
22.029	Angiotensin-1-7_Metadynamics	bio	Metadynamics, Angiotensin-(1-7), peptide	L.-América Chi	LOWER_WALLS WHOLEMOLECULES COORDINATION UPPER_WALLS GYRATION GROUP PRINT METAD FLUSH	core bias colvar generic
22.028	N-glycan conformer distributions in atomistic simulation	bio	REST2, RECT, N-glycan, pucker	Isabell Grothaus	READ MOLINFO HISTOGRAM TORSION PRINT METAD CONVERT_TO_FES DUMPGRID PUCKERING	gridtools colvar bias generic
22.027	Molecular Dynamics simulations of BANAL-236 RBD-hACE2 complexes	bio	SARS-CoV-2, COVID-19, MD, human-ACE2, spike, BANAL-236, receptor-binding domain	Max Bonomi	RMSD PRINT	colvar generic
22.001	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	UPPER_WALLS UNITS METAD FLUSH OPT_ADAM POSITION INCLUDE BF_LEGENDRE BF_CHEBYSHEV PRINT ENERGY VES_OUTPUT_BASISFUNCTIONS TD_UNIFORM DISTANCE BF_GAUSSIANS OPT_AVERAGED_SGD TD_WELLTEMPERED BF_WAVELETS VES_LINEAR_EXPANSION COORDINATION BF_CUBIC_B_SPLINES	colvar setup bias ves generic
21.035	CmuMD simulations of NaCl(aq) at NaCl	chemistry	CmuMD, interface	Aaron Finney	RESTRAINT DISTANCE FIXEDATOM LOAD PRINT GROUP	colvar core generic bias vatom setup
21.022	Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly	materials	parallel bias metadynamics, adsorption, peptide	Xin Qi	MOLINFO LOWER_WALLS PBMETAD UPPER_WALLS GYRATION DISTANCE COM PRINT ENERGY	bias colvar 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	RESTRAINT MOLINFO WHOLEMOLECULES COORDINATION STATS PRINT	function bias colvar generic
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	MOLINFO DIHCOR WHOLEMOLECULES STATS TORSION PARABETARMSD FLUSH ENDPLUMED INCLUDE PBMETAD METAINFERENCE PRINT GYRATION COMBINE COORDINATION CS2BACKBONE ENSEMBLE ANTIBETARMSD ALPHARMSD GROUP	function colvar core isdb multicolvar secondarystructure bias generic
20.010	Phase equilibrium of liquid water and hexagonal ice from enhanced sampling molecular dynamics simulations	materials	water, ice, TIP4P, crystallization, EnvironmentSimilarity, RefCV, kernel, VES, variationally enhanced sampling	Pablo Piaggi	RESTART ENVIRONMENTSIMILARITY VES_LINEAR_EXPANSION OPT_DUMMY BF_LEGENDRE VOLUME Q6 UPPER_WALLS OPT_AVERAGED_SGD PRINT TD_WELLTEMPERED MATHEVAL	function colvar envsim symfunc generic bias ves setup
20.009	The dynamics of linear polyubiquitin	bio	saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics	Carlo Camilloni	MOLINFO PBMETAD WHOLEMOLECULES GYRATION DISTANCE TORSION STATS ENSEMBLE ALPHABETA METAINFERENCE PRINT CENTER SAXS FLUSH	function colvar isdb multicolvar bias vatom 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	ENDPLUMED MOVINGRESTRAINT GYRATION UNITS PRINT	bias colvar generic setup
19.075	PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python	other	Python, automatic differentiation	Toni Giorgino	RESTRAINT ENDPLUMED DUMPDERIVATIVES COMBINE DISTANCE TORSION PRINT CENTER GROUP ANGLE CUSTOM	function colvar core bias vatom generic
19.070	Unexpected Dynamics in the UUCG RNA Tetraloop	bio	well-tempered metadynamics, RNA, UUCG, maximum entropy	Sandro Bottaro	MOLINFO WHOLEMOLECULES DISTANCE RMSD ERMSD TORSION PRINT METAD	colvar bias generic
19.052	Gibbs free energy of homogeneous nucleation	materials	nucleation, surface excess free energy	Gareth Tribello	ENDPLUMED FCCUBIC PRINT UPPER_WALLS UNITS METAD CELL	colvar setup symfunc bias generic
19.042	Harmonic Linear Discriminant Analysis (HLDA)	methods	metadynamics, chemistry, HLDA	GiovanniMaria Piccini	PRINT UPPER_WALLS DISTANCE COMBINE UNITS METAD ENERGY FLUSH	function colvar setup bias generic
19.020	PTMetaD-WTE simulation of the Ntail IDP	bio	metadynamics, IDPs, protein folding	Mattia Bernetti	ENDPLUMED MOLINFO WHOLEMOLECULES GYRATION ALPHARMSD PRINT METAD ENERGY	bias colvar secondarystructure generic
19.005	Cmyc small molecule interaction	bio	metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP	Gabriella Heller	INCLUDE MOLINFO PBMETAD WHOLEMOLECULES COORDINATION GYRATION CS2BACKBONE DISTANCE ALPHABETA METAINFERENCE PRINT CENTER GROUP	colvar core isdb multicolvar bias vatom generic
19.002	EMMI STRA6	bio	metainference, cryo-EM	Max Bonomi	BIASVALUE MOLINFO EMMI PRINT GROUP	bias core generic isdb
25.018	Metainference simulation for dimerization of RNA binding protein	bio	Metainference, Metadynamics, SAXS, protein dimer	Debadutta Patra	SAXS CENTER MOLINFO GYRATION STATS DISTANCE UPPER_WALLS METAINFERENCE PBMETAD TORSION FLUSH WHOLEMOLECULES PRINT ENSEMBLE	bias vatom isdb function generic colvar
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	INCLUDE CENTER MOLINFO GYRATION VOLUME DISTANCE ENERGY READ DUMPATOMS RESTART PBMETAD TORSION UPDATE_IF WHOLEMOLECULES PRINT	bias vatom setup generic 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	COORDINATION COMBINE MOLINFO GYRATION OPES_METAD DISTANCE TORSION CUSTOM ALPHARMSD WHOLEMOLECULES PRINT	secondarystructure function generic colvar opes
24.014	Learning Collective Variables with Synthetic Data Augmentation through Physics-inspired Geodesic Interpolation	methods	data augmentation, geodesic interpolation, collective variables, protein folding	Juno Nam	COORDINATION MOLINFO LOWER_WALLS METAD UPPER_WALLS PYTORCH_MODEL DRR FLUSH WHOLEMOLECULES RMSD PRINT	bias drr pytorch generic colvar
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 MOLINFO DISTANCE METAD ENERGY COORDINATIONNUMBER COMMITTOR BIASVALUE RESTART TORSION MATHEVAL FLUSH PRINT	symfunc bias function setup generic colvar
24.011	Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble	methods	committor, machine learning	Peilin Kang	MOLINFO UNITS UPPER_WALLS CELL RMSD POSITION LOWER_WALLS PRINT GROUP INCLUDE COORDINATION ENDPLUMED ENERGY BIASVALUE LOAD MATHEVAL WHOLEMOLECULES DISTANCE TORSION CUSTOM	bias core function setup generic colvar
24.007	SWISH-X	bio	swish-x, SWISH-X, swish, expanded SWISH	Alberto Borsatto	INCLUDE ECV_MULTITHERMAL MOLINFO ENERGY UPPER_WALLS OPES_EXPANDED CONTACTMAP WHOLEMOLECULES PRINT	bias generic colvar opes
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	SAXS GROUP CENTER MOLINFO STATS DISTANCE UPPER_WALLS BIASVALUE WRAPAROUND RMSD PRINT ENSEMBLE	bias core vatom isdb function generic colvar
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 LOCAL_Q6 COMBINE MOVINGRESTRAINT LOWER_WALLS COORDINATIONNUMBER METAD MFILTER_MORE Q6 PRINT	symfunc bias core generic multicolvar 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	MOLINFO DISTANCE METAD HISTOGRAM READ CONVERT_TO_FES MATHEVAL REWEIGHT_METAD WHOLEMOLECULES RMSD PRINT DUMPGRID	bias gridtools generic function colvar
23.003	Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations	methods	metadynamics, alchemical variable, alchemical free energy calculations	Wei-Tse Hsu	EXTRACV METAD READ TORSION PRINT	bias generic 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	INCLUDE ECV_UMBRELLAS_LINE ENVIRONMENTSIMILARITY LOWER_WALLS UPPER_WALLS OPES_EXPANDED PRINT	bias envsim generic opes
22.018	Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations	bio	ligand binding, docking, EMMI, LAT1	Max Bonomi	GROUP MOLINFO BIASVALUE EMMIVOX LOAD WHOLEMOLECULES PRINT	bias core isdb setup generic
22.009	Glycosylation in calixarenes capsule	chemistry	Metadynamics, glycosylation, supramolecular catalysis	GiovanniMaria Piccini	GROUP COMBINE COORDINATION UNITS DISTANCE UPPER_WALLS LOWER_WALLS FIT_TO_TEMPLATE DISTANCES METAD ANGLE BRIDGE MATHEVAL FLUSH WHOLEMOLECULES RMSD PRINT	bias core adjmat generic setup multicolvar function colvar
22.002	GAMBES_SAMPL5_RATES	other	GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding	Jayashrita Debnath	GROUP CENTER COORDINATION ENDPLUMED DISTANCE UPPER_WALLS PYTORCH_MODEL FIT_TO_TEMPLATE ENERGY COMMITTOR ANGLE FIXEDATOM LOAD MATHEVAL FLUSH WHOLEMOLECULES PRINT	bias core vatom function setup pytorch generic colvar
21.052	On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets	materials	Ibuprofen, unbinding, WTmetaD	Matteo Salvalaglio	CENTER ENDPLUMED DISTANCE METAD COORDINATIONNUMBER COMMITTOR TORSION PRINT	symfunc bias vatom generic colvar
21.038	Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics	materials	metadynamics, SGOOP, nucleation, urea	Ziyue Zou	INCLUDE GROUP CENTER COMBINE VOLUME ENERGY METAD COORDINATIONNUMBER LOAD PRINT	symfunc bias core vatom function setup generic colvar
21.019	Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations	materials	Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen	Matteo Salvalaglio	COM TORSIONS KDE DISTANCE MATHEVAL PRINT	vatom gridtools generic multicolvar function colvar
21.011	CmuMD simulations of NaCl(aq) at graphite	chemistry	CmuMD, DFS clustering	Aaron Finney	AROUND GROUP RESTRAINT DFSCLUSTERING DENSITY COORDINATIONNUMBER CONTACT_MATRIX MULTICOLVARDENS MFILTER_MORE FIXEDATOM CLUSTER_DISTRIBUTION LOAD CLUSTER_NATOMS PRINT DUMPGRID	symfunc bias clusters core vatom volumes adjmat gridtools setup multicolvar generic
21.003	aSYN SAXS metainference	bio	metainference, SAXS	Kresten Lindorff-Larsen	GROUP SAXS EEFSOLV CENTER MOLINFO GYRATION METAINFERENCE BIASVALUE PBMETAD FLUSH ALPHARMSD WHOLEMOLECULES PRINT	bias core vatom isdb secondarystructure generic 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	GROUP COM DISTANCE WHOLEMOLECULES PRINT	vatom generic colvar core
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
20.031	Soft fluorescent nanoshuttles targeting receptors	chemistry	polymers, receptors, nanoparticles, fluorescent probes	Adriana Pietropaolo	CENTER COORDINATION PBMETAD WHOLEMOLECULES PRINT	bias generic colvar vatom
20.026	Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor	bio	Metadynamics, Umbrella sampling	Brandon Peters	RESTRAINT MULTI_RMSD METAD HISTOGRAM CONVERT_TO_FES REWEIGHT_METAD PRINT DUMPGRID	bias generic gridtools colvar
20.015	Rational design of ASCT2 inhibitors using an integrated experimental-computational approach	bio	ASCT2 transporter, small-molecules, cryo-EM, metainference	Max Bonomi	GROUP MOLINFO BIASVALUE EMMIVOX DUMPATOMS LOAD WHOLEMOLECULES PRINT	bias core isdb setup generic
20.011	Uremic toxin analysis	bio	metadynamics, uremic toxin, serum albumin	Jim Pfaendtner	GROUP CENTER COORDINATION DISTANCE DISTANCES RESTART WHOLEMOLECULES PRINT	core vatom setup multicolvar generic colvar
19.066	Finding ligand unbinding reaction pathways	methods	maze, ligand unbinding	Jakub Rydzewski	POSITION UNITS MAZE_OPTIMIZER_BIAS MAZE_SIMULATED_ANNEALING MAZE_LOSS PRINT	maze setup generic colvar
19.049	Determining the sizes of solid/liquid clusters in MD trajectories of nucleation	methods	nucleation, metadynamics, clustering, Steinhardt order parameters	Gareth Tribello	LOCAL_Q6 MORE_THAN CLUSTER_PROPERTIES DFSCLUSTERING SMAC CONTACT_MATRIX ONES METAD COORDINATIONNUMBER DISTANCES Q6 CLUSTER_DISTRIBUTION MATRIX_VECTOR_PRODUCT CUSTOM CLUSTER_NATOMS OUTER_PRODUCT PRINT OUTPUT_CLUSTER	symfunc bias clusters matrixtools adjmat generic multicolvar function
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	GROUP POSITION COORDINATION UNITS LOWER_WALLS UPPER_WALLS METAD RESTART FLUSH PRINT	bias core setup generic colvar
19.040	Optimal Metric for Path Collective Variables	bio	metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path	Francesco Luigi Gervasio	ENDPLUMED METAD TORSION MATHEVAL PRINT	bias generic colvar function
19.038	native state dynamics of human and mouse b2m	bio	metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation	Carlo Camilloni	GROUP MOLINFO ANTIBETARMSD ALPHABETA ENDPLUMED LOWER_WALLS UPPER_WALLS BIASVALUE RESTART PBMETAD FLUSH WHOLEMOLECULES PRINT CS2BACKBONE	bias core isdb secondarystructure setup multicolvar generic
19.036	Thermodynamics and kinetics of G protein-coupled receptor activation	bio	metadynamics, allostery, receptor conformation, GPCR, pharmacology	Davide Provasi	COM FUNCPATHMSD ENDPLUMED DISTANCE METAD CONTACTMAP WHOLEMOLECULES RMSD PRINT	bias vatom generic function colvar
19.029	WTE-metaD of FF domain of URNF1 C57D variant	bio	metadynamics, mutations, post-translational modification, ff domain	Elena Papaleo	GROUP MOLINFO ALPHABETA GYRATION LOWER_WALLS UPPER_WALLS METAD WHOLEMOLECULES PRINT	bias core multicolvar generic colvar
19.028	pRAVE	methods	RAVE, reaction coordinate, deep learning, metadynamics, kinetics	Pratyush Tiwary	COM COMBINE ALPHABETA DISTANCE COMMITTOR RESTART TORSION EXTERNAL WHOLEMOLECULES PRINT	bias vatom function setup multicolvar generic colvar
19.019	FA-MetaD-JCP-Wang-et-al	bio	Frequency adaptive metadynamics; peptide	Kresten Lindorff-Larsen	COMBINE MOLINFO ALPHABETA METAD COMMITTOR FLUSH PRINT	bias multicolvar function generic
19.007	EMMI Microtubules	bio	metainference, cryo-EM	Max Bonomi	GROUP MOLINFO EMMI BIASVALUE WHOLEMOLECULES PRINT	bias isdb generic core

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