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
26.008	Ensemble Dynamics	methods	State Exploration, Protein Folding, Drug Binding, Phase Transition	Florian M. Dietrich	CUSTOM LOAD TORSION DISTANCE BIASVALUE PRINT POSITION UNITS OPES_METAD_EXPLORE GROUP CELL	bias setup generic colvar function opes core
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	CENTER RMSD WRAPAROUND UPPER_WALLS MATHEVAL COMMITTOR CUSTOM METAD LOWER_WALLS PRINT FUNNEL FUNNEL_PS WHOLEMOLECULES COORDINATION DISTANCE TORSION OPES_METAD COM ENDPLUMED GROUP	vatom bias opes generic colvar function funnel core
25.006	Characterizing the conformational ensemble of PROTAC degraders in solutions via atomistic simulations	methods	Enhanced sampling, Atomistic simulations, Conformational ensemble, PROTACs, Targeted Protein Degradation, Chamelonic molecules	Shikshya Bhusal, Omar Valsson	VOLUME CENTER TORSION READ DISTANCE PRINT INCLUDE ENERGY RESTART MOLINFO GYRATION UPDATE_IF DUMPATOMS PBMETAD WHOLEMOLECULES	vatom bias setup generic colvar
24.026	Constant pH metadynamics of RNA oligomers	bio	metadynamics, pH, RNA	Giovanni Bussi	METAD PUCKERING TORSION PRINT RESTART MOLINFO	colvar bias setup generic
24.018	A new route to the prebiotic synthesis of glycine via ab initio-based machine learning calculations	chemistry	prebiotic chemistry, glycine, Strecker synthesis, ab initio calculations, machine learning	Léon HUET	DISTANCE PRINT	colvar generic
24.008	yCD Metadynamics	bio	volume-based MetaD, path CVs, infrequent MetaD, product release	James McCarty	PATH READ RMSD CONTACTMAP MOLINFO WRAPAROUND MATHEVAL UPPER_WALLS COMMITTOR METAD FLUSH PRINT FIXEDATOM DUMPGRID WHOLEMOLECULES COORDINATION DISTANCE INCLUDE FIT_TO_TEMPLATE HISTOGRAM REWEIGHT_METAD CONVERT_TO_FES COM ENDPLUMED GROUP	bias vatom generic mapping gridtools colvar function core
24.004	Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables	materials	metadynamics, nucleation, machine learning	Ziyue Zou	LOAD METAD PRINT INCLUDE RESTART GROUP	bias core setup generic
23.033	DNA G-quadruplex and G-hairpin folding with ST-metaD protocol	bio	DNA, G4, GQ, quadruplex, hairpin, folding, metadynamics, REST2, ST-metaD	Pavlína Pokorná	METAD COORDINATION BIASVALUE PRINT GHBFIX ERMSD MOLINFO COMBINE WHOLEMOLECULES	function colvar bias generic
23.031	Identifying small molecules binding sites in RNA conformational ensembles with SHAMAN	bio	RNA, metadynamics, probes, mixed-solvent MD, small molecules, binding sites	Max Bonomi	METAD CENTER SHADOW PRINT POSITION FIT_TO_TEMPLATE MOLINFO WRAPAROUND GROUP UPPER_WALLS DISTANCES WHOLEMOLECULES	vatom bias isdb generic colvar multicolvar core
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	REWEIGHT_METAD METAD DUMPGRID READ DISTANCE PRINT CONVERT_TO_FES RMSD MOLINFO MATHEVAL HISTOGRAM WHOLEMOLECULES	bias generic gridtools colvar function
23.015	MPCs aggregation	bio	opes_explore, dimerization, MPCs, self-assembly	Vikas Tiwari	CUSTOM METAD COORDINATION LOWER_WALLS CENTER DISTANCE PRINT COM OPES_METAD_EXPLORE GROUP UPPER_WALLS WHOLEMOLECULES	vatom bias generic colvar function opes core
23.011	OneOPES, a combined enhanced sampling method to rule them all	bio	OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding	Valerio Rizzi	METAD TORSION DISTANCE PRINT ENERGY ENDPLUMED OPES_EXPANDED ECV_MULTITHERMAL MOLINFO OPES_METAD_EXPLORE	colvar bias opes generic
23.008	PBMetaD simulations of Histatin5	bio	metadynamics, IDP, Rg, PPII	Francesco Pesce	TORSION PRINT GYRATION MOLINFO GROUP PBMETAD WHOLEMOLECULES	colvar bias core generic
23.006	Transcription factor unbinding	bio	metadynamics, DNA, conformational changes	Malin Lüking	ALPHARMSD METAD DISTANCE ANGLE PRINT COM DUMPFORCES CONTACTMAP MOLINFO	vatom bias secondarystructure generic colvar
22.045	Binding mode and mechanism of enzymatic polyethylene terephthalate degradation	bio	metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation	Francesco Colizzi	METAD LOWER_WALLS DISTANCE ANGLE PRINT COM MOVINGRESTRAINT UPPER_WALLS WHOLEMOLECULES	vatom colvar bias generic
22.044	Colloid Crystallisation Analyses	materials	Q4, Q6, Pair Entropy, DFS	Aaron Finney	DFSCLUSTERING LOCAL_Q6 CLUSTER_NATOMS PRINT CONTACT_MATRIX MFILTER_LESS COORDINATIONNUMBER Q6 MFILTER_MORE GROUP LOCAL_AVERAGE LOCAL_Q4 COMBINE Q4	generic symfunc adjmat clusters multicolvar function core
22.041	Skipping the Replica Exchange Ladder with Normalizing Flows	methods	OPES, alanine, normalizing flows, replica exchange	Michele Invernizzi	TORSION OPES_METAD PRINT POSITION UNITS ENERGY ENDPLUMED OPES_EXPANDED ECV_MULTITHERMAL	colvar opes setup generic
22.021	Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations	chemistry	Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella	Sigbjørn Løland Bore	LOWER_WALLS ENVIRONMENTSIMILARITY PRINT INCLUDE ECV_UMBRELLAS_LINE OPES_EXPANDED UPPER_WALLS	envsim bias opes generic
21.042	Peptoid-mediated Au nanocrystal growth	materials	parallel-bias metadynamics, peptoid, Au	Xin Qi	DISTANCE PRINT COM UPPER_WALLS GYRATION MOLINFO PBMETAD	colvar vatom generic bias
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	VOLUME BF_LEGENDRE ENVIRONMENTSIMILARITY PRINT MATHEVAL ENERGY OPT_AVERAGED_SGD ECV_UMBRELLAS_LINE VES_LINEAR_EXPANSION RESTART OPES_EXPANDED TD_UNIFORM ECV_MULTITHERMAL_MULTIBARIC Q6 UPPER_WALLS	bias setup generic symfunc colvar envsim function ves opes
20.000	Muscarinic M2 receptor-ligand funnel metadynamics	bio	multiple walker metadynamics, well-tempered metadynamics, funnel metadynamics, MC-HLDA, GPCR, receptor, Adiabatic Bias MD	Riccardo Capelli	REWEIGHT_METAD METAD LOWER_WALLS DUMPGRID READ DISTANCE ABMD PRINT COM MATHEVAL CONVERT_TO_FES ENDPLUMED UPPER_WALLS HISTOGRAM COMBINE	vatom bias generic gridtools colvar function
19.065	Molecular Enhanced Sampling with Autoencoders	methods	enhanced sampling, collective variables, deep learning	Wei Chen	POSITION COM ANN COMBINE RESTRAINT	vatom bias colvar annfunc function
19.064	Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations	materials	metadynamics, peptide-surface binding	Jim Pfaendtner	METAD DISTANCE PRINT COM ENERGY GYRATION MOLINFO UPPER_WALLS	vatom colvar bias generic
19.040	Optimal Metric for Path Collective Variables	bio	metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path	Francesco Luigi Gervasio	METAD TORSION PRINT ENDPLUMED MATHEVAL	function colvar bias generic
19.038	native state dynamics of human and mouse b2m	bio	metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation	Carlo Camilloni	ANTIBETARMSD LOWER_WALLS PBMETAD FLUSH BIASVALUE PRINT ENDPLUMED RESTART MOLINFO ALPHABETA GROUP UPPER_WALLS CS2BACKBONE WHOLEMOLECULES	bias setup isdb secondarystructure generic multicolvar core
19.028	pRAVE	methods	RAVE, reaction coordinate, deep learning, metadynamics, kinetics	Pratyush Tiwary	TORSION DISTANCE PRINT COM RESTART EXTERNAL COMMITTOR ALPHABETA COMBINE WHOLEMOLECULES	vatom bias setup generic colvar multicolvar function
19.020	PTMetaD-WTE simulation of the Ntail IDP	bio	metadynamics, IDPs, protein folding	Mattia Bernetti	ALPHARMSD METAD PRINT ENERGY ENDPLUMED GYRATION MOLINFO WHOLEMOLECULES	colvar secondarystructure generic bias
19.017	Ligand binding pathways exploration	bio	metadynamics, ligand binding	Riccardo Capelli	REWEIGHT_METAD METAD COORDINATION DUMPGRID FLUSH READ POSITION COM PRINT MATHEVAL FIT_TO_TEMPLATE CONVERT_TO_FES ENDPLUMED WRAPAROUND GROUP UPPER_WALLS HISTOGRAM WHOLEMOLECULES	vatom bias generic gridtools colvar function core
19.010	Multi-domain protein dynamics	bio	metainference, NMR, protein dynamics	Carlo Camilloni	RESTRAINT RDC CENTER ALPHABETA TORSION DISTANCE PRINT ENDPLUMED DHENERGY METAINFERENCE ENSEMBLE MOLINFO UPPER_WALLS DIHCOR GROUP PBMETAD STATS WHOLEMOLECULES	vatom bias isdb generic colvar multicolvar function core
19.000	VesDeltaF	methods	VES, convergence, suboptimal CVs	Michele Invernizzi	LOAD METAD TORSION PRINT POSITION UNITS ENERGY ENDPLUMED RESTART VES_DELTA_F	bias setup generic colvar ves
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	RMSD CENTER PATH OPES_EXPANDED PATHMSD LOWER_WALLS VOLUME ENERGY ECV_MULTITHERMAL CUSTOM COORDINATION UPPER_WALLS OPES_METAD_EXPLORE GROUP PRINT DISTANCE	core mapping vatom function colvar opes bias generic
25.030	Committor Regularization	methods	metadynamics, enhanced sampling, mlcvs, committor, machine learning	Florian Dietrich	MOVINGRESTRAINT METAD UNITS PRINT	bias setup generic
25.029	Energetic Constraints in the Enzymatic Depolymerization of Crystalline PET from enhanced molecular simulations	bio	HREX-Metadynamics, PETase, crystalline PET, amorphous PET, conformational ensembles, substrate binding, chain detachment	Ania Di Pede-Mattatelli and Francesco Colizzi	METAD HISTOGRAM REWEIGHT_BIAS WHOLEMOLECULES LOWER_WALLS FIXEDATOM UPPER_WALLS COM CONVERT_TO_FES DUMPGRID MOLINFO PRINT DISTANCE	gridtools vatom colvar bias generic
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	SMAC DISTANCES TORSIONS DUMPMULTICOLVAR PRINT	symfunc multicolvar generic
25.012	A Machine Learning-Driven, Probability-Based Approach to Enzyme Catalysis	bio	enzyme catalysis, transition state, structure-activity relationship, free energy surface, reaction mechanism, water, alpha-amylase, sugar, QM/MM MD, OPES, committor function, machine learning	Sudip Das	CELL OPES_METAD POSITION LOAD MATHEVAL UNITS FLUSH ENERGY TORSION COORDINATION CUSTOM COMBINE BIASVALUE INCLUDE PRINT DISTANCE	setup function colvar opes bias generic
25.010	Kinetic rates calculation with Ratchet&Pawl MD	methods	kinetics, ligand binding, ABMD, ratchet&pawl MD	Riccardo Capelli	ABMD WHOLEMOLECULES FLUSH COM COMMITTOR GROUP PRINT DISTANCE	core vatom colvar bias generic
24.031	DeepLNE	methods	PATHCV, OPES, OneOPES	Thorben Fröhlking	OPES_EXPANDED PYTORCH_MODEL VOLUME ENERGY RESTART ECV_MULTITHERMAL ERMSD COORDINATION OPES_METAD_EXPLORE COMBINE MOLINFO PRINT	setup pytorch function colvar opes generic
24.029	Combination of OPES and OPES-Explore	methods	OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin	Dhiman Ray	RMSD UNITS FIXEDATOM ENDPLUMED CUSTOM OPES_METAD_EXPLORE FIT_TO_TEMPLATE GROUP PYTORCH_MODEL COORDINATION CONTACTMAP DISTANCE CENTER METAD OPES_METAD WHOLEMOLECULES LOWER_WALLS ENERGY COMBINE UPPER_WALLS INCLUDE PRINT POSITION MATHEVAL FLUSH BIASVALUE MOLINFO	core setup pytorch vatom function colvar opes bias generic
23.032	Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics	bio	metadynamics, tSNE, neural network, machine learning, trp-cage, folding	Vojtech Spiwok	METAD POSITION WHOLEMOLECULES ANN ALPHARMSD COMBINE FIT_TO_TEMPLATE MOLINFO PRINT	secondarystructure function annfunc colvar bias generic
23.025	Probing ion binding to G-quadruplexes and related events	chemistry	metadynamics, repulsive potential, nucleic acids, G-quadruplexes	Marcelo Poleto	METAD POSITION DISTANCES WHOLEMOLECULES UNITS WRAPAROUND LOWER_WALLS MATHEVAL FLUSH RESTART COM UPPER_WALLS FIT_TO_TEMPLATE DUMPATOMS GROUP PRINT DISTANCE	core setup vatom function multicolvar colvar bias generic
23.023	Rational design of novel biomimetic sequence-defined polymers for mineralization applications	methods	metadynamics, surface binding, biomimetic mineralization	Kaylyn Torkelson	PBMETAD COORDINATION GYRATION UPPER_WALLS COM PRINT DISTANCE	bias vatom colvar 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	METAD CONSTANT WHOLEMOLECULES MATHEVAL LOWER_WALLS UPPER_WALLS BIASVALUE PRINT DISTANCE	bias function colvar generic
23.001	Quantum phase diagram of water	chemistry	Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella	Sigbjørn-Løland Bore	ENVIRONMENTSIMILARITY OPES_EXPANDED LOWER_WALLS RESTART UPPER_WALLS INCLUDE PRINT ECV_UMBRELLAS_LINE	opes setup envsim 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	METAD PATHMSD FLUSH CUSTOM DRR BIASVALUE PRINT	drr function colvar bias generic
22.004	Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques	chemistry	reaction discovery, OPES, collective variables	Umberto Raucci	OPES_METAD LOAD MATHEVAL UNITS PYTORCH_MODEL LOWER_WALLS COORDINATION CUSTOM COM UPPER_WALLS OPES_METAD_EXPLORE GROUP PRINT DISTANCE	core setup pytorch vatom function colvar opes bias generic
21.052	On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets	materials	Ibuprofen, unbinding, WTmetaD	Matteo Salvalaglio	METAD CENTER COORDINATIONNUMBER ENDPLUMED TORSION COMMITTOR PRINT DISTANCE	symfunc vatom colvar bias generic
21.035	CmuMD simulations of NaCl(aq) at NaCl	chemistry	CmuMD, interface	Aaron Finney	LOAD RESTRAINT FIXEDATOM GROUP PRINT DISTANCE	core setup vatom colvar bias generic
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	METAD RANDOM_EXCHANGES PBMETAD ENDPLUMED TORSION INCLUDE PRINT	bias colvar generic
21.031	Photo-switchable sulfonulureas in KATP channel	bio	metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels	Katarzyna Walczewska-Szewc	METAD WHOLEMOLECULES UNITS LOWER_WALLS UPPER_WALLS COM PRINT DISTANCE	setup vatom colvar bias generic
21.030	Thermodynamic Basis for Stabilization of Helical Peptoids by Chiral Sidechains	bio	parallel bias parallel tempered metadynamics in WTE, synthetic foldamers, self-assembly, peptoid secondary structure	Jim Pfaendtner	METAD PBMETAD ENERGY TORSION COORDINATION GYRATION COM INCLUDE ALPHABETA PRINT DISTANCE	vatom multicolvar colvar bias generic
21.029	Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs	bio	metadynamics, small peptide, machine learning	Pratyush Tiwary	EXTERNAL FLUSH ENERGY RESTART TORSION MOLINFO PRINT	bias setup colvar generic
21.023	Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling	methods	enhanced sampling, collective variables, machine learning	Jakub Rydzewski	METAD REWEIGHT_METAD CONSTANT UNITS ENERGY TORSION CUSTOM BIASVALUE INCLUDE PRINT DISTANCE	setup function colvar bias generic
21.022	Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly	materials	parallel bias metadynamics, adsorption, peptide	Xin Qi	LOWER_WALLS PBMETAD ENERGY GYRATION COM UPPER_WALLS MOLINFO PRINT DISTANCE	bias vatom colvar generic
21.011	CmuMD simulations of NaCl(aq) at graphite	chemistry	CmuMD, DFS clustering	Aaron Finney	MULTICOLVARDENS MFILTER_MORE AROUND LOAD COORDINATIONNUMBER RESTRAINT CLUSTER_NATOMS CLUSTER_DISTRIBUTION DENSITY FIXEDATOM CONTACT_MATRIX DFSCLUSTERING DUMPGRID GROUP PRINT	core symfunc clusters setup gridtools adjmat vatom multicolvar volumes bias generic
20.034	Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations	bio	RNA, SARS-CoV-2, partial tempering	Sandro Bottaro	CENTER RESTART ERMSD TORSION ABMD MOLINFO PRINT DISTANCE	setup vatom colvar bias generic
20.032	Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil	materials	clustering, conformational isomers	Matteo Salvalaglio	ENDPLUMED TORSION PRINT	colvar generic
20.026	Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor	bio	Metadynamics, Umbrella sampling	Brandon Peters	METAD REWEIGHT_METAD HISTOGRAM RESTRAINT MULTI_RMSD CONVERT_TO_FES DUMPGRID PRINT	generic bias colvar gridtools
20.004	Data-driven collective variables for enhanced sampling	methods	collective variables, machine learning, deep-lda	Luigi Bonati	OPES_METAD LOAD MATHEVAL PYTORCH_MODEL UNITS LOWER_WALLS FLUSH ENDPLUMED TORSION COM UPPER_WALLS GROUP PRINT DISTANCE	core setup pytorch vatom function colvar opes bias generic
19.082	Ammonia Borane Dehydrogenation	chemistry	metadynamics, reaction discovery, hydrogen production, chemistry	Valerio Rizzi	METAD EXTERNAL COORDINATIONNUMBER UNITS FLUSH RESTART ENDPLUMED COMBINE GROUP PRINT	core symfunc setup function bias generic
19.071	Time-independent free energies from metadynamics via Mean Force Integration	methods	metadynamics, mean force integration, MFI, thermodynamic integration	Matteo Salvalaglio	METAD EXTERNAL HISTOGRAM REWEIGHT_METAD REWEIGHT_BIAS MATHEVAL TORSION DUMPGRID CONVERT_TO_FES BIASVALUE COMMITTOR PRINT READ DISTANCE	gridtools function colvar bias generic
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	METAD POSITION UNITS LOWER_WALLS FLUSH RESTART COORDINATION UPPER_WALLS GROUP PRINT	core setup colvar bias 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	METAD ENERGY UPPER_WALLS COM PRINT DISTANCE	bias vatom colvar generic
19.035	Dimerization of GPCRs from coarse-grained umbrella sampling	bio	Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization	Davide Provasi	RESTRAINT TORSION COM GROUP PRINT DISTANCE	core vatom colvar bias generic
19.025	Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide	bio	metainference, NMR, protein dynamics, force-fields	Carlo Camilloni	STATS METAINFERENCE WHOLEMOLECULES PBMETAD JCOUPLING FLUSH ENDPLUMED TORSION GYRATION ENSEMBLE RDC CS2BACKBONE BIASVALUE MOLINFO PRINT	isdb function colvar bias generic
19.019	FA-MetaD-JCP-Wang-et-al	bio	Frequency adaptive metadynamics; peptide	Kresten Lindorff-Larsen	METAD FLUSH COMBINE COMMITTOR ALPHABETA MOLINFO PRINT	bias function multicolvar generic
19.011	Automatic Gradient Computation for Collective Variables	other	gradient, differentiation, curvature	Toni Giorgino	ENDPLUMED	generic
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	COORDINATION RMSD FUNNEL PRINT FUNNEL_PS UPPER_WALLS WRAPAROUND WHOLEMOLECULES PYTORCH_MODEL ENERGY DISTANCE METAD LOWER_WALLS COM MATHEVAL GROUP	function pytorch core bias funnel generic vatom colvar
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	PRINT MOVINGRESTRAINT SAXS GYRATION INCLUDE UPPER_WALLS WHOLEMOLECULES DISTANCE METAD CENTER MOLINFO GROUP	core bias isdb generic vatom colvar
25.019	The Arch from the Stones. Understanding Protein Folding Energy Landscapes via Bio-inspired Collective Variables	bio	protein folding, OPES, OneOPES, binding free energy	Valerio Rizzi	COORDINATION RMSD PRINT COMBINE OPES_METAD_EXPLORE OPES_EXPANDED GHOST ENERGY DISTANCE ECV_MULTITHERMAL CENTER MOLINFO CUSTOM GROUP	function core opes generic 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	PRINT EMMIVOX WHOLEMOLECULES BIASVALUE MOLINFO GROUP	generic core bias isdb
25.014	Atomic resolution ensembles of intrinsically disordered proteins with Alphafold	bio	bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement	Vincent Schnapka	PRINT BAIES BIASVALUE GROUP	generic core bias isdb
25.001	RNA G-quadruplex folding with ST-metaD protocol	bio	RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD	Pavlína Pokorná	COMBINE WHOLEMOLECULES METAD MOLINFO ERMSD	generic function bias colvar
24.036	Leveraging cryptic ligand envelopes through enhanced molecular simulations	bio	HREX, conformational heterogeneity, drug discovery, ligand binding, plitidepsin, aplidin, ligand-target complexes, cryptic ligand envelope	Francesco Colizzi	COORDINATION PRINT DUMPGRID WHOLEMOLECULES DISTANCE HISTOGRAM TORSION ANGLE CONVERT_TO_FES GROUP	generic gridtools core colvar
24.034	Umbrella sampling of ion in transporter SLC26A7	bio	umbrella sampling, transporter, ions	Xiaoli Lu	POSITION UNITS PRINT RESTRAINT	generic bias setup colvar
24.028	All-atom simulations of RNA-membrane interactions	bio	metadynamics, membrane, RNA	Giovanni Bussi	PRINT COMBINE DISTANCES GYRATION UPPER_WALLS MATHEVAL WHOLEMOLECULES GHOST DISTANCE METAD CENTER PUCKERING MOLINFO LOWER_WALLS POSITION SORT GROUP	function core multicolvar bias generic vatom colvar
24.017	Absolute Binding Free Energies with OneOPES	methods	protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy	Francesco Gervasio	RMSD OPES_METAD_EXPLORE OPES_EXPANDED PROJECTION_ON_AXIS RESTART GROUP PRINT COM MATHEVAL WRAPAROUND WHOLEMOLECULES MOLINFO BIASVALUE COORDINATION CONSTANT INCLUDE UPPER_WALLS CONTACTMAP ENERGY ECV_MULTITHERMAL METAD TORSION LOWER_WALLS CUSTOM	function core vatom setup bias generic opes colvar
24.010	Oxytocin metadynamics simulation	bio	metadynamics, oxytocin, peptide	Jan Beránek	PRINT FLUSH WHOLEMOLECULES METAD TORSION RESTART	generic bias setup colvar
24.009	Weighted Shape Gaussian Mixture Models	bio	metadynamics, clustering	Glen Hocky	PRINT UNITS METAD TORSION GROUP	core bias setup generic colvar
23.039	Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation	chemistry	metadynamics, ligand dissociation	Eric Beyerle	RESTRAINT COMBINE PRINT DUMPMASSCHARGE UPPER_WALLS DISTANCE FIXEDATOM METAD CENTER MOLINFO	function bias generic vatom colvar
23.021	Into the Dynamics of Rotaxanes at Atomistic Resolution	materials	metadynamics, rotaxanes, molecular shuttles, molecular machines	Luigi Leanza	PRINT UPPER_WALLS DISTANCE FIXEDATOM METAD CENTER TORSION CUSTOM MATHEVAL	function bias generic vatom colvar
23.018	Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention	materials	metadynamics, surface binding, peptide adsorption	Kaylyn Torkelson	PRINT GYRATION UPPER_WALLS DISTANCE COM PBMETAD	generic vatom bias colvar
23.013	Path meta-eABF simulation of large scale conformational change in STING protein	methods	meta-eABF, path CV, large scale conformational change, STING protein, reciprocal barrier restraint	Istvan Kolossvary	PRINT UPPER_WALLS UNITS PATHMSD FLUSH DRR TIME METAD BIASVALUE LOWER_WALLS CUSTOM	function bias setup drr generic colvar
22.038	Enhanced Sampling Aided Design of Molecular Photoswitches	chemistry	reaction discovery, OPES explore, graph CV	Umberto Raucci	COORDINATION PRINT OPES_METAD_EXPLORE UNITS PYTORCH_MODEL CUSTOM	function pytorch setup generic opes colvar
22.034	Rationalising the difference in crystallisability of two Sulflowers using efficient in silico methods	materials	metadynamics, crystallizability, crystal structure prediction, sulflower, persulforated coronene	Matteo Salvalaglio	PRINT UPPER_WALLS MATHEVAL COMMITTOR DRMSD METAD LOWER_WALLS CUSTOM CELL	generic function bias colvar
22.024	Conformational Entropy as a Potential Liability of Computationally Designed Antibodies	bio	metadynamics, conformational entropy, antibody, nanobody	Thomas Löhr	RESTART ALPHABETA PRINT ALPHARMSD ANTIBETARMSD WHOLEMOLECULES MOLINFO TORSION COM PBMETAD	multicolvar setup bias generic vatom secondarystructure colvar
22.005	Collective Variable for Metadynamics Derived from AlphaFold Output	bio	AlphaFold, protein folding, protein structure prediction, metadynamics, deep learning, free energy simulation, collective variable	Vojtech Spiwok	LOAD PRINT METAD WHOLEMOLECULES	generic bias setup
21.049	Multiple-path-metadynamics and PathMaps	methods	path-CV, metadynamics, multiple-walker, multiple paths, pathmap	Alberto Pérez-de-Alba-Ortíz	PRINT COMBINE RESTRAINT MOVINGRESTRAINT CONSTANT UNITS UPPER_WALLS ENSEMBLE LOAD METAD TORSION LOWER_WALLS CUSTOM	function bias setup generic colvar
21.046	Ubiquitin Interacting Motifs, Duality Between Structured and Disordered Motifs	bio	wt metadynamics, ubiquitin, ataxin-3, short linear motifs, ubiquitin binding motif, moonlight functions, intrinsic disorder	Elena Papaleo	ALPHABETA PRINT ENDPLUMED GYRATION UPPER_WALLS WHOLEMOLECULES METAD LOWER_WALLS GROUP	core multicolvar bias generic 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	COORDINATION PRINT COMBINE VOLUME ENDPLUMED METAD CUSTOM	generic function bias colvar
21.026	Probing allosteric regulations with coevolution-driven molecular simulations	bio	metadynamics, coevolution, allostery, adenylate cyclase	Francesco Colizzi	PRINT UPPER_WALLS UNITS PATHMSD WHOLEMOLECULES DISTANCE METAD COM	bias setup generic vatom colvar
21.012	NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition	bio	funnel metadynamics	Jim Pfaendtner	FUNNEL_PS FUNNEL PRINT UPPER_WALLS DISTANCE METAD LOWER_WALLS COM	bias funnel generic vatom colvar
20.030	Converging experimental and computational views of the knotting mechanism of the smallest knotted protein	bio	phi-values, transition state, knotted proteins	Cristina Paissoni	COORDINATION RESTRAINT COMBINE PRINT WHOLEMOLECULES MOLINFO STATS	generic function bias colvar
20.025	The role of water in host-guest interaction	bio	ligand binding, water, opes, SAMPL5	Valerio Rizzi	COORDINATION PRINT GROUP ENDPLUMED UPPER_WALLS PYTORCH_MODEL WHOLEMOLECULES ENERGY DISTANCE FIXEDATOM FIT_TO_TEMPLATE CENTER OPES_METAD MATHEVAL ANGLE	function pytorch core bias opes generic vatom 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	PRINT CONSTANT INCLUDE FUNCPATHGENERAL UPPER_WALLS WHOLEMOLECULES COM CONTACTMAP DISTANCE LOAD METAD BIASVALUE LOWER_WALLS MOLINFO PROJECTION_ON_AXIS MATHEVAL GROUP	function core bias setup generic vatom colvar
19.077	Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations	materials	metadynamics, peptide-surface binding	Jim Pfaendtner	PRINT GYRATION UPPER_WALLS ENERGY DISTANCE METAD MOLINFO COM	generic vatom bias colvar
19.070	Unexpected Dynamics in the UUCG RNA Tetraloop	bio	well-tempered metadynamics, RNA, UUCG, maximum entropy	Sandro Bottaro	RMSD PRINT WHOLEMOLECULES DISTANCE METAD TORSION MOLINFO ERMSD	generic bias colvar
19.068	Rethinking Metadynamics	methods	metadynamics, opes, convergence	Michele Invernizzi	POSITION PRINT ENDPLUMED UNITS EXTERNAL METAD TORSION OPES_METAD	bias setup generic opes colvar
19.043	Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA)	methods	metadynamics, chemistry, HLDA	GiovanniMaria Piccini	PRINT COMBINE DISTANCES UNITS UPPER_WALLS FLUSH DISTANCE METAD RESTART	function multicolvar bias setup generic colvar
19.029	WTE-metaD of FF domain of URNF1 C57D variant	bio	metadynamics, mutations, post-translational modification, ff domain	Elena Papaleo	ALPHABETA PRINT GYRATION UPPER_WALLS WHOLEMOLECULES METAD MOLINFO LOWER_WALLS GROUP	core multicolvar bias generic colvar
19.018	Excited state FEP/Metadynamics simulations	chemistry	metadynamics, FEP, excited states, conjugated polymers, torsional potential	Adriana Pietropaolo	PRINT CONSTANT WHOLEMOLECULES METAD BIASVALUE TORSION MATHEVAL	generic function bias colvar
25.022	Imidazole Diffusion in SALEM-2 MOF	materials	OPES, Diffusion, Ring opening, MOFs, Machine Learning Potentials	Sudheesh Kumar Ethirajan	CENTER PROJECTION_ON_AXIS UNITS MOLINFO DISTANCE GROUP ENDPLUMED WHOLEMOLECULES PRINT DISTANCES OPES_METAD	generic core colvar setup opes multicolvar vatom
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	CENTER FIXEDATOM MATHEVAL ENERGY DISTANCE GROUP COORDINATION WHOLEMOLECULES FIT_TO_TEMPLATE UPPER_WALLS PRINT OPES_METAD_EXPLORE ANGLE	generic core colvar function bias opes vatom
25.018	Metainference simulation for dimerization of RNA binding protein	bio	Metainference, Metadynamics, SAXS, protein dimer	Debadutta Patra	SAXS CENTER STATS ENSEMBLE PBMETAD MOLINFO DISTANCE METAINFERENCE WHOLEMOLECULES FLUSH UPPER_WALLS PRINT TORSION GYRATION	generic bias function colvar isdb vatom
25.016	Advancing in silico drug design with Bayesian refinement of AlphaFold models	bio	bAIes, AlphaFold, Bayesian refinement, virtual screening, docking, small-molecule, enrichment	Samiran Sen	GROUP PRINT BAIES BIASVALUE	generic isdb bias core
24.033	Transient interactions between the fuzzy coat and the cross-b core of brain-derived Ab42 filaments	bio	CryoEM, MEMMI, Metadynamics, Metainference, Ab42 Fibrils, structural ensemble	Maria Milanesi	RMSD CENTER EMMI BIASVALUE PBMETAD PARABETARMSD MOLINFO DISTANCE GROUP DUMPATOMS WHOLEMOLECULES DUMPMASSCHARGE UPPER_WALLS ALPHARMSD PRINT COORDINATION COM	generic core bias colvar secondarystructure isdb vatom
24.032	DeepLNE++	methods	PATHCV, OPES	Thorben Fröhlking	ENERGY DISTANCE GROUP LOAD CUSTOM PRINT COORDINATION COMBINE TORSION OPES_METAD	generic core colvar function setup opes
24.023	Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21. A Machine-Learning-Aided Enhanced Sampling Study	bio	RNA, miRNA, OneOPES, ligand binding, conformational changes	Valerio Rizzi	ECV_MULTITHERMAL ENERGY DISTANCE GROUP RESTART COORDINATION OPES_EXPANDED CUSTOM PRINT OPES_METAD_EXPLORE COMBINE TORSION	generic core colvar setup function opes
24.002	Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes	chemistry	metadynamics, ligand design, solvent extraction	Xiaoyu Wang	METAD PRINT RESTART UNITS TORSION	generic colvar bias setup
23.040	Supramolecular capsules assembly dynamics	chemistry	Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics	Riccardo Capelli	CENTER METAD UNITS DISTANCE GROUP WHOLEMOLECULES CUSTOM POSITION PRINT DISTANCES FLUSH COM	generic core colvar bias setup function multicolvar vatom
23.036	Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water?	bio	NaCl, nucleation, metadynamics	Ruiyu Wang	COORDINATIONNUMBER METAD MATHEVAL ENERGY Q4 Q6 VOLUME PRINT COMBINE	generic symfunc bias colvar function
23.026	Machine Learning Nucleation Collective Variables with Graph Neural Networks	chemistry	Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks	Florian Dietrich	MFILTER_MORE COORDINATIONNUMBER LOCAL_Q6 LOWER_WALLS METAD Q6 GROUP MOVINGRESTRAINT PRINT COMBINE	generic symfunc core bias function multicolvar
23.024	Permutationally Invariant Networks for Enhanced Sampling (PINES)	methods	collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent	Nicholas Herringer	PBMETAD LOAD PRINT	generic bias setup
23.014	Structural basis of dimerization of chemokine receptors CCR5 and CXCR4	bio	metadynamics, oligomerization, chemokine receptors, GPCR, membrane	Vittorio Limongelli	METAD DISTANCE WHOLEMOLECULES FLUSH UPPER_WALLS PRINT COMBINE TORSION COM	generic colvar bias function vatom
23.002	Critical comparison of general-purpose collective variables for crystal nucleation	methods	metadynamics, umbrella sampling, commitor, entropy, PIV	Julien Lam	METAD FUNCPATHMSD UNITS ENERGY Q4 Q6 PIV PAIRENTROPY LOCAL_AVERAGE CUSTOM RESTRAINT UPPER_WALLS VOLUME PRINT	generic symfunc gridtools colvar bias function setup piv
22.036	Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction	bio	Well-tempered MetaDynamics with Hamiltonian Replica Exchange	Miroslav Krepl	METAD BIASVALUE MOLINFO GROUP LOAD GHBFIX CUSTOM FLUSH UPPER_WALLS PRINT COORDINATION COMBINE	generic core colvar bias setup function
22.020	Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix–Junction–Helix RNA	bio	RNA force field, Helix-Junction-Helix RNA, SAXS, Well tempered metadynamics	Weiwei He	METAD DISTANCE GROUP WHOLEMOLECULES PRINT TORSION COM	generic core colvar bias vatom
22.018	Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations	bio	ligand binding, docking, EMMI, LAT1	Max Bonomi	BIASVALUE MOLINFO GROUP LOAD WHOLEMOLECULES EMMIVOX PRINT	generic core bias setup isdb
22.001	Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials	methods	enhanced sampling, variationally enhanced sampling, ves, metadynamics, bias representation, wavelets, adam	Benjamin Pampel	VES_LINEAR_EXPANSION BF_LEGENDRE OPT_ADAM UPPER_WALLS BF_CUBIC_B_SPLINES BF_WAVELETS OPT_AVERAGED_SGD ENERGY DISTANCE POSITION PRINT COORDINATION BF_CHEBYSHEV FLUSH BF_GAUSSIANS UNITS METAD VES_OUTPUT_BASISFUNCTIONS TD_WELLTEMPERED TD_UNIFORM INCLUDE	generic colvar bias setup ves
21.051	Automatic learning of hydrogen-bond fixes in an AMBER RNA force field	methods	force field, RNA	Giovanni Bussi	METAD BIASVALUE MOLINFO ERMSD WHOLEMOLECULES PRINT COORDINATION COMBINE	generic colvar bias function
21.048	Enhancing ligand exploration within a channel pore and fenestrations using metadynamics	bio	well-tempered metadynamics, protein-ligand enhanced sampling, sodium channel, Nav, small molecule drug	Elaine Tao	METAD LOWER_WALLS UNITS DISTANCE CUSTOM UPPER_WALLS PRINT TORSION COM	generic colvar function bias setup vatom
21.043	Predicting the Conformational Variability of Oncogenic GTP-bound G12D Mutated KRas-4B Proteins at Cell Membranes	chemistry	well-tempered metadynamics, KRas-4B, anionic membrane, conformational variability	Huixia Lu	METAD FIXEDATOM FIT_TO_TEMPLATE PRINT TORSION	generic colvar bias vatom
21.013	Role of vibrational excitation in heterogeneous catalysis	chemistry	catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption	Kristof Bal	REWEIGHT_BIAS COORDINATIONNUMBER HISTOGRAM VES_LINEAR_EXPANSION RESTRAINT UPPER_WALLS LOWER_WALLS OPT_AVERAGED_SGD TD_GRID DISTANCE ANGLES LOAD PRINT COORDINATION UWALLS BF_CHEBYSHEV FLUSH UNITS CONVERT_TO_FES DISTANCES METAD DUMPGRID EXTERNAL COMBINE REWEIGHT_METAD	generic symfunc gridtools colvar bias ves setup function multicolvar
21.008	Multi-replica biased sampling for photoisomerization processes in conjugated polymers	methods	metadynamics, FEP, replica-exchange	Adriana Pietropaolo	CONSTANT BIASVALUE MATHEVAL PBMETAD RESTART WHOLEMOLECULES PRINT TORSION	generic colvar bias function setup
20.024	Gaussian Mixture Based Enhanced Sampling (GAMBES)	methods	enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias	Jayashrita Debnath	LOWER_WALLS COMBINE UNITS ENERGY DISTANCE GROUP LOAD UPPER_WALLS PRINT DISTANCES TORSION	generic core colvar bias function setup multicolvar
20.019	Systematic finite-temperature reduction of crystal energy landscapes	materials	crystals, organics, structure prediction	Matteo Salvalaglio	METAD LOWER_WALLS MATHEVAL ENERGY CELL UPPER_WALLS VOLUME PRINT	generic colvar bias function
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 FUNCPATHMSD ABMD UPPER_WALLS LOWER_WALLS MOLINFO DISTANCE WHOLEMOLECULES PRINT READ CONTACTMAP FLUSH CONVERT_TO_FES COM METAD ENDPLUMED DUMPGRID COMBINE REWEIGHT_METAD	generic gridtools colvar bias function vatom
20.002	Exploring conformational dynamics of the extracellular Venus flytrap domain of the GABAB receptor, a path-metadynamics study	bio	Metadynamics, path CVs	Riccardo Ocello	METAD PATHMSD MOLINFO GROUP RESTART WHOLEMOLECULES UPPER_WALLS PRINT	generic core colvar bias setup
19.075	PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python	other	Python, automatic differentiation	Toni Giorgino	DUMPDERIVATIVES CENTER DISTANCE ENDPLUMED GROUP RESTRAINT CUSTOM PRINT COMBINE TORSION ANGLE	generic core bias colvar function vatom
19.063	Protein-ligand binding through metadynamics with path CVs	bio	metadynamics, path CVs, ligand binding	Mattia Bernetti	METAD LOWER_WALLS PATHMSD WHOLEMOLECULES UPPER_WALLS PRINT	generic colvar bias
19.058	Constrained MD for maintaining a cavity in a calculation	chemistry	constrained MD, porous molecules, porosity, cavity	Kim Jelfs	RESTART MOVINGRESTRAINT FLUSH PRINT INPLANEDISTANCES DISTANCES COM	generic bias setup multicolvar vatom
19.049	Determining the sizes of solid/liquid clusters in MD trajectories of nucleation	methods	nucleation, metadynamics, clustering, Steinhardt order parameters	Gareth Tribello	LOCAL_Q6 OUTER_PRODUCT COORDINATIONNUMBER METAD CLUSTER_DISTRIBUTION SMAC CONTACT_MATRIX Q6 MATRIX_VECTOR_PRODUCT OUTPUT_CLUSTER ONES DFSCLUSTERING CUSTOM CLUSTER_PROPERTIES CLUSTER_NATOMS MORE_THAN PRINT DISTANCES	adjmat generic symfunc bias clusters function matrixtools multicolvar
19.048	Understanding Ligand Binding Selectivity in a Prototypical GPCR Family	bio	metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding	Francesco Gervasio	CONSTANT METAD LOWER_WALLS BIASVALUE MATHEVAL DISTANCE WHOLEMOLECULES UPPER_WALLS PRINT COM	generic colvar bias function vatom
19.042	Harmonic Linear Discriminant Analysis (HLDA)	methods	metadynamics, chemistry, HLDA	GiovanniMaria Piccini	METAD UNITS ENERGY DISTANCE FLUSH UPPER_WALLS PRINT COMBINE	generic colvar bias setup function
19.037	Scission free energy of organic dyes	chemistry	metadynamics, multiple walkers, matheval/lepton	Paolo Raiteri	METAD MATHEVAL UNITS DISTANCE RESTART FLUSH UPPER_WALLS PRINT	generic colvar bias function setup
19.026	Ice Nucleation on Cholesterol Crystals	materials	forward flux sampling, crystal nucleation, water, ice, organic crystals	Gabriele Cesare Sosso	CLUSTER_WITHSURFACE MFILTER_MORE LOCAL_Q6 COMMITTOR CONTACT_MATRIX Q6 ENDPLUMED DFSCLUSTERING CLUSTER_NATOMS FLUSH OUTPUT_CLUSTER	generic adjmat symfunc clusters multicolvar
19.016	Succinnic acid gamma polymorph	materials	Succinnic acid, conformers, polymorphs, metadynamics	Matteo Salvalaglio	LOWER_WALLS METAD MATHEVAL ENERGY CELL ENDPLUMED UPPER_WALLS VOLUME PRINT COMBINE TORSION	generic colvar bias function
19.014	MIL101(Cr) SBUs assembly	materials	MOFs, nucleation, self-assembly, metadynamics	Matteo Salvalaglio	COORDINATIONNUMBER METAD ENDPLUMED RESTART PRINT DISTANCES GYRATION	generic symfunc bias setup colvar multicolvar
19.013	RNA FF FITTING	methods	force field, RNA	Giovanni Bussi	CONSTANT BIASVALUE MATHEVAL PUCKERING MOLINFO INCLUDE TORSION	generic colvar bias function
19.009	RNA tetraloops folding	bio	metadynamics, RNA, folding	Giovanni Bussi	RMSD METAD MOLINFO ENDPLUMED ERMSD WHOLEMOLECULES PRINT	bias generic colvar
26.006	Metadynamics simulations of buried phosphorylation sites and proline isomerisation	bio	metadynamics	Julian Streit	PRINT COORDINATION WHOLEMOLECULES MOLINFO TORSION METAD	colvar bias generic
25.007	Shaping the glycan landscape. Hidden relationships between linkage and ring distortion induced by carbohydrate-active enzmyes	bio	REST-RECT, REST2, glycan, enzyme, CAZyme, steered	Isabell Grothaus	RESTRAINT PRINT DISTANCE TORSION MOLINFO RESTART MOVINGRESTRAINT PUCKERING METAD	colvar bias generic setup
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	UPPER_WALLS PRINT DISTANCES COMMITTOR DISTANCE OPES_METAD GROUP FLUSH FIXEDATOM ZDISTANCES CUSTOM COORDINATIONNUMBER UNITS	function vatom generic bias multicolvar opes symfunc setup colvar core
25.002	M3_PCV-ABMD	chemistry	Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor	Gian Marco Elisi	UPPER_WALLS PRINT PATHMSD ENDPLUMED ABMD UNITS	colvar bias generic setup
24.027	Proline cis and trans subensembles of a disordered peptide	bio	intrinsically disordered proteins, proline cis trans isomerisation, metadynamics, collective variables	Alice Pettitt	PRINT ALPHARMSD GYRATION DISTANCE GROUP FLUSH INCLUDE ENDPLUMED COMBINE PBMETAD WHOLEMOLECULES MOLINFO PARABETARMSD DIHCOR TORSION ANTIBETARMSD COORDINATION	function secondarystructure generic bias multicolvar colvar core
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	PRINT ALPHARMSD GYRATION DISTANCE OPES_METAD CUSTOM COMBINE WHOLEMOLECULES TORSION MOLINFO COORDINATION	function secondarystructure generic opes colvar
24.016	Cryo-EM guided simulations of ribozyme	bio	metainference, cryo-EM	Giovanni Bussi	EMMIVOX PRINT RESTRAINT GROUP INCLUDE ERMSD WHOLEMOLECULES MOLINFO BIASVALUE	generic isdb bias colvar core
24.012	Molecular simulations to investigate the impact of N6-methylation in RNA recognition	bio	metadynamics, alchemistry, RNA modification, RNA:protein interactions	Giovanni Bussi	UPPER_WALLS PRINT GHBFIX LOWER_WALLS DISTANCE GROUP COMBINE DEBUG MOLINFO COM METAD BIASVALUE CENTER COORDINATION	function vatom generic bias colvar core
24.006	Water vapor condensation	chemistry	metadynamics, homogeneous condensation, chemical potential	Shenghui Zhong	UPPER_WALLS PRINT COORDINATIONNUMBER CLUSTER_NATOMS CONTACT_MATRIX CLUSTER_PROPERTIES DFSCLUSTERING METAD UNITS	generic bias adjmat clusters setup symfunc
23.028	Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process	chemistry	Ammonia decomposition; Dynamics;OPES; Neural Network potential	Manyi Yang	UPPER_WALLS PRINT DISTANCES COMMITTOR LOWER_WALLS DISTANCE ENERGY MATHEVAL GROUP OPES_METAD FLUSH FIXEDATOM ZDISTANCES CUSTOM COORDINATIONNUMBER COM UNITS	function vatom generic bias multicolvar opes symfunc setup colvar core
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	UPPER_WALLS PRINT FIT_TO_TEMPLATE LOWER_WALLS DISTANCE OPES_METAD GROUP FIXEDATOM CUSTOM PYTORCH_MODEL WHOLEMOLECULES TORSION CENTER OPES_METAD_EXPLORE PATH COORDINATION UNITS	function pytorch vatom generic bias setup opes mapping colvar core
23.009	Deep Learning Collective Variables from Transition Path Ensemble	methods	TPI-Deep-TDA, Deep-TDA, Transition Path, OPES, OPES Flooding, Machine Learning, Protein folding, Ligand binding	Dhiman Ray	CONTACTMAP GROUP WHOLEMOLECULES PYTORCH_MODEL PRINT DISTANCE OPES_METAD ENERGY INCLUDE CUSTOM CENTER COORDINATION UPPER_WALLS FIT_TO_TEMPLATE RMSD COMBINE MOLINFO ANGLE COMMITTOR LOWER_WALLS MATHEVAL ENDPLUMED FIXEDATOM	function pytorch vatom generic bias opes colvar core
22.017	Water regulates the residence time of Benzamidine in Trypsin	bio	ligand binding, water, opes, benzamidine trypsin, unbinding rates, machine learning, Deep-LDA, Deep-TICA	Narjes Ansari	UPPER_WALLS PRINT COMMITTOR FIT_TO_TEMPLATE LOWER_WALLS DISTANCE OPES_METAD MATHEVAL GROUP FIXEDATOM RMSD CUSTOM WHOLEMOLECULES PYTORCH_MODEL CENTER COORDINATION	function pytorch vatom generic bias opes colvar core
22.015	Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome	bio	photodynamics, bacteriophytochrome, variationally enhanced sampling	Jakub Rydzewski	PRINT TD_UNIFORM TORSION VES_LINEAR_EXPANSION BF_FOURIER OPT_AVERAGED_SGD	colvar generic ves
22.008	Ab initio metadynamics determination of temperature-dependent free-energy landscape in ultrasmall silver clusters	materials	Well tempered metadynamics, ab-initio, ase	Daniel Sucerquia	UPPER_WALLS COORDINATION GYRATION LOWER_WALLS DISTANCE FLUSH COMBINE COORDINATIONNUMBER COM METAD UNITS	function vatom generic bias setup symfunc colvar
22.002	GAMBES_SAMPL5_RATES	other	GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding	Jayashrita Debnath	UPPER_WALLS PRINT ANGLE FIT_TO_TEMPLATE COMMITTOR DISTANCE ENERGY MATHEVAL GROUP FLUSH FIXEDATOM ENDPLUMED LOAD WHOLEMOLECULES PYTORCH_MODEL CENTER COORDINATION	function pytorch vatom generic bias setup colvar core
22.000	Amyloid precursor protein processing by human γ-secretase	bio	Bias Exchange Metadynamics, Helix unfolding, coupled binding	Xiaoli Lu	RANDOM_EXCHANGES PRINT ALPHARMSD COORDINATION DISTANCE CONTACTMAP INCLUDE MOLINFO ANTIBETARMSD CENTER METAD UNITS	secondarystructure vatom generic bias setup colvar
21.032	Metal-coupled folding mechanism to metallothionein	bio	parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination	Manuel-Peris Diaz	GROUP PBMETAD WHOLEMOLECULES COORDINATION UNITS	generic bias setup colvar core
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 READ GROUP HISTOGRAM WHOLEMOLECULES CONVERT_TO_FES POSITION PRINT DISTANCE COORDINATION METAD UPPER_WALLS FLUSH RMSD MATHEVAL DUMPGRID FIXEDATOM ENDPLUMED COM	function vatom generic bias core colvar gridtools
21.016	MD SAXS GTPase associated center	bio	metadynamics, RNA, folding, SAXS	Giovanni Bussi	SAXS UPPER_WALLS PRINT GYRATION LOWER_WALLS GROUP INCLUDE ERMSD CUSTOM WHOLEMOLECULES MOLINFO METAD	function generic isdb bias colvar core
21.009	Nucleation rates from small scale atomistic simulations and transition state theory	materials	kinetics, free energy barriers, nucleation, droplets, metadynamics	Kristof Bal	UPPER_WALLS PRINT COMMITTOR REWEIGHT_METAD FLUSH DUMPGRID HISTOGRAM LOAD COORDINATIONNUMBER CONVERT_TO_FES MOVINGRESTRAINT METAD UNITS	generic bias setup symfunc gridtools
21.000	Uremic toxin time scale dynamics	bio	uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs)	Jim Pfaendtner	PRINT DISTANCE GROUP WHOLEMOLECULES COM	colvar vatom generic core
20.031	Soft fluorescent nanoshuttles targeting receptors	chemistry	polymers, receptors, nanoparticles, fluorescent probes	Adriana Pietropaolo	PRINT PBMETAD WHOLEMOLECULES CENTER COORDINATION	colvar vatom bias 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 FIT_TO_TEMPLATE DISTANCE RESTART CENTER METAD	vatom generic bias setup colvar
20.022	Unified Approach to Enhanced Sampling	methods	OPES, expanded ensembles, importance sampling	Michele Invernizzi	ECV_UMBRELLAS_LINE WHOLEMOLECULES ECV_MULTITHERMAL POSITION PRINT ENERGY ENVIRONMENTSIMILARITY CUSTOM UPPER_WALLS VOLUME ECV_LINEAR OPES_EXPANDED RMSD LOAD TORSION MOLINFO MATHEVAL Q6 ENDPLUMED ECV_MULTITHERMAL_MULTIBARIC UNITS	function envsim generic bias setup opes symfunc colvar
20.018	Free energy barriers from biased molecular dynamics simulations	methods	kinetics, free energy barriers, chemical reactions, nucleation, metadynamics	Kristof Bal	REWEIGHT_METAD DENSITY HISTOGRAM CONVERT_TO_FES PAIRENTROPY PRINT DISTANCE ENERGY CENTER COORDINATION METAD UPPER_WALLS VOLUME FLUSH COMBINE LOAD COORDINATIONNUMBER LOWER_WALLS LOCAL_AVERAGE SPRINT Q6 DUMPGRID REWEIGHT_BIAS CONTACT_MATRIX UNITS	function vatom sprint generic bias adjmat volumes setup symfunc colvar gridtools
20.016	Predicting polymorphism in molecular crystals using orientational entropy	materials	metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy	Pablo Piaggi	UPPER_WALLS PRINT VOLUME GROUP INCLUDE LOAD CENTER METAD	vatom generic bias setup colvar core
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	ALPHARMSD GROUP WHOLEMOLECULES PRINT INCLUDE PBMETAD DIHCOR COORDINATION GYRATION FLUSH COMBINE MOLINFO TORSION ANTIBETARMSD CS2BACKBONE METAINFERENCE STATS ENDPLUMED PARABETARMSD ENSEMBLE	function secondarystructure generic isdb bias colvar multicolvar core
19.072	SINE hairpin MD+NMR	bio	metadynamics, RNA, NMR	Giovanni Bussi	PRINT COORDINATION SORT DISTANCE MATHEVAL FLUSH INCLUDE MAXENT WHOLEMOLECULES MOLINFO TORSION COM METAD	function vatom generic bias 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	RANDOM_EXCHANGES PRINT INCLUDE TORSION METAD	colvar bias generic
19.052	Gibbs free energy of homogeneous nucleation	materials	nucleation, surface excess free energy	Gareth Tribello	UPPER_WALLS PRINT CELL ENDPLUMED FCCUBIC METAD UNITS	generic bias setup symfunc 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	UPPER_WALLS BRIDGE DISTANCES ALPHABETA REWEIGHT_METAD LOWER_WALLS DISTANCE PRINT GROUP FUNNEL RMSD COMBINE WHOLEMOLECULES MOLINFO TORSION COM METAD	function vatom generic bias adjmat multicolvar funnel colvar core
19.015	Ibuprofen conformational dynamics and thermodynamics surface	materials	Ibuprofen, crystal, surface, solvents, conformers, metadynamics	Matteo Salvalaglio	UPPER_WALLS PRINT COMMITTOR LOWER_WALLS DISTANCE TORSION CENTER METAD	colvar vatom bias generic
19.007	EMMI Microtubules	bio	metainference, cryo-EM	Max Bonomi	PRINT EMMI GROUP WHOLEMOLECULES MOLINFO BIASVALUE	isdb bias generic core
19.001	RNA SHAPE	bio	metadynamics, RNA, ligand binding	Giovanni Bussi	RANDOM_EXCHANGES UPPER_WALLS PRINT DISTANCES ANGLE LOWER_WALLS DISTANCE FLUSH INCLUDE ERMSD COMBINE MOLINFO METAD	function generic bias multicolvar colvar
25.008	Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting	methods	metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting	Dhiman Ray	PYTORCH_MODEL ENDPLUMED RMSD UNITS METAD TORSION DISTANCE ENERGY OPES_METAD POSITION LOWER_WALLS GROUP MOLINFO BIASVALUE CUSTOM WHOLEMOLECULES PRINT UPPER_WALLS	opes function bias core colvar generic setup pytorch
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	COM UNITS METAD DISTANCE FLUSH COMBINE COORDINATIONNUMBER DISTANCES ANGLE LOWER_WALLS RESTRAINT FIXEDATOM COORDINATION GROUP PRINT UPPER_WALLS	function vatom bias core colvar generic symfunc setup multicolvar
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	UNITS DISTANCE COMMITTOR OPES_METAD LOWER_WALLS GROUP COORDINATION RESTART CUSTOM PRINT UPPER_WALLS	opes function bias core colvar generic setup
24.024	Host-Guest binding free energies à la carte, an automated OneOPES protocol	bio	OneOPES, ligand binding, binding free energy,SAMPL challenge, host-guest	Valerio Rizzi	ENDPLUMED DISTANCE TORSION CENTER FIT_TO_TEMPLATE COORDINATION OPES_METAD_EXPLORE MATHEVAL LOWER_WALLS GROUP ANGLE FIXEDATOM ENERGY ECV_MULTITHERMAL OPES_EXPANDED WHOLEMOLECULES PRINT UPPER_WALLS	opes function vatom bias core colvar generic
24.001	A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations	bio	OPES, OPES-Flooding, QM/MM, Kinetics, Enzyme Catalysis	Dhiman Ray	UNITS DISTANCE FLUSH COMMITTOR COMBINE TORSION OPES_METAD LOWER_WALLS CUSTOM PRINT UPPER_WALLS	opes function bias colvar generic setup
23.043	Modeling the ferroelectric phase transition in barium titanate with DFT accuracy and converged sampling	materials	Barium Titanate, ferroelectric phase transition, Machine Learning, polarization order parameters	Lorenzo Gigli	METAD INCLUDE TRANSPOSE FLUSH MATHEVAL SUM SELECT_COMPONENTS PRINT	function bias matrixtools generic valtools
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	WRAPAROUND RMSD STATS ENSEMBLE DISTANCE CENTER SAXS BIASVALUE MOLINFO GROUP PRINT UPPER_WALLS	function vatom bias core colvar isdb generic
23.020	FEP simulations of ATOX1 homodimer	chemistry	parallel bias metadynamics, FEP, free-energy of metal ion dissociation	Adriana Pietropaolo	CONSTANT DISTANCE MATHEVAL BIASVALUE ANGLE PBMETAD WHOLEMOLECULES PRINT	function generic colvar bias
22.030	Mixing physics across temperatures with generative artificial intelligence	methods	REMD, Generative AI, DDPM	Yihang Wang	WHOLEMOLECULES PRINT TORSION	generic colvar
22.029	Angiotensin-1-7_Metadynamics	bio	Metadynamics, Angiotensin-(1-7), peptide	L.-América Chi	GYRATION METAD FLUSH LOWER_WALLS GROUP COORDINATION WHOLEMOLECULES PRINT UPPER_WALLS	core generic colvar bias
21.037	Molecular Dynamics simulations of RBD/hACE2 complexes	bio	SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain	Max Bonomi	RMSD DISTANCE PRINT	generic colvar
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 ENVIRONMENTSIMILARITY OPT_DUMMY VOLUME MATHEVAL TD_WELLTEMPERED RESTART Q6 OPT_AVERAGED_SGD PRINT UPPER_WALLS VES_LINEAR_EXPANSION	function bias colvar ves symfunc generic envsim setup
19.083	Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis	chemistry	metadynamics, chemical reactions, reaction discovery	Valerio Rizzi	ENDPLUMED UNITS METAD COMBINE COORDINATIONNUMBER DISTANCES FLUSH GROUP RESTART PRINT UPPER_WALLS	function bias core symfunc generic setup multicolvar
19.053	Capillary fluctuations with PLUMED	methods	nucleation, surface tension, capillary fluctuations	Gareth Tribello	UNITS MORE_THAN FOURIER_TRANSFORM DUMPGRID GROUP CENTER FCCUBIC MULTICOLVARDENS FIND_CONTOUR_SURFACE	function fourier vatom contour core symfunc setup gridtools
19.051	Solid liquid interfacial free energy out of equilibrium	materials	metadynamics, nucleation, surface excess free energy	Gareth Tribello	ENDPLUMED UNITS METAD LOWER_WALLS CELL AROUND FCCUBIC PRINT UPPER_WALLS	bias colvar generic symfunc volumes setup
19.021	Coarse-Grained Directed Simulation	methods	experiment directed simulation, coarse-grain, bias	Glen Hocky	DISTANCE COMBINE TORSION RESTRAINT EDS PRINT	function bias colvar generic eds
26.007	Metadynamics Simulations Reveal the Protonation-Dependent Conformational Landscape of GSK-3β Dual Inhibitors	chemistry	metadynamics, ligand unbinding, path CVs, funnel metadynamics	Gian Marco Elisi	METAD WHOLEMOLECULES UNITS FUNNEL_PS FUNNEL COM MATHEVAL PATHMSD LOWER_WALLS UPPER_WALLS PRINT ENDPLUMED ANGLE DISTANCE COMBINE RMSD MOLINFO	vatom generic colvar function bias setup funnel
26.001	Molecular simulations Alx riboswitch	bio	RNA, riboswitch	Giovanni Bussi	PRINT MATHEVAL DISTANCE MOVINGRESTRAINT ERMSD RESTRAINT MOLINFO	bias colvar generic function
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	METAD WHOLEMOLECULES PRINT MATHEVAL LOWER_WALLS UPPER_WALLS GYRATION COORDINATION DISTANCE COMBINE CENTER GROUP	generic core function bias vatom colvar
25.026	Deciphering the Molecular Mechanisms of Startle Disease - the Role of the Asn46Lys Mutation in the Glycine Receptor	bio	metadynamics, glycine receptors, funnel metadynamics	Jacob Adam Clark	METAD FUNNEL_PS FUNNEL COM LOWER_WALLS PRINT UPPER_WALLS	bias vatom funnel generic
25.024	Sampling glycan-glycan interactions for B22 calculations	bio	B22, glycan, carbohydrates, distance, REST2, metadynamics, RECT, replica exchange	Isabell Louise Grothaus	METAD PRINT COM POSITION DISTANCE COMBINE RESTRAINT	generic function bias vatom colvar
25.023	Molecular simulations of Tau-protein oligomers	bio	metadynamics, proteins, aggregation	Giovanni Bussi	METAD CONVERT_TO_FES PRINT RESTART CUSTOM REWEIGHT_BIAS RMSD HISTOGRAM DUMPGRID CONTACTMAP FLUSH RESTRAINT	gridtools generic function bias setup colvar
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	GHOST DISTANCES PRINT LOWER_WALLS OPES_EXPANDED PATHMSD UPPER_WALLS OPES_METAD_EXPLORE CUSTOM ECV_MULTITHERMAL DISTANCE COORDINATION RMSD CENTER ENERGY GROUP	generic core opes multicolvar function bias vatom colvar
25.003	Surrogate Model CV	methods	Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding	Sompriya Chatterjee	WHOLEMOLECULES OPES_METAD PRINT MATHEVAL ENDPLUMED CUSTOM DISTANCE COMMITTOR COMBINE GROUP PYTORCH_MODEL TORSION ENERGY MOLINFO	generic pytorch core opes function colvar
24.000	Ammonia Decomposition on Non-stoichiometric Lithium Imide	chemistry	ammonia decomposition, non-stoichiometric lithium imide, machine learning interatomic potentials, enhanced sampling, heterogeneous catalysis	Francesco Mambretti	ZDISTANCES UNITS OPES_METAD PRINT COORDINATIONNUMBER UPPER_WALLS DISTANCE FIXEDATOM FLUSH GROUP	vatom generic core symfunc opes multicolvar bias setup colvar
23.027	CmuMD simulations of NaCl(aq) at NaCl	chemistry	CmuMD, DFS, Q3, Pair Entropy	Aaron Finney	LOCAL_Q3 UNITS CONTACT_MATRIX Q3 AROUND PRINT FIXEDATOM COORDINATIONNUMBER DFSCLUSTERING LOAD CLUSTER_NATOMS HISTOGRAM CLUSTER_DISTRIBUTION LOCAL_AVERAGE DUMPGRID DENSITY RESTRAINT GROUP	volumes vatom gridtools generic adjmat core symfunc bias setup clusters
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 LOWER_WALLS OPES_EXPANDED RESTART UPPER_WALLS HISTOGRAM ECV_UMBRELLAS_LINE DUMPGRID ENVIRONMENTSIMILARITY	gridtools generic envsim opes bias setup
22.043	Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES	bio	OPES, RNA, Tetraloop, Folding	Gül Zerze	WHOLEMOLECULES PRINT OPES_EXPANDED ECV_MULTITHERMAL ECV_UMBRELLAS_LINE CONTACTMAP ENERGY	colvar generic opes
22.035	Deciphering the alphabet of disorder — Glu and Asp act differently on local but not global properties	bio	intrinsically disordered proteins, parallel bias metadynamics, protein	Kresten Lindorff-Larsen	WHOLEMOLECULES PBMETAD GYRATION TORSION MOLINFO	bias colvar generic
22.033	Reciprocal barrier restraint. Application to PROTAC passive permeability prediction	methods	PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR	Istvan Kolossvary	METAD UNITS PRINT COM BIASVALUE CUSTOM DISTANCE DRR FLUSH	vatom generic drr function bias setup colvar
22.028	N-glycan conformer distributions in atomistic simulation	bio	REST2, RECT, N-glycan, pucker	Isabell Grothaus	METAD CONVERT_TO_FES PRINT PUCKERING READ HISTOGRAM TORSION DUMPGRID MOLINFO	bias gridtools colvar generic
22.009	Glycosylation in calixarenes capsule	chemistry	Metadynamics, glycosylation, supramolecular catalysis	GiovanniMaria Piccini	METAD BRIDGE DISTANCES WHOLEMOLECULES UNITS LOWER_WALLS MATHEVAL FIT_TO_TEMPLATE PRINT ANGLE UPPER_WALLS DISTANCE COORDINATION COMBINE RMSD FLUSH GROUP	generic adjmat core multicolvar function bias setup colvar
22.007	Characterization of a natural variant of human NDP52 and its functional consequences on mitophagy	bio	metadynamics, well-tempered, protein-protein interactions, disordered proteins, mutations autophagy	Elena Papaleo	METAD WHOLEMOLECULES PRINT ANGLE UPPER_WALLS ALPHARMSD DISTANCE COORDINATION ALPHABETA TORSION FLUSH MOLINFO	generic secondarystructure multicolvar bias colvar
22.003	Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling	methods	opes, metadynamics, reweighting, alanine, muller	Michele Invernizzi	METAD UNITS OPES_METAD PRINT ENDPLUMED OPES_EXPANDED PBMETAD LOWER_WALLS BIASVALUE OPES_METAD_EXPLORE ECV_MULTITHERMAL POSITION UPPER_WALLS CUSTOM ECV_UMBRELLAS_FILE TORSION ENERGY	generic opes function bias setup colvar
21.050	N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity	methods	bio	Isabell Louise Grothaus	DISTANCE CENTER PRINT	vatom colvar generic
21.019	Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations	materials	Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen	Matteo Salvalaglio	PRINT MATHEVAL COM TORSIONS DISTANCE KDE	gridtools generic multicolvar function vatom colvar
21.017	All-atom simulations of the Vav1 AD construct	bio	metadynamics, parallel-bias, well-tempered	Simone Orioli	METAD WHOLEMOLECULES PBMETAD PRINT RESTART ALPHARMSD GROUP REWEIGHT_BIAS ALPHABETA CONTACTMAP MOLINFO	generic secondarystructure core multicolvar bias setup colvar
21.010	Step by Step Strecker Amino Acid Synthesis from Ab Initio Prebiotic Chemistry	chemistry	Strecker reaction, free energy landscape, ab initio molecular dynamics, glycine, prebiotic synthesis	Théo Magrino	PRINT	generic
20.017	FISST	methods	FISST, force, peptide, sampling, tempering	Glen Hocky	UNITS PRINT MATHEVAL BIASVALUE GYRATION DISTANCE FISST ENERGY RESTRAINT GROUP	fisst generic core function bias setup colvar
20.001	Conformational stability and dynamics in solution and in crystals report similarly on unfolding and aggregation propensity of amyloidogenic proteins	bio	metainference, metadynamics, NMR, protein dynamics, b2m, protein crystals	Carlo Camilloni	WHOLEMOLECULES PBMETAD PRINT LOWER_WALLS BIASVALUE ENDPLUMED UPPER_WALLS ANTIBETARMSD GROUP ALPHABETA FLUSH CS2BACKBONE MOLINFO	generic secondarystructure core isdb multicolvar bias
19.076	Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones	bio	molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics	Salvatore Assenza	UNITS PRINT ENDPLUMED GYRATION MOVINGRESTRAINT	bias setup colvar generic
19.067	Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways	bio	metadynamics, ligand unbinding	Jakub Rydzewski	METAD UNITS PRINT LOWER_WALLS RESTART PATHMSD UPPER_WALLS	bias setup colvar generic
19.066	Finding ligand unbinding reaction pathways	methods	maze, ligand unbinding	Jakub Rydzewski	UNITS PRINT POSITION MAZE_SIMULATED_ANNEALING MAZE_OPTIMIZER_BIAS MAZE_LOSS	maze setup colvar generic
19.056	maze	methods	maze, ligand unbinding	Jakub Rydzewski	UNITS PRINT POSITION MAZE_SIMULATED_ANNEALING MAZE_OPTIMIZER_BIAS MAZE_LOSS	maze setup colvar generic
19.036	Thermodynamics and kinetics of G protein-coupled receptor activation	bio	metadynamics, allostery, receptor conformation, GPCR, pharmacology	Davide Provasi	METAD WHOLEMOLECULES PRINT ENDPLUMED COM FUNCPATHMSD DISTANCE RMSD CONTACTMAP	generic function bias vatom colvar
19.024	PT-MetaD-WTE	methods	metadynamics, WTE, trp cage, PT	Jim Pfaendtner	METAD EXTERNAL COORDINATION ENERGY GROUP	bias core colvar
19.022	eABF simulation of NANMA (alanine dipeptide)	methods	eABF, DRR, alanine dipeptide	Haochuan Chen	DRR TORSION PRINT	colvar generic drr
25.009	Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water	chemistry	metadynamics, nitrate photolysis	Kam-Tung Chan	METAD HISTOGRAM DUMPGRID READ RESTART DISTANCE UPPER_WALLS GROUP CUSTOM FLUSH COORDINATION REWEIGHT_METAD PRINT	gridtools generic setup bias core colvar function
24.030	NMR guided simulation of dsRBD	bio	Metainference, NMR, protein dynamics	Debadutta Patra	WHOLEMOLECULES MOLINFO ALPHABETA STATS METAINFERENCE ENSEMBLE DISTANCE GROUP RDC FLUSH PRINT	generic core isdb multicolvar colvar function
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	METAD MOLINFO COMMITTOR ENERGY RESTART DISTANCE COORDINATIONNUMBER TORSION RESTRAINT FLUSH MATHEVAL BIASVALUE PRINT	symfunc generic setup bias colvar function
24.011	Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble	methods	committor, machine learning	Peilin Kang	MOLINFO GROUP COORDINATION MATHEVAL CELL UNITS ENERGY LOWER_WALLS INCLUDE BIASVALUE PRINT WHOLEMOLECULES POSITION ENDPLUMED DISTANCE UPPER_WALLS TORSION CUSTOM LOAD RMSD	generic setup bias core colvar function
24.007	SWISH-X	bio	swish-x, SWISH-X, swish, expanded SWISH	Alberto Borsatto	OPES_EXPANDED WHOLEMOLECULES MOLINFO ENERGY UPPER_WALLS ECV_MULTITHERMAL INCLUDE CONTACTMAP PRINT	bias opes colvar generic
24.005	Learning Markovian Dynamics with Spectral Maps	methods	spectral map, collective variables, machine learning	Jakub Rydzewski	UNITS DISTANCE CUSTOM BIASVALUE PRINT	generic setup bias colvar function
24.003	Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations	chemistry	steered molecular dynamics, foldamers, peptoids, bio-inspired	Kaylyn Torkelson	WHOLEMOLECULES ALPHABETA DISTANCE MOVINGRESTRAINT GYRATION TORSION INCLUDE COORDINATION COM PRINT	generic bias vatom multicolvar colvar
23.046	Lasso Peptides - HLDA CV	bio	metadynamics, protein folding, HLDA, harmonic	Gabriel da Hora	WHOLEMOLECULES METAD UNITS DISTANCE COMBINE PRINT	generic setup bias colvar function
23.035	An Extended Metadynamics Protocol for Binding/Unbinding of Peptide Ligands to Class A G-Protein Coupled Receptors	bio	G protein coupled receptor, peptide ligands, metadynamics, multiple-walker	Timothy Clark	WHOLEMOLECULES METAD CONSTANT LOWER_WALLS DISTANCE UPPER_WALLS CENTER MATHEVAL BIASVALUE PRINT	generic bias vatom colvar 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	MOLINFO GROUP FIT_TO_TEMPLATE COORDINATION MATHEVAL OPES_METAD_EXPLORE CENTER WRAPAROUND COM COMMITTOR UNITS ENERGY LOWER_WALLS FLUSH BIASVALUE PRINT WHOLEMOLECULES POSITION ENDPLUMED OPES_METAD DISTANCE UPPER_WALLS TORSION CUSTOM	generic opes setup bias vatom core colvar function
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	METAD READ EXTRACV TORSION PRINT	bias colvar generic
22.025	Bubble nucleation rate predictions in a Lennard-Jones fluid	materials	free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation	Kristof Bal	COMMITTOR DUMPGRID ANN HISTOGRAM UNITS COORDINATIONNUMBER REWEIGHT_BIAS UPPER_WALLS MOVINGRESTRAINT CUSTOM FLUSH RESTRAINT LOAD CONVERT_TO_FES VOLUME BIASVALUE PRINT	gridtools symfunc generic annfunc setup bias colvar function
21.044	NaCl nucleation	chemistry	metadynamics, DFS clustering	Aaron Finney	MFILTER_MORE METAD CONTACT_MATRIX DFSCLUSTERING FIXEDATOM Q6 HISTOGRAM INSPHERE DUMPGRID LOCAL_Q6 COORDINATIONNUMBER GROUP CLUSTER_NATOMS COMBINE CLUSTER_DISTRIBUTION PRINT	adjmat gridtools symfunc generic bias vatom core clusters volumes multicolvar function
21.039	Deep learning the slow modes for rare events sampling	methods	collective variables, machine learning, slow modes, deep-tica, opes	Luigi Bonati	MOLINFO GROUP CONTACTMAP VOLUME OPES_EXPANDED COMBINE ENVIRONMENTSIMILARITY UNITS ENERGY INCLUDE FLUSH PRINT WHOLEMOLECULES PYTORCH_MODEL Q6 ENDPLUMED OPES_METAD DISTANCE ECV_MULTITHERMAL TORSION LOAD RMSD	envsim symfunc generic opes setup pytorch core colvar function
21.033	Multiple-path-metadynamics applied to DNA base-pairing transitions	bio	path-CV, metadynamics, multiple-walker, dna	Alberto Pérez-de-Alba-Ortíz	METAD CONSTANT MOVINGRESTRAINT UPPER_WALLS RESTRAINT INCLUDE COMBINE PRINT	bias function generic
21.028	From Enhanced Sampling to Reaction Profiles	methods	collective variables, multi-state, machine learning, Deep-TDA	Enrico Trizio	FIXEDATOM DISTANCES ANGLE GROUP FIT_TO_TEMPLATE COORDINATION MATHEVAL CENTER UNITS LOWER_WALLS PRINT WHOLEMOLECULES PYTORCH_MODEL ENDPLUMED OPES_METAD DISTANCE UPPER_WALLS TORSION LOAD	generic opes setup bias vatom pytorch core multicolvar colvar function
21.020	Reweighted Jarzynski sampling	methods	free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions	Kristof Bal	METAD CONSTANT VES_LINEAR_EXPANSION OPT_AVERAGED_SGD COORDINATIONNUMBER BF_CHEBYSHEV TD_WELLTEMPERED COMBINE REWEIGHT_METAD DUMPGRID UNITS MOVINGRESTRAINT FLUSH REWEIGHT_BIAS BIASVALUE PRINT HISTOGRAM ANN OPES_METAD DISTANCE UPPER_WALLS RESTRAINT CUSTOM LOAD CONVERT_TO_FES	gridtools symfunc generic opes annfunc setup ves bias colvar function
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 POSITION RESTART RESTRAINT COORDINATION CENTER MATHEVAL REWEIGHT_BIAS PRINT	generic setup bias vatom colvar function
21.006	OPES, On-the-fly Probability Enhanced Sampling Method	methods	opes, alanine dipeptide, well-tempered, multithermal, multiumbrella	Michele Invernizzi	OPES_EXPANDED ENDPLUMED ENERGY OPES_METAD ECV_MULTITHERMAL TORSION ECV_UMBRELLAS_LINE PRINT	opes colvar generic
21.003	aSYN SAXS metainference	bio	metainference, SAXS	Kresten Lindorff-Larsen	WHOLEMOLECULES MOLINFO SAXS ALPHARMSD METAINFERENCE PBMETAD GROUP GYRATION FLUSH CENTER EEFSOLV BIASVALUE PRINT	generic bias secondarystructure vatom core isdb colvar
20.029	High Conformational Flexibility of the E2F1/DP1/DNA complex	bio	SAXS, protein-DNA complex, hySAXS, ensemble determination	Cristina Paissoni	WHOLEMOLECULES MOLINFO SAXS ENSEMBLE DISTANCE GROUP PRINT RESTRAINT INCLUDE CENTER BIASVALUE STATS	generic bias vatom core isdb colvar function
20.020	Parallel Bias Metadynamics	methods	pbmetad, trp-cage, folding	Max Bonomi	WHOLEMOLECULES MOLINFO ALPHABETA PBMETAD GYRATION DIHCOR INCLUDE COORDINATION PRINT	bias multicolvar colvar generic
20.015	Rational design of ASCT2 inhibitors using an integrated experimental-computational approach	bio	ASCT2 transporter, small-molecules, cryo-EM, metainference	Max Bonomi	WHOLEMOLECULES MOLINFO DUMPATOMS GROUP EMMIVOX LOAD BIASVALUE PRINT	generic setup bias core isdb
20.011	Uremic toxin analysis	bio	metadynamics, uremic toxin, serum albumin	Jim Pfaendtner	WHOLEMOLECULES DISTANCES RESTART DISTANCE GROUP COORDINATION CENTER PRINT	generic setup vatom core multicolvar colvar
19.069	Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen	materials	ibuprofen, crystal, solvent, surface	Matteo Salvalaglio	ENDPLUMED DISTANCE GROUP INCLUDE CENTER PRINT	vatom colvar core generic
19.032	Chemical reaction in solution using path collective variables based on coordination patterns	chemistry	chemical reactions, solutions, metadynamics, coordination patterns	Fabio Pietrucci	METAD DISTANCES RESTART PATH UPPER_WALLS FLUSH PRINT	mapping generic setup bias 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	PYTORCH_MODEL TORSION COORDINATION FIXEDATOM DISTANCE GROUP FIT_TO_TEMPLATE PRINT CUSTOM UPPER_WALLS WHOLEMOLECULES RESTART OPES_METAD PATH CENTER LOWER_WALLS	pytorch generic setup bias opes vatom colvar function mapping core
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 DRR COORDINATION RMSD MOLINFO PRINT FLUSH UPPER_WALLS WHOLEMOLECULES LOWER_WALLS METAD	pytorch generic drr bias colvar
23.041	Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference	methods	EMMIVox, cryo-EM, single-structure refinement, ensemble refinement, Bayesian inference, B-factors, structural ensembles	Samuel Hoff	DISTANCE GROUP MOLINFO PRINT EMMIVOX UPPER_WALLS WHOLEMOLECULES WRAPAROUND BIASVALUE INCLUDE	generic bias colvar isdb core
23.037	Estimating binding free energy of solid binding peptides without extensive sampling	bio	metadynamics, solid binding peptides	Xin Qi	DISTANCE MOLINFO PRINT UPPER_WALLS COM PBMETAD GYRATION LOWER_WALLS	vatom colvar bias 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	PYTORCH_MODEL ENDPLUMED PRINT POSITION UPPER_WALLS CUSTOM UNITS OPES_METAD BIASVALUE LOWER_WALLS	pytorch generic setup bias opes colvar function
23.019	Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors	bio	binding pathway, binding energy, sketch-map, drug development	Raitis Bobrovs	COLLECT_FRAMES VORONOI DISTANCE LANDMARK_SELECT_FPS TRANSPOSE VSTACK PRINT PATHMSD SKETCHMAP_PROJECTION CUSTOM UPPER_WALLS WHOLEMOLECULES COM SKETCHMAP DISSIMILARITIES METAD	dimred generic valtools landmarks matrixtools bias vatom colvar function
23.012	JAK2 2D meta-eABF PMF with statistical analysis	bio	2D meta-eABF, path CV, PMF	Istvan Kolossvary	DRR PRINT PATHMSD FLUSH CUSTOM UPPER_WALLS BIASVALUE LOWER_WALLS METAD	generic drr bias colvar function
23.007	Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains	bio	metadynamics, peptoids, parallel-bias metadynamics	Jim Pfaendtner	TORSION COORDINATION PRINT RESTRAINT INCLUDE WHOLEMOLECULES COM PBMETAD GYRATION	vatom colvar bias generic
23.000	Atomistic simulations of RNA tetraloop folding via PTWTE-WTM	bio	parallel tempering, well-tempered metadynamics, well-tempered ensemble, RNA, Tetraloop, Folding	Gül Zerze	PRINT UPPER_WALLS WHOLEMOLECULES CONTACTMAP ENERGY LOWER_WALLS METAD	colvar bias generic
22.042	Metadynamics of NSP10 and variants	bio	metadynamics, NSP10, crystal structure, variants	Shozeb Haider	TORSION PRINT METAD	colvar bias generic
22.040	From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure	bio	SARS-CoV-2, Spike, Omicron	Miłosz Wieczór	METAD PRINT UPPER_WALLS WHOLEMOLECULES LOWER_WALLS PCAVARS	bias mapping generic
22.039	Driving and characterizing nucleation of urea and glycine polymorphs in water	bio	metadynamics, nucleation, amino acids, polymorphism	Eric Beyerle	MATHEVAL COORDINATIONNUMBER LOAD GROUP PRINT PAIRENTROPY INCLUDE Q4 COMBINE CENTER Q6 METAD	gridtools generic setup bias vatom symfunc function core
22.023	Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy	bio	CryoEM, MEMMI,EMMI, Metadynamics, Metainference, IAPP, structural ensemble	Faidon Brotzakis	COORDINATION TORSION EMMI RMSD GROUP MOLINFO PRINT UPPER_WALLS BIASVALUE WHOLEMOLECULES RESTART COM PBMETAD	generic setup bias vatom colvar isdb core
22.022	Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir	bio	RMSD, protein-ligand interactions	Isabell Grothaus	RMSD PRINT	colvar generic
22.019	Exploring aspartic protease inhibitor binding to design selective antimalarials	bio	ligand binding, loop opening, path CV, funnel metadynamics, drug development	Raitis Bobrovs	DISTANCE PRINT PATHMSD FUNNEL_PS FUNNEL UPPER_WALLS WHOLEMOLECULES COM LOWER_WALLS METAD	generic bias vatom colvar funnel
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	HISTOGRAM ENVIRONMENTSIMILARITY VOLUME PRINT AROUND CUSTOM UPPER_WALLS OPES_METAD RESTART DUMPGRID ENERGY	gridtools generic setup envsim bias opes colvar function volumes
22.013	Ligand dissociation from PreQ1 riboswitch	bio	ligand, RNA, metadynamics, pRAVE	Yihang Wang	COORDINATIONNUMBER COMMITTOR DISTANCE RMSD MOLINFO PRINT WHOLEMOLECULES COM COMBINE METAD	generic bias vatom symfunc colvar 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	DISTANCE CONTACTMAP CENTER PRINT	vatom colvar generic
22.006	Peptide framework for screening the effects of amino acids on assembly	bio	metadynamics, peptides	Andrew White	CONVERT_TO_FES DISTANCES HISTOGRAM GROUP PRINT INCLUDE COM REWEIGHT_BIAS GYRATION DUMPGRID COMBINE METAD	gridtools multicolvar generic bias vatom colvar function core
21.047	Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations	materials	pair entropy, metadynamics, ves, solids, crystallization	Pablo Piaggi	TD_WELLTEMPERED LOAD VOLUME BF_LEGENDRE PRINT VES_LINEAR_EXPANSION PAIRENTROPY OPT_AVERAGED_SGD RESTART COMBINE ENERGY METAD	gridtools generic setup ves bias colvar function
21.001	Substrate recognition and catalysis by glycosaminoglycan sulfotransferases	bio	metadynamics, well-tempered metadynamics, puckering, coordination	Tarsis Ferreira	HISTOGRAM COORDINATION DISTANCE GROUP MOLINFO PRINT RANDOM_EXCHANGES UPPER_WALLS WHOLEMOLECULES INCLUDE ENERGY PUCKERING DUMPGRID REWEIGHT_METAD LOWER_WALLS METAD	gridtools generic bias colvar core
20.023	metadynminer and metadynminer3d	methods	metadynamics, visualization, R	Vojtech Spiwok	TORSION PRINT METAD	colvar bias generic
20.021	Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins.	bio	phi-values, restrained MD, transition-state, protein folding, disordered proteins, protein evolution	Cristina Paissoni	COORDINATION MOLINFO PRINT RESTRAINT STATS WHOLEMOLECULES	colvar bias function generic
20.009	The dynamics of linear polyubiquitin	bio	saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics	Carlo Camilloni	TORSION DISTANCE METAINFERENCE ENSEMBLE MOLINFO ALPHABETA PRINT STATS FLUSH WHOLEMOLECULES SAXS PBMETAD GYRATION CENTER	multicolvar generic bias vatom colvar isdb function
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 COORDINATION PRINT CUSTOM UNITS METAD	multicolvar setup generic bias colvar function
20.007	Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics	bio	metadynamics, loop movement, artificial intelligence	Pratyush Tiwary	TORSION DISTANCE RMSD MOLINFO PRINT UPPER_WALLS WHOLEMOLECULES RESTART COMBINE METAD	setup generic bias colvar function
20.006	Class B GPCR activation mechanism	bio	metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding	Francesco Gervasio	MATHEVAL RMSD DISTANCE MOLINFO PRINT UPPER_WALLS WHOLEMOLECULES COMBINE CENTER ENERGY LOWER_WALLS METAD	generic bias vatom colvar function
19.080	Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium	methods	ves, variationally enhanced sampling, vibrational excitation, chemical reactions	Kristof Bal	CONVERT_TO_FES TD_WELLTEMPERED HISTOGRAM COORDINATION BF_CHEBYSHEV DISTANCE EXTERNAL TD_GRID PRINT ANGLE VES_LINEAR_EXPANSION FLUSH UPPER_WALLS UNITS OPT_AVERAGED_SGD COMBINE DUMPGRID LOWER_WALLS	gridtools generic setup ves bias colvar function
19.074	Asymmetric base pair opening in nucleic acids	bio	double helix, DNA, RNA, unwindability	Giovanni Bussi	ENDPLUMED COORDINATION DISTANCE RESTRAINT WHOLEMOLECULES LOWER_WALLS	colvar bias generic
19.061	Diffusion in porous materials	materials	metadynamics, porous materials, diffusion	Kim E. Jelfs	DISTANCE GROUP PRINT UPPER_WALLS RESTART COM CENTER LOWER_WALLS METAD	setup generic bias vatom colvar core
19.060	Neural networks-based variationally enhanced sampling	methods	ves, neural networks	Luigi Bonati	ENDPLUMED TORSION LOAD ENVIRONMENTSIMILARITY PRINT POSITION UNITS ENERGY Q6	setup generic envsim symfunc 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	CONVERT_TO_FES HISTOGRAM READ PRINT UPPER_WALLS RESTART REWEIGHT_BIAS DISTANCE_FROM_CONTOUR DUMPGRID COMBINE METAD	gridtools contour setup generic bias function
19.030	Coarse-Grained MetaDynamics (CG-MetaD)	bio	Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy	Vittorio Limongelli	DISTANCE PRINT UPPER_WALLS WHOLEMOLECULES COM LOWER_WALLS METAD	vatom colvar bias generic
19.023	RECT	methods	metadynamics, replica exchange	Giovanni Bussi	TORSION PRINT WHOLEMOLECULES GYRATION METAD	colvar bias generic
19.005	Cmyc small molecule interaction	bio	metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP	Gabriella Heller	CS2BACKBONE COORDINATION DISTANCE GROUP METAINFERENCE MOLINFO ALPHABETA PRINT INCLUDE WHOLEMOLECULES PBMETAD GYRATION CENTER	multicolvar generic bias vatom colvar isdb core
19.003	EMMI ClpP	bio	metainference, cryo-EM	Max Bonomi	EMMI GROUP MOLINFO PRINT BIASVALUE	core isdb bias 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	DISTANCE PRINT ANGLE METAD WHOLEMOLECULES	colvar generic bias
26.000	OPES simulations of disordered proteins	bio	OPES, IDPs	Julian Streit	RESTART PRINT OPES_EXPANDED ECV_MULTITHERMAL ENERGY	opes colvar generic setup
25.013	Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices	bio	umbrella sampling, temperature ramping	Alexander Berlaga	DISTANCE PRINT PYTORCH_MODEL RESTRAINT GYRATION	colvar generic pytorch bias
25.011	Chiral perovskite nucleation	chemistry	metadynamics, chiral perovskites, nucleation	Adriana Pietropaolo	RESTART MULTI_RMSD PRINT DISTANCE MATHEVAL UNITS UPPER_WALLS LOWER_WALLS PBMETAD	colvar generic setup bias function
25.000	Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer	bio	metadynamics, pathCV	Sahithya Sridharan Iyer	RESTART FUNCPATHGENERAL COM PRINT DISTANCE GROUP UPPER_WALLS METAD WHOLEMOLECULES MOLINFO	colvar generic setup bias vatom core function
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	FIT_TO_TEMPLATE CENTER MATHEVAL COMBINE COORDINATION DISTANCE GROUP ANGLE RMSD OPES_METAD PRINT TORSION FIXEDATOM METAD CONTACTMAP ENDPLUMED MOLINFO CUSTOM UPPER_WALLS COMMITTOR WHOLEMOLECULES	opes colvar generic bias core vatom function
24.021	Ab initio machine learning simulation of calcium carbonate from aqueous solutions to the solid state	chemistry	ion pairing, caco3, opes, proton transfer, crystallization	Pablo Piaggi	COORDINATION DISTANCE PRINT OPES_METAD UPPER_WALLS ENERGY	opes colvar generic bias
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	LOAD PRINT GROUP TORSION COMMITTOR METAD	colvar generic setup bias core
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	METAD PRINT DISTANCE ALPHARMSD FUNCPATHMSD UPPER_WALLS INCLUDE LOWER_WALLS CONTACTMAP PATHMSD MOLINFO	colvar generic bias secondarystructure function
23.044	Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition	materials	metadynamics, interlocked molecules	Luigi Leanza	CONVERT_TO_FES COORDINATION PRINT GROUP READ HISTOGRAM DUMPGRID COMMITTOR METAD ENDPLUMED	colvar generic bias core gridtools
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	PRINT DISTANCE MATHEVAL RMSD METAD WHOLEMOLECULES MOLINFO	colvar generic bias function
23.034	Urea nucleation in water: do long-range forces matter?	materials	LMF theory, Metadynamics, Nucleation	Ziyue Zou	COORDINATIONNUMBER LOAD PRINT GROUP CENTER INCLUDE METAD	generic setup bias core symfunc vatom
23.005	A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs	bio	metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A	Timothy Clark	CONVERT_TO_FES PRINT DISTANCE MATHEVAL RMSD REWEIGHT_METAD READ HISTOGRAM DUMPGRID METAD WHOLEMOLECULES MOLINFO	colvar generic bias gridtools function
22.037	Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site	chemistry	metadynamics, DNA, abasic	Mike Jones	METAD DISTANCES DISTANCE PRINT	colvar generic multicolvar bias
22.031	Rare Event Kinetics from Adaptive Bias Enhanced Sampling	methods	OPES Flooding, Kinetics, Rate, OPES, Machine Learning	Dhiman Ray	COMBINE CONSTANT DISTANCE GROUP RMSD OPES_METAD PRINT PYTORCH_MODEL TORSION BIASVALUE UNITS POSITION CONTACTMAP ENDPLUMED MOLINFO CUSTOM INCLUDE COMMITTOR ENERGY WHOLEMOLECULES	opes colvar generic setup bias core pytorch 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	colvar generic
22.026	Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification	materials	Peptoid, silica	Jim Pfaendtner	COM PRINT DISTANCE MOLINFO UPPER_WALLS GYRATION PBMETAD	vatom generic colvar bias
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	ALPHABETA COM CUSTOM PRINT DISTANCE LOWER_WALLS MATHEVAL COMBINE TORSION UPPER_WALLS ZANGLES YANGLES METAD WHOLEMOLECULES XANGLES MOLINFO	colvar generic bias multicolvar vatom function
21.040	A structural ensemble of a tau-microtubule complex reveals regulatory tau phosphorylation and acetylation mechanisms	bio	EMMI, CryoEM, tau-microtubules, post-translational modifications, chemical mutagenesis, structural ensemble, Metainference	Faidon Brotzakis	RESTART COM PRINT DISTANCE GROUP BIASVALUE UPPER_WALLS EMMI WHOLEMOLECULES MOLINFO	colvar generic setup bias isdb core vatom
21.038	Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics	materials	metadynamics, SGOOP, nucleation, urea	Ziyue Zou	COORDINATIONNUMBER VOLUME LOAD PRINT GROUP CENTER COMBINE INCLUDE METAD ENERGY	colvar generic setup bias core symfunc vatom function
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	COORDINATION PRINT GROUP LOWER_WALLS PARABETARMSD DIHCOR RANDOM_EXCHANGES UPPER_WALLS ANTIBETARMSD METAD ENERGY WHOLEMOLECULES GYRATION ALPHARMSD MOLINFO	colvar generic bias secondarystructure multicolvar core
21.027	EGFR activating mutations mechanism	bio	metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA	Francesco Gervasio	PRINT DISTANCE LOWER_WALLS CONTACTMAP MATHEVAL UPPER_WALLS INCLUDE METAD ENERGY WHOLEMOLECULES ALPHARMSD MOLINFO	colvar generic bias secondarystructure function
21.025	Computational and biochemical analysis of type IV pilus dynamics and stability	bio	molecular dynamics, calcium binding, Type IV pilus	Yasaman Karami	DISTANCE LOWER_WALLS UPPER_WALLS PRINT	colvar generic bias
21.014	how to determine statistically accurate conformational ensembles	bio	metadynamics, metainference, errors, cv, SAXS, ensemble determination	Cristina Paissoni	ALPHABETA PRINT PBMETAD SAXS CENTER TORSION BIASVALUE ENSEMBLE ANTIBETARMSD STATS METAD CONTACTMAP WHOLEMOLECULES GYRATION MOLINFO	colvar generic bias isdb multicolvar secondarystructure vatom function
21.005	Crystallization Collective Variable	methods	Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA	Tarak Karmakar	FLUSH LOAD PRINT GROUP PYTORCH_MODEL MATHEVAL OPES_METAD UPPER_WALLS LOWER_WALLS	opes generic setup bias core pytorch function
21.004	Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy	bio	machine learning, well-tempered metadynamics, path collective variable, potential of mean force, standard binding free energy calculations, host-guest, protein-ligand unbinding	Dorothea Gobbo	METAD RESTART PRINT UPPER_WALLS LOWER_WALLS WHOLEMOLECULES PATHMSD	colvar generic setup bias
20.033	COVID-19 Spike protein opening transition mechanism	bio	EMMI, CryoEM, COVID-19, Spike, Metainference	Faidon Brotzakis	CONVERT_TO_FES PRINT GROUP READ HISTOGRAM RMSD BIASVALUE DISTANCES EMMI DUMPGRID WHOLEMOLECULES MOLINFO	colvar generic bias isdb multicolvar core gridtools
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	METAD DISTANCE TORSION PRINT	colvar generic bias
19.081	Calculation of phase diagrams in the multithermal-multibaric ensemble	methods	VES, variationally enhanced sampling, multithermal-multibaric, energy, Wang Landau, RefCV, kernel, bcc, fcc, sodium, aluminum	Pablo Piaggi	LOAD MATHEVAL COMBINE REWEIGHT_TEMP_PRESS RESTART VOLUME READ DUMPGRID OPT_DUMMY PRINT VES_LINEAR_EXPANSION TD_WELLTEMPERED BF_LEGENDRE TD_MULTITHERMAL_MULTIBARIC HISTOGRAM REWEIGHT_BIAS CONVERT_TO_FES Q6 UPPER_WALLS CELL OPT_AVERAGED_SGD LOWER_WALLS ENERGY	colvar generic setup bias ves gridtools symfunc function
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	COORDINATIONNUMBER PRINT LOWER_WALLS DISTANCES UPPER_WALLS METAD ENERGY ENDPLUMED GYRATION	colvar generic bias multicolvar symfunc
19.062	Elucidating molecular design principles for charge-alternating peptides	bio	peptide folding, metadynamics, well-tempered ensemble, parallel tempering	Jim Pfaendtner	PRINT METAD ENERGY WHOLEMOLECULES GYRATION	colvar generic bias
19.057	SAXS ensembles using Martini-Beads multi-scale SAXS	methods	metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics	Cristina Paissoni	ALPHABETA COORDINATION PRINT GROUP ANGLE SAXS CENTER MATHEVAL COMBINE WHOLEMOLECULES MOLINFO BIASVALUE ENSEMBLE INCLUDE STATS ENDPLUMED PBMETAD	colvar generic bias isdb multicolvar core vatom function
19.054	MetaFEP	methods	metadynamics, chemistry, free energy perturbation	GiovanniMaria Piccini	FLUSH PRINT DISTANCE LOWER_WALLS COMBINE UNITS UPPER_WALLS METAD ENERGY	colvar generic setup bias function
19.039	Funnel Metadynamics	bio	funnel-metadynamics, absolute binding free energy, ligand-receptor complexes	Vittorio Limongelli	METAD COM PRINT DISTANCE FUNNEL RMSD UPPER_WALLS FUNNEL_PS LOWER_WALLS WHOLEMOLECULES	colvar generic bias funnel vatom
19.031	Ice nucleation using PIV-based path coordinates	materials	phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics	Silvio Pipolo	PIV PRINT LOWER_WALLS FUNCPATHMSD UPPER_WALLS CELL METAD	colvar generic bias piv function
19.012	Martini-Beads multi-scale SAXS	methods	metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex	Carlo Camilloni	PRINT DISTANCE SAXS GROUP ENDPLUMED CENTER RMSD BIASVALUE UPPER_WALLS INCLUDE STATS RESTRAINT WHOLEMOLECULES MOLINFO	colvar generic bias isdb core vatom function
19.004	MI Ubiquitin	bio	metainference, NMR	Max Bonomi	CS2BACKBONE PRINT GROUP RDC METAINFERENCE WHOLEMOLECULES MOLINFO	isdb core generic
19.002	EMMI STRA6	bio	metainference, cryo-EM	Max Bonomi	PRINT GROUP BIASVALUE EMMI MOLINFO	isdb core generic bias

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