Browse the eggs in PLUMED-NEST

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

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

plumID	Name	Category	Keywords	Contributor	Actions	Modules
25.026	Deciphering the Molecular Mechanisms of Startle Disease - the Role of the Asn46Lys Mutation in the Glycine Receptor	bio	metadynamics, glycine receptors, funnel metadynamics	Jacob Adam Clark	METAD UPPER_WALLS FUNNEL LOWER_WALLS PRINT COM FUNNEL_PS	bias generic funnel vatom
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	OPES_EXPANDED CUSTOM MOLINFO ECV_MULTITHERMAL GROUP RMSD DISTANCE COORDINATION GHOST COMBINE CENTER ENERGY PRINT OPES_METAD_EXPLORE	colvar function vatom opes core generic
25.017	Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity	bio	EMMIVox, cryo-EM, allostery, decamer, filament, ensemble refinement, glutamine synthetase	Samuel Hoff	EMMIVOX WHOLEMOLECULES GROUP MOLINFO PRINT BIASVALUE	core generic isdb bias
25.010	Kinetic rates calculation with Ratchet&Pawl MD	methods	kinetics, ligand binding, ABMD, ratchet&pawl MD	Riccardo Capelli	ABMD WHOLEMOLECULES GROUP DISTANCE COMMITTOR FLUSH PRINT COM	colvar vatom core generic bias
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	OPES_EXPANDED MATHEVAL ANGLE WHOLEMOLECULES UPPER_WALLS GROUP ENDPLUMED ECV_MULTITHERMAL FIT_TO_TEMPLATE FIXEDATOM DISTANCE COORDINATION CENTER LOWER_WALLS TORSION ENERGY PRINT OPES_METAD_EXPLORE	colvar function vatom opes core generic bias
24.000	Ammonia Decomposition on Non-stoichiometric Lithium Imide	chemistry	ammonia decomposition, non-stoichiometric lithium imide, machine learning interatomic potentials, enhanced sampling, heterogeneous catalysis	Francesco Mambretti	UNITS UPPER_WALLS GROUP FIXEDATOM DISTANCE COORDINATIONNUMBER ZDISTANCES FLUSH OPES_METAD PRINT	symfunc colvar vatom opes core generic multicolvar bias setup
23.023	Rational design of novel biomimetic sequence-defined polymers for mineralization applications	methods	metadynamics, surface binding, biomimetic mineralization	Kaylyn Torkelson	UPPER_WALLS DISTANCE COORDINATION PBMETAD GYRATION PRINT COM	bias generic colvar vatom
23.022	A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar	methods	collective variables, machine learning, toy model	Enrico Trizio	CUSTOM PYTORCH_MODEL UNITS UPPER_WALLS ENDPLUMED POSITION LOWER_WALLS OPES_METAD PRINT BIASVALUE	colvar function opes generic bias setup pytorch
23.008	PBMetaD simulations of Histatin5	bio	metadynamics, IDP, Rg, PPII	Francesco Pesce	WHOLEMOLECULES GROUP TORSION PBMETAD GYRATION MOLINFO PRINT	core generic colvar bias
22.037	Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site	chemistry	metadynamics, DNA, abasic	Mike Jones	DISTANCE DISTANCES PRINT METAD	bias generic colvar multicolvar
22.015	Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome	bio	photodynamics, bacteriophytochrome, variationally enhanced sampling	Jakub Rydzewski	OPT_AVERAGED_SGD VES_LINEAR_EXPANSION BF_FOURIER TORSION PRINT TD_UNIFORM	generic colvar ves
22.011	Accelerating all-atom simulations and gaining mechanistic understanding of biophysical systems through State Predictive Information Bottleneck	methods	metadynamics, membrane permeation, protein folding	Shams Mehdi	CUSTOM MATHEVAL XANGLES METAD ZANGLES WHOLEMOLECULES UPPER_WALLS DISTANCE YANGLES LOWER_WALLS COMBINE TORSION MOLINFO PRINT COM ALPHABETA	colvar function vatom generic multicolvar bias
22.002	GAMBES_SAMPL5_RATES	other	GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding	Jayashrita Debnath	PYTORCH_MODEL MATHEVAL ANGLE WHOLEMOLECULES GROUP UPPER_WALLS ENDPLUMED FIT_TO_TEMPLATE FIXEDATOM DISTANCE COORDINATION FLUSH COMMITTOR ENERGY PRINT LOAD CENTER	colvar function vatom core generic bias setup pytorch
21.046	Ubiquitin Interacting Motifs, Duality Between Structured and Disordered Motifs	bio	wt metadynamics, ubiquitin, ataxin-3, short linear motifs, ubiquitin binding motif, moonlight functions, intrinsic disorder	Elena Papaleo	METAD WHOLEMOLECULES UPPER_WALLS GROUP ENDPLUMED LOWER_WALLS GYRATION PRINT ALPHABETA	colvar core generic multicolvar bias
21.025	Computational and biochemical analysis of type IV pilus dynamics and stability	bio	molecular dynamics, calcium binding, Type IV pilus	Yasaman Karami	DISTANCE PRINT UPPER_WALLS LOWER_WALLS	bias generic colvar
21.023	Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling	methods	enhanced sampling, collective variables, machine learning	Jakub Rydzewski	CUSTOM METAD INCLUDE UNITS REWEIGHT_METAD DISTANCE CONSTANT TORSION ENERGY PRINT BIASVALUE	colvar function generic bias setup
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	RESTART METAD WHOLEMOLECULES UPPER_WALLS PATHMSD LOWER_WALLS PRINT	bias generic setup colvar
20.034	Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations	bio	RNA, SARS-CoV-2, partial tempering	Sandro Bottaro	ABMD ERMSD DISTANCE RESTART TORSION MOLINFO PRINT CENTER	colvar vatom generic bias setup
20.026	Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor	bio	Metadynamics, Umbrella sampling	Brandon Peters	RESTRAINT CONVERT_TO_FES METAD HISTOGRAM DUMPGRID MULTI_RMSD REWEIGHT_METAD PRINT	bias generic gridtools colvar
20.017	FISST	methods	FISST, force, peptide, sampling, tempering	Glen Hocky	RESTRAINT MATHEVAL UNITS GROUP DISTANCE GYRATION FISST ENERGY PRINT BIASVALUE	colvar function core generic bias setup fisst
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	COORDINATION COMBINE DIHCOR ENDPLUMED PARABETARMSD INCLUDE METAINFERENCE GROUP TORSION FLUSH MOLINFO PRINT ENSEMBLE CS2BACKBONE WHOLEMOLECULES ANTIBETARMSD PBMETAD GYRATION ALPHARMSD STATS	colvar isdb function core generic multicolvar secondarystructure bias
20.006	Class B GPCR activation mechanism	bio	metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding	Francesco Gervasio	MATHEVAL METAD MOLINFO WHOLEMOLECULES UPPER_WALLS RMSD DISTANCE LOWER_WALLS COMBINE ENERGY PRINT CENTER	colvar function vatom generic bias
20.001	Conformational stability and dynamics in solution and in crystals report similarly on unfolding and aggregation propensity of amyloidogenic proteins	bio	metainference, metadynamics, NMR, protein dynamics, b2m, protein crystals	Carlo Camilloni	CS2BACKBONE UPPER_WALLS GROUP WHOLEMOLECULES ANTIBETARMSD ENDPLUMED PBMETAD FLUSH LOWER_WALLS MOLINFO PRINT BIASVALUE ALPHABETA	isdb core generic multicolvar secondarystructure bias
19.069	Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen	materials	ibuprofen, crystal, solvent, surface	Matteo Salvalaglio	INCLUDE GROUP ENDPLUMED DISTANCE PRINT CENTER	core generic colvar vatom
19.063	Protein-ligand binding through metadynamics with path CVs	bio	metadynamics, path CVs, ligand binding	Mattia Bernetti	METAD WHOLEMOLECULES UPPER_WALLS PATHMSD LOWER_WALLS PRINT	bias generic colvar
19.046	Optimal Collective from short simulations for Benzamidine-Trypsin ligand binding	bio	VAC-MetaD, optimised collective variables, binding free energy, unbinding rates, benzamidine trypsin, Structure Activity Relation	Faidon Brotzakis	METAD BRIDGE DISTANCES UPPER_WALLS WHOLEMOLECULES GROUP REWEIGHT_METAD RMSD FUNNEL DISTANCE LOWER_WALLS COMBINE TORSION MOLINFO PRINT COM ALPHABETA	colvar function vatom funnel core generic multicolvar adjmat bias
19.037	Scission free energy of organic dyes	chemistry	metadynamics, multiple walkers, matheval/lepton	Paolo Raiteri	MATHEVAL METAD UNITS UPPER_WALLS DISTANCE FLUSH RESTART PRINT	colvar function generic bias setup
19.029	WTE-metaD of FF domain of URNF1 C57D variant	bio	metadynamics, mutations, post-translational modification, ff domain	Elena Papaleo	METAD UPPER_WALLS WHOLEMOLECULES GROUP LOWER_WALLS GYRATION MOLINFO PRINT ALPHABETA	colvar core generic multicolvar bias
19.007	EMMI Microtubules	bio	metainference, cryo-EM	Max Bonomi	EMMI WHOLEMOLECULES GROUP MOLINFO PRINT BIASVALUE	core generic isdb bias
19.004	MI Ubiquitin	bio	metainference, NMR	Max Bonomi	CS2BACKBONE METAINFERENCE RDC WHOLEMOLECULES GROUP MOLINFO PRINT	core generic isdb
19.001	RNA SHAPE	bio	metadynamics, RNA, ligand binding	Giovanni Bussi	METAD RANDOM_EXCHANGES ANGLE INCLUDE UPPER_WALLS ERMSD DISTANCE FLUSH LOWER_WALLS COMBINE MOLINFO PRINT DISTANCES	colvar function generic multicolvar bias
26.002	A Transferable and Robust Computational Framework for Class A GPCR Activation Free Energies	bio	OneOPES, GPCR, ADRB1, activation, euclidean path, microswitches, conformational changes, allostery	Valerio Rizzi	CUSTOM OPES_EXPANDED ECV_MULTITHERMAL ENERGY PATH LOWER_WALLS VOLUME COORDINATION DISTANCE OPES_METAD_EXPLORE CENTER PRINT PATHMSD RMSD UPPER_WALLS GROUP	opes function bias colvar core mapping vatom generic
25.030	Committor Regularization	methods	metadynamics, enhanced sampling, mlcvs, committor, machine learning	Florian Dietrich	PRINT METAD UNITS MOVINGRESTRAINT	generic bias setup
25.018	Metainference simulation for dimerization of RNA binding protein	bio	Metainference, Metadynamics, SAXS, protein dimer	Debadutta Patra	TORSION GYRATION ENSEMBLE PBMETAD DISTANCE METAINFERENCE CENTER STATS SAXS WHOLEMOLECULES PRINT FLUSH UPPER_WALLS MOLINFO	function bias colvar vatom generic isdb
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	DUMPATOMS READ RESTART TORSION ENERGY UPDATE_IF GYRATION VOLUME PBMETAD DISTANCE CENTER PRINT WHOLEMOLECULES MOLINFO INCLUDE	bias colvar vatom 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	CUSTOM ZDISTANCES UNITS OPES_METAD COMMITTOR DISTANCE FIXEDATOM PRINT FLUSH COORDINATIONNUMBER UPPER_WALLS GROUP DISTANCES	opes function bias multicolvar colvar core vatom generic symfunc setup
24.034	Umbrella sampling of ion in transporter SLC26A7	bio	umbrella sampling, transporter, ions	Xiaoli Lu	RESTRAINT PRINT POSITION UNITS	colvar generic bias setup
24.029	Combination of OPES and OPES-Explore	methods	OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin	Dhiman Ray	CONTACTMAP COORDINATION OPES_METAD_EXPLORE FIXEDATOM ENDPLUMED WHOLEMOLECULES POSITION FLUSH GROUP CUSTOM BIASVALUE LOWER_WALLS METAD DISTANCE MATHEVAL UPPER_WALLS MOLINFO CENTER PRINT RMSD COMBINE ENERGY UNITS OPES_METAD PYTORCH_MODEL FIT_TO_TEMPLATE INCLUDE	opes pytorch function bias colvar core vatom generic setup
24.023	Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21. A Machine-Learning-Aided Enhanced Sampling Study	bio	RNA, miRNA, OneOPES, ligand binding, conformational changes	Valerio Rizzi	CUSTOM OPES_EXPANDED RESTART TORSION ENERGY ECV_MULTITHERMAL COORDINATION DISTANCE OPES_METAD_EXPLORE PRINT COMBINE GROUP	opes function colvar core generic setup
24.018	A new route to the prebiotic synthesis of glycine via ab initio-based machine learning calculations	chemistry	prebiotic chemistry, glycine, Strecker synthesis, ab initio calculations, machine learning	Léon HUET	PRINT DISTANCE	colvar generic
24.014	Learning Collective Variables with Synthetic Data Augmentation through Physics-inspired Geodesic Interpolation	methods	data augmentation, geodesic interpolation, collective variables, protein folding	Juno Nam	LOWER_WALLS PYTORCH_MODEL COORDINATION METAD PRINT WHOLEMOLECULES FLUSH RMSD UPPER_WALLS MOLINFO DRR	pytorch bias colvar generic drr
23.040	Supramolecular capsules assembly dynamics	chemistry	Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics	Riccardo Capelli	CUSTOM UNITS METAD DISTANCE CENTER PRINT POSITION WHOLEMOLECULES COM FLUSH GROUP DISTANCES	function bias multicolvar colvar core vatom generic setup
23.026	Machine Learning Nucleation Collective Variables with Graph Neural Networks	chemistry	Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks	Florian Dietrich	Q6 LOCAL_Q6 MOVINGRESTRAINT LOWER_WALLS METAD PRINT MFILTER_MORE COORDINATIONNUMBER COMBINE GROUP	function bias multicolvar core generic symfunc
23.018	Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention	materials	metadynamics, surface binding, peptide adsorption	Kaylyn Torkelson	GYRATION PBMETAD DISTANCE PRINT COM UPPER_WALLS	vatom colvar generic bias
23.001	Quantum phase diagram of water	chemistry	Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella	Sigbjørn-Løland Bore	OPES_EXPANDED RESTART LOWER_WALLS PRINT ECV_UMBRELLAS_LINE UPPER_WALLS INCLUDE ENVIRONMENTSIMILARITY	opes bias generic envsim setup
22.044	Colloid Crystallisation Analyses	materials	Q4, Q6, Pair Entropy, DFS	Aaron Finney	Q6 LOCAL_Q6 CONTACT_MATRIX PRINT CLUSTER_NATOMS MFILTER_LESS LOCAL_AVERAGE Q4 COORDINATIONNUMBER MFILTER_MORE DFSCLUSTERING COMBINE GROUP LOCAL_Q4	function multicolvar core generic symfunc adjmat clusters
22.036	Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction	bio	Well-tempered MetaDynamics with Hamiltonian Replica Exchange	Miroslav Krepl	CUSTOM BIASVALUE GHBFIX COORDINATION METAD PRINT FLUSH COMBINE LOAD UPPER_WALLS MOLINFO GROUP	function bias colvar core generic setup
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	LOWER_WALLS FUNNEL_PS METAD DISTANCE PRINT WHOLEMOLECULES PATHMSD COM FUNNEL UPPER_WALLS	bias funnel colvar vatom generic
21.026	Probing allosteric regulations with coevolution-driven molecular simulations	bio	metadynamics, coevolution, allostery, adenylate cyclase	Francesco Colizzi	UNITS METAD DISTANCE PRINT WHOLEMOLECULES PATHMSD COM UPPER_WALLS	bias colvar vatom generic setup
21.015	Coarse-grained metadynamics and umbrella sampling simulations to investigate interactions of carbohydrate-binding modules with chitin	bio	metadynamics, umbrella sampling, coarse-grained, MARTINI, chitin, carbohydrate-binding module	Gaston Courtade	RESTART REWEIGHT_BIAS COORDINATION METAD CENTER MATHEVAL RESTRAINT PRINT WHOLEMOLECULES POSITION	function bias colvar vatom generic setup
20.030	Converging experimental and computational views of the knotting mechanism of the smallest knotted protein	bio	phi-values, transition state, knotted proteins	Cristina Paissoni	MOLINFO COORDINATION RESTRAINT STATS PRINT WHOLEMOLECULES COMBINE	function colvar generic bias
20.025	The role of water in host-guest interaction	bio	ligand binding, water, opes, SAMPL5	Valerio Rizzi	ENERGY OPES_METAD COORDINATION PYTORCH_MODEL DISTANCE FIXEDATOM CENTER MATHEVAL ENDPLUMED PRINT WHOLEMOLECULES FIT_TO_TEMPLATE ANGLE UPPER_WALLS GROUP	opes pytorch function bias colvar core vatom generic
20.010	Phase equilibrium of liquid water and hexagonal ice from enhanced sampling molecular dynamics simulations	materials	water, ice, TIP4P, crystallization, EnvironmentSimilarity, RefCV, kernel, VES, variationally enhanced sampling	Pablo Piaggi	Q6 RESTART TD_WELLTEMPERED BF_LEGENDRE VOLUME OPT_AVERAGED_SGD MATHEVAL PRINT OPT_DUMMY UPPER_WALLS VES_LINEAR_EXPANSION ENVIRONMENTSIMILARITY	function bias ves colvar generic symfunc envsim setup
19.058	Constrained MD for maintaining a cavity in a calculation	chemistry	constrained MD, porous molecules, porosity, cavity	Kim Jelfs	MOVINGRESTRAINT RESTART INPLANEDISTANCES PRINT COM FLUSH DISTANCES	bias multicolvar vatom generic setup
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	RESTART UNITS LOWER_WALLS COORDINATION METAD PRINT POSITION FLUSH UPPER_WALLS GROUP	bias colvar core generic setup
19.032	Chemical reaction in solution using path collective variables based on coordination patterns	chemistry	chemical reactions, solutions, metadynamics, coordination patterns	Fabio Pietrucci	RESTART PATH METAD PRINT FLUSH UPPER_WALLS DISTANCES	bias multicolvar mapping generic setup
19.028	pRAVE	methods	RAVE, reaction coordinate, deep learning, metadynamics, kinetics	Pratyush Tiwary	ALPHABETA EXTERNAL RESTART TORSION COMMITTOR DISTANCE PRINT WHOLEMOLECULES COM COMBINE	function bias multicolvar colvar vatom generic setup
26.006	Metadynamics simulations of buried phosphorylation sites and proline isomerisation	bio	metadynamics	Julian Streit	WHOLEMOLECULES PRINT MOLINFO COORDINATION TORSION METAD	bias generic colvar
25.024	Sampling glycan-glycan interactions for B22 calculations	bio	B22, glycan, carbohydrates, distance, REST2, metadynamics, RECT, replica exchange	Isabell Louise Grothaus	DISTANCE COM PRINT COMBINE POSITION RESTRAINT METAD	bias generic function vatom colvar
25.022	Imidazole Diffusion in SALEM-2 MOF	materials	OPES, Diffusion, Ring opening, MOFs, Machine Learning Potentials	Sudheesh Kumar Ethirajan	CENTER WHOLEMOLECULES ENDPLUMED DISTANCE PRINT GROUP DISTANCES UNITS MOLINFO PROJECTION_ON_AXIS OPES_METAD	generic setup multicolvar vatom opes core colvar
25.016	Advancing in silico drug design with Bayesian refinement of AlphaFold models	bio	bAIes, AlphaFold, Bayesian refinement, virtual screening, docking, small-molecule, enrichment	Samiran Sen	BIASVALUE PRINT BAIES GROUP	core bias generic isdb
25.015	Assessment of Force Fields for Describing Conformational Polymorphic Crystals of ROY	materials	Molecular crystal, Force Field, Collective Variable	Pradip Si and Omar Valsson	DUMPMULTICOLVAR TORSIONS PRINT DISTANCES SMAC	generic multicolvar symfunc
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	LOWER_WALLS DISTANCE PRINT GROUP UNITS COORDINATION COMMITTOR RESTART UPPER_WALLS CUSTOM OPES_METAD	bias setup generic function opes core colvar
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	WHOLEMOLECULES CENTER DUMPMASSCHARGE DISTANCE BIASVALUE COM PBMETAD PRINT GROUP DUMPATOMS MOLINFO COORDINATION ALPHARMSD EMMI UPPER_WALLS RMSD PARABETARMSD	secondarystructure bias generic isdb vatom core colvar
24.030	NMR guided simulation of dsRBD	bio	Metainference, NMR, protein dynamics	Debadutta Patra	WHOLEMOLECULES FLUSH METAINFERENCE DISTANCE PRINT RDC ALPHABETA GROUP MOLINFO STATS ENSEMBLE	generic function multicolvar isdb core colvar
24.020	Graph Neural Network-State Predictive Information Bottleneck (GNN-SPIB) approach for learning molecular thermodynamics and kinetics	bio	LJ7, alanine, well-tempered metadynamics, infrequent metadynamics, machine learning	Ziyue Zou, Dedi Wang, Pratyush Tiwary	LOAD PRINT GROUP COMMITTOR TORSION METAD	bias generic setup core colvar
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	FLUSH LOWER_WALLS DISTANCE PRINT COMBINE UNITS COMMITTOR UPPER_WALLS TORSION CUSTOM OPES_METAD	bias generic function setup opes 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	WHOLEMOLECULES DISTANCE BIASVALUE PRINT GROUP WRAPAROUND MOLINFO UPPER_WALLS EMMIVOX INCLUDE	bias generic isdb core colvar
23.021	Into the Dynamics of Rotaxanes at Atomistic Resolution	materials	metadynamics, rotaxanes, molecular shuttles, molecular machines	Luigi Leanza	CENTER FIXEDATOM DISTANCE PRINT UPPER_WALLS TORSION METAD MATHEVAL CUSTOM	bias generic function vatom colvar
23.012	JAK2 2D meta-eABF PMF with statistical analysis	bio	2D meta-eABF, path CV, PMF	Istvan Kolossvary	FLUSH LOWER_WALLS BIASVALUE PRINT PATHMSD DRR UPPER_WALLS METAD CUSTOM	drr bias generic function colvar
22.042	Metadynamics of NSP10 and variants	bio	metadynamics, NSP10, crystal structure, variants	Shozeb Haider	PRINT TORSION METAD	bias generic colvar
22.026	Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification	materials	Peptoid, silica	Jim Pfaendtner	DISTANCE COM PRINT PBMETAD GYRATION MOLINFO UPPER_WALLS	bias generic colvar vatom
22.020	Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix–Junction–Helix RNA	bio	RNA force field, Helix-Junction-Helix RNA, SAXS, Well tempered metadynamics	Weiwei He	WHOLEMOLECULES DISTANCE COM PRINT GROUP TORSION METAD	bias generic vatom core colvar
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	FLUSH LOWER_WALLS DISTANCE COM COMBINE GYRATION UNITS COORDINATION COORDINATIONNUMBER UPPER_WALLS METAD	bias generic function setup symfunc vatom colvar
21.033	Multiple-path-metadynamics applied to DNA base-pairing transitions	bio	path-CV, metadynamics, multiple-walker, dna	Alberto Pérez-de-Alba-Ortíz	MOVINGRESTRAINT PRINT CONSTANT COMBINE RESTRAINT UPPER_WALLS METAD INCLUDE	bias generic function
21.027	EGFR activating mutations mechanism	bio	metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA	Francesco Gervasio	WHOLEMOLECULES LOWER_WALLS DISTANCE PRINT CONTACTMAP MOLINFO ALPHARMSD ENERGY UPPER_WALLS METAD MATHEVAL INCLUDE	secondarystructure bias generic function colvar
21.019	Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations	materials	Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen	Matteo Salvalaglio	TORSIONS DISTANCE COM PRINT KDE MATHEVAL	generic function multicolvar gridtools vatom colvar
21.013	Role of vibrational excitation in heterogeneous catalysis	chemistry	catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption	Kristof Bal	LOAD OPT_AVERAGED_SGD CONVERT_TO_FES TD_GRID UNITS UPPER_WALLS UWALLS DUMPGRID LOWER_WALLS EXTERNAL HISTOGRAM DISTANCES REWEIGHT_METAD METAD VES_LINEAR_EXPANSION FLUSH REWEIGHT_BIAS DISTANCE COORDINATION RESTRAINT ANGLES PRINT BF_CHEBYSHEV COMBINE COORDINATIONNUMBER	bias setup multicolvar generic function symfunc ves gridtools colvar
20.027	Allosteric Regulation of SARS-CoV-2 Protease. Towards Informed Structure-Based Drug Discovery	bio	SARS-CoV2, MPro, Covid-19, Molecular Dynamics, Metadynamics, Computer-Aided Drug Discovery	Khaled Abdel-Maksoud	PRINT TORSION METAD DISTANCE	bias generic colvar
20.018	Free energy barriers from biased molecular dynamics simulations	methods	kinetics, free energy barriers, chemical reactions, nucleation, metadynamics	Kristof Bal	LOAD DENSITY CONVERT_TO_FES UNITS UPPER_WALLS DUMPGRID LOWER_WALLS HISTOGRAM LOCAL_AVERAGE REWEIGHT_METAD ENERGY METAD FLUSH VOLUME REWEIGHT_BIAS DISTANCE COORDINATION PAIRENTROPY SPRINT CENTER PRINT Q6 COMBINE CONTACT_MATRIX COORDINATIONNUMBER	bias setup generic function symfunc volumes gridtools sprint adjmat 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	WHOLEMOLECULES LOAD LOWER_WALLS DISTANCE BIASVALUE COM PRINT CONSTANT CONTACTMAP GROUP FUNCPATHGENERAL MOLINFO UPPER_WALLS METAD MATHEVAL PROJECTION_ON_AXIS INCLUDE	bias generic setup function vatom core colvar
20.004	Data-driven collective variables for enhanced sampling	methods	collective variables, machine learning, deep-lda	Luigi Bonati	FLUSH LOAD ENDPLUMED LOWER_WALLS DISTANCE PRINT COM GROUP UNITS PYTORCH_MODEL UPPER_WALLS TORSION MATHEVAL OPES_METAD	bias generic setup function pytorch vatom opes core colvar
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	DUMPGRID ENDPLUMED LOWER_WALLS DISTANCE COM PRINT CONVERT_TO_FES HISTOGRAM COMBINE READ REWEIGHT_METAD UPPER_WALLS METAD MATHEVAL ABMD	bias generic function gridtools vatom colvar
19.080	Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium	methods	ves, variationally enhanced sampling, vibrational excitation, chemical reactions	Kristof Bal	VES_LINEAR_EXPANSION FLUSH DUMPGRID LOWER_WALLS EXTERNAL OPT_AVERAGED_SGD DISTANCE PRINT HISTOGRAM CONVERT_TO_FES BF_CHEBYSHEV COMBINE TD_GRID UNITS COORDINATION ANGLE UPPER_WALLS TD_WELLTEMPERED	bias generic function setup ves gridtools colvar
19.076	Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones	bio	molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics	Salvatore Assenza	ENDPLUMED MOVINGRESTRAINT PRINT GYRATION UNITS	bias generic setup colvar
19.073	On the role of enthalpic and entropic contributions on the conformational free energy landscape of MIL-101(Cr) building units	materials	metadynamics, MOF, MIL101Cr, conformational	Matteo Salvalaglio	ENDPLUMED LOWER_WALLS PRINT DISTANCES GYRATION ENERGY COORDINATIONNUMBER UPPER_WALLS METAD	bias generic multicolvar symfunc colvar
19.053	Capillary fluctuations with PLUMED	methods	nucleation, surface tension, capillary fluctuations	Gareth Tribello	CENTER FOURIER_TRANSFORM DUMPGRID FCCUBIC GROUP FIND_CONTOUR_SURFACE MORE_THAN UNITS MULTICOLVARDENS	function setup symfunc fourier gridtools contour vatom core
19.043	Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA)	methods	metadynamics, chemistry, HLDA	GiovanniMaria Piccini	FLUSH DISTANCE PRINT COMBINE DISTANCES UNITS RESTART UPPER_WALLS METAD	generic setup function multicolvar bias colvar
19.019	FA-MetaD-JCP-Wang-et-al	bio	Frequency adaptive metadynamics; peptide	Kresten Lindorff-Larsen	FLUSH PRINT ALPHABETA COMBINE MOLINFO COMMITTOR METAD	bias generic function multicolvar
19.018	Excited state FEP/Metadynamics simulations	chemistry	metadynamics, FEP, excited states, conjugated polymers, torsional potential	Adriana Pietropaolo	WHOLEMOLECULES BIASVALUE PRINT CONSTANT TORSION METAD MATHEVAL	bias generic function colvar
19.014	MIL101(Cr) SBUs assembly	materials	MOFs, nucleation, self-assembly, metadynamics	Matteo Salvalaglio	ENDPLUMED PRINT DISTANCES GYRATION RESTART COORDINATIONNUMBER METAD	generic setup multicolvar bias symfunc colvar
26.011	Lets Stalk About Membranes. Committor-Based Enhanced Sampling of Stalk Formation.	bio	committor, machine learning, enhanced sampling, OPES, membrane fusion, stalk formation, nanoparticles	Giorgia Rossi	COORDINATION CUSTOM PRINT BIASVALUE GROUP CENTER LOWER_WALLS LOAD OPES_METAD_EXPLORE	opes function colvar bias vatom generic setup core
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 UNITS MATHEVAL PATHMSD PRINT RMSD MOLINFO ENDPLUMED ANGLE LOWER_WALLS COMBINE FUNNEL UPPER_WALLS DISTANCE WHOLEMOLECULES COM FUNNEL_PS	function colvar bias funnel vatom generic setup
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 PRINT CONVERT_TO_FES HISTOGRAM REWEIGHT_BIAS MOLINFO LOWER_WALLS DUMPGRID UPPER_WALLS DISTANCE FIXEDATOM WHOLEMOLECULES COM	gridtools bias colvar vatom generic
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 COORDINATION MATHEVAL GYRATION WHOLEMOLECULES PRINT CENTER LOWER_WALLS COMBINE UPPER_WALLS DISTANCE GROUP	function colvar bias vatom generic core
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	COORDINATION ENERGY MATHEVAL PRINT FIT_TO_TEMPLATE OPES_METAD_EXPLORE ANGLE GROUP CENTER UPPER_WALLS DISTANCE FIXEDATOM WHOLEMOLECULES	opes function colvar bias vatom generic core
25.011	Chiral perovskite nucleation	chemistry	metadynamics, chiral perovskites, nucleation	Adriana Pietropaolo	UNITS MATHEVAL PBMETAD MULTI_RMSD PRINT RESTART LOWER_WALLS UPPER_WALLS DISTANCE	function colvar bias generic setup
24.032	DeepLNE++	methods	PATHCV, OPES	Thorben Fröhlking	COORDINATION CUSTOM ENERGY PRINT OPES_METAD TORSION COMBINE LOAD DISTANCE GROUP	opes function colvar generic setup core
24.026	Constant pH metadynamics of RNA oligomers	bio	metadynamics, pH, RNA	Giovanni Bussi	METAD PRINT RESTART TORSION MOLINFO PUCKERING	generic colvar bias setup
24.016	Cryo-EM guided simulations of ribozyme	bio	metainference, cryo-EM	Giovanni Bussi	EMMIVOX WHOLEMOLECULES PRINT MOLINFO BIASVALUE ERMSD INCLUDE GROUP RESTRAINT	colvar bias generic isdb core
24.007	SWISH-X	bio	swish-x, SWISH-X, swish, expanded SWISH	Alberto Borsatto	ENERGY INCLUDE PRINT MOLINFO CONTACTMAP UPPER_WALLS OPES_EXPANDED ECV_MULTITHERMAL WHOLEMOLECULES	generic opes colvar bias
24.006	Water vapor condensation	chemistry	metadynamics, homogeneous condensation, chemical potential	Shenghui Zhong	METAD UNITS CLUSTER_PROPERTIES PRINT CONTACT_MATRIX DFSCLUSTERING UPPER_WALLS COORDINATIONNUMBER CLUSTER_NATOMS	bias generic setup clusters adjmat symfunc
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 PATHMSD FUNCPATHMSD PRINT ALPHARMSD MOLINFO LOWER_WALLS UPPER_WALLS DISTANCE INCLUDE CONTACTMAP	function colvar bias generic secondarystructure
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 PRINT ALPHARMSD FIT_TO_TEMPLATE MOLINFO COMBINE ANN WHOLEMOLECULES POSITION	function colvar bias generic annfunc secondarystructure
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	UNITS OPES_METAD FIT_TO_TEMPLATE MOLINFO TORSION WHOLEMOLECULES GROUP POSITION ENERGY BIASVALUE COM MATHEVAL PRINT CENTER LOWER_WALLS OPES_METAD_EXPLORE COORDINATION CUSTOM WRAPAROUND ENDPLUMED COMMITTOR UPPER_WALLS DISTANCE FLUSH	opes function colvar bias vatom generic setup core
23.028	Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process	chemistry	Ammonia decomposition; Dynamics;OPES; Neural Network potential	Manyi Yang	CUSTOM UNITS MATHEVAL ENERGY COMMITTOR PRINT COORDINATIONNUMBER OPES_METAD ZDISTANCES COM LOWER_WALLS DISTANCES UPPER_WALLS DISTANCE FIXEDATOM GROUP FLUSH	opes function colvar bias vatom generic multicolvar setup symfunc core
23.027	CmuMD simulations of NaCl(aq) at NaCl	chemistry	CmuMD, DFS, Q3, Pair Entropy	Aaron Finney	Q3 UNITS PRINT RESTRAINT HISTOGRAM DENSITY AROUND CONTACT_MATRIX DFSCLUSTERING LOCAL_Q3 CLUSTER_DISTRIBUTION LOCAL_AVERAGE LOAD COORDINATIONNUMBER FIXEDATOM GROUP DUMPGRID CLUSTER_NATOMS	gridtools bias vatom generic volumes setup clusters symfunc adjmat core
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	METAD DRR CUSTOM UNITS PATHMSD PRINT BIASVALUE LOWER_WALLS UPPER_WALLS TIME FLUSH	function colvar bias generic setup drr
23.003	Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations	methods	metadynamics, alchemical variable, alchemical free energy calculations	Wei-Tse Hsu	METAD PRINT READ TORSION EXTRACV	generic colvar bias
22.039	Driving and characterizing nucleation of urea and glycine polymorphs in water	bio	metadynamics, nucleation, amino acids, polymorphism	Eric Beyerle	PAIRENTROPY METAD MATHEVAL INCLUDE PRINT Q4 CENTER LOAD COMBINE COORDINATIONNUMBER Q6 GROUP	function gridtools bias vatom generic setup symfunc core
22.018	Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations	bio	ligand binding, docking, EMMI, LAT1	Max Bonomi	EMMIVOX PRINT MOLINFO BIASVALUE GROUP LOAD WHOLEMOLECULES	bias generic setup isdb 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	COORDINATION CUSTOM COMMITTOR MATHEVAL PRINT OPES_METAD RMSD FIT_TO_TEMPLATE GROUP CENTER LOWER_WALLS PYTORCH_MODEL UPPER_WALLS DISTANCE FIXEDATOM WHOLEMOLECULES	opes function colvar bias pytorch vatom generic core
21.049	Multiple-path-metadynamics and PathMaps	methods	path-CV, metadynamics, multiple-walker, multiple paths, pathmap	Alberto Pérez-de-Alba-Ortíz	METAD ENSEMBLE UNITS CUSTOM PRINT TORSION CONSTANT LOWER_WALLS COMBINE LOAD MOVINGRESTRAINT UPPER_WALLS RESTRAINT	function colvar bias generic setup
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 CUSTOM UNITS PRINT TORSION LOWER_WALLS UPPER_WALLS DISTANCE COM	function colvar bias vatom generic setup
21.047	Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations	materials	pair entropy, metadynamics, ves, solids, crystallization	Pablo Piaggi	PAIRENTROPY METAD ENERGY BF_LEGENDRE VOLUME PRINT RESTART TD_WELLTEMPERED LOAD COMBINE OPT_AVERAGED_SGD VES_LINEAR_EXPANSION	function gridtools bias ves colvar generic setup
21.044	NaCl nucleation	chemistry	metadynamics, DFS clustering	Aaron Finney	METAD DUMPGRID PRINT HISTOGRAM MFILTER_MORE Q6 INSPHERE COMBINE LOCAL_Q6 CONTACT_MATRIX DFSCLUSTERING COORDINATIONNUMBER FIXEDATOM GROUP CLUSTER_DISTRIBUTION CLUSTER_NATOMS	function gridtools bias vatom generic multicolvar volumes clusters symfunc adjmat core
21.043	Predicting the Conformational Variability of Oncogenic GTP-bound G12D Mutated KRas-4B Proteins at Cell Membranes	chemistry	well-tempered metadynamics, KRas-4B, anionic membrane, conformational variability	Huixia Lu	METAD PRINT TORSION FIT_TO_TEMPLATE FIXEDATOM	generic colvar bias vatom
21.041	Nucleating a Different Coordination in a Crystal under Pressure. A Study of the B1−B2 Transition in NaCl by Metadynamics	methods	metadynamics, structural phase transitions, pressure-induced phase transition, martensitic transitions	Matej Badin	METAD COORDINATION CUSTOM VOLUME PRINT ENDPLUMED COMBINE	generic function colvar bias
21.040	A structural ensemble of a tau-microtubule complex reveals regulatory tau phosphorylation and acetylation mechanisms	bio	EMMI, CryoEM, tau-microtubules, post-translational modifications, chemical mutagenesis, structural ensemble, Metainference	Faidon Brotzakis	PRINT RESTART UPPER_WALLS MOLINFO BIASVALUE GROUP EMMI DISTANCE WHOLEMOLECULES COM	colvar bias vatom generic setup isdb core
21.038	Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics	materials	metadynamics, SGOOP, nucleation, urea	Ziyue Zou	METAD ENERGY PRINT VOLUME CENTER LOAD COMBINE COORDINATIONNUMBER INCLUDE GROUP	function colvar bias vatom generic setup symfunc core
21.037	Molecular Dynamics simulations of RBD/hACE2 complexes	bio	SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain	Max Bonomi	PRINT RMSD DISTANCE	generic colvar
21.016	MD SAXS GTPase associated center	bio	metadynamics, RNA, folding, SAXS	Giovanni Bussi	METAD CUSTOM GYRATION WHOLEMOLECULES PRINT ERMSD MOLINFO LOWER_WALLS SAXS UPPER_WALLS INCLUDE GROUP	function colvar bias generic isdb core
21.009	Nucleation rates from small scale atomistic simulations and transition state theory	materials	kinetics, free energy barriers, nucleation, droplets, metadynamics	Kristof Bal	METAD UNITS DUMPGRID PRINT CONVERT_TO_FES HISTOGRAM REWEIGHT_METAD MOVINGRESTRAINT COMMITTOR LOAD UPPER_WALLS COORDINATIONNUMBER FLUSH	gridtools bias generic setup symfunc
20.028	Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane	bio	metadynamics, KRas-4B, anionic membrane	Huixia Lu	METAD PRINT RESTART FIT_TO_TEMPLATE CENTER DISTANCE	colvar bias vatom generic setup
20.024	Gaussian Mixture Based Enhanced Sampling (GAMBES)	methods	enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias	Jayashrita Debnath	UNITS ENERGY PRINT TORSION LOWER_WALLS LOAD DISTANCES COMBINE UPPER_WALLS DISTANCE GROUP	function colvar bias generic multicolvar setup core
19.077	Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations	materials	metadynamics, peptide-surface binding	Jim Pfaendtner	METAD ENERGY GYRATION PRINT MOLINFO UPPER_WALLS DISTANCE COM	generic colvar bias vatom
19.067	Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways	bio	metadynamics, ligand unbinding	Jakub Rydzewski	METAD UNITS PATHMSD PRINT RESTART LOWER_WALLS UPPER_WALLS	setup colvar bias generic
19.060	Neural networks-based variationally enhanced sampling	methods	ves, neural networks	Luigi Bonati	UNITS ENERGY PRINT TORSION ENDPLUMED LOAD ENVIRONMENTSIMILARITY Q6 POSITION	colvar generic setup symfunc envsim
19.057	SAXS ensembles using Martini-Beads multi-scale SAXS	methods	metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics	Cristina Paissoni	COORDINATION ENSEMBLE MATHEVAL PBMETAD ALPHABETA STATS PRINT MOLINFO ANGLE BIASVALUE ENDPLUMED GROUP CENTER COMBINE SAXS INCLUDE WHOLEMOLECULES	function colvar bias vatom generic multicolvar isdb core
19.054	MetaFEP	methods	metadynamics, chemistry, free energy perturbation	GiovanniMaria Piccini	METAD UNITS ENERGY PRINT LOWER_WALLS COMBINE UPPER_WALLS DISTANCE FLUSH	function colvar bias generic setup
19.052	Gibbs free energy of homogeneous nucleation	materials	nucleation, surface excess free energy	Gareth Tribello	METAD UNITS FCCUBIC PRINT ENDPLUMED UPPER_WALLS CELL	colvar bias generic setup symfunc
19.042	Harmonic Linear Discriminant Analysis (HLDA)	methods	metadynamics, chemistry, HLDA	GiovanniMaria Piccini	METAD UNITS ENERGY PRINT COMBINE UPPER_WALLS DISTANCE FLUSH	function colvar bias generic setup
19.036	Thermodynamics and kinetics of G protein-coupled receptor activation	bio	metadynamics, allostery, receptor conformation, GPCR, pharmacology	Davide Provasi	METAD FUNCPATHMSD PRINT RMSD ENDPLUMED CONTACTMAP DISTANCE WHOLEMOLECULES COM	function colvar bias vatom generic
19.026	Ice Nucleation on Cholesterol Crystals	materials	forward flux sampling, crystal nucleation, water, ice, organic crystals	Gabriele Cesare Sosso	CLUSTER_WITHSURFACE ENDPLUMED MFILTER_MORE CONTACT_MATRIX DFSCLUSTERING COMMITTOR LOCAL_Q6 OUTPUT_CLUSTER Q6 FLUSH CLUSTER_NATOMS	generic multicolvar clusters adjmat symfunc
19.022	eABF simulation of NANMA (alanine dipeptide)	methods	eABF, DRR, alanine dipeptide	Haochuan Chen	PRINT DRR TORSION	generic colvar drr
19.017	Ligand binding pathways exploration	bio	metadynamics, ligand binding	Riccardo Capelli	METAD COORDINATION MATHEVAL WHOLEMOLECULES PRINT CONVERT_TO_FES READ HISTOGRAM FIT_TO_TEMPLATE WRAPAROUND ENDPLUMED REWEIGHT_METAD COM DUMPGRID UPPER_WALLS GROUP FLUSH POSITION	function colvar bias gridtools vatom generic core
19.012	Martini-Beads multi-scale SAXS	methods	metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex	Carlo Camilloni	PRINT STATS RMSD MOLINFO BIASVALUE GROUP ENDPLUMED CENTER SAXS UPPER_WALLS DISTANCE INCLUDE WHOLEMOLECULES RESTRAINT	function colvar bias vatom generic isdb core
19.011	Automatic Gradient Computation for Collective Variables	other	gradient, differentiation, curvature	Toni Giorgino	ENDPLUMED	generic
19.000	VesDeltaF	methods	VES, convergence, suboptimal CVs	Michele Invernizzi	METAD UNITS ENERGY PRINT RESTART TORSION ENDPLUMED VES_DELTA_F LOAD POSITION	colvar bias ves generic setup
26.008	Ensemble Dynamics	methods	State Exploration, Protein Folding, Drug Binding, Phase Transition	Florian M. Dietrich	GROUP LOAD DISTANCE POSITION PRINT BIASVALUE OPES_METAD_EXPLORE UNITS TORSION CELL CUSTOM	generic core opes bias colvar function setup
26.004	Resolving the ambiguous binding site of quercetin at the calcineurin subunit junction using funnel metadynamics with deep learning collective variables	bio	metadynamics, funnel metadynamics, DeepTICA	Jason Loo	GROUP DISTANCE ENERGY PYTORCH_MODEL WRAPAROUND PRINT RMSD FUNNEL_PS METAD FUNNEL UPPER_WALLS WHOLEMOLECULES COORDINATION LOWER_WALLS MATHEVAL COM	generic core funnel vatom pytorch bias colvar function
26.001	Molecular simulations Alx riboswitch	bio	RNA, riboswitch	Giovanni Bussi	DISTANCE ERMSD PRINT MOLINFO MOVINGRESTRAINT RESTRAINT MATHEVAL	function generic bias colvar
25.014	Atomic resolution ensembles of intrinsically disordered proteins with Alphafold	bio	bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement	Vincent Schnapka	GROUP BAIES BIASVALUE PRINT	bias generic core isdb
25.013	Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices	bio	umbrella sampling, temperature ramping	Alexander Berlaga	DISTANCE PYTORCH_MODEL PRINT GYRATION RESTRAINT	bias generic pytorch colvar
25.012	A Machine Learning-Driven, Probability-Based Approach to Enzyme Catalysis	bio	enzyme catalysis, transition state, structure-activity relationship, free energy surface, reaction mechanism, water, alpha-amylase, sugar, QM/MM MD, OPES, committor function, machine learning	Sudip Das	LOAD DISTANCE ENERGY POSITION PRINT MATHEVAL BIASVALUE INCLUDE COORDINATION OPES_METAD TORSION FLUSH UNITS COMBINE CELL CUSTOM	generic colvar opes bias function setup
25.007	Shaping the glycan landscape. Hidden relationships between linkage and ring distortion induced by carbohydrate-active enzmyes	bio	REST-RECT, REST2, glycan, enzyme, CAZyme, steered	Isabell Grothaus	DISTANCE RESTART PRINT METAD MOVINGRESTRAINT MOLINFO PUCKERING RESTRAINT TORSION	setup generic bias colvar
25.002	M3_PCV-ABMD	chemistry	Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor	Gian Marco Elisi	PRINT PATHMSD ENDPLUMED UPPER_WALLS UNITS ABMD	setup generic bias colvar
24.019	Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning	bio	OPES, machine learning, protein folding, adaptive sampling	Mingyuan Zhang	DISTANCE PRINT ALPHARMSD MOLINFO GYRATION OPES_METAD WHOLEMOLECULES COORDINATION TORSION COMBINE CUSTOM	generic opes colvar secondarystructure function
24.017	Absolute Binding Free Energies with OneOPES	methods	protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy	Francesco Gervasio	ENERGY PRINT BIASVALUE INCLUDE COORDINATION CONTACTMAP LOWER_WALLS COM RESTART ECV_MULTITHERMAL WRAPAROUND RMSD MOLINFO UPPER_WALLS GROUP OPES_EXPANDED OPES_METAD_EXPLORE WHOLEMOLECULES PROJECTION_ON_AXIS CONSTANT MATHEVAL METAD TORSION CUSTOM	generic core opes vatom bias colvar function setup
24.012	Molecular simulations to investigate the impact of N6-methylation in RNA recognition	bio	metadynamics, alchemistry, RNA modification, RNA:protein interactions	Giovanni Bussi	GROUP DISTANCE PRINT GHBFIX MOLINFO BIASVALUE METAD UPPER_WALLS COMBINE COORDINATION DEBUG CENTER LOWER_WALLS COM	generic core colvar vatom bias function
23.044	Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition	materials	metadynamics, interlocked molecules	Luigi Leanza	GROUP PRINT ENDPLUMED DUMPGRID METAD READ HISTOGRAM COORDINATION CONVERT_TO_FES COMMITTOR	generic core bias gridtools colvar
23.037	Estimating binding free energy of solid binding peptides without extensive sampling	bio	metadynamics, solid binding peptides	Xin Qi	DISTANCE PRINT MOLINFO UPPER_WALLS PBMETAD GYRATION LOWER_WALLS COM	generic vatom bias colvar
23.033	DNA G-quadruplex and G-hairpin folding with ST-metaD protocol	bio	DNA, G4, GQ, quadruplex, hairpin, folding, metadynamics, REST2, ST-metaD	Pavlína Pokorná	ERMSD PRINT GHBFIX MOLINFO BIASVALUE METAD WHOLEMOLECULES COORDINATION COMBINE	function generic bias colvar
23.025	Probing ion binding to G-quadruplexes and related events	chemistry	metadynamics, repulsive potential, nucleic acids, G-quadruplexes	Marcelo Poleto	GROUP DISTANCE DUMPATOMS DISTANCES WRAPAROUND POSITION RESTART PRINT FIT_TO_TEMPLATE METAD UPPER_WALLS WHOLEMOLECULES FLUSH UNITS LOWER_WALLS MATHEVAL COM	generic core vatom bias multicolvar colvar function setup
23.020	FEP simulations of ATOX1 homodimer	chemistry	parallel bias metadynamics, FEP, free-energy of metal ion dissociation	Adriana Pietropaolo	DISTANCE ANGLE PRINT BIASVALUE PBMETAD WHOLEMOLECULES CONSTANT MATHEVAL	function generic bias colvar
23.017	How and When Does an Enzyme React? Unraveling α-Amylase Catalytic Activity with Enhanced Sampling Techniques	bio	enzymatic reaction discovery, reaction mechanism, catalysis, ligand-binding modes, water, alpha-amylase, sugar, QM/MM MD, OPES, OPES explore, graph CV, machine learning, Deep TDA CV, path CV	Sudip Das	GROUP DISTANCE PYTORCH_MODEL PRINT FIT_TO_TEMPLATE UPPER_WALLS OPES_METAD_EXPLORE COORDINATION OPES_METAD WHOLEMOLECULES PATH LOWER_WALLS UNITS CUSTOM CENTER TORSION FIXEDATOM	generic core mapping opes vatom bias pytorch colvar function setup
23.002	Critical comparison of general-purpose collective variables for crystal nucleation	methods	metadynamics, umbrella sampling, commitor, entropy, PIV	Julien Lam	Q6 ENERGY LOCAL_AVERAGE PRINT VOLUME METAD FUNCPATHMSD UPPER_WALLS PAIRENTROPY RESTRAINT UNITS CUSTOM Q4 PIV	generic piv colvar bias gridtools symfunc function setup
22.033	Reciprocal barrier restraint. Application to PROTAC passive permeability prediction	methods	PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR	Istvan Kolossvary	DISTANCE PRINT METAD BIASVALUE DRR FLUSH UNITS CUSTOM COM	generic drr bias vatom colvar function setup
22.031	Rare Event Kinetics from Adaptive Bias Enhanced Sampling	methods	OPES Flooding, Kinetics, Rate, OPES, Machine Learning	Dhiman Ray	ENERGY PRINT BIASVALUE INCLUDE CONTACTMAP POSITION RMSD MOLINFO GROUP PYTORCH_MODEL ENDPLUMED WHOLEMOLECULES UNITS COMBINE COMMITTOR CONSTANT DISTANCE OPES_METAD TORSION CUSTOM	generic core opes pytorch bias colvar function setup
22.006	Peptide framework for screening the effects of amino acids on assembly	bio	metadynamics, peptides	Andrew White	DISTANCES GROUP REWEIGHT_BIAS PRINT DUMPGRID METAD GYRATION INCLUDE HISTOGRAM CONVERT_TO_FES COMBINE COM	generic core vatom bias gridtools multicolvar colvar function
22.004	Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques	chemistry	reaction discovery, OPES, collective variables	Umberto Raucci	DISTANCE GROUP PYTORCH_MODEL LOAD PRINT UPPER_WALLS OPES_METAD_EXPLORE COORDINATION OPES_METAD LOWER_WALLS UNITS CUSTOM MATHEVAL COM	generic core opes vatom pytorch bias colvar function setup
22.003	Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling	methods	opes, metadynamics, reweighting, alanine, muller	Michele Invernizzi	ENERGY ECV_MULTITHERMAL POSITION PRINT OPES_EXPANDED ENDPLUMED ECV_UMBRELLAS_FILE METAD BIASVALUE PBMETAD OPES_METAD_EXPLORE OPES_METAD UPPER_WALLS LOWER_WALLS UNITS TORSION CUSTOM	generic opes bias colvar function setup
21.051	Automatic learning of hydrogen-bond fixes in an AMBER RNA force field	methods	force field, RNA	Giovanni Bussi	ERMSD PRINT METAD MOLINFO BIASVALUE WHOLEMOLECULES COORDINATION COMBINE	function generic bias 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 core bias colvar setup
21.029	Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs	bio	metadynamics, small peptide, machine learning	Pratyush Tiwary	RESTART ENERGY PRINT MOLINFO EXTERNAL FLUSH TORSION	colvar generic bias setup
21.017	All-atom simulations of the Vav1 AD construct	bio	metadynamics, parallel-bias, well-tempered	Simone Orioli	GROUP RESTART REWEIGHT_BIAS PRINT ALPHARMSD ALPHABETA MOLINFO METAD PBMETAD WHOLEMOLECULES CONTACTMAP	generic core secondarystructure bias multicolvar colvar setup
21.014	how to determine statistically accurate conformational ensembles	bio	metadynamics, metainference, errors, cv, SAXS, ensemble determination	Cristina Paissoni	ANTIBETARMSD ENSEMBLE PRINT ALPHABETA STATS METAD MOLINFO BIASVALUE GYRATION PBMETAD WHOLEMOLECULES CONTACTMAP CENTER TORSION SAXS	generic colvar secondarystructure vatom bias multicolvar isdb function
21.006	OPES, On-the-fly Probability Enhanced Sampling Method	methods	opes, alanine dipeptide, well-tempered, multithermal, multiumbrella	Michele Invernizzi	ECV_UMBRELLAS_LINE ENERGY ECV_MULTITHERMAL OPES_EXPANDED PRINT ENDPLUMED OPES_METAD TORSION	opes generic colvar
20.023	metadynminer and metadynminer3d	methods	metadynamics, visualization, R	Vojtech Spiwok	TORSION METAD PRINT	generic bias colvar
20.020	Parallel Bias Metadynamics	methods	pbmetad, trp-cage, folding	Max Bonomi	DIHCOR PRINT ALPHABETA MOLINFO GYRATION INCLUDE WHOLEMOLECULES COORDINATION PBMETAD	multicolvar generic bias colvar
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	PRINT DUMPGRID READ CONTACTMAP FLUSH LOWER_WALLS COM MOLINFO UPPER_WALLS REWEIGHT_METAD ENDPLUMED WHOLEMOLECULES COMBINE ABMD DISTANCE METAD FUNCPATHMSD HISTOGRAM CONVERT_TO_FES	generic vatom bias gridtools colvar function
19.083	Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis	chemistry	metadynamics, chemical reactions, reaction discovery	Valerio Rizzi	GROUP DISTANCES RESTART PRINT ENDPLUMED METAD COORDINATIONNUMBER UPPER_WALLS FLUSH UNITS COMBINE	generic core bias multicolvar symfunc function setup
19.064	Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations	materials	metadynamics, peptide-surface binding	Jim Pfaendtner	DISTANCE ENERGY PRINT METAD MOLINFO GYRATION UPPER_WALLS COM	generic vatom bias colvar
19.049	Determining the sizes of solid/liquid clusters in MD trajectories of nucleation	methods	nucleation, metadynamics, clustering, Steinhardt order parameters	Gareth Tribello	LOCAL_Q6 Q6 DISTANCES CLUSTER_NATOMS SMAC PRINT OUTPUT_CLUSTER METAD OUTER_PRODUCT MORE_THAN COORDINATIONNUMBER MATRIX_VECTOR_PRODUCT ONES CLUSTER_PROPERTIES CLUSTER_DISTRIBUTION CONTACT_MATRIX CUSTOM DFSCLUSTERING	generic adjmat bias clusters multicolvar symfunc function matrixtools
19.040	Optimal Metric for Path Collective Variables	bio	metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path	Francesco Luigi Gervasio	PRINT ENDPLUMED METAD TORSION MATHEVAL	function generic bias colvar
19.031	Ice nucleation using PIV-based path coordinates	materials	phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics	Silvio Pipolo	PRINT METAD FUNCPATHMSD UPPER_WALLS LOWER_WALLS CELL PIV	generic piv bias colvar function
19.024	PT-MetaD-WTE	methods	metadynamics, WTE, trp cage, PT	Jim Pfaendtner	GROUP ENERGY METAD EXTERNAL COORDINATION	core bias colvar
25.008	Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting	methods	metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting	Dhiman Ray	ENERGY RMSD LOWER_WALLS PRINT UNITS GROUP POSITION DISTANCE METAD MOLINFO ENDPLUMED BIASVALUE CUSTOM PYTORCH_MODEL OPES_METAD UPPER_WALLS TORSION WHOLEMOLECULES	bias setup function generic opes core pytorch colvar
25.005	Mechanism of Nanocluster Formation from Machine-Learned Potential-based Simulations	chemistry	WT-metadynamics, metal nanoclusters, nucleation, neural network potential, deepMD	Vikas Tiwari, Tarak Karmakar	LOWER_WALLS PRINT UNITS GROUP COORDINATION COMBINE ANGLE DISTANCE COORDINATIONNUMBER METAD COM RESTRAINT FIXEDATOM UPPER_WALLS FLUSH DISTANCES	symfunc bias setup function multicolvar vatom generic core colvar
24.009	Weighted Shape Gaussian Mixture Models	bio	metadynamics, clustering	Glen Hocky	PRINT UNITS GROUP METAD TORSION	bias setup generic core colvar
24.003	Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations	chemistry	steered molecular dynamics, foldamers, peptoids, bio-inspired	Kaylyn Torkelson	GYRATION ALPHABETA PRINT INCLUDE COORDINATION DISTANCE COM TORSION MOVINGRESTRAINT WHOLEMOLECULES	bias multicolvar vatom generic colvar
23.046	Lasso Peptides - HLDA CV	bio	metadynamics, protein folding, HLDA, harmonic	Gabriel da Hora	PRINT UNITS COMBINE DISTANCE METAD WHOLEMOLECULES	setup bias function generic colvar
23.010	An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G‑Protein-Coupled Receptor Ligands	bio	GPCR, binding free energy, free energy surface	Timothy Clark	MATHEVAL LOWER_WALLS PRINT DISTANCE METAD BIASVALUE CONSTANT UPPER_WALLS WHOLEMOLECULES	bias generic 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	GYRATION PRINT INCLUDE COORDINATION RESTRAINT COM PBMETAD TORSION WHOLEMOLECULES	vatom generic colvar bias
22.038	Enhanced Sampling Aided Design of Molecular Photoswitches	chemistry	reaction discovery, OPES explore, graph CV	Umberto Raucci	OPES_METAD_EXPLORE PRINT UNITS COORDINATION PYTORCH_MODEL CUSTOM	setup function generic opes pytorch colvar
22.023	Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy	bio	CryoEM, MEMMI,EMMI, Metadynamics, Metainference, IAPP, structural ensemble	Faidon Brotzakis	RMSD RESTART PRINT GROUP COORDINATION EMMI COM MOLINFO BIASVALUE PBMETAD UPPER_WALLS TORSION WHOLEMOLECULES	setup bias isdb vatom generic core colvar
22.013	Ligand dissociation from PreQ1 riboswitch	bio	ligand, RNA, metadynamics, pRAVE	Yihang Wang	RMSD PRINT COMBINE COMMITTOR DISTANCE COORDINATIONNUMBER METAD COM MOLINFO WHOLEMOLECULES	symfunc bias function vatom generic 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
20.021	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	STATS PRINT COORDINATION RESTRAINT MOLINFO WHOLEMOLECULES	generic colvar function bias
20.008	Simulating solvation and acidity in complex mixtures with first-principles accuracy. The case of CH3SO3H and H2O2 in phenol	chemistry	proton trasfer, metadynamics	Kevin Rossi	PRINT UNITS COORDINATION METAD CUSTOM DISTANCES	setup bias function multicolvar generic colvar
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	ENERGY MATHEVAL PRINT COMBINE VES_LINEAR_EXPANSION LOAD TD_WELLTEMPERED Q6 HISTOGRAM TD_MULTITHERMAL_MULTIBARIC OPT_AVERAGED_SGD VOLUME LOWER_WALLS DUMPGRID OPT_DUMMY UPPER_WALLS READ REWEIGHT_TEMP_PRESS CONVERT_TO_FES CELL REWEIGHT_BIAS BF_LEGENDRE RESTART	symfunc setup bias ves function generic gridtools colvar
19.066	Finding ligand unbinding reaction pathways	methods	maze, ligand unbinding	Jakub Rydzewski	MAZE_SIMULATED_ANNEALING PRINT UNITS POSITION MAZE_LOSS MAZE_OPTIMIZER_BIAS	generic setup colvar maze
19.065	Molecular Enhanced Sampling with Autoencoders	methods	enhanced sampling, collective variables, deep learning	Wei Chen	RESTRAINT POSITION COMBINE COM ANN	bias function vatom annfunc colvar
19.062	Elucidating molecular design principles for charge-alternating peptides	bio	peptide folding, metadynamics, well-tempered ensemble, parallel tempering	Jim Pfaendtner	ENERGY GYRATION PRINT METAD WHOLEMOLECULES	generic colvar bias
19.061	Diffusion in porous materials	materials	metadynamics, porous materials, diffusion	Kim E. Jelfs	LOWER_WALLS PRINT RESTART GROUP DISTANCE METAD COM UPPER_WALLS CENTER	bias setup vatom generic core colvar
19.025	Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide	bio	metainference, NMR, protein dynamics, force-fields	Carlo Camilloni	GYRATION RDC STATS METAINFERENCE PRINT CS2BACKBONE MOLINFO BIASVALUE PBMETAD JCOUPLING ENSEMBLE ENDPLUMED FLUSH TORSION WHOLEMOLECULES	bias isdb function generic colvar
26.012	Buprenorphine Restricts the Conformational Landscape of the μ-Opioid Receptor	bio	OneOPES, GPCR, MOR, activation, euclidean path, conformational changes, allostery	Simone Aureli	DISTANCE PATH RMSD ECV_MULTITHERMAL PRINT CUSTOM UPPER_WALLS GROUP COORDINATION ENERGY VOLUME OPES_METAD_EXPLORE OPES_EXPANDED CENTER	function opes bias generic colvar mapping core vatom
26.010	Solvation-Mediated Ammonia Synthesis in a Nanoheterogeneous Liquid Alloy	materials	OPES, Catalysis, Ammonia Synthesis	Axel Tosello Gardini	DISTANCE PRINT COORDINATIONNUMBER FLUSH CUSTOM GROUP UPPER_WALLS COORDINATION INCLUDE UNITS OPES_METAD_EXPLORE OPES_METAD DISTANCES	function opes bias generic colvar symfunc multicolvar setup core
25.003	Surrogate Model CV	methods	Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding	Sompriya Chatterjee	DISTANCE COMMITTOR MOLINFO PRINT COMBINE TORSION CUSTOM ENERGY GROUP MATHEVAL OPES_METAD PYTORCH_MODEL ENDPLUMED WHOLEMOLECULES	function opes generic colvar core pytorch
24.036	Leveraging cryptic ligand envelopes through enhanced molecular simulations	bio	HREX, conformational heterogeneity, drug discovery, ligand binding, plitidepsin, aplidin, ligand-target complexes, cryptic ligand envelope	Francesco Colizzi	DISTANCE ANGLE PRINT HISTOGRAM TORSION GROUP COORDINATION CONVERT_TO_FES DUMPGRID WHOLEMOLECULES	gridtools generic colvar core
24.028	All-atom simulations of RNA-membrane interactions	bio	metadynamics, membrane, RNA	Giovanni Bussi	SORT DISTANCE METAD POSITION GHOST GYRATION MOLINFO PRINT PUCKERING COMBINE GROUP LOWER_WALLS UPPER_WALLS DISTANCES MATHEVAL CENTER WHOLEMOLECULES	function bias generic colvar multicolvar core vatom
24.027	Proline cis and trans subensembles of a disordered peptide	bio	intrinsically disordered proteins, proline cis trans isomerisation, metadynamics, collective variables	Alice Pettitt	DISTANCE PARABETARMSD GYRATION MOLINFO PBMETAD PRINT FLUSH COMBINE GROUP TORSION ALPHARMSD INCLUDE COORDINATION ANTIBETARMSD WHOLEMOLECULES ENDPLUMED DIHCOR	function bias generic colvar multicolvar secondarystructure core
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	METAD RMSD COMMITTOR ANGLE UPPER_WALLS COORDINATION CENTER WHOLEMOLECULES MOLINFO COMBINE CUSTOM GROUP MATHEVAL ENDPLUMED DISTANCE FIXEDATOM OPES_METAD FIT_TO_TEMPLATE CONTACTMAP PRINT TORSION	function opes bias generic colvar core vatom
24.005	Learning Markovian Dynamics with Spectral Maps	methods	spectral map, collective variables, machine learning	Jakub Rydzewski	BIASVALUE DISTANCE PRINT CUSTOM UNITS	function bias generic colvar 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 PRINT FLUSH SELECT_COMPONENTS MATHEVAL INCLUDE SUM TRANSPOSE	function valtools bias generic matrixtools
23.039	Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation	chemistry	metadynamics, ligand dissociation	Eric Beyerle	DISTANCE METAD RESTRAINT MOLINFO PRINT DUMPMASSCHARGE COMBINE FIXEDATOM UPPER_WALLS CENTER	function bias generic colvar vatom
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	DISTANCE RMSD METAD MOLINFO PRINT MATHEVAL WHOLEMOLECULES	function generic colvar bias
23.031	Identifying small molecules binding sites in RNA conformational ensembles with SHAMAN	bio	RNA, metadynamics, probes, mixed-solvent MD, small molecules, binding sites	Max Bonomi	SHADOW METAD WRAPAROUND POSITION MOLINFO PRINT GROUP UPPER_WALLS DISTANCES CENTER FIT_TO_TEMPLATE WHOLEMOLECULES	isdb bias generic colvar multicolvar core vatom
23.015	MPCs aggregation	bio	opes_explore, dimerization, MPCs, self-assembly	Vikas Tiwari	DISTANCE METAD PRINT COM CUSTOM GROUP UPPER_WALLS COORDINATION LOWER_WALLS OPES_METAD_EXPLORE CENTER WHOLEMOLECULES	function opes bias generic colvar core vatom
23.006	Transcription factor unbinding	bio	metadynamics, DNA, conformational changes	Malin Lüking	DISTANCE METAD DUMPFORCES CONTACTMAP ANGLE MOLINFO COM PRINT ALPHARMSD	bias generic colvar secondarystructure vatom
22.041	Skipping the Replica Exchange Ladder with Normalizing Flows	methods	OPES, alanine, normalizing flows, replica exchange	Michele Invernizzi	POSITION ECV_MULTITHERMAL PRINT TORSION OPES_EXPANDED ENERGY UNITS OPES_METAD ENDPLUMED	generic opes colvar setup
22.030	Mixing physics across temperatures with generative artificial intelligence	methods	REMD, Generative AI, DDPM	Yihang Wang	WHOLEMOLECULES PRINT TORSION	generic colvar
21.039	Deep learning the slow modes for rare events sampling	methods	collective variables, machine learning, slow modes, deep-tica, opes	Luigi Bonati	RMSD ECV_MULTITHERMAL WHOLEMOLECULES ENVIRONMENTSIMILARITY LOAD Q6 MOLINFO COMBINE GROUP ENDPLUMED DISTANCE FLUSH OPES_EXPANDED ENERGY OPES_METAD PYTORCH_MODEL CONTACTMAP PRINT TORSION VOLUME INCLUDE UNITS	function opes envsim generic colvar symfunc setup core pytorch
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	DISTANCE ALPHABETA METAD GYRATION PBMETAD COM PRINT TORSION ENERGY COORDINATION INCLUDE	bias generic colvar multicolvar vatom
21.008	Multi-replica biased sampling for photoisomerization processes in conjugated polymers	methods	metadynamics, FEP, replica-exchange	Adriana Pietropaolo	BIASVALUE CONSTANT PRINT PBMETAD TORSION MATHEVAL RESTART WHOLEMOLECULES	function bias generic colvar setup
21.003	aSYN SAXS metainference	bio	metainference, SAXS	Kresten Lindorff-Larsen	BIASVALUE METAINFERENCE GYRATION MOLINFO PRINT PBMETAD FLUSH GROUP ALPHARMSD SAXS CENTER EEFSOLV WHOLEMOLECULES	isdb bias generic colvar secondarystructure core vatom
21.001	Substrate recognition and catalysis by glycosaminoglycan sulfotransferases	bio	metadynamics, well-tempered metadynamics, puckering, coordination	Tarsis Ferreira	DISTANCE METAD REWEIGHT_METAD PUCKERING PRINT MOLINFO RANDOM_EXCHANGES GROUP UPPER_WALLS LOWER_WALLS ENERGY COORDINATION INCLUDE HISTOGRAM DUMPGRID WHOLEMOLECULES	bias generic colvar gridtools core
20.031	Soft fluorescent nanoshuttles targeting receptors	chemistry	polymers, receptors, nanoparticles, fluorescent probes	Adriana Pietropaolo	PRINT PBMETAD COORDINATION CENTER WHOLEMOLECULES	generic vatom colvar bias
19.082	Ammonia Borane Dehydrogenation	chemistry	metadynamics, reaction discovery, hydrogen production, chemistry	Valerio Rizzi	METAD EXTERNAL PRINT COORDINATIONNUMBER FLUSH COMBINE GROUP UNITS ENDPLUMED RESTART	function bias generic symfunc setup core
19.075	PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python	other	Python, automatic differentiation	Toni Giorgino	DISTANCE DUMPDERIVATIVES RESTRAINT ANGLE PRINT COMBINE CUSTOM GROUP TORSION CENTER ENDPLUMED	function bias generic colvar core vatom
19.071	Time-independent free energies from metadynamics via Mean Force Integration	methods	metadynamics, mean force integration, MFI, thermodynamic integration	Matteo Salvalaglio	BIASVALUE DISTANCE METAD EXTERNAL COMMITTOR REWEIGHT_METAD PRINT TORSION MATHEVAL CONVERT_TO_FES READ HISTOGRAM DUMPGRID REWEIGHT_BIAS	function bias generic colvar gridtools
19.050	Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes	chemistry	metadynamics, membranes, Willard Chandler surface	Gareth Tribello	METAD DISTANCE_FROM_CONTOUR PRINT RESTART COMBINE UPPER_WALLS CONVERT_TO_FES READ HISTOGRAM DUMPGRID REWEIGHT_BIAS	function bias generic contour setup gridtools
19.048	Understanding Ligand Binding Selectivity in a Prototypical GPCR Family	bio	metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding	Francesco Gervasio	BIASVALUE CONSTANT METAD DISTANCE PRINT COM UPPER_WALLS LOWER_WALLS MATHEVAL WHOLEMOLECULES	function bias generic colvar vatom
19.030	Coarse-Grained MetaDynamics (CG-MetaD)	bio	Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy	Vittorio Limongelli	DISTANCE METAD PRINT COM UPPER_WALLS LOWER_WALLS WHOLEMOLECULES	generic vatom colvar bias
19.010	Multi-domain protein dynamics	bio	metainference, NMR, protein dynamics	Carlo Camilloni	DISTANCE ALPHABETA METAINFERENCE RESTRAINT RDC DIHCOR MOLINFO PBMETAD ENSEMBLE STATS TORSION GROUP UPPER_WALLS PRINT DHENERGY CENTER ENDPLUMED WHOLEMOLECULES	function isdb bias generic colvar multicolvar core vatom
19.009	RNA tetraloops folding	bio	metadynamics, RNA, folding	Giovanni Bussi	METAD RMSD MOLINFO PRINT ERMSD ENDPLUMED WHOLEMOLECULES	generic colvar bias
19.005	Cmyc small molecule interaction	bio	metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP	Gabriella Heller	ALPHABETA METAINFERENCE DISTANCE CS2BACKBONE GYRATION MOLINFO PBMETAD PRINT GROUP COORDINATION INCLUDE CENTER WHOLEMOLECULES	isdb bias generic colvar multicolvar core vatom
26.013	Characterizing Partially Unfolded States of the C-Terminal Domain in WT and 3PA Mouse Prion Protein	bio	parallel-bias metadynamics, PBMetaD, metadynamics, mouse prion protein, prion protein, protein folding, partially unfolded states, molecular dynamics	Sonali M. Jadhav	COORDINATION PBMETAD GROUP WHOLEMOLECULES DUMPMASSCHARGE COM DISTANCE MOLINFO PRINT GYRATION INCLUDE ALPHARMSD CONTACTMAP	bias colvar secondarystructure generic core vatom
26.009	Exploring the Conformational Landscape of HIV-1 TAR RNA by PT-WTE	bio	RNA, PT-WTE, HIV-1 TAR	Stefano Bosio	GROUP WHOLEMOLECULES METAD PRINT MOLINFO ENERGY	bias colvar generic core
26.000	OPES simulations of disordered proteins	bio	OPES, IDPs	Julian Streit	ECV_MULTITHERMAL PRINT OPES_EXPANDED RESTART ENERGY	opes setup colvar generic
25.023	Molecular simulations of Tau-protein oligomers	bio	metadynamics, proteins, aggregation	Giovanni Bussi	RMSD CUSTOM HISTOGRAM CONVERT_TO_FES METAD PRINT RESTART REWEIGHT_BIAS RESTRAINT DUMPGRID CONTACTMAP FLUSH	bias colvar generic gridtools function setup
25.001	RNA G-quadruplex folding with ST-metaD protocol	bio	RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD	Pavlína Pokorná	COMBINE WHOLEMOLECULES ERMSD METAD MOLINFO	function bias colvar generic
24.025	Correlating Enzymatic Reactivity for Different Substrates using Transferable Data-Driven Collective Variables	bio	enzymatic reactivity, k_cat, transfer learning, data-driven CVs, catalysis, ligand-binding modes, water, alpha-amylase, sugar, classical MD, OPES, machine learning, Deep TDA CV, path CV	Sudip Das	COORDINATION UPPER_WALLS OPES_METAD CUSTOM GROUP WHOLEMOLECULES FIT_TO_TEMPLATE TORSION DISTANCE FIXEDATOM PRINT CENTER RESTART LOWER_WALLS PYTORCH_MODEL PATH	pytorch bias colvar mapping generic core function opes setup vatom
24.010	Oxytocin metadynamics simulation	bio	metadynamics, oxytocin, peptide	Jan Beránek	WHOLEMOLECULES TORSION METAD PRINT RESTART FLUSH	setup bias colvar generic
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	CONSTANT UPPER_WALLS WHOLEMOLECULES DISTANCE METAD MATHEVAL BIASVALUE PRINT CENTER LOWER_WALLS	bias colvar generic function vatom
23.034	Urea nucleation in water: do long-range forces matter?	materials	LMF theory, Metadynamics, Nucleation	Ziyue Zou	GROUP LOAD METAD PRINT CENTER INCLUDE COORDINATIONNUMBER	bias generic core symfunc setup vatom
23.029	An accurate and efficient SAXS/SANS implementation including solvation layer effects suitable for restrained Molecular Dynamics simulations	bio	SAXS, SANS, SAS, metainference, proteins, nucleic-acid	Federico Ballabio	UPPER_WALLS STATS RMSD GROUP DISTANCE PRINT MOLINFO BIASVALUE CENTER ENSEMBLE WRAPAROUND SAXS	bias colvar isdb generic core function vatom
23.024	Permutationally Invariant Networks for Enhanced Sampling (PINES)	methods	collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent	Nicholas Herringer	LOAD PRINT PBMETAD	setup bias generic
23.016	Activation/deactivation free-energy profiles for the β2-adrenergic receptor: Ligand modes of action	bio	G protein coupled receptor, beta-adrenergic, receptor activation, partial agonism, metadynamics	Timothy Clark	RMSD CONVERT_TO_FES REWEIGHT_METAD HISTOGRAM WHOLEMOLECULES DISTANCE METAD MOLINFO MATHEVAL PRINT DUMPGRID READ	bias colvar generic gridtools function
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	OPES_METAD RMSD CUSTOM FIT_TO_TEMPLATE DISTANCE MATHEVAL CONTACTMAP UPPER_WALLS CENTER ENDPLUMED ANGLE COMBINE WHOLEMOLECULES FIXEDATOM MOLINFO LOWER_WALLS PYTORCH_MODEL COMMITTOR ENERGY COORDINATION GROUP PRINT INCLUDE	pytorch bias colvar generic core function opes 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	RMSD CONVERT_TO_FES REWEIGHT_METAD HISTOGRAM WHOLEMOLECULES DISTANCE METAD MOLINFO MATHEVAL PRINT DUMPGRID READ	bias colvar generic gridtools function
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	UPPER_WALLS HISTOGRAM PRINT OPES_EXPANDED RESTART LOWER_WALLS ENVIRONMENTSIMILARITY ECV_UMBRELLAS_LINE DUMPGRID	bias envsim generic gridtools opes setup
22.043	Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES	bio	OPES, RNA, Tetraloop, Folding	Gül Zerze	ECV_MULTITHERMAL WHOLEMOLECULES PRINT OPES_EXPANDED ECV_UMBRELLAS_LINE CONTACTMAP ENERGY	opes colvar generic
22.040	From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure	bio	SARS-CoV-2, Spike, Omicron	Miłosz Wieczór	UPPER_WALLS WHOLEMOLECULES METAD PRINT LOWER_WALLS PCAVARS	bias mapping generic
22.012	Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT	bio	contact maps, protein-protein interactions	Isabell-Louise Grothaus	CENTER CONTACTMAP DISTANCE PRINT	colvar generic vatom
21.050	N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity	methods	bio	Isabell Louise Grothaus	CENTER DISTANCE PRINT	colvar generic vatom
21.022	Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly	materials	parallel bias metadynamics, adsorption, peptide	Xin Qi	UPPER_WALLS PBMETAD COM DISTANCE MOLINFO PRINT GYRATION LOWER_WALLS ENERGY	bias colvar generic vatom
20.029	High Conformational Flexibility of the E2F1/DP1/DNA complex	bio	SAXS, protein-DNA complex, hySAXS, ensemble determination	Cristina Paissoni	STATS GROUP WHOLEMOLECULES DISTANCE MOLINFO PRINT BIASVALUE CENTER ENSEMBLE INCLUDE RESTRAINT SAXS	bias colvar isdb generic core function vatom
20.022	Unified Approach to Enhanced Sampling	methods	OPES, expanded ensembles, importance sampling	Michele Invernizzi	ECV_MULTITHERMAL RMSD CUSTOM UNITS MATHEVAL ECV_UMBRELLAS_LINE UPPER_WALLS Q6 POSITION LOAD ENDPLUMED ECV_LINEAR TORSION WHOLEMOLECULES MOLINFO ENVIRONMENTSIMILARITY ENERGY VOLUME PRINT OPES_EXPANDED ECV_MULTITHERMAL_MULTIBARIC	bias colvar envsim generic symfunc function opes setup
20.016	Predicting polymorphism in molecular crystals using orientational entropy	materials	metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy	Pablo Piaggi	UPPER_WALLS GROUP VOLUME LOAD METAD PRINT CENTER INCLUDE	bias colvar generic core setup vatom
20.015	Rational design of ASCT2 inhibitors using an integrated experimental-computational approach	bio	ASCT2 transporter, small-molecules, cryo-EM, metainference	Max Bonomi	GROUP LOAD WHOLEMOLECULES BIASVALUE MOLINFO PRINT EMMIVOX DUMPATOMS	bias isdb generic core setup
20.011	Uremic toxin analysis	bio	metadynamics, uremic toxin, serum albumin	Jim Pfaendtner	COORDINATION GROUP WHOLEMOLECULES DISTANCE PRINT CENTER RESTART DISTANCES	colvar generic core setup vatom multicolvar
20.007	Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics	bio	metadynamics, loop movement, artificial intelligence	Pratyush Tiwary	UPPER_WALLS RMSD COMBINE TORSION WHOLEMOLECULES DISTANCE METAD PRINT MOLINFO RESTART	bias colvar generic function setup
19.074	Asymmetric base pair opening in nucleic acids	bio	double helix, DNA, RNA, unwindability	Giovanni Bussi	COORDINATION WHOLEMOLECULES DISTANCE LOWER_WALLS ENDPLUMED RESTRAINT	bias colvar generic
19.070	Unexpected Dynamics in the UUCG RNA Tetraloop	bio	well-tempered metadynamics, RNA, UUCG, maximum entropy	Sandro Bottaro	RMSD WHOLEMOLECULES ERMSD DISTANCE TORSION METAD MOLINFO PRINT	bias colvar generic
19.068	Rethinking Metadynamics	methods	metadynamics, opes, convergence	Michele Invernizzi	OPES_METAD POSITION UNITS TORSION METAD PRINT ENDPLUMED EXTERNAL	bias colvar generic opes setup
19.059	cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide	bio	bias-exchange metadynamics, cis-trans isomerization	Fabrizio Marinelli	TORSION METAD PRINT INCLUDE RANDOM_EXCHANGES	bias colvar generic
19.056	maze	methods	maze, ligand unbinding	Jakub Rydzewski	POSITION UNITS MAZE_OPTIMIZER_BIAS MAZE_SIMULATED_ANNEALING MAZE_LOSS PRINT	maze setup colvar generic
19.051	Solid liquid interfacial free energy out of equilibrium	materials	metadynamics, nucleation, surface excess free energy	Gareth Tribello	FCCUBIC UPPER_WALLS UNITS METAD PRINT LOWER_WALLS ENDPLUMED CELL AROUND	bias colvar generic volumes symfunc setup
19.039	Funnel Metadynamics	bio	funnel-metadynamics, absolute binding free energy, ligand-receptor complexes	Vittorio Limongelli	UPPER_WALLS RMSD FUNNEL WHOLEMOLECULES DISTANCE COM METAD PRINT LOWER_WALLS FUNNEL_PS	bias colvar generic funnel vatom
19.035	Dimerization of GPCRs from coarse-grained umbrella sampling	bio	Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization	Davide Provasi	GROUP TORSION COM DISTANCE PRINT RESTRAINT	bias colvar generic core vatom
19.021	Coarse-Grained Directed Simulation	methods	experiment directed simulation, coarse-grain, bias	Glen Hocky	COMBINE TORSION DISTANCE PRINT EDS RESTRAINT	bias colvar generic function eds
19.015	Ibuprofen conformational dynamics and thermodynamics surface	materials	Ibuprofen, crystal, surface, solvents, conformers, metadynamics	Matteo Salvalaglio	UPPER_WALLS TORSION DISTANCE METAD PRINT CENTER LOWER_WALLS COMMITTOR	bias colvar generic vatom
25.025	Enhanced Sampling of Ligand Binding Coupled to RNA Conformational Dynamics	bio	OPES, OPES Flooding , Metadynamics, RNA, Ligand binding, Free Energy, Kinetics, Funnel	Revanth Elangovan and Dhiman Ray	FUNNEL_PS OPES_METAD WRAPAROUND COMMITTOR LOWER_WALLS WHOLEMOLECULES COM FUNNEL RMSD PRINT METAD DISTANCE UPPER_WALLS ENDPLUMED COORDINATION CUSTOM GROUP MATHEVAL CENTER TORSION	colvar function bias generic vatom core opes funnel
24.021	Ab initio machine learning simulation of calcium carbonate from aqueous solutions to the solid state	chemistry	ion pairing, caco3, opes, proton transfer, crystallization	Pablo Piaggi	DISTANCE UPPER_WALLS COORDINATION ENERGY OPES_METAD PRINT	generic colvar bias opes
24.002	Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes	chemistry	metadynamics, ligand design, solvent extraction	Xiaoyu Wang	UNITS TORSION PRINT RESTART METAD	generic setup colvar bias
23.014	Structural basis of dimerization of chemokine receptors CCR5 and CXCR4	bio	metadynamics, oligomerization, chemokine receptors, GPCR, membrane	Vittorio Limongelli	FLUSH COMBINE DISTANCE WHOLEMOLECULES COM UPPER_WALLS TORSION PRINT METAD	colvar function bias generic vatom
22.035	Deciphering the alphabet of disorder — Glu and Asp act differently on local but not global properties	bio	intrinsically disordered proteins, parallel bias metadynamics, protein	Kresten Lindorff-Larsen	MOLINFO WHOLEMOLECULES PBMETAD TORSION GYRATION	generic colvar bias
22.034	Rationalising the difference in crystallisability of two Sulflowers using efficient in silico methods	materials	metadynamics, crystallizability, crystal structure prediction, sulflower, persulforated coronene	Matteo Salvalaglio	LOWER_WALLS CELL UPPER_WALLS CUSTOM MATHEVAL DRMSD PRINT COMMITTOR METAD	generic colvar function bias
22.028	N-glycan conformer distributions in atomistic simulation	bio	REST2, RECT, N-glycan, pucker	Isabell Grothaus	MOLINFO PUCKERING CONVERT_TO_FES DUMPGRID HISTOGRAM TORSION PRINT METAD READ	generic colvar gridtools bias
22.027	Molecular Dynamics simulations of BANAL-236 RBD-hACE2 complexes	bio	SARS-CoV-2, COVID-19, MD, human-ACE2, spike, BANAL-236, receptor-binding domain	Max Bonomi	RMSD PRINT	generic colvar
22.025	Bubble nucleation rate predictions in a Lennard-Jones fluid	materials	free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation	Kristof Bal	FLUSH UPPER_WALLS COORDINATIONNUMBER REWEIGHT_BIAS CUSTOM UNITS ANN HISTOGRAM CONVERT_TO_FES VOLUME DUMPGRID RESTRAINT PRINT MOVINGRESTRAINT BIASVALUE COMMITTOR LOAD	colvar symfunc bias function generic setup annfunc gridtools
22.024	Conformational Entropy as a Potential Liability of Computationally Designed Antibodies	bio	metadynamics, conformational entropy, antibody, nanobody	Thomas Löhr	MOLINFO WHOLEMOLECULES PBMETAD COM ANTIBETARMSD ALPHABETA TORSION PRINT RESTART ALPHARMSD	colvar bias secondarystructure generic vatom setup multicolvar
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 ECV_UMBRELLAS_LINE UPPER_WALLS INCLUDE PRINT OPES_EXPANDED	generic envsim bias opes
22.009	Glycosylation in calixarenes capsule	chemistry	Metadynamics, glycosylation, supramolecular catalysis	GiovanniMaria Piccini	LOWER_WALLS FLUSH COMBINE BRIDGE DISTANCE WHOLEMOLECULES DISTANCES UPPER_WALLS UNITS GROUP COORDINATION MATHEVAL RMSD ANGLE PRINT METAD FIT_TO_TEMPLATE	colvar function bias generic setup core multicolvar adjmat
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	FLUSH MOLINFO DISTANCE WHOLEMOLECULES UPPER_WALLS COORDINATION ALPHABETA ANGLE TORSION PRINT METAD ALPHARMSD	colvar bias secondarystructure generic multicolvar
22.005	Collective Variable for Metadynamics Derived from AlphaFold Output	bio	AlphaFold, protein folding, protein structure prediction, metadynamics, deep learning, free energy simulation, collective variable	Vojtech Spiwok	PRINT METAD LOAD WHOLEMOLECULES	generic setup bias
22.001	Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials	methods	enhanced sampling, variationally enhanced sampling, ves, metadynamics, bias representation, wavelets, adam	Benjamin Pampel	TD_UNIFORM PRINT POSITION METAD VES_LINEAR_EXPANSION TD_WELLTEMPERED FLUSH DISTANCE UPPER_WALLS BF_LEGENDRE UNITS COORDINATION BF_GAUSSIANS BF_CUBIC_B_SPLINES BF_CHEBYSHEV OPT_ADAM BF_WAVELETS VES_OUTPUT_BASISFUNCTIONS ENERGY INCLUDE OPT_AVERAGED_SGD	colvar bias ves generic setup
21.052	On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets	materials	Ibuprofen, unbinding, WTmetaD	Matteo Salvalaglio	DISTANCE COORDINATIONNUMBER ENDPLUMED CENTER TORSION PRINT COMMITTOR METAD	colvar symfunc bias generic vatom
21.042	Peptoid-mediated Au nanocrystal growth	materials	parallel-bias metadynamics, peptoid, Au	Xin Qi	MOLINFO DISTANCE COM UPPER_WALLS PBMETAD PRINT GYRATION	generic vatom colvar bias
21.028	From Enhanced Sampling to Reaction Profiles	methods	collective variables, multi-state, machine learning, Deep-TDA	Enrico Trizio	DISTANCES OPES_METAD LOWER_WALLS WHOLEMOLECULES PRINT LOAD DISTANCE UPPER_WALLS ENDPLUMED UNITS COORDINATION ANGLE FIXEDATOM FIT_TO_TEMPLATE GROUP MATHEVAL CENTER TORSION PYTORCH_MODEL	colvar function bias generic setup vatom core multicolvar pytorch opes
21.018	Localized Volume-based Metadynamics	bio	LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification	Riccardo Capelli	DUMPGRID REWEIGHT_METAD WHOLEMOLECULES COM RMSD PRINT POSITION METAD FLUSH DISTANCE UPPER_WALLS ENDPLUMED CONVERT_TO_FES COORDINATION HISTOGRAM FIXEDATOM READ GROUP MATHEVAL	colvar function bias generic vatom core gridtools
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	ENVIRONMENTSIMILARITY ECV_UMBRELLAS_LINE UPPER_WALLS ECV_MULTITHERMAL_MULTIBARIC TD_UNIFORM BF_LEGENDRE ENERGY MATHEVAL VOLUME PRINT OPES_EXPANDED RESTART OPT_AVERAGED_SGD Q6 VES_LINEAR_EXPANSION	envsim colvar bias ves function symfunc generic setup opes
19.072	SINE hairpin MD+NMR	bio	metadynamics, RNA, NMR	Giovanni Bussi	FLUSH MAXENT MOLINFO DISTANCE COM WHOLEMOLECULES SORT COORDINATION MATHEVAL INCLUDE TORSION PRINT METAD	colvar function bias generic vatom
19.023	RECT	methods	metadynamics, replica exchange	Giovanni Bussi	WHOLEMOLECULES TORSION PRINT METAD GYRATION	generic colvar bias
19.020	PTMetaD-WTE simulation of the Ntail IDP	bio	metadynamics, IDPs, protein folding	Mattia Bernetti	MOLINFO WHOLEMOLECULES ENDPLUMED ENERGY PRINT METAD ALPHARMSD GYRATION	generic colvar bias secondarystructure
19.016	Succinnic acid gamma polymorph	materials	Succinnic acid, conformers, polymorphs, metadynamics	Matteo Salvalaglio	LOWER_WALLS COMBINE UPPER_WALLS ENDPLUMED MATHEVAL ENERGY VOLUME TORSION PRINT CELL METAD	generic colvar function bias
26.005	Cryptic pocket discovery in Alzheimer disease risk proteins BIN1, PICALM, and CD2AP via well-tempered metadynamics	methods	cryptic pockets, Alzheimer disease, BIN1, PICALM, CD2AP, well-tempered metadynamics, endocytosis, clathrin-mediated trafficking, virtual screening	Cagrı Ozkurt	METAD DISTANCE PRINT ANGLE WHOLEMOLECULES	generic bias 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	UPPER_WALLS INCLUDE GROUP SAXS MOLINFO METAD GYRATION DISTANCE PRINT CENTER MOVINGRESTRAINT WHOLEMOLECULES	generic core bias vatom colvar isdb
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	UPPER_WALLS COORDINATION OPES_EXPANDED CUSTOM OPES_METAD_EXPLORE LOWER_WALLS GROUP ECV_MULTITHERMAL GHOST DISTANCES RMSD DISTANCE ENERGY CENTER PRINT PATHMSD	core generic bias vatom function opes colvar multicolvar
25.009	Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water	chemistry	metadynamics, nitrate photolysis	Kam-Tung Chan	UPPER_WALLS COORDINATION FLUSH CUSTOM DUMPGRID RESTART GROUP METAD HISTOGRAM REWEIGHT_METAD DISTANCE READ PRINT	generic core setup bias gridtools function colvar
25.000	Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer	bio	metadynamics, pathCV	Sahithya Sridharan Iyer	UPPER_WALLS RESTART GROUP MOLINFO COM METAD FUNCPATHGENERAL DISTANCE PRINT WHOLEMOLECULES	core generic setup bias vatom function colvar
24.031	DeepLNE	methods	PATHCV, OPES, OneOPES	Thorben Fröhlking	COORDINATION ERMSD PYTORCH_MODEL OPES_METAD_EXPLORE RESTART MOLINFO ECV_MULTITHERMAL ENERGY VOLUME PRINT OPES_EXPANDED COMBINE	generic setup function opes colvar pytorch
24.013	Estimating Free Energy Surfaces and their Convergence from multiple, independent static and history-dependent biased molecular-dynamics simulations with Mean Force Integration	methods	Mean Force Integration, Convergence, FES, Umbrella Sampling	Matteo Salvalaglio	FLUSH RESTART RESTRAINT MOLINFO METAD COORDINATIONNUMBER TORSION MATHEVAL DISTANCE PRINT ENERGY COMMITTOR BIASVALUE	generic setup bias function colvar symfunc
24.011	Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble	methods	committor, machine learning	Peilin Kang	COORDINATION GROUP ENERGY CELL INCLUDE TORSION BIASVALUE UPPER_WALLS POSITION LOWER_WALLS UNITS DISTANCE ENDPLUMED CUSTOM MOLINFO LOAD MATHEVAL RMSD PRINT WHOLEMOLECULES	core generic setup bias function colvar
24.008	yCD Metadynamics	bio	volume-based MetaD, path CVs, infrequent MetaD, product release	James McCarty	COORDINATION CONVERT_TO_FES GROUP FLUSH CONTACTMAP DUMPGRID INCLUDE METAD FIXEDATOM WRAPAROUND REWEIGHT_METAD UPPER_WALLS COM ENDPLUMED DISTANCE READ WHOLEMOLECULES COMMITTOR MOLINFO HISTOGRAM MATHEVAL FIT_TO_TEMPLATE RMSD PRINT PATH	core generic bias vatom mapping gridtools function colvar
24.004	Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables	materials	metadynamics, nucleation, machine learning	Ziyue Zou	INCLUDE RESTART GROUP METAD LOAD PRINT	generic bias core setup
23.036	Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water?	bio	NaCl, nucleation, metadynamics	Ruiyu Wang	Q4 Q6 METAD COORDINATIONNUMBER MATHEVAL ENERGY VOLUME PRINT COMBINE	generic bias function colvar symfunc
23.019	Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors	bio	binding pathway, binding energy, sketch-map, drug development	Raitis Bobrovs	UPPER_WALLS SKETCHMAP VSTACK CUSTOM LANDMARK_SELECT_FPS SKETCHMAP_PROJECTION DISSIMILARITIES METAD COM COLLECT_FRAMES DISTANCE PRINT TRANSPOSE VORONOI PATHMSD WHOLEMOLECULES	landmarks generic bias dimred valtools vatom function matrixtools colvar
23.011	OneOPES, a combined enhanced sampling method to rule them all	bio	OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding	Valerio Rizzi	OPES_METAD_EXPLORE MOLINFO TORSION ECV_MULTITHERMAL METAD DISTANCE ENERGY PRINT OPES_EXPANDED ENDPLUMED	generic bias colvar opes
23.000	Atomistic simulations of RNA tetraloop folding via PTWTE-WTM	bio	parallel tempering, well-tempered metadynamics, well-tempered ensemble, RNA, Tetraloop, Folding	Gül Zerze	UPPER_WALLS CONTACTMAP LOWER_WALLS METAD PRINT ENERGY WHOLEMOLECULES	generic bias colvar
22.045	Binding mode and mechanism of enzymatic polyethylene terephthalate degradation	bio	metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation	Francesco Colizzi	UPPER_WALLS LOWER_WALLS METAD COM DISTANCE PRINT MOVINGRESTRAINT ANGLE WHOLEMOLECULES	generic bias colvar vatom
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	DRR FLUSH CUSTOM METAD PRINT PATHMSD BIASVALUE	generic bias function colvar drr
22.029	Angiotensin-1-7_Metadynamics	bio	Metadynamics, Angiotensin-(1-7), peptide	L.-América Chi	UPPER_WALLS COORDINATION FLUSH LOWER_WALLS GROUP METAD GYRATION PRINT WHOLEMOLECULES	generic bias colvar core
22.016	Homogeneous ice nucleation in an ab initio machine learning model of water	chemistry	ice, water, nucleation, seeding, environment similarity, interfacial free energy, interfaces	Pablo Piaggi	UPPER_WALLS CUSTOM DUMPGRID RESTART OPES_METAD ENVIRONMENTSIMILARITY AROUND HISTOGRAM ENERGY VOLUME PRINT	generic envsim setup bias gridtools volumes function opes colvar
22.000	Amyloid precursor protein processing by human γ-secretase	bio	Bias Exchange Metadynamics, Helix unfolding, coupled binding	Xiaoli Lu	COORDINATION RANDOM_EXCHANGES CONTACTMAP INCLUDE MOLINFO METAD UNITS ALPHARMSD ANTIBETARMSD DISTANCE CENTER PRINT	generic setup bias vatom secondarystructure colvar
21.036	Modelling the structure and interactions of intrinsically disordered peptides with multiple-replica, metadynamics-based sampling methods and force-field combinations	bio	Bias Exchange Metadynamics, PTWTE-metaD	Matteo Salvalaglio	UPPER_WALLS RANDOM_EXCHANGES COORDINATION PARABETARMSD LOWER_WALLS GROUP MOLINFO METAD GYRATION ALPHARMSD PRINT ANTIBETARMSD ENERGY DIHCOR WHOLEMOLECULES	generic core bias secondarystructure colvar multicolvar
21.035	CmuMD simulations of NaCl(aq) at NaCl	chemistry	CmuMD, interface	Aaron Finney	RESTRAINT GROUP LOAD FIXEDATOM DISTANCE PRINT	core generic setup bias vatom colvar
21.034	Efficient sampling of high-dimensional free energy landscapes using adaptive reinforced dynamics	bio	reinforced dynamics, bias-exchange metadynamics, parallel-bias metadynamics	Dongdong Wang	RANDOM_EXCHANGES INCLUDE PBMETAD TORSION METAD PRINT ENDPLUMED	generic bias colvar
21.031	Photo-switchable sulfonulureas in KATP channel	bio	metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels	Katarzyna Walczewska-Szewc	UPPER_WALLS LOWER_WALLS METAD COM UNITS DISTANCE PRINT WHOLEMOLECULES	generic setup bias vatom colvar
21.020	Reweighted Jarzynski sampling	methods	free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions	Kristof Bal	CONVERT_TO_FES VES_LINEAR_EXPANSION BF_CHEBYSHEV FLUSH DUMPGRID OPES_METAD METAD REWEIGHT_METAD MOVINGRESTRAINT TD_WELLTEMPERED BIASVALUE UPPER_WALLS REWEIGHT_BIAS RESTRAINT UNITS ANN DISTANCE CUSTOM OPT_AVERAGED_SGD COORDINATIONNUMBER LOAD HISTOGRAM PRINT COMBINE CONSTANT	generic setup ves bias gridtools annfunc function opes colvar symfunc
21.012	NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition	bio	funnel metadynamics	Jim Pfaendtner	UPPER_WALLS LOWER_WALLS METAD COM FUNNEL_PS DISTANCE PRINT FUNNEL	generic funnel bias vatom colvar
21.011	CmuMD simulations of NaCl(aq) at graphite	chemistry	CmuMD, DFS clustering	Aaron Finney	DUMPGRID CLUSTER_DISTRIBUTION GROUP RESTRAINT DFSCLUSTERING COORDINATIONNUMBER FIXEDATOM AROUND DENSITY CONTACT_MATRIX CLUSTER_NATOMS PRINT LOAD MULTICOLVARDENS MFILTER_MORE	core generic setup bias vatom gridtools volumes clusters adjmat symfunc multicolvar
21.005	Crystallization Collective Variable	methods	Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA	Tarak Karmakar	UPPER_WALLS FLUSH PYTORCH_MODEL LOWER_WALLS OPES_METAD GROUP LOAD MATHEVAL PRINT	generic core setup bias function opes pytorch
21.000	Uremic toxin time scale dynamics	bio	uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs)	Jim Pfaendtner	GROUP COM DISTANCE PRINT WHOLEMOLECULES	core vatom colvar generic
20.033	COVID-19 Spike protein opening transition mechanism	bio	EMMI, CryoEM, COVID-19, Spike, Metainference	Faidon Brotzakis	EMMI DUMPGRID CONVERT_TO_FES GROUP MOLINFO HISTOGRAM RMSD PRINT READ WHOLEMOLECULES DISTANCES BIASVALUE	core generic bias gridtools colvar isdb multicolvar
20.032	Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil	materials	clustering, conformational isomers	Matteo Salvalaglio	ENDPLUMED PRINT TORSION	generic colvar
20.019	Systematic finite-temperature reduction of crystal energy landscapes	materials	crystals, organics, structure prediction	Matteo Salvalaglio	UPPER_WALLS CELL LOWER_WALLS METAD MATHEVAL ENERGY VOLUME PRINT	function bias colvar generic
20.009	The dynamics of linear polyubiquitin	bio	saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics	Carlo Camilloni	ALPHABETA FLUSH STATS SAXS PBMETAD TORSION MOLINFO METAINFERENCE GYRATION DISTANCE PRINT CENTER ENSEMBLE WHOLEMOLECULES	generic bias vatom function colvar isdb multicolvar
20.002	Exploring conformational dynamics of the extracellular Venus flytrap domain of the GABAB receptor, a path-metadynamics study	bio	Metadynamics, path CVs	Riccardo Ocello	UPPER_WALLS RESTART GROUP MOLINFO METAD PRINT PATHMSD WHOLEMOLECULES	core generic setup bias colvar
19.041	Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces	bio	metadynamics, collective variables, conformational changes, multiple walkers, Well-Tempered MetaD, peptide, binding, phosphorylation, post-transitional motif, sio2, adsorption	Jim Pfaendtner	UPPER_WALLS COM METAD DISTANCE ENERGY PRINT	generic bias colvar vatom
19.038	native state dynamics of human and mouse b2m	bio	metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation	Carlo Camilloni	ALPHABETA UPPER_WALLS FLUSH LOWER_WALLS RESTART GROUP PBMETAD MOLINFO CS2BACKBONE ENDPLUMED ANTIBETARMSD PRINT WHOLEMOLECULES BIASVALUE	generic core setup bias secondarystructure isdb multicolvar
19.013	RNA FF FITTING	methods	force field, RNA	Giovanni Bussi	PUCKERING INCLUDE MOLINFO TORSION MATHEVAL CONSTANT BIASVALUE	generic function colvar bias
19.003	EMMI ClpP	bio	metainference, cryo-EM	Max Bonomi	EMMI GROUP MOLINFO PRINT BIASVALUE	core bias isdb generic
19.002	EMMI STRA6	bio	metainference, cryo-EM	Max Bonomi	EMMI GROUP MOLINFO PRINT BIASVALUE	core bias isdb generic

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