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
26.002	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	CUSTOM PRINT GROUP CENTER DISTANCE PATH COORDINATION ECV_MULTITHERMAL UPPER_WALLS VOLUME OPES_EXPANDED RMSD OPES_METAD_EXPLORE ENERGY PATHMSD LOWER_WALLS	colvar vatom bias mapping core function opes generic
25.024	Sampling glycan-glycan interactions for B22 calculations	bio	B22, glycan, carbohydrates, distance, REST2, metadynamics, RECT, replica exchange	Isabell Louise Grothaus	POSITION PRINT METAD DISTANCE COM RESTRAINT COMBINE	colvar vatom bias function generic
24.036	Leveraging cryptic ligand envelopes through enhanced molecular simulations	bio	HREX, conformational heterogeneity, drug discovery, ligand binding, plitidepsin, aplidin, ligand-target complexes, cryptic ligand envelope	Francesco Colizzi	PRINT GROUP CONVERT_TO_FES DISTANCE COORDINATION HISTOGRAM WHOLEMOLECULES DUMPGRID TORSION ANGLE	gridtools colvar core generic
24.031	DeepLNE	methods	PATHCV, OPES, OneOPES	Thorben Fröhlking	PRINT ERMSD MOLINFO RESTART COORDINATION VOLUME ECV_MULTITHERMAL PYTORCH_MODEL OPES_EXPANDED COMBINE OPES_METAD_EXPLORE ENERGY	colvar pytorch opes function setup generic
24.020	Graph Neural Network-State Predictive Information Bottleneck (GNN-SPIB) approach for learning molecular thermodynamics and kinetics	bio	LJ7, alanine, well-tempered metadynamics, infrequent metadynamics, machine learning	Ziyue Zou, Dedi Wang, Pratyush Tiwary	PRINT GROUP METAD LOAD COMMITTOR TORSION	colvar bias core setup generic
24.009	Weighted Shape Gaussian Mixture Models	bio	metadynamics, clustering	Glen Hocky	GROUP UNITS PRINT METAD TORSION	colvar bias core setup generic
24.003	Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations	chemistry	steered molecular dynamics, foldamers, peptoids, bio-inspired	Kaylyn Torkelson	PRINT ALPHABETA MOVINGRESTRAINT GYRATION DISTANCE COM COORDINATION WHOLEMOLECULES INCLUDE TORSION	colvar vatom bias multicolvar generic
23.044	Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition	materials	metadynamics, interlocked molecules	Luigi Leanza	GROUP PRINT CONVERT_TO_FES METAD READ ENDPLUMED COORDINATION HISTOGRAM COMMITTOR DUMPGRID	colvar bias gridtools core generic
23.034	Urea nucleation in water: do long-range forces matter?	materials	LMF theory, Metadynamics, Nucleation	Ziyue Zou	GROUP PRINT COORDINATIONNUMBER CENTER METAD LOAD INCLUDE	vatom bias core symfunc setup generic
23.027	CmuMD simulations of NaCl(aq) at NaCl	chemistry	CmuMD, DFS, Q3, Pair Entropy	Aaron Finney	GROUP UNITS Q3 PRINT COORDINATIONNUMBER CLUSTER_NATOMS LOCAL_AVERAGE AROUND LOAD FIXEDATOM RESTRAINT HISTOGRAM DFSCLUSTERING CONTACT_MATRIX DENSITY LOCAL_Q3 DUMPGRID CLUSTER_DISTRIBUTION	clusters volumes vatom bias gridtools adjmat core symfunc setup generic
23.008	PBMetaD simulations of Histatin5	bio	metadynamics, IDP, Rg, PPII	Francesco Pesce	GROUP PRINT GYRATION MOLINFO WHOLEMOLECULES PBMETAD TORSION	colvar bias core generic
23.007	Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains	bio	metadynamics, peptoids, parallel-bias metadynamics	Jim Pfaendtner	PRINT GYRATION COM COORDINATION RESTRAINT WHOLEMOLECULES INCLUDE PBMETAD TORSION	colvar bias vatom generic
23.004	Melting curves of ice polymorphs in the vicinity of the liquid-liquid critical point	chemistry	water, liquid-liquid transition, second critical point, ice, polymorphs, melting curves, environment similarity, opes, density-functional theory, scan, machine learning potential	Pablo Piaggi	PRINT RESTART ENVIRONMENTSIMILARITY HISTOGRAM UPPER_WALLS OPES_EXPANDED DUMPGRID ECV_UMBRELLAS_LINE LOWER_WALLS	bias gridtools envsim opes setup generic
23.001	Quantum phase diagram of water	chemistry	Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella	Sigbjørn-Løland Bore	PRINT RESTART ENVIRONMENTSIMILARITY UPPER_WALLS INCLUDE OPES_EXPANDED ECV_UMBRELLAS_LINE LOWER_WALLS	bias envsim opes setup generic
22.036	Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction	bio	Well-tempered MetaDynamics with Hamiltonian Replica Exchange	Miroslav Krepl	GROUP CUSTOM PRINT METAD MOLINFO LOAD COORDINATION GHBFIX FLUSH BIASVALUE UPPER_WALLS COMBINE	colvar bias core function setup generic
22.031	Rare Event Kinetics from Adaptive Bias Enhanced Sampling	methods	OPES Flooding, Kinetics, Rate, OPES, Machine Learning	Dhiman Ray	PRINT UNITS WHOLEMOLECULES COMBINE ENERGY CUSTOM ENDPLUMED BIASVALUE TORSION RMSD POSITION GROUP CONSTANT CONTACTMAP DISTANCE COMMITTOR MOLINFO PYTORCH_MODEL OPES_METAD INCLUDE	colvar bias pytorch opes core function setup generic
22.026	Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification	materials	Peptoid, silica	Jim Pfaendtner	PRINT GYRATION MOLINFO DISTANCE COM UPPER_WALLS PBMETAD	colvar bias vatom generic
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	CUSTOM PRINT ALPHABETA XANGLES METAD MOLINFO DISTANCE MATHEVAL COM ZANGLES YANGLES UPPER_WALLS WHOLEMOLECULES COMBINE TORSION LOWER_WALLS	colvar vatom bias multicolvar function generic
21.052	On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets	materials	Ibuprofen, unbinding, WTmetaD	Matteo Salvalaglio	PRINT COORDINATIONNUMBER CENTER METAD DISTANCE ENDPLUMED COMMITTOR TORSION	colvar vatom bias symfunc generic
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	GROUP ALPHABETA PRINT METAD GYRATION ENDPLUMED UPPER_WALLS WHOLEMOLECULES LOWER_WALLS	colvar bias core multicolvar generic
21.026	Probing allosteric regulations with coevolution-driven molecular simulations	bio	metadynamics, coevolution, allostery, adenylate cyclase	Francesco Colizzi	PRINT UNITS METAD DISTANCE COM UPPER_WALLS WHOLEMOLECULES PATHMSD	colvar vatom bias setup generic
21.016	MD SAXS GTPase associated center	bio	metadynamics, RNA, folding, SAXS	Giovanni Bussi	GROUP CUSTOM PRINT ERMSD GYRATION MOLINFO METAD SAXS UPPER_WALLS WHOLEMOLECULES INCLUDE LOWER_WALLS	colvar bias core function isdb generic
21.000	Uremic toxin time scale dynamics	bio	uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs)	Jim Pfaendtner	GROUP PRINT DISTANCE COM WHOLEMOLECULES	colvar vatom core generic
20.028	Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane	bio	metadynamics, KRas-4B, anionic membrane	Huixia Lu	PRINT METAD CENTER FIT_TO_TEMPLATE DISTANCE RESTART	colvar vatom bias setup generic
20.025	The role of water in host-guest interaction	bio	ligand binding, water, opes, SAMPL5	Valerio Rizzi	GROUP PRINT CENTER FIT_TO_TEMPLATE DISTANCE MATHEVAL ENDPLUMED FIXEDATOM COORDINATION UPPER_WALLS WHOLEMOLECULES PYTORCH_MODEL OPES_METAD ENERGY ANGLE	colvar vatom bias pytorch core function opes generic
20.011	Uremic toxin analysis	bio	metadynamics, uremic toxin, serum albumin	Jim Pfaendtner	GROUP PRINT CENTER DISTANCES DISTANCE RESTART COORDINATION WHOLEMOLECULES	colvar vatom core multicolvar setup generic
19.065	Molecular Enhanced Sampling with Autoencoders	methods	enhanced sampling, collective variables, deep learning	Wei Chen	POSITION ANN RESTRAINT COM COMBINE	colvar annfunc vatom bias function
19.056	maze	methods	maze, ligand unbinding	Jakub Rydzewski	POSITION UNITS PRINT MAZE_LOSS MAZE_SIMULATED_ANNEALING MAZE_OPTIMIZER_BIAS	colvar setup maze generic
19.043	Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA)	methods	metadynamics, chemistry, HLDA	GiovanniMaria Piccini	PRINT UNITS METAD DISTANCE DISTANCES RESTART UPPER_WALLS FLUSH COMBINE	colvar bias multicolvar function setup generic
19.041	Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces	bio	metadynamics, collective variables, conformational changes, multiple walkers, Well-Tempered MetaD, peptide, binding, phosphorylation, post-transitional motif, sio2, adsorption	Jim Pfaendtner	PRINT METAD DISTANCE COM UPPER_WALLS ENERGY	colvar bias vatom generic
19.039	Funnel Metadynamics	bio	funnel-metadynamics, absolute binding free energy, ligand-receptor complexes	Vittorio Limongelli	PRINT METAD DISTANCE COM UPPER_WALLS WHOLEMOLECULES FUNNEL_PS FUNNEL RMSD LOWER_WALLS	colvar vatom bias generic funnel
19.014	MIL101(Cr) SBUs assembly	materials	MOFs, nucleation, self-assembly, metadynamics	Matteo Salvalaglio	PRINT COORDINATIONNUMBER METAD GYRATION DISTANCES ENDPLUMED RESTART	colvar bias multicolvar symfunc setup generic
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 METAD DISTANCE ANGLE PRINT	colvar bias generic
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	COORDINATION RMSD ECV_MULTITHERMAL ENERGY DISTANCES CUSTOM GROUP DISTANCE OPES_METAD_EXPLORE GHOST LOWER_WALLS OPES_EXPANDED PRINT CENTER UPPER_WALLS PATHMSD	function colvar bias generic core vatom opes multicolvar
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	COORDINATION ENERGY OPES_METAD DISTANCE PRINT UPPER_WALLS	colvar bias opes generic
24.017	Absolute Binding Free Energies with OneOPES	methods	protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy	Francesco Gervasio	BIASVALUE COORDINATION INCLUDE WHOLEMOLECULES RMSD ECV_MULTITHERMAL GROUP CUSTOM OPES_METAD_EXPLORE PRINT WRAPAROUND UPPER_WALLS MATHEVAL ENERGY METAD COM TORSION RESTART LOWER_WALLS CONTACTMAP OPES_EXPANDED CONSTANT PROJECTION_ON_AXIS MOLINFO	function colvar bias setup generic core vatom opes
24.016	Cryo-EM guided simulations of ribozyme	bio	metainference, cryo-EM	Giovanni Bussi	EMMIVOX WHOLEMOLECULES GROUP BIASVALUE ERMSD RESTRAINT PRINT INCLUDE MOLINFO	colvar bias generic core isdb
23.038	Determinants of Neutral Antagonism and Inverse Agonism in the β2-adrenergic receptor	bio	protein coupled receptor, beta-adrenergic, receptor activation, antagonism, inverse agonism, metadynamics	Timothy Clark	WHOLEMOLECULES RMSD METAD DISTANCE PRINT MOLINFO MATHEVAL	colvar bias function generic
23.024	Permutationally Invariant Networks for Enhanced Sampling (PINES)	methods	collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent	Nicholas Herringer	PRINT PBMETAD LOAD	bias setup 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	WHOLEMOLECULES RMSD METAD DUMPGRID HISTOGRAM DISTANCE REWEIGHT_METAD PRINT MOLINFO CONVERT_TO_FES MATHEVAL READ	function gridtools colvar bias generic
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	TIME DRR METAD FLUSH CUSTOM BIASVALUE LOWER_WALLS PRINT UNITS UPPER_WALLS PATHMSD	function drr colvar bias setup generic
22.045	Binding mode and mechanism of enzymatic polyethylene terephthalate degradation	bio	metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation	Francesco Colizzi	WHOLEMOLECULES METAD DISTANCE COM ANGLE LOWER_WALLS PRINT UPPER_WALLS MOVINGRESTRAINT	colvar bias vatom generic
22.035	Deciphering the alphabet of disorder — Glu and Asp act differently on local but not global properties	bio	intrinsically disordered proteins, parallel bias metadynamics, protein	Kresten Lindorff-Larsen	GYRATION WHOLEMOLECULES PBMETAD TORSION MOLINFO	colvar bias generic
22.034	Rationalising the difference in crystallisability of two Sulflowers using efficient in silico methods	materials	metadynamics, crystallizability, crystal structure prediction, sulflower, persulforated coronene	Matteo Salvalaglio	METAD PRINT CUSTOM CELL COMMITTOR LOWER_WALLS DRMSD UPPER_WALLS MATHEVAL	function colvar bias generic
22.029	Angiotensin-1-7_Metadynamics	bio	Metadynamics, Angiotensin-(1-7), peptide	L.-América Chi	GYRATION COORDINATION WHOLEMOLECULES METAD FLUSH GROUP LOWER_WALLS PRINT UPPER_WALLS	colvar bias core generic
22.003	Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling	methods	opes, metadynamics, reweighting, alanine, muller	Michele Invernizzi	ECV_MULTITHERMAL ENERGY PBMETAD ENDPLUMED METAD CUSTOM ECV_UMBRELLAS_FILE OPES_METAD BIASVALUE TORSION OPES_METAD_EXPLORE POSITION LOWER_WALLS OPES_EXPANDED PRINT UNITS UPPER_WALLS	function colvar bias setup generic opes
22.000	Amyloid precursor protein processing by human γ-secretase	bio	Bias Exchange Metadynamics, Helix unfolding, coupled binding	Xiaoli Lu	COORDINATION ANTIBETARMSD RANDOM_EXCHANGES UNITS METAD INCLUDE CENTER DISTANCE CONTACTMAP PRINT ALPHARMSD MOLINFO	colvar bias setup generic vatom secondarystructure
21.051	Automatic learning of hydrogen-bond fixes in an AMBER RNA force field	methods	force field, RNA	Giovanni Bussi	COORDINATION WHOLEMOLECULES METAD COMBINE BIASVALUE ERMSD PRINT MOLINFO	colvar bias function 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 GROUP COORDINATION UNITS	colvar bias setup generic core
21.020	Reweighted Jarzynski sampling	methods	free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions	Kristof Bal	REWEIGHT_BIAS OPES_METAD BIASVALUE REWEIGHT_METAD LOAD MOVINGRESTRAINT FLUSH VES_LINEAR_EXPANSION CUSTOM HISTOGRAM DISTANCE RESTRAINT PRINT UPPER_WALLS BF_CHEBYSHEV COMBINE METAD OPT_AVERAGED_SGD CONVERT_TO_FES UNITS CONSTANT COORDINATIONNUMBER TD_WELLTEMPERED ANN DUMPGRID	function gridtools colvar bias setup generic annfunc opes 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	REWEIGHT_METAD COORDINATION READ WHOLEMOLECULES RMSD FLUSH GROUP HISTOGRAM DISTANCE FIXEDATOM PRINT UPPER_WALLS MATHEVAL ENDPLUMED METAD COM POSITION CONVERT_TO_FES DUMPGRID	function gridtools colvar bias generic core vatom
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 METAD PRINT REWEIGHT_BIAS POSITION RESTART RESTRAINT COORDINATION CENTER MATHEVAL	function colvar bias setup generic vatom
21.011	CmuMD simulations of NaCl(aq) at graphite	chemistry	CmuMD, DFS clustering	Aaron Finney	DFSCLUSTERING COORDINATIONNUMBER DENSITY CLUSTER_DISTRIBUTION RESTRAINT GROUP MULTICOLVARDENS DUMPGRID FIXEDATOM CLUSTER_NATOMS AROUND PRINT MFILTER_MORE LOAD CONTACT_MATRIX	gridtools bias setup adjmat generic volumes core vatom symfunc multicolvar clusters
21.001	Substrate recognition and catalysis by glycosaminoglycan sulfotransferases	bio	metadynamics, well-tempered metadynamics, puckering, coordination	Tarsis Ferreira	PUCKERING WHOLEMOLECULES COORDINATION ENERGY RANDOM_EXCHANGES METAD GROUP DUMPGRID HISTOGRAM DISTANCE REWEIGHT_METAD LOWER_WALLS PRINT INCLUDE MOLINFO UPPER_WALLS	gridtools colvar bias generic core
20.023	metadynminer and metadynminer3d	methods	metadynamics, visualization, R	Vojtech Spiwok	METAD TORSION PRINT	colvar bias generic
20.016	Predicting polymorphism in molecular crystals using orientational entropy	materials	metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy	Pablo Piaggi	METAD GROUP CENTER VOLUME PRINT INCLUDE UPPER_WALLS LOAD	colvar bias setup generic core vatom
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	BF_LEGENDRE TD_WELLTEMPERED Q6 VES_LINEAR_EXPANSION ENVIRONMENTSIMILARITY OPT_AVERAGED_SGD VOLUME RESTART PRINT UPPER_WALLS MATHEVAL OPT_DUMMY	function colvar bias setup generic envsim ves symfunc
20.004	Data-driven collective variables for enhanced sampling	methods	collective variables, machine learning, deep-lda	Luigi Bonati	PYTORCH_MODEL ENDPLUMED FLUSH GROUP OPES_METAD DISTANCE TORSION COM LOWER_WALLS PRINT UNITS UPPER_WALLS LOAD MATHEVAL	function colvar bias setup generic pytorch core vatom opes
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	WHOLEMOLECULES METAD GROUP RESTART PRINT MOLINFO UPPER_WALLS PATHMSD	colvar bias setup generic core
20.001	Conformational stability and dynamics in solution and in crystals report similarly on unfolding and aggregation propensity of amyloidogenic proteins	bio	metainference, metadynamics, NMR, protein dynamics, b2m, protein crystals	Carlo Camilloni	ALPHABETA WHOLEMOLECULES ANTIBETARMSD CS2BACKBONE PBMETAD ENDPLUMED FLUSH GROUP BIASVALUE LOWER_WALLS PRINT MOLINFO UPPER_WALLS	bias generic core secondarystructure multicolvar isdb
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	ENDPLUMED COMBINE METAD CONVERT_TO_FES DUMPGRID HISTOGRAM DISTANCE COM ABMD REWEIGHT_METAD LOWER_WALLS PRINT UPPER_WALLS MATHEVAL READ	function gridtools colvar bias generic vatom
19.060	Neural networks-based variationally enhanced sampling	methods	ves, neural networks	Luigi Bonati	ENERGY Q6 ENDPLUMED ENVIRONMENTSIMILARITY TORSION POSITION PRINT UNITS LOAD	colvar setup generic envsim symfunc
19.058	Constrained MD for maintaining a cavity in a calculation	chemistry	constrained MD, porous molecules, porosity, cavity	Kim Jelfs	INPLANEDISTANCES DISTANCES FLUSH COM RESTART PRINT MOVINGRESTRAINT	bias setup generic vatom multicolvar
19.035	Dimerization of GPCRs from coarse-grained umbrella sampling	bio	Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization	Davide Provasi	GROUP DISTANCE TORSION COM RESTRAINT PRINT	colvar bias generic core vatom
19.020	PTMetaD-WTE simulation of the Ntail IDP	bio	metadynamics, IDPs, protein folding	Mattia Bernetti	GYRATION WHOLEMOLECULES ENERGY ENDPLUMED METAD PRINT ALPHARMSD MOLINFO	colvar bias secondarystructure generic
19.018	Excited state FEP/Metadynamics simulations	chemistry	metadynamics, FEP, excited states, conjugated polymers, torsional potential	Adriana Pietropaolo	CONSTANT WHOLEMOLECULES METAD BIASVALUE TORSION PRINT MATHEVAL	colvar bias function generic
19.016	Succinnic acid gamma polymorph	materials	Succinnic acid, conformers, polymorphs, metadynamics	Matteo Salvalaglio	ENERGY ENDPLUMED METAD COMBINE CELL TORSION VOLUME LOWER_WALLS PRINT UPPER_WALLS MATHEVAL	colvar bias function generic
19.011	Automatic Gradient Computation for Collective Variables	other	gradient, differentiation, curvature	Toni Giorgino	ENDPLUMED	generic
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	WRAPAROUND UPPER_WALLS GROUP TORSION RMSD OPES_METAD COMMITTOR COM WHOLEMOLECULES FUNNEL_PS LOWER_WALLS FUNNEL CUSTOM CENTER METAD PRINT COORDINATION MATHEVAL	core colvar generic opes funnel bias vatom function
25.016	Advancing in silico drug design with Bayesian refinement of AlphaFold models	bio	bAIes, AlphaFold, Bayesian refinement, virtual screening, docking, small-molecule, enrichment	Samiran Sen	BAIES PRINT GROUP BIASVALUE	bias core isdb generic
25.014	Atomic resolution ensembles of intrinsically disordered proteins with Alphafold	bio	bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement	Vincent Schnapka	BAIES PRINT GROUP BIASVALUE	bias core isdb generic
25.000	Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer	bio	metadynamics, pathCV	Sahithya Sridharan Iyer	MOLINFO DISTANCE UPPER_WALLS GROUP RESTART COM WHOLEMOLECULES METAD PRINT FUNCPATHGENERAL	setup core colvar generic function bias vatom
24.008	yCD Metadynamics	bio	volume-based MetaD, path CVs, infrequent MetaD, product release	James McCarty	WRAPAROUND HISTOGRAM COMMITTOR FIT_TO_TEMPLATE COM PATH CONVERT_TO_FES PRINT FLUSH MOLINFO READ RMSD WHOLEMOLECULES GROUP FIXEDATOM CONTACTMAP ENDPLUMED REWEIGHT_METAD DUMPGRID INCLUDE MATHEVAL UPPER_WALLS METAD DISTANCE COORDINATION	mapping core colvar generic function gridtools bias vatom
24.001	A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations	bio	OPES, OPES-Flooding, QM/MM, Kinetics, Enzyme Catalysis	Dhiman Ray	DISTANCE UPPER_WALLS TORSION UNITS OPES_METAD LOWER_WALLS COMBINE CUSTOM PRINT COMMITTOR FLUSH	setup opes colvar generic function bias
23.039	Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation	chemistry	metadynamics, ligand dissociation	Eric Beyerle	MOLINFO RESTRAINT DISTANCE UPPER_WALLS FIXEDATOM DUMPMASSCHARGE COMBINE CENTER METAD PRINT	colvar generic function bias vatom
23.035	An Extended Metadynamics Protocol for Binding/Unbinding of Peptide Ligands to Class A G-Protein Coupled Receptors	bio	G protein coupled receptor, peptide ligands, metadynamics, multiple-walker	Timothy Clark	DISTANCE UPPER_WALLS BIASVALUE WHOLEMOLECULES LOWER_WALLS CENTER METAD PRINT CONSTANT MATHEVAL	colvar generic function bias vatom
23.026	Machine Learning Nucleation Collective Variables with Graph Neural Networks	chemistry	Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks	Florian Dietrich	MOVINGRESTRAINT GROUP LOWER_WALLS COMBINE LOCAL_Q6 MFILTER_MORE METAD PRINT Q6 COORDINATIONNUMBER	core symfunc bias generic function multicolvar
23.020	FEP simulations of ATOX1 homodimer	chemistry	parallel bias metadynamics, FEP, free-energy of metal ion dissociation	Adriana Pietropaolo	PBMETAD ANGLE DISTANCE BIASVALUE WHOLEMOLECULES PRINT CONSTANT MATHEVAL	colvar bias generic function
22.043	Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES	bio	OPES, RNA, Tetraloop, Folding	Gül Zerze	OPES_EXPANDED CONTACTMAP ENERGY WHOLEMOLECULES ECV_UMBRELLAS_LINE ECV_MULTITHERMAL PRINT	opes colvar generic
22.042	Metadynamics of NSP10 and variants	bio	metadynamics, NSP10, crystal structure, variants	Shozeb Haider	METAD PRINT TORSION	colvar bias generic
22.032	Reciprocal barrier restraint. Application to path-meta-eABF	methods	restraint, upper wall, lower wall, path colvar, meta-eABF, metadynamics, DRR, protein conformational transition, PROTAC	Istvan Kolossvary	PATHMSD BIASVALUE DRR CUSTOM METAD PRINT FLUSH	colvar generic function drr bias
22.021	Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations	chemistry	Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella	Sigbjørn Løland Bore	OPES_EXPANDED UPPER_WALLS LOWER_WALLS ECV_UMBRELLAS_LINE PRINT INCLUDE ENVIRONMENTSIMILARITY	opes bias envsim generic
22.017	Water regulates the residence time of Benzamidine in Trypsin	bio	ligand binding, water, opes, benzamidine trypsin, unbinding rates, machine learning, Deep-LDA, Deep-TICA	Narjes Ansari	DISTANCE UPPER_WALLS GROUP FIXEDATOM OPES_METAD RMSD COMMITTOR FIT_TO_TEMPLATE WHOLEMOLECULES PYTORCH_MODEL LOWER_WALLS CUSTOM CENTER PRINT COORDINATION MATHEVAL	function core colvar generic opes bias vatom pytorch
22.002	GAMBES_SAMPL5_RATES	other	GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding	Jayashrita Debnath	ANGLE DISTANCE UPPER_WALLS GROUP FIXEDATOM LOAD ENDPLUMED COMMITTOR FIT_TO_TEMPLATE ENERGY WHOLEMOLECULES PYTORCH_MODEL CENTER PRINT COORDINATION FLUSH MATHEVAL	setup core colvar generic function bias vatom pytorch
21.049	Multiple-path-metadynamics and PathMaps	methods	path-CV, metadynamics, multiple-walker, multiple paths, pathmap	Alberto Pérez-de-Alba-Ortíz	RESTRAINT UPPER_WALLS TORSION UNITS LOAD LOWER_WALLS ENSEMBLE COMBINE CUSTOM MOVINGRESTRAINT METAD PRINT CONSTANT	setup colvar generic function bias
21.036	Modelling the structure and interactions of intrinsically disordered peptides with multiple-replica, metadynamics-based sampling methods and force-field combinations	bio	Bias Exchange Metadynamics, PTWTE-metaD	Matteo Salvalaglio	MOLINFO UPPER_WALLS GROUP ANTIBETARMSD RANDOM_EXCHANGES ENERGY WHOLEMOLECULES LOWER_WALLS ALPHARMSD DIHCOR METAD PRINT COORDINATION PARABETARMSD GYRATION	multicolvar secondarystructure core colvar generic bias
21.010	Step by Step Strecker Amino Acid Synthesis from Ab Initio Prebiotic Chemistry	chemistry	Strecker reaction, free energy landscape, ab initio molecular dynamics, glycine, prebiotic synthesis	Théo Magrino	PRINT	generic
21.005	Crystallization Collective Variable	methods	Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA	Tarak Karmakar	UPPER_WALLS GROUP OPES_METAD LOAD PYTORCH_MODEL LOWER_WALLS PRINT FLUSH MATHEVAL	function setup core generic opes bias pytorch
20.031	Soft fluorescent nanoshuttles targeting receptors	chemistry	polymers, receptors, nanoparticles, fluorescent probes	Adriana Pietropaolo	PBMETAD WHOLEMOLECULES CENTER PRINT COORDINATION	colvar bias vatom generic
20.029	High Conformational Flexibility of the E2F1/DP1/DNA complex	bio	SAXS, protein-DNA complex, hySAXS, ensemble determination	Cristina Paissoni	MOLINFO RESTRAINT DISTANCE GROUP BIASVALUE WHOLEMOLECULES ENSEMBLE SAXS CENTER INCLUDE PRINT STATS	core colvar isdb generic function bias vatom
19.030	Coarse-Grained MetaDynamics (CG-MetaD)	bio	Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy	Vittorio Limongelli	DISTANCE UPPER_WALLS COM WHOLEMOLECULES LOWER_WALLS METAD PRINT	colvar generic bias vatom
19.024	PT-MetaD-WTE	methods	metadynamics, WTE, trp cage, PT	Jim Pfaendtner	GROUP ENERGY EXTERNAL METAD COORDINATION	colvar bias core
19.012	Martini-Beads multi-scale SAXS	methods	metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex	Carlo Camilloni	MOLINFO DISTANCE RESTRAINT UPPER_WALLS GROUP RMSD ENDPLUMED BIASVALUE WHOLEMOLECULES SAXS CENTER INCLUDE PRINT STATS	core colvar isdb generic function bias vatom
19.009	RNA tetraloops folding	bio	metadynamics, RNA, folding	Giovanni Bussi	MOLINFO ENDPLUMED RMSD WHOLEMOLECULES ERMSD METAD PRINT	colvar bias generic
19.000	VesDeltaF	methods	VES, convergence, suboptimal CVs	Michele Invernizzi	RESTART VES_DELTA_F TORSION ENDPLUMED UNITS LOAD ENERGY METAD PRINT POSITION	ves setup colvar generic bias
26.000	OPES simulations of disordered proteins	bio	OPES, IDPs	Julian Streit	PRINT ENERGY RESTART OPES_EXPANDED ECV_MULTITHERMAL	opes generic setup colvar
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	COMBINE LOWER_WALLS GROUP PRINT COORDINATION CENTER UPPER_WALLS DISTANCE WHOLEMOLECULES MATHEVAL GYRATION METAD	function vatom colvar generic core 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	SAXS GROUP INCLUDE PRINT MOLINFO UPPER_WALLS CENTER MOVINGRESTRAINT DISTANCE WHOLEMOLECULES GYRATION METAD	vatom bias colvar generic core isdb
25.026	Deciphering the Molecular Mechanisms of Startle Disease - the Role of the Asn46Lys Mutation in the Glycine Receptor	bio	metadynamics, glycine receptors, funnel metadynamics	Jacob Adam Clark	FUNNEL_PS LOWER_WALLS PRINT COM FUNNEL UPPER_WALLS METAD	bias generic vatom funnel
25.013	Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices	bio	umbrella sampling, temperature ramping	Alexander Berlaga	PRINT RESTRAINT PYTORCH_MODEL DISTANCE GYRATION	bias generic colvar pytorch
25.006	Characterizing the conformational ensemble of PROTAC degraders in solutions via atomistic simulations	methods	Enhanced sampling, Atomistic simulations, Conformational ensemble, PROTACs, Targeted Protein Degradation, Chamelonic molecules	Shikshya Bhusal, Omar Valsson	PBMETAD INCLUDE TORSION PRINT ENERGY RESTART READ DUMPATOMS MOLINFO VOLUME CENTER UPDATE_IF DISTANCE WHOLEMOLECULES GYRATION	vatom colvar generic bias setup
25.001	RNA G-quadruplex folding with ST-metaD protocol	bio	RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD	Pavlína Pokorná	COMBINE MOLINFO WHOLEMOLECULES ERMSD METAD	bias function colvar generic
24.027	Proline cis and trans subensembles of a disordered peptide	bio	intrinsically disordered proteins, proline cis trans isomerisation, metadynamics, collective variables	Alice Pettitt	COMBINE FLUSH DIHCOR PBMETAD INCLUDE GROUP TORSION PRINT ANTIBETARMSD COORDINATION MOLINFO WHOLEMOLECULES DISTANCE ALPHARMSD PARABETARMSD ENDPLUMED GYRATION	function multicolvar colvar generic core bias secondarystructure
24.013	Estimating Free Energy Surfaces and their Convergence from multiple, independent static and history-dependent biased molecular-dynamics simulations with Mean Force Integration	methods	Mean Force Integration, Convergence, FES, Umbrella Sampling	Matteo Salvalaglio	FLUSH TORSION PRINT ENERGY RESTART RESTRAINT BIASVALUE COORDINATIONNUMBER COMMITTOR MOLINFO DISTANCE METAD MATHEVAL	function colvar generic symfunc bias setup
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	FLUSH OPES_METAD GROUP PRINT FIXEDATOM COORDINATIONNUMBER UPPER_WALLS DISTANCE ZDISTANCES UNITS	bias colvar multicolvar opes generic core symfunc vatom setup
23.046	Lasso Peptides - HLDA CV	bio	metadynamics, protein folding, HLDA, harmonic	Gabriel da Hora	COMBINE PRINT DISTANCE WHOLEMOLECULES UNITS METAD	function colvar generic bias setup
23.045	Minute-timescale simulations of G Protein Coupled Receptor A2A activation mechanism reveal a receptor pseudo-active state	bio	Path CVs Metadynamics, GPCRs activation transition	Vittorio Limongelli	LOWER_WALLS INCLUDE PATHMSD PRINT FUNCPATHMSD MOLINFO UPPER_WALLS DISTANCE ALPHARMSD CONTACTMAP METAD	function colvar generic bias secondarystructure
23.043	Modeling the ferroelectric phase transition in barium titanate with DFT accuracy and converged sampling	materials	Barium Titanate, ferroelectric phase transition, Machine Learning, polarization order parameters	Lorenzo Gigli	FLUSH INCLUDE PRINT SELECT_COMPONENTS TRANSPOSE SUM METAD MATHEVAL	function matrixtools generic valtools bias
23.040	Supramolecular capsules assembly dynamics	chemistry	Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics	Riccardo Capelli	FLUSH DISTANCES GROUP PRINT CUSTOM COM POSITION CENTER DISTANCE WHOLEMOLECULES UNITS METAD	function bias multicolvar colvar generic core vatom setup
23.032	Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics	bio	metadynamics, tSNE, neural network, machine learning, trp-cage, folding	Vojtech Spiwok	COMBINE ALPHARMSD ANN PRINT MOLINFO POSITION WHOLEMOLECULES FIT_TO_TEMPLATE METAD	function annfunc colvar generic bias secondarystructure
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	DISTANCES GROUP PRINT SHADOW MOLINFO POSITION UPPER_WALLS CENTER WHOLEMOLECULES WRAPAROUND FIT_TO_TEMPLATE METAD	bias vatom colvar multicolvar generic core isdb
23.018	Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention	materials	metadynamics, surface binding, peptide adsorption	Kaylyn Torkelson	PBMETAD PRINT COM UPPER_WALLS DISTANCE GYRATION	bias generic vatom colvar
23.017	How and When Does an Enzyme React? Unraveling α-Amylase Catalytic Activity with Enhanced Sampling Techniques	bio	enzymatic reaction discovery, reaction mechanism, catalysis, ligand-binding modes, water, alpha-amylase, sugar, QM/MM MD, OPES, OPES explore, graph CV, machine learning, Deep TDA CV, path CV	Sudip Das	LOWER_WALLS PATH TORSION GROUP PRINT OPES_METAD CUSTOM OPES_METAD_EXPLORE FIXEDATOM COORDINATION CENTER PYTORCH_MODEL UPPER_WALLS DISTANCE WHOLEMOLECULES FIT_TO_TEMPLATE UNITS	function vatom colvar opes generic mapping pytorch core bias setup
23.014	Structural basis of dimerization of chemokine receptors CCR5 and CXCR4	bio	metadynamics, oligomerization, chemokine receptors, GPCR, membrane	Vittorio Limongelli	COMBINE FLUSH TORSION PRINT COM UPPER_WALLS DISTANCE WHOLEMOLECULES METAD	function bias colvar generic vatom
23.012	JAK2 2D meta-eABF PMF with statistical analysis	bio	2D meta-eABF, path CV, PMF	Istvan Kolossvary	FLUSH LOWER_WALLS PATHMSD PRINT CUSTOM DRR UPPER_WALLS BIASVALUE METAD	function colvar generic bias drr
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	TORSION PRINT READ EXTRACV METAD	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	FLUSH DISTANCE PRINT CUSTOM COM DRR BIASVALUE METAD UNITS	function bias colvar generic vatom drr setup
22.022	Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir	bio	RMSD, protein-ligand interactions	Isabell Grothaus	PRINT RMSD	generic colvar
22.020	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	GROUP TORSION PRINT COM DISTANCE WHOLEMOLECULES METAD	bias colvar generic core vatom
22.015	Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome	bio	photodynamics, bacteriophytochrome, variationally enhanced sampling	Jakub Rydzewski	TORSION PRINT TD_UNIFORM OPT_AVERAGED_SGD VES_LINEAR_EXPANSION BF_FOURIER	generic ves colvar
22.009	Glycosylation in calixarenes capsule	chemistry	Metadynamics, glycosylation, supramolecular catalysis	GiovanniMaria Piccini	COMBINE FLUSH DISTANCES LOWER_WALLS GROUP PRINT FIT_TO_TEMPLATE MATHEVAL COORDINATION RMSD UPPER_WALLS WHOLEMOLECULES DISTANCE ANGLE BRIDGE UNITS METAD	function adjmat multicolvar colvar generic core bias setup
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	TORSION PRINT FIXEDATOM METAD FIT_TO_TEMPLATE	vatom generic bias colvar
21.039	Deep learning the slow modes for rare events sampling	methods	collective variables, machine learning, slow modes, deep-tica, opes	Luigi Bonati	INCLUDE GROUP LOAD MOLINFO WHOLEMOLECULES ENVIRONMENTSIMILARITY ECV_MULTITHERMAL CONTACTMAP FLUSH OPES_METAD ENERGY RMSD DISTANCE PRINT Q6 OPES_EXPANDED COMBINE TORSION VOLUME PYTORCH_MODEL ENDPLUMED UNITS	function envsim colvar opes generic pytorch core symfunc setup
21.037	Molecular Dynamics simulations of RBD/hACE2 complexes	bio	SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain	Max Bonomi	DISTANCE PRINT RMSD	generic colvar
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	PBMETAD TORSION INCLUDE PRINT RANDOM_EXCHANGES METAD ENDPLUMED	bias generic colvar
21.023	Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling	methods	enhanced sampling, collective variables, machine learning	Jakub Rydzewski	DISTANCE INCLUDE TORSION PRINT CUSTOM ENERGY REWEIGHT_METAD BIASVALUE METAD CONSTANT UNITS	function colvar generic bias setup
20.032	Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil	materials	clustering, conformational isomers	Matteo Salvalaglio	PRINT ENDPLUMED TORSION	generic colvar
20.027	Allosteric Regulation of SARS-CoV-2 Protease. Towards Informed Structure-Based Drug Discovery	bio	SARS-CoV2, MPro, Covid-19, Molecular Dynamics, Metadynamics, Computer-Aided Drug Discovery	Khaled Abdel-Maksoud	PRINT METAD DISTANCE TORSION	bias generic colvar
20.022	Unified Approach to Enhanced Sampling	methods	OPES, expanded ensembles, importance sampling	Michele Invernizzi	LOAD MOLINFO WHOLEMOLECULES ENVIRONMENTSIMILARITY ECV_MULTITHERMAL CUSTOM ENERGY POSITION RMSD ECV_MULTITHERMAL_MULTIBARIC PRINT Q6 ECV_LINEAR UPPER_WALLS OPES_EXPANDED MATHEVAL TORSION VOLUME ECV_UMBRELLAS_LINE ENDPLUMED UNITS	function envsim colvar opes generic symfunc bias setup
20.021	Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins.	bio	phi-values, restrained MD, transition-state, protein folding, disordered proteins, protein evolution	Cristina Paissoni	PRINT COORDINATION RESTRAINT MOLINFO STATS WHOLEMOLECULES	bias generic function colvar
20.008	Simulating solvation and acidity in complex mixtures with first-principles accuracy. The case of CH3SO3H and H2O2 in phenol	chemistry	proton trasfer, metadynamics	Kevin Rossi	DISTANCES PRINT CUSTOM COORDINATION METAD UNITS	function colvar multicolvar generic bias setup
19.082	Ammonia Borane Dehydrogenation	chemistry	metadynamics, reaction discovery, hydrogen production, chemistry	Valerio Rizzi	COMBINE FLUSH EXTERNAL GROUP PRINT RESTART COORDINATIONNUMBER METAD ENDPLUMED UNITS	function generic core symfunc bias setup
19.081	Calculation of phase diagrams in the multithermal-multibaric ensemble	methods	VES, variationally enhanced sampling, multithermal-multibaric, energy, Wang Landau, RefCV, kernel, bcc, fcc, sodium, aluminum	Pablo Piaggi	BF_LEGENDRE LOWER_WALLS OPT_DUMMY READ LOAD REWEIGHT_TEMP_PRESS ENERGY RESTART CELL OPT_AVERAGED_SGD TD_WELLTEMPERED PRINT Q6 REWEIGHT_BIAS UPPER_WALLS VES_LINEAR_EXPANSION MATHEVAL CONVERT_TO_FES COMBINE TD_MULTITHERMAL_MULTIBARIC VOLUME HISTOGRAM DUMPGRID	function colvar generic symfunc gridtools bias setup ves
19.070	Unexpected Dynamics in the UUCG RNA Tetraloop	bio	well-tempered metadynamics, RNA, UUCG, maximum entropy	Sandro Bottaro	TORSION PRINT MOLINFO RMSD DISTANCE WHOLEMOLECULES ERMSD METAD	bias generic colvar
19.063	Protein-ligand binding through metadynamics with path CVs	bio	metadynamics, path CVs, ligand binding	Mattia Bernetti	LOWER_WALLS PATHMSD PRINT UPPER_WALLS WHOLEMOLECULES METAD	bias generic colvar
19.046	Optimal Collective from short simulations for Benzamidine-Trypsin ligand binding	bio	VAC-MetaD, optimised collective variables, binding free energy, unbinding rates, benzamidine trypsin, Structure Activity Relation	Faidon Brotzakis	ALPHABETA COMBINE LOWER_WALLS DISTANCES GROUP TORSION PRINT COM REWEIGHT_METAD FUNNEL MOLINFO UPPER_WALLS RMSD DISTANCE WHOLEMOLECULES BRIDGE METAD	function vatom adjmat colvar multicolvar generic funnel core bias
19.038	native state dynamics of human and mouse b2m	bio	metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation	Carlo Camilloni	ALPHABETA PBMETAD FLUSH LOWER_WALLS GROUP PRINT ANTIBETARMSD RESTART MOLINFO UPPER_WALLS BIASVALUE WHOLEMOLECULES ENDPLUMED CS2BACKBONE	multicolvar isdb generic core bias setup secondarystructure
19.026	Ice Nucleation on Cholesterol Crystals	materials	forward flux sampling, crystal nucleation, water, ice, organic crystals	Gabriele Cesare Sosso	FLUSH LOCAL_Q6 CLUSTER_NATOMS CLUSTER_WITHSURFACE Q6 CONTACT_MATRIX OUTPUT_CLUSTER MFILTER_MORE COMMITTOR ENDPLUMED DFSCLUSTERING	adjmat multicolvar clusters generic symfunc
19.017	Ligand binding pathways exploration	bio	metadynamics, ligand binding	Riccardo Capelli	FLUSH GROUP PRINT FIT_TO_TEMPLATE COM ENDPLUMED REWEIGHT_METAD READ COORDINATION CONVERT_TO_FES POSITION UPPER_WALLS HISTOGRAM WHOLEMOLECULES WRAPAROUND MATHEVAL DUMPGRID METAD	function bias colvar generic core gridtools vatom
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 UPPER_WALLS PRINT MOLINFO METAD REWEIGHT_BIAS WHOLEMOLECULES CONVERT_TO_FES FIXEDATOM DISTANCE DUMPGRID COM LOWER_WALLS	gridtools colvar bias vatom generic
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 PRINT MOLINFO ECV_MULTITHERMAL COORDINATION OPES_METAD_EXPLORE RMSD CUSTOM CENTER DISTANCE COMBINE GHOST OPES_EXPANDED GROUP	function colvar opes core vatom generic
25.010	Kinetic rates calculation with Ratchet&Pawl MD	methods	kinetics, ligand binding, ABMD, ratchet&pawl MD	Riccardo Capelli	PRINT FLUSH COMMITTOR WHOLEMOLECULES DISTANCE ABMD COM GROUP	colvar bias core vatom generic
25.003	Surrogate Model CV	methods	Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding	Sompriya Chatterjee	ENERGY PRINT MOLINFO ENDPLUMED MATHEVAL TORSION CUSTOM PYTORCH_MODEL COMMITTOR OPES_METAD WHOLEMOLECULES DISTANCE COMBINE GROUP	function colvar opes core generic pytorch
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	UPPER_WALLS PRINT MOLINFO PBMETAD COORDINATION PARABETARMSD ALPHARMSD RMSD WHOLEMOLECULES EMMI CENTER DISTANCE COM DUMPATOMS BIASVALUE DUMPMASSCHARGE GROUP	colvar secondarystructure bias core vatom generic isdb
24.029	Combination of OPES and OPES-Explore	methods	OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin	Dhiman Ray	PRINT CENTER COMBINE BIASVALUE ENERGY CONTACTMAP POSITION FIT_TO_TEMPLATE RMSD CUSTOM PYTORCH_MODEL OPES_METAD UNITS DISTANCE MOLINFO ENDPLUMED METAD COORDINATION INCLUDE OPES_METAD_EXPLORE WHOLEMOLECULES FIXEDATOM LOWER_WALLS GROUP UPPER_WALLS FLUSH MATHEVAL	setup function colvar opes bias core vatom generic pytorch
24.007	SWISH-X	bio	swish-x, SWISH-X, swish, expanded SWISH	Alberto Borsatto	ENERGY UPPER_WALLS CONTACTMAP PRINT MOLINFO ECV_MULTITHERMAL INCLUDE WHOLEMOLECULES OPES_EXPANDED	opes generic bias colvar
23.023	Rational design of novel biomimetic sequence-defined polymers for mineralization applications	methods	metadynamics, surface binding, biomimetic mineralization	Kaylyn Torkelson	UPPER_WALLS PRINT PBMETAD COORDINATION GYRATION DISTANCE COM	generic bias colvar vatom
23.006	Transcription factor unbinding	bio	metadynamics, DNA, conformational changes	Malin Lüking	CONTACTMAP PRINT MOLINFO METAD DUMPFORCES ALPHARMSD DISTANCE ANGLE COM	colvar secondarystructure bias vatom generic
22.040	From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure	bio	SARS-CoV-2, Spike, Omicron	Miłosz Wieczór	UPPER_WALLS PRINT METAD WHOLEMOLECULES LOWER_WALLS PCAVARS	mapping generic bias
22.039	Driving and characterizing nucleation of urea and glycine polymorphs in water	bio	metadynamics, nucleation, amino acids, polymorphism	Eric Beyerle	LOAD PRINT COORDINATIONNUMBER Q6 METAD Q4 MATHEVAL INCLUDE CENTER PAIRENTROPY COMBINE GROUP	setup gridtools function symfunc bias core 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 PRINT DISTANCE DISTANCES	multicolvar generic bias colvar
22.019	Exploring aspartic protease inhibitor binding to design selective antimalarials	bio	ligand binding, loop opening, path CV, funnel metadynamics, drug development	Raitis Bobrovs	UPPER_WALLS PRINT FUNNEL METAD FUNNEL_PS WHOLEMOLECULES DISTANCE COM LOWER_WALLS PATHMSD	colvar bias vatom generic funnel
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	UPPER_WALLS PRINT MOLINFO FLUSH METAD COORDINATION ALPHABETA ALPHARMSD TORSION WHOLEMOLECULES DISTANCE ANGLE	multicolvar colvar secondarystructure bias generic
21.047	Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations	materials	pair entropy, metadynamics, ves, solids, crystallization	Pablo Piaggi	LOAD ENERGY PRINT RESTART VOLUME VES_LINEAR_EXPANSION METAD OPT_AVERAGED_SGD PAIRENTROPY COMBINE TD_WELLTEMPERED BF_LEGENDRE	setup gridtools function colvar bias generic ves
21.045	QM/MM metadynamics of thiol-disulfide exchange between methylthiolate and dimethyldisulfide in water with an imposed external electrostatic potential (ESP)	chemistry	metadynamics, QM/MM, electrostatic potential, thiol-disulfide exchange	Denis Maag	UPPER_WALLS PRINT COORDINATIONNUMBER METAD COORDINATION DISTANCE COMBINE LOWER_WALLS	function colvar symfunc bias generic
21.044	NaCl nucleation	chemistry	metadynamics, DFS clustering	Aaron Finney	HISTOGRAM PRINT COORDINATIONNUMBER Q6 INSPHERE METAD CONTACT_MATRIX DFSCLUSTERING CLUSTER_DISTRIBUTION LOCAL_Q6 MFILTER_MORE CLUSTER_NATOMS COMBINE FIXEDATOM DUMPGRID GROUP	multicolvar gridtools function clusters symfunc bias core vatom volumes generic adjmat
21.029	Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs	bio	metadynamics, small peptide, machine learning	Pratyush Tiwary	ENERGY PRINT RESTART MOLINFO FLUSH TORSION EXTERNAL	setup generic bias colvar
21.025	Computational and biochemical analysis of type IV pilus dynamics and stability	bio	molecular dynamics, calcium binding, Type IV pilus	Yasaman Karami	UPPER_WALLS PRINT LOWER_WALLS DISTANCE	generic bias colvar
21.019	Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations	materials	Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen	Matteo Salvalaglio	PRINT TORSIONS MATHEVAL DISTANCE COM KDE	multicolvar gridtools function colvar vatom generic
21.006	OPES, On-the-fly Probability Enhanced Sampling Method	methods	opes, alanine dipeptide, well-tempered, multithermal, multiumbrella	Michele Invernizzi	ENERGY PRINT ENDPLUMED ECV_UMBRELLAS_LINE ECV_MULTITHERMAL TORSION OPES_METAD OPES_EXPANDED	opes generic colvar
21.004	Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy	bio	machine learning, well-tempered metadynamics, path collective variable, potential of mean force, standard binding free energy calculations, host-guest, protein-ligand unbinding	Dorothea Gobbo	UPPER_WALLS PRINT RESTART METAD WHOLEMOLECULES LOWER_WALLS PATHMSD	setup generic bias colvar
21.003	aSYN SAXS metainference	bio	metainference, SAXS	Kresten Lindorff-Larsen	PRINT FLUSH MOLINFO EEFSOLV PBMETAD SAXS ALPHARMSD WHOLEMOLECULES CENTER GYRATION METAINFERENCE BIASVALUE GROUP	colvar secondarystructure bias core vatom generic isdb
21.002	Phase equilibrium of water with hexagonal and cubic ice using the SCAN functional	materials	ice, water, SCAN, OPES, VES, multithermal, crystallization, environment similarity, refcv, reweighting	Pablo Piaggi	ENERGY UPPER_WALLS PRINT RESTART VOLUME VES_LINEAR_EXPANSION ENVIRONMENTSIMILARITY Q6 ECV_UMBRELLAS_LINE MATHEVAL OPT_AVERAGED_SGD ECV_MULTITHERMAL_MULTIBARIC TD_UNIFORM OPES_EXPANDED BF_LEGENDRE	setup function colvar symfunc opes bias generic envsim ves
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	ERMSD PRINT MOLINFO RESTART TORSION CENTER DISTANCE ABMD	setup colvar bias vatom generic
20.033	COVID-19 Spike protein opening transition mechanism	bio	EMMI, CryoEM, COVID-19, Spike, Metainference	Faidon Brotzakis	HISTOGRAM PRINT MOLINFO READ RMSD DISTANCES WHOLEMOLECULES EMMI CONVERT_TO_FES DUMPGRID BIASVALUE GROUP	multicolvar gridtools colvar bias core generic isdb
20.020	Parallel Bias Metadynamics	methods	pbmetad, trp-cage, folding	Max Bonomi	PRINT MOLINFO PBMETAD COORDINATION ALPHABETA DIHCOR INCLUDE WHOLEMOLECULES GYRATION	multicolvar generic bias colvar
20.017	FISST	methods	FISST, force, peptide, sampling, tempering	Glen Hocky	ENERGY PRINT RESTRAINT MATHEVAL UNITS GYRATION DISTANCE FISST BIASVALUE GROUP	setup function colvar bias core generic fisst
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	HISTOGRAM PRINT COMBINE COM CONTACTMAP READ DISTANCE ABMD FUNCPATHMSD MOLINFO ENDPLUMED METAD WHOLEMOLECULES REWEIGHT_METAD DUMPGRID LOWER_WALLS UPPER_WALLS FLUSH CONVERT_TO_FES	gridtools function colvar bias vatom generic
19.067	Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways	bio	metadynamics, ligand unbinding	Jakub Rydzewski	UPPER_WALLS PRINT RESTART METAD UNITS LOWER_WALLS PATHMSD	setup generic bias colvar
19.052	Gibbs free energy of homogeneous nucleation	materials	nucleation, surface excess free energy	Gareth Tribello	UPPER_WALLS PRINT ENDPLUMED FCCUBIC METAD UNITS CELL	setup colvar symfunc bias generic
25.023	Molecular simulations of Tau-protein oligomers	bio	metadynamics, proteins, aggregation	Giovanni Bussi	METAD RMSD CUSTOM CONTACTMAP REWEIGHT_BIAS RESTRAINT PRINT FLUSH HISTOGRAM CONVERT_TO_FES DUMPGRID RESTART	generic bias gridtools colvar function setup
25.021	All You Need Is Water. Converging Ligand Binding Simulations with Hydration Collective Variables	bio	OPES Explore, ligand binding, binding free energy, water, hydration CVs, SAMPL challenge, host-guest	Valerio Rizzi	ENERGY MATHEVAL DISTANCE ANGLE UPPER_WALLS FIT_TO_TEMPLATE WHOLEMOLECULES FIXEDATOM COORDINATION OPES_METAD_EXPLORE GROUP PRINT CENTER	generic bias vatom core opes colvar function
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	COMBINE METAD DISTANCE ANGLE UNITS COORDINATIONNUMBER UPPER_WALLS LOWER_WALLS COORDINATION FIXEDATOM FLUSH COM RESTRAINT GROUP PRINT DISTANCES	generic bias vatom colvar core multicolvar symfunc function 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	COMBINE ENERGY ANGLE GROUP OPES_METAD CUSTOM RMSD MATHEVAL UPPER_WALLS COMMITTOR LOWER_WALLS FIXEDATOM MOLINFO CONTACTMAP DISTANCE WHOLEMOLECULES PRINT ENDPLUMED INCLUDE CENTER PYTORCH_MODEL FIT_TO_TEMPLATE COORDINATION	generic bias function vatom opes pytorch colvar core
22.030	Mixing physics across temperatures with generative artificial intelligence	methods	REMD, Generative AI, DDPM	Yihang Wang	WHOLEMOLECULES PRINT TORSION	generic colvar
22.028	N-glycan conformer distributions in atomistic simulation	bio	REST2, RECT, N-glycan, pucker	Isabell Grothaus	METAD READ TORSION PUCKERING HISTOGRAM PRINT MOLINFO CONVERT_TO_FES DUMPGRID	generic bias gridtools colvar
22.006	Peptide framework for screening the effects of amino acids on assembly	bio	metadynamics, peptides	Andrew White	COMBINE METAD REWEIGHT_BIAS HISTOGRAM PRINT COM GYRATION CONVERT_TO_FES GROUP DUMPGRID DISTANCES INCLUDE	generic bias vatom core multicolvar gridtools colvar function
21.022	Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly	materials	parallel bias metadynamics, adsorption, peptide	Xin Qi	ENERGY DISTANCE UPPER_WALLS PBMETAD LOWER_WALLS PRINT COM MOLINFO GYRATION	generic bias vatom colvar
21.017	All-atom simulations of the Vav1 AD construct	bio	metadynamics, parallel-bias, well-tempered	Simone Orioli	ALPHARMSD METAD CONTACTMAP ALPHABETA REWEIGHT_BIAS PBMETAD WHOLEMOLECULES PRINT MOLINFO GROUP RESTART	generic bias core multicolvar colvar secondarystructure setup
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	COMBINE STATS WHOLEMOLECULES RESTRAINT MOLINFO COORDINATION PRINT	generic bias function colvar
20.024	Gaussian Mixture Based Enhanced Sampling (GAMBES)	methods	enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias	Jayashrita Debnath	COMBINE ENERGY LOAD DISTANCE TORSION UNITS UPPER_WALLS LOWER_WALLS PRINT GROUP DISTANCES	generic bias core multicolvar colvar function setup
20.006	Class B GPCR activation mechanism	bio	metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding	Francesco Gervasio	COMBINE METAD ENERGY RMSD MATHEVAL DISTANCE UPPER_WALLS LOWER_WALLS WHOLEMOLECULES PRINT MOLINFO CENTER	generic bias vatom colvar function
19.029	WTE-metaD of FF domain of URNF1 C57D variant	bio	metadynamics, mutations, post-translational modification, ff domain	Elena Papaleo	METAD UPPER_WALLS ALPHABETA LOWER_WALLS WHOLEMOLECULES PRINT MOLINFO GYRATION GROUP	generic bias multicolvar colvar core
19.022	eABF simulation of NANMA (alanine dipeptide)	methods	eABF, DRR, alanine dipeptide	Haochuan Chen	PRINT DRR TORSION	generic colvar drr
19.013	RNA FF FITTING	methods	force field, RNA	Giovanni Bussi	CONSTANT BIASVALUE MATHEVAL TORSION PUCKERING MOLINFO INCLUDE	generic bias function colvar
25.012	A Machine Learning-Driven, Probability-Based Approach to Enzyme Catalysis	bio	enzyme catalysis, transition state, structure-activity relationship, free energy surface, reaction mechanism, water, alpha-amylase, sugar, QM/MM MD, OPES, committor function, machine learning	Sudip Das	UNITS COORDINATION CUSTOM PRINT TORSION DISTANCE INCLUDE ENERGY LOAD BIASVALUE COMBINE CELL OPES_METAD MATHEVAL POSITION FLUSH	opes generic colvar setup bias function
24.034	Umbrella sampling of ion in transporter SLC26A7	bio	umbrella sampling, transporter, ions	Xiaoli Lu	UNITS POSITION RESTRAINT PRINT	bias generic colvar setup
24.026	Constant pH metadynamics of RNA oligomers	bio	metadynamics, pH, RNA	Giovanni Bussi	PUCKERING METAD MOLINFO TORSION RESTART PRINT	bias generic colvar setup
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 COORDINATION TORSION DISTANCE OPES_METAD_EXPLORE ENERGY OPES_EXPANDED GROUP COMBINE ECV_MULTITHERMAL RESTART PRINT	opes generic colvar setup core function
24.005	Learning Markovian Dynamics with Spectral Maps	methods	spectral map, collective variables, machine learning	Jakub Rydzewski	UNITS CUSTOM DISTANCE BIASVALUE PRINT	generic colvar setup bias function
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	COORDINATION TORSION OPES_METAD_EXPLORE WHOLEMOLECULES LOWER_WALLS CENTER MATHEVAL OPES_METAD PRINT CUSTOM UNITS MOLINFO ENERGY COM BIASVALUE ENDPLUMED UPPER_WALLS WRAPAROUND FLUSH COMMITTOR FIT_TO_TEMPLATE DISTANCE GROUP POSITION	opes generic colvar setup bias vatom core function
23.015	MPCs aggregation	bio	opes_explore, dimerization, MPCs, self-assembly	Vikas Tiwari	CUSTOM COORDINATION METAD UPPER_WALLS DISTANCE OPES_METAD_EXPLORE GROUP WHOLEMOLECULES COM LOWER_WALLS CENTER PRINT	opes generic colvar bias vatom core 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	METAD UPPER_WALLS CONTACTMAP ENERGY WHOLEMOLECULES LOWER_WALLS PRINT	bias generic colvar
22.038	Enhanced Sampling Aided Design of Molecular Photoswitches	chemistry	reaction discovery, OPES explore, graph CV	Umberto Raucci	UNITS COORDINATION CUSTOM OPES_METAD_EXPLORE PYTORCH_MODEL PRINT	pytorch opes generic colvar setup function
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	generic colvar
22.025	Bubble nucleation rate predictions in a Lennard-Jones fluid	materials	free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation	Kristof Bal	UNITS CUSTOM COMMITTOR UPPER_WALLS MOVINGRESTRAINT LOAD VOLUME ANN HISTOGRAM BIASVALUE COORDINATIONNUMBER REWEIGHT_BIAS CONVERT_TO_FES FLUSH RESTRAINT DUMPGRID PRINT	symfunc generic colvar setup annfunc bias gridtools function
22.016	Homogeneous ice nucleation in an ab initio machine learning model of water	chemistry	ice, water, nucleation, seeding, environment similarity, interfacial free energy, interfaces	Pablo Piaggi	CUSTOM ENVIRONMENTSIMILARITY UPPER_WALLS ENERGY VOLUME HISTOGRAM AROUND OPES_METAD DUMPGRID RESTART PRINT	opes generic colvar setup bias envsim volumes gridtools function
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	CONTACTMAP DISTANCE CENTER PRINT	generic colvar vatom
22.001	Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials	methods	enhanced sampling, variationally enhanced sampling, ves, metadynamics, bias representation, wavelets, adam	Benjamin Pampel	COORDINATION METAD VES_OUTPUT_BASISFUNCTIONS BF_WAVELETS PRINT UNITS VES_LINEAR_EXPANSION INCLUDE ENERGY UPPER_WALLS TD_WELLTEMPERED BF_LEGENDRE FLUSH OPT_ADAM DISTANCE BF_CHEBYSHEV OPT_AVERAGED_SGD TD_UNIFORM BF_GAUSSIANS POSITION BF_CUBIC_B_SPLINES	generic colvar ves setup bias
21.040	A structural ensemble of a tau-microtubule complex reveals regulatory tau phosphorylation and acetylation mechanisms	bio	EMMI, CryoEM, tau-microtubules, post-translational modifications, chemical mutagenesis, structural ensemble, Metainference	Faidon Brotzakis	UPPER_WALLS MOLINFO DISTANCE GROUP EMMI COM WHOLEMOLECULES BIASVALUE RESTART PRINT	isdb generic colvar setup bias vatom core
21.027	EGFR activating mutations mechanism	bio	metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA	Francesco Gervasio	METAD UPPER_WALLS MOLINFO DISTANCE CONTACTMAP INCLUDE ENERGY WHOLEMOLECULES LOWER_WALLS MATHEVAL ALPHARMSD PRINT	generic colvar bias secondarystructure function
21.014	how to determine statistically accurate conformational ensembles	bio	metadynamics, metainference, errors, cv, SAXS, ensemble determination	Cristina Paissoni	ANTIBETARMSD MOLINFO METAD SAXS TORSION ENSEMBLE CONTACTMAP GYRATION ALPHABETA WHOLEMOLECULES BIASVALUE PBMETAD CENTER STATS PRINT	isdb generic colvar multicolvar secondarystructure bias vatom function
21.009	Nucleation rates from small scale atomistic simulations and transition state theory	materials	kinetics, free energy barriers, nucleation, droplets, metadynamics	Kristof Bal	UNITS COMMITTOR METAD UPPER_WALLS MOVINGRESTRAINT LOAD FLUSH HISTOGRAM COORDINATIONNUMBER CONVERT_TO_FES DUMPGRID REWEIGHT_METAD PRINT	symfunc generic setup bias gridtools
20.009	The dynamics of linear polyubiquitin	bio	saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics	Carlo Camilloni	METAINFERENCE MOLINFO ENSEMBLE SAXS TORSION DISTANCE GYRATION ALPHABETA FLUSH WHOLEMOLECULES PBMETAD CENTER STATS PRINT	isdb generic colvar multicolvar bias vatom function
19.069	Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen	materials	ibuprofen, crystal, solvent, surface	Matteo Salvalaglio	ENDPLUMED DISTANCE INCLUDE GROUP CENTER PRINT	generic colvar vatom core
19.053	Capillary fluctuations with PLUMED	methods	nucleation, surface tension, capillary fluctuations	Gareth Tribello	UNITS FOURIER_TRANSFORM FCCUBIC FIND_CONTOUR_SURFACE MULTICOLVARDENS GROUP MORE_THAN CENTER DUMPGRID	symfunc function contour setup vatom gridtools core fourier
19.045	Adsorption free energy of Ca/CO3 ions on calcite steps in contact with water	materials	metadynamics, well-tempered, multiple walkers, LAMMPS	Marco De La Pierre	UNITS COORDINATION METAD UPPER_WALLS PRINT GROUP LOWER_WALLS POSITION RESTART FLUSH	generic colvar setup bias core
19.028	pRAVE	methods	RAVE, reaction coordinate, deep learning, metadynamics, kinetics	Pratyush Tiwary	COMMITTOR TORSION DISTANCE ALPHABETA WHOLEMOLECULES COM COMBINE EXTERNAL RESTART PRINT	generic colvar multicolvar setup bias vatom function
19.025	Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide	bio	metainference, NMR, protein dynamics, force-fields	Carlo Camilloni	ENDPLUMED METAINFERENCE MOLINFO ENSEMBLE TORSION RDC GYRATION PRINT WHOLEMOLECULES BIASVALUE PBMETAD STATS CS2BACKBONE JCOUPLING FLUSH	isdb generic colvar bias function
19.010	Multi-domain protein dynamics	bio	metainference, NMR, protein dynamics	Carlo Camilloni	METAINFERENCE UPPER_WALLS MOLINFO ENSEMBLE TORSION DISTANCE RDC ENDPLUMED ALPHABETA GROUP WHOLEMOLECULES RESTRAINT DHENERGY PBMETAD CENTER STATS DIHCOR PRINT	isdb generic colvar multicolvar bias vatom core function
19.005	Cmyc small molecule interaction	bio	metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP	Gabriella Heller	COORDINATION METAINFERENCE MOLINFO DISTANCE GYRATION INCLUDE ALPHABETA GROUP WHOLEMOLECULES PBMETAD CENTER CS2BACKBONE PRINT	isdb generic colvar multicolvar bias vatom core
19.002	EMMI STRA6	bio	metainference, cryo-EM	Max Bonomi	MOLINFO GROUP EMMI BIASVALUE PRINT	bias generic core isdb
19.001	RNA SHAPE	bio	metadynamics, RNA, ligand binding	Giovanni Bussi	METAD UPPER_WALLS MOLINFO ANGLE DISTANCE ERMSD INCLUDE RANDOM_EXCHANGES FLUSH COMBINE LOWER_WALLS DISTANCES PRINT	generic colvar multicolvar bias 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	GROUP LOWER_WALLS FUNNEL COM FUNNEL_PS RMSD METAD ENERGY DISTANCE WRAPAROUND PRINT PYTORCH_MODEL UPPER_WALLS MATHEVAL WHOLEMOLECULES COORDINATION	function bias funnel vatom colvar pytorch core generic
26.001	Molecular simulations Alx riboswitch	bio	RNA, riboswitch	Giovanni Bussi	ERMSD MOLINFO DISTANCE PRINT RESTRAINT MOVINGRESTRAINT MATHEVAL	function generic bias colvar
24.035	Data efficient machine learning potentials for modeling catalytic reactivity via active learning and enhanced sampling	chemistry	opes, catalysis, ammonia, machine learning potentials	Luigi Bonati	RESTART GROUP UNITS LOWER_WALLS DISTANCE CUSTOM PRINT OPES_METAD COMMITTOR UPPER_WALLS COORDINATION	function bias opes colvar setup core generic
24.030	NMR guided simulation of dsRBD	bio	Metainference, NMR, protein dynamics	Debadutta Patra	GROUP RDC ENSEMBLE STATS ALPHABETA MOLINFO DISTANCE PRINT FLUSH METAINFERENCE WHOLEMOLECULES	function multicolvar colvar core isdb generic
24.011	Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble	methods	committor, machine learning	Peilin Kang	LOAD DISTANCE ENDPLUMED WHOLEMOLECULES GROUP UNITS CELL INCLUDE MATHEVAL LOWER_WALLS POSITION MOLINFO CUSTOM PRINT UPPER_WALLS COORDINATION TORSION BIASVALUE RMSD ENERGY	function bias colvar setup core generic
23.041	Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference	methods	EMMIVox, cryo-EM, single-structure refinement, ensemble refinement, Bayesian inference, B-factors, structural ensembles	Samuel Hoff	GROUP BIASVALUE EMMIVOX MOLINFO DISTANCE PRINT WRAPAROUND INCLUDE UPPER_WALLS WHOLEMOLECULES	bias colvar core isdb generic
23.037	Estimating binding free energy of solid binding peptides without extensive sampling	bio	metadynamics, solid binding peptides	Xin Qi	COM LOWER_WALLS PBMETAD MOLINFO DISTANCE PRINT GYRATION UPPER_WALLS	vatom generic bias colvar
23.036	Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water?	bio	NaCl, nucleation, metadynamics	Ruiyu Wang	Q4 METAD COMBINE COORDINATIONNUMBER ENERGY PRINT VOLUME Q6 MATHEVAL	function bias colvar generic symfunc
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	GHBFIX BIASVALUE METAD COMBINE ERMSD MOLINFO PRINT WHOLEMOLECULES COORDINATION	function generic bias colvar
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	GROUP SAXS BIASVALUE ENSEMBLE RMSD STATS CENTER MOLINFO DISTANCE PRINT WRAPAROUND UPPER_WALLS	function bias vatom colvar core isdb generic
23.025	Probing ion binding to G-quadruplexes and related events	chemistry	metadynamics, repulsive potential, nucleic acids, G-quadruplexes	Marcelo Poleto	RESTART FIT_TO_TEMPLATE GROUP LOWER_WALLS UNITS COM POSITION METAD DUMPATOMS DISTANCE WRAPAROUND DISTANCES PRINT FLUSH UPPER_WALLS MATHEVAL WHOLEMOLECULES	function bias vatom multicolvar colvar setup core generic
23.022	A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar	methods	collective variables, machine learning, toy model	Enrico Trizio	BIASVALUE UNITS LOWER_WALLS POSITION CUSTOM PRINT OPES_METAD ENDPLUMED PYTORCH_MODEL UPPER_WALLS	function bias opes colvar setup pytorch generic
23.010	An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G‑Protein-Coupled Receptor Ligands	bio	GPCR, binding free energy, free energy surface	Timothy Clark	BIASVALUE LOWER_WALLS METAD DISTANCE PRINT UPPER_WALLS MATHEVAL WHOLEMOLECULES CONSTANT	function colvar generic bias
23.005	A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs	bio	metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A	Timothy Clark	REWEIGHT_METAD CONVERT_TO_FES RMSD METAD READ MOLINFO DISTANCE PRINT HISTOGRAM DUMPGRID MATHEVAL WHOLEMOLECULES	function gridtools bias colvar generic
22.044	Colloid Crystallisation Analyses	materials	Q4, Q6, Pair Entropy, DFS	Aaron Finney	Q4 LOCAL_Q4 GROUP COMBINE MFILTER_MORE COORDINATIONNUMBER CONTACT_MATRIX DFSCLUSTERING MFILTER_LESS LOCAL_AVERAGE PRINT LOCAL_Q6 Q6 CLUSTER_NATOMS	function multicolvar adjmat clusters core generic symfunc
22.024	Conformational Entropy as a Potential Liability of Computationally Designed Antibodies	bio	metadynamics, conformational entropy, antibody, nanobody	Thomas Löhr	RESTART TORSION COM ALPHARMSD PBMETAD ALPHABETA MOLINFO PRINT ANTIBETARMSD WHOLEMOLECULES	bias vatom multicolvar colvar setup secondarystructure generic
22.018	Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations	bio	ligand binding, docking, EMMI, LAT1	Max Bonomi	GROUP BIASVALUE LOAD EMMIVOX MOLINFO PRINT WHOLEMOLECULES	bias setup core isdb generic
22.013	Ligand dissociation from PreQ1 riboswitch	bio	ligand, RNA, metadynamics, pRAVE	Yihang Wang	COM RMSD COMBINE METAD COORDINATIONNUMBER MOLINFO DISTANCE PRINT COMMITTOR WHOLEMOLECULES	function bias vatom colvar generic symfunc
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	LOWER_WALLS UNITS METAD COMBINE COM COORDINATIONNUMBER DISTANCE GYRATION FLUSH UPPER_WALLS COORDINATION	function bias vatom colvar setup generic symfunc
21.042	Peptoid-mediated Au nanocrystal growth	materials	parallel-bias metadynamics, peptoid, Au	Xin Qi	COM PBMETAD MOLINFO DISTANCE PRINT GYRATION UPPER_WALLS	vatom generic bias colvar
21.035	CmuMD simulations of NaCl(aq) at NaCl	chemistry	CmuMD, interface	Aaron Finney	GROUP LOAD DISTANCE PRINT RESTRAINT FIXEDATOM	bias vatom colvar setup core generic
21.033	Multiple-path-metadynamics applied to DNA base-pairing transitions	bio	path-CV, metadynamics, multiple-walker, dna	Alberto Pérez-de-Alba-Ortíz	METAD COMBINE PRINT INCLUDE RESTRAINT MOVINGRESTRAINT UPPER_WALLS CONSTANT	function generic bias
21.030	Thermodynamic Basis for Stabilization of Helical Peptoids by Chiral Sidechains	bio	parallel bias parallel tempered metadynamics in WTE, synthetic foldamers, self-assembly, peptoid secondary structure	Jim Pfaendtner	TORSION COM METAD PBMETAD ALPHABETA ENERGY DISTANCE INCLUDE PRINT GYRATION COORDINATION	bias vatom multicolvar colvar generic
21.008	Multi-replica biased sampling for photoisomerization processes in conjugated polymers	methods	metadynamics, FEP, replica-exchange	Adriana Pietropaolo	RESTART TORSION BIASVALUE PBMETAD PRINT MATHEVAL WHOLEMOLECULES CONSTANT	function bias colvar setup generic
20.015	Rational design of ASCT2 inhibitors using an integrated experimental-computational approach	bio	ASCT2 transporter, small-molecules, cryo-EM, metainference	Max Bonomi	GROUP BIASVALUE LOAD EMMIVOX MOLINFO DUMPATOMS PRINT WHOLEMOLECULES	bias setup core isdb generic
19.077	Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations	materials	metadynamics, peptide-surface binding	Jim Pfaendtner	COM METAD ENERGY MOLINFO DISTANCE PRINT GYRATION UPPER_WALLS	vatom generic bias colvar
19.071	Time-independent free energies from metadynamics via Mean Force Integration	methods	metadynamics, mean force integration, MFI, thermodynamic integration	Matteo Salvalaglio	REWEIGHT_METAD CONVERT_TO_FES TORSION BIASVALUE REWEIGHT_BIAS METAD HISTOGRAM DISTANCE PRINT EXTERNAL COMMITTOR READ DUMPGRID MATHEVAL	function gridtools bias colvar generic
19.064	Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations	materials	metadynamics, peptide-surface binding	Jim Pfaendtner	COM METAD ENERGY MOLINFO DISTANCE PRINT GYRATION UPPER_WALLS	vatom generic bias colvar
19.062	Elucidating molecular design principles for charge-alternating peptides	bio	peptide folding, metadynamics, well-tempered ensemble, parallel tempering	Jim Pfaendtner	METAD ENERGY PRINT GYRATION WHOLEMOLECULES	colvar generic bias
19.040	Optimal Metric for Path Collective Variables	bio	metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path	Francesco Luigi Gervasio	TORSION METAD PRINT ENDPLUMED MATHEVAL	function generic bias colvar
19.037	Scission free energy of organic dyes	chemistry	metadynamics, multiple walkers, matheval/lepton	Paolo Raiteri	RESTART UNITS METAD DISTANCE PRINT FLUSH UPPER_WALLS MATHEVAL	function bias colvar setup generic
19.036	Thermodynamics and kinetics of G protein-coupled receptor activation	bio	metadynamics, allostery, receptor conformation, GPCR, pharmacology	Davide Provasi	COM RMSD METAD CONTACTMAP DISTANCE FUNCPATHMSD PRINT ENDPLUMED WHOLEMOLECULES	function bias vatom colvar generic
19.031	Ice nucleation using PIV-based path coordinates	materials	phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics	Silvio Pipolo	LOWER_WALLS METAD CELL PIV FUNCPATHMSD PRINT UPPER_WALLS	function bias colvar piv generic
19.023	RECT	methods	metadynamics, replica exchange	Giovanni Bussi	TORSION METAD PRINT GYRATION WHOLEMOLECULES	generic bias colvar
19.004	MI Ubiquitin	bio	metainference, NMR	Max Bonomi	GROUP RDC CS2BACKBONE MOLINFO PRINT METAINFERENCE WHOLEMOLECULES	isdb generic core
25.022	Imidazole Diffusion in SALEM-2 MOF	materials	OPES, Diffusion, Ring opening, MOFs, Machine Learning Potentials	Sudheesh Kumar Ethirajan	OPES_METAD MOLINFO DISTANCE ENDPLUMED CENTER UNITS PROJECTION_ON_AXIS DISTANCES PRINT WHOLEMOLECULES GROUP	core opes multicolvar generic setup vatom colvar
25.018	Metainference simulation for dimerization of RNA binding protein	bio	Metainference, Metadynamics, SAXS, protein dimer	Debadutta Patra	SAXS MOLINFO GYRATION DISTANCE TORSION UPPER_WALLS PBMETAD CENTER PRINT ENSEMBLE WHOLEMOLECULES METAINFERENCE STATS FLUSH	isdb generic bias function vatom colvar
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	MOLINFO BIASVALUE PRINT EMMIVOX WHOLEMOLECULES GROUP	core generic bias isdb
25.011	Chiral perovskite nucleation	chemistry	metadynamics, chiral perovskites, nucleation	Adriana Pietropaolo	DISTANCE RESTART MATHEVAL UPPER_WALLS MULTI_RMSD PBMETAD UNITS PRINT LOWER_WALLS	generic bias setup function colvar
25.009	Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water	chemistry	metadynamics, nitrate photolysis	Kam-Tung Chan	DISTANCE RESTART REWEIGHT_METAD METAD HISTOGRAM DUMPGRID UPPER_WALLS COORDINATION CUSTOM PRINT READ FLUSH GROUP	core generic bias setup function gridtools colvar
25.004	Machine Learning-Driven Molecular Dynamics Unveil a Bulk Phase Transformation Driving Ammonia Synthesis on Barium Hydride	chemistry	OPES, OPES flooding, Catalysis, Ammonia Synthesis	Axel Tosello Gardini	ZDISTANCES OPES_METAD FIXEDATOM DISTANCE COMMITTOR UPPER_WALLS DISTANCES UNITS CUSTOM PRINT COORDINATIONNUMBER FLUSH GROUP	core opes multicolvar generic bias symfunc setup function vatom colvar
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	MOLINFO ENDPLUMED TORSION CENTER GROUP FIT_TO_TEMPLATE FIXEDATOM MATHEVAL RMSD UPPER_WALLS COORDINATION COMBINE DISTANCE METAD COMMITTOR CUSTOM OPES_METAD CONTACTMAP ANGLE PRINT WHOLEMOLECULES	core opes generic bias function vatom 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	OPES_METAD MOLINFO GYRATION DISTANCE TORSION CUSTOM COORDINATION COMBINE PRINT ALPHARMSD WHOLEMOLECULES	opes generic secondarystructure function colvar
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	PYTORCH_MODEL MOLINFO METAD RMSD UPPER_WALLS COORDINATION DRR LOWER_WALLS PRINT WHOLEMOLECULES FLUSH	drr pytorch generic bias colvar
24.012	Molecular simulations to investigate the impact of N6-methylation in RNA recognition	bio	metadynamics, alchemistry, RNA modification, RNA:protein interactions	Giovanni Bussi	MOLINFO DISTANCE METAD UPPER_WALLS BIASVALUE CENTER COORDINATION COMBINE PRINT GHBFIX COM DEBUG LOWER_WALLS GROUP	core generic bias function vatom colvar
24.002	Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes	chemistry	metadynamics, ligand design, solvent extraction	Xiaoyu Wang	RESTART TORSION METAD UNITS PRINT	bias generic colvar setup
23.019	Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors	bio	binding pathway, binding energy, sketch-map, drug development	Raitis Bobrovs	VORONOI DISSIMILARITIES DISTANCE COLLECT_FRAMES PATHMSD METAD TRANSPOSE UPPER_WALLS LANDMARK_SELECT_FPS SKETCHMAP CUSTOM SKETCHMAP_PROJECTION VSTACK PRINT COM WHOLEMOLECULES	landmarks valtools bias generic dimred function matrixtools vatom colvar
23.002	Critical comparison of general-purpose collective variables for crystal nucleation	methods	metadynamics, umbrella sampling, commitor, entropy, PIV	Julien Lam	ENERGY Q4 METAD PAIRENTROPY UPPER_WALLS LOCAL_AVERAGE CUSTOM UNITS PIV PRINT Q6 FUNCPATHMSD VOLUME RESTRAINT	piv generic bias symfunc setup function gridtools colvar
22.041	Skipping the Replica Exchange Ladder with Normalizing Flows	methods	OPES, alanine, normalizing flows, replica exchange	Michele Invernizzi	ENERGY OPES_METAD ENDPLUMED TORSION POSITION OPES_EXPANDED UNITS PRINT ECV_MULTITHERMAL	generic opes colvar setup
22.004	Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques	chemistry	reaction discovery, OPES, collective variables	Umberto Raucci	OPES_METAD_EXPLORE LOAD PYTORCH_MODEL DISTANCE OPES_METAD MATHEVAL UPPER_WALLS COORDINATION CUSTOM UNITS PRINT COM LOWER_WALLS GROUP	core pytorch opes generic bias setup function vatom colvar
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	ENDPLUMED METAD CUSTOM COORDINATION COMBINE PRINT VOLUME	function colvar generic bias
21.038	Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics	materials	metadynamics, SGOOP, nucleation, urea	Ziyue Zou	INCLUDE LOAD ENERGY METAD CENTER COMBINE PRINT COORDINATIONNUMBER VOLUME GROUP	core generic bias symfunc setup function vatom colvar
21.013	Role of vibrational excitation in heterogeneous catalysis	chemistry	catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption	Kristof Bal	REWEIGHT_BIAS DUMPGRID UNITS RESTRAINT EXTERNAL LOAD OPT_AVERAGED_SGD UWALLS REWEIGHT_METAD UPPER_WALLS COORDINATION COMBINE FLUSH CONVERT_TO_FES DISTANCE TD_GRID METAD HISTOGRAM ANGLES LOWER_WALLS DISTANCES PRINT COORDINATIONNUMBER VES_LINEAR_EXPANSION BF_CHEBYSHEV	setup multicolvar generic bias symfunc ves function gridtools colvar
21.012	NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition	bio	funnel metadynamics	Jim Pfaendtner	DISTANCE METAD UPPER_WALLS FUNNEL PRINT COM FUNNEL_PS LOWER_WALLS	generic bias funnel vatom colvar
20.026	Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor	bio	Metadynamics, Umbrella sampling	Brandon Peters	REWEIGHT_METAD METAD MULTI_RMSD HISTOGRAM DUMPGRID PRINT RESTRAINT CONVERT_TO_FES	gridtools colvar generic bias
20.019	Systematic finite-temperature reduction of crystal energy landscapes	materials	crystals, organics, structure prediction	Matteo Salvalaglio	ENERGY MATHEVAL METAD UPPER_WALLS PRINT CELL VOLUME LOWER_WALLS	function bias generic colvar
20.014	amyloid beta small molecule interaction	bio	intrinsically disordered proteins, disordered proteins, IDPs, fuzzy binding, small molecule, drugs, entropy, binding, Alzheimer’s disease, amyloid beta	Gabriella Heller	MOLINFO ENDPLUMED TORSION PBMETAD ENSEMBLE ANTIBETARMSD GROUP COORDINATION COMBINE METAINFERENCE FLUSH GYRATION PARABETARMSD STATS INCLUDE DIHCOR PRINT ALPHARMSD WHOLEMOLECULES CS2BACKBONE	core isdb multicolvar generic bias secondarystructure function colvar
20.012	Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies	bio	metadynamics, well-tempered ensemble, ligand binding, binding affinity calculations, novel COLVAR, funnel restraints, Hamiltonian replica-exchange, PathCV, COMetPath, SWISH	Francesco Gervasio	INCLUDE LOAD DISTANCE MOLINFO MATHEVAL CONTACTMAP CONSTANT METAD UPPER_WALLS BIASVALUE PROJECTION_ON_AXIS PRINT COM WHOLEMOLECULES FUNCPATHGENERAL LOWER_WALLS GROUP	core generic bias setup function vatom colvar
19.083	Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis	chemistry	metadynamics, chemical reactions, reaction discovery	Valerio Rizzi	RESTART ENDPLUMED METAD UPPER_WALLS DISTANCES UNITS COMBINE PRINT COORDINATIONNUMBER FLUSH GROUP	core multicolvar generic bias symfunc setup function
19.076	Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones	bio	molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics	Salvatore Assenza	GYRATION ENDPLUMED UNITS PRINT MOVINGRESTRAINT	bias generic colvar setup
19.075	PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python	other	Python, automatic differentiation	Toni Giorgino	DISTANCE TORSION ENDPLUMED ANGLE CENTER CUSTOM DUMPDERIVATIVES COMBINE PRINT RESTRAINT GROUP	core generic bias function vatom colvar
19.073	On the role of enthalpic and entropic contributions on the conformational free energy landscape of MIL-101(Cr) building units	materials	metadynamics, MOF, MIL101Cr, conformational	Matteo Salvalaglio	ENERGY GYRATION ENDPLUMED METAD UPPER_WALLS DISTANCES PRINT COORDINATIONNUMBER LOWER_WALLS	multicolvar generic bias symfunc colvar
19.072	SINE hairpin MD+NMR	bio	metadynamics, RNA, NMR	Giovanni Bussi	INCLUDE MAXENT MOLINFO DISTANCE MATHEVAL TORSION METAD COORDINATION SORT PRINT COM WHOLEMOLECULES FLUSH	generic bias function vatom colvar
19.068	Rethinking Metadynamics	methods	metadynamics, opes, convergence	Michele Invernizzi	EXTERNAL OPES_METAD TORSION METAD ENDPLUMED POSITION UNITS PRINT	opes generic bias setup colvar
19.066	Finding ligand unbinding reaction pathways	methods	maze, ligand unbinding	Jakub Rydzewski	MAZE_OPTIMIZER_BIAS POSITION MAZE_LOSS UNITS MAZE_SIMULATED_ANNEALING PRINT	maze generic colvar setup
19.061	Diffusion in porous materials	materials	metadynamics, porous materials, diffusion	Kim E. Jelfs	DISTANCE RESTART METAD UPPER_WALLS CENTER PRINT COM LOWER_WALLS GROUP	core generic bias setup 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	INCLUDE TORSION METAD RANDOM_EXCHANGES PRINT	bias generic colvar
19.054	MetaFEP	methods	metadynamics, chemistry, free energy perturbation	GiovanniMaria Piccini	ENERGY DISTANCE METAD UPPER_WALLS UNITS LOWER_WALLS COMBINE PRINT FLUSH	generic bias setup function colvar
19.051	Solid liquid interfacial free energy out of equilibrium	materials	metadynamics, nucleation, surface excess free energy	Gareth Tribello	FCCUBIC ENDPLUMED METAD AROUND UPPER_WALLS UNITS PRINT CELL LOWER_WALLS	volumes generic bias symfunc setup colvar
19.050	Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes	chemistry	metadynamics, membranes, Willard Chandler surface	Gareth Tribello	REWEIGHT_BIAS RESTART METAD HISTOGRAM DUMPGRID UPPER_WALLS COMBINE PRINT READ DISTANCE_FROM_CONTOUR CONVERT_TO_FES	generic bias setup contour function gridtools
19.049	Determining the sizes of solid/liquid clusters in MD trajectories of nucleation	methods	nucleation, metadynamics, clustering, Steinhardt order parameters	Gareth Tribello	SMAC DFSCLUSTERING CLUSTER_PROPERTIES METAD CONTACT_MATRIX OUTPUT_CLUSTER ONES DISTANCES CUSTOM MATRIX_VECTOR_PRODUCT CLUSTER_DISTRIBUTION CLUSTER_NATOMS PRINT LOCAL_Q6 Q6 MORE_THAN COORDINATIONNUMBER OUTER_PRODUCT	adjmat multicolvar generic bias clusters symfunc function matrixtools
19.032	Chemical reaction in solution using path collective variables based on coordination patterns	chemistry	chemical reactions, solutions, metadynamics, coordination patterns	Fabio Pietrucci	RESTART METAD UPPER_WALLS PATH DISTANCES PRINT FLUSH	mapping multicolvar generic bias setup
19.021	Coarse-Grained Directed Simulation	methods	experiment directed simulation, coarse-grain, bias	Glen Hocky	DISTANCE TORSION EDS COMBINE PRINT RESTRAINT	generic bias function colvar eds
19.019	FA-MetaD-JCP-Wang-et-al	bio	Frequency adaptive metadynamics; peptide	Kresten Lindorff-Larsen	MOLINFO METAD COMMITTOR COMBINE ALPHABETA PRINT FLUSH	multicolvar function generic bias
19.007	EMMI Microtubules	bio	metainference, cryo-EM	Max Bonomi	MOLINFO BIASVALUE EMMI PRINT WHOLEMOLECULES GROUP	core generic bias isdb
25.030	Committor Regularization	methods	metadynamics, enhanced sampling, mlcvs, committor, machine learning	Florian Dietrich	PRINT MOVINGRESTRAINT METAD UNITS	setup generic bias
25.015	Assessment of Force Fields for Describing Conformational Polymorphic Crystals of ROY	materials	Molecular crystal, Force Field, Collective Variable	Pradip Si and Omar Valsson	TORSIONS SMAC PRINT DUMPMULTICOLVAR DISTANCES	generic symfunc multicolvar
25.008	Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting	methods	metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting	Dhiman Ray	ENDPLUMED UPPER_WALLS ENERGY TORSION DISTANCE GROUP LOWER_WALLS UNITS CUSTOM PRINT PYTORCH_MODEL BIASVALUE WHOLEMOLECULES MOLINFO METAD RMSD POSITION OPES_METAD	core setup function colvar generic bias opes pytorch
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	DISTANCE TORSION MOVINGRESTRAINT RESTART PRINT RESTRAINT MOLINFO METAD PUCKERING	generic colvar setup bias
25.002	M3_PCV-ABMD	chemistry	Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor	Gian Marco Elisi	ENDPLUMED UPPER_WALLS ABMD UNITS PRINT PATHMSD	setup colvar generic bias
24.032	DeepLNE++	methods	PATHCV, OPES	Thorben Fröhlking	LOAD DISTANCE GROUP CUSTOM TORSION ENERGY COMBINE PRINT COORDINATION OPES_METAD	core setup function colvar generic opes
24.028	All-atom simulations of RNA-membrane interactions	bio	metadynamics, membrane, RNA	Giovanni Bussi	GHOST UPPER_WALLS MATHEVAL DISTANCE GROUP SORT LOWER_WALLS DISTANCES PRINT COMBINE PUCKERING WHOLEMOLECULES MOLINFO METAD GYRATION POSITION CENTER	core function colvar generic bias vatom multicolvar
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	UPPER_WALLS DISTANCE GROUP TORSION RESTART CUSTOM LOWER_WALLS PRINT PYTORCH_MODEL FIT_TO_TEMPLATE WHOLEMOLECULES PATH COORDINATION FIXEDATOM OPES_METAD CENTER	opes core mapping setup function colvar generic bias vatom pytorch
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	ENDPLUMED UPPER_WALLS MATHEVAL DISTANCE GROUP TORSION LOWER_WALLS OPES_METAD_EXPLORE ENERGY ECV_MULTITHERMAL PRINT CENTER FIT_TO_TEMPLATE OPES_EXPANDED WHOLEMOLECULES COORDINATION FIXEDATOM ANGLE	vatom core function colvar generic bias opes
24.018	A new route to the prebiotic synthesis of glycine via ab initio-based machine learning calculations	chemistry	prebiotic chemistry, glycine, Strecker synthesis, ab initio calculations, machine learning	Léon HUET	PRINT DISTANCE	colvar generic
24.010	Oxytocin metadynamics simulation	bio	metadynamics, oxytocin, peptide	Jan Beránek	FLUSH TORSION RESTART PRINT WHOLEMOLECULES METAD	bias colvar generic setup
24.006	Water vapor condensation	chemistry	metadynamics, homogeneous condensation, chemical potential	Shenghui Zhong	UPPER_WALLS CLUSTER_NATOMS UNITS DFSCLUSTERING PRINT CLUSTER_PROPERTIES METAD COORDINATIONNUMBER CONTACT_MATRIX	adjmat setup symfunc generic bias clusters
24.004	Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables	materials	metadynamics, nucleation, machine learning	Ziyue Zou	LOAD GROUP RESTART INCLUDE PRINT METAD	generic setup core bias
23.028	Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process	chemistry	Ammonia decomposition; Dynamics;OPES; Neural Network potential	Manyi Yang	FLUSH UPPER_WALLS MATHEVAL ENERGY GROUP UNITS DISTANCE ZDISTANCES LOWER_WALLS CUSTOM PRINT COMMITTOR DISTANCES OPES_METAD COM COORDINATIONNUMBER FIXEDATOM	vatom core setup symfunc function colvar generic bias opes multicolvar
23.021	Into the Dynamics of Rotaxanes at Atomistic Resolution	materials	metadynamics, rotaxanes, molecular shuttles, molecular machines	Luigi Leanza	UPPER_WALLS MATHEVAL DISTANCE TORSION CUSTOM PRINT METAD FIXEDATOM CENTER	function colvar generic bias vatom
23.011	OneOPES, a combined enhanced sampling method to rule them all	bio	OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding	Valerio Rizzi	ENDPLUMED DISTANCE ENERGY TORSION OPES_METAD_EXPLORE ECV_MULTITHERMAL PRINT OPES_EXPANDED MOLINFO METAD	colvar generic bias opes
22.023	Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy	bio	CryoEM, MEMMI,EMMI, Metadynamics, Metainference, IAPP, structural ensemble	Faidon Brotzakis	UPPER_WALLS GROUP TORSION RESTART EMMI PRINT PBMETAD BIASVALUE WHOLEMOLECULES MOLINFO RMSD COORDINATION COM	core setup isdb colvar generic bias vatom
22.005	Collective Variable for Metadynamics Derived from AlphaFold Output	bio	AlphaFold, protein folding, protein structure prediction, metadynamics, deep learning, free energy simulation, collective variable	Vojtech Spiwok	PRINT LOAD METAD WHOLEMOLECULES	bias generic setup
21.050	N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity	methods	bio	Isabell Louise Grothaus	PRINT DISTANCE CENTER	colvar generic vatom
21.048	Enhancing ligand exploration within a channel pore and fenestrations using metadynamics	bio	well-tempered metadynamics, protein-ligand enhanced sampling, sodium channel, Nav, small molecule drug	Elaine Tao	UPPER_WALLS DISTANCE TORSION UNITS CUSTOM LOWER_WALLS PRINT METAD COM	setup function colvar generic bias vatom
21.031	Photo-switchable sulfonulureas in KATP channel	bio	metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels	Katarzyna Walczewska-Szewc	UPPER_WALLS LOWER_WALLS DISTANCE UNITS PRINT WHOLEMOLECULES METAD COM	setup colvar generic bias vatom
21.028	From Enhanced Sampling to Reaction Profiles	methods	collective variables, multi-state, machine learning, Deep-TDA	Enrico Trizio	UPPER_WALLS LOWER_WALLS LOAD UNITS FIXEDATOM PRINT PYTORCH_MODEL OPES_METAD ANGLE ENDPLUMED MATHEVAL GROUP WHOLEMOLECULES CENTER FIT_TO_TEMPLATE DISTANCE TORSION COORDINATION DISTANCES	opes core setup multicolvar function colvar generic bias vatom pytorch
20.018	Free energy barriers from biased molecular dynamics simulations	methods	kinetics, free energy barriers, chemical reactions, nucleation, metadynamics	Kristof Bal	FLUSH VOLUME UPPER_WALLS LOAD LOWER_WALLS UNITS DUMPGRID PAIRENTROPY CONTACT_MATRIX COMBINE REWEIGHT_BIAS PRINT SPRINT DENSITY CONVERT_TO_FES LOCAL_AVERAGE HISTOGRAM ENERGY Q6 CENTER DISTANCE REWEIGHT_METAD METAD COORDINATION COORDINATIONNUMBER	gridtools adjmat setup symfunc volumes sprint function colvar generic bias vatom
20.007	Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics	bio	metadynamics, loop movement, artificial intelligence	Pratyush Tiwary	UPPER_WALLS DISTANCE TORSION RESTART COMBINE PRINT WHOLEMOLECULES RMSD METAD MOLINFO	setup function colvar generic bias
19.080	Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium	methods	ves, variationally enhanced sampling, vibrational excitation, chemical reactions	Kristof Bal	BF_CHEBYSHEV FLUSH UPPER_WALLS EXTERNAL TD_WELLTEMPERED DISTANCE LOWER_WALLS UNITS HISTOGRAM VES_LINEAR_EXPANSION PRINT COMBINE TD_GRID DUMPGRID COORDINATION OPT_AVERAGED_SGD CONVERT_TO_FES ANGLE	gridtools ves setup function colvar generic bias
19.074	Asymmetric base pair opening in nucleic acids	bio	double helix, DNA, RNA, unwindability	Giovanni Bussi	ENDPLUMED LOWER_WALLS DISTANCE RESTRAINT WHOLEMOLECULES COORDINATION	colvar generic bias
19.057	SAXS ensembles using Martini-Beads multi-scale SAXS	methods	metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics	Cristina Paissoni	SAXS ENSEMBLE ENDPLUMED MATHEVAL GROUP ALPHABETA INCLUDE COMBINE PRINT CENTER PBMETAD BIASVALUE STATS WHOLEMOLECULES MOLINFO COORDINATION ANGLE	function core isdb colvar generic bias vatom multicolvar
19.048	Understanding Ligand Binding Selectivity in a Prototypical GPCR Family	bio	metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding	Francesco Gervasio	UPPER_WALLS MATHEVAL LOWER_WALLS DISTANCE CONSTANT PRINT BIASVALUE WHOLEMOLECULES METAD COM	function colvar generic bias vatom
19.042	Harmonic Linear Discriminant Analysis (HLDA)	methods	metadynamics, chemistry, HLDA	GiovanniMaria Piccini	FLUSH UPPER_WALLS ENERGY DISTANCE UNITS COMBINE PRINT METAD	setup function colvar generic bias
19.015	Ibuprofen conformational dynamics and thermodynamics surface	materials	Ibuprofen, crystal, surface, solvents, conformers, metadynamics	Matteo Salvalaglio	UPPER_WALLS DISTANCE LOWER_WALLS TORSION PRINT COMMITTOR METAD CENTER	colvar generic bias vatom
19.003	EMMI ClpP	bio	metainference, cryo-EM	Max Bonomi	GROUP EMMI PRINT BIASVALUE MOLINFO	isdb generic core bias

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