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
25.027	Enhanced-sampling MD simulations of a protein-peptide complex integrating SAXS and XL-MS experimental information	bio	steered MD, metadynamics, SAXS, XL-MS, ensemble reconstruction	Mattia Bernetti	PRINT MOLINFO UPPER_WALLS GYRATION WHOLEMOLECULES METAD MOVINGRESTRAINT DISTANCE CENTER GROUP INCLUDE SAXS	colvar core generic bias isdb vatom
25.023	Molecular simulations of Tau-protein oligomers	bio	metadynamics, proteins, aggregation	Giovanni Bussi	PRINT RESTRAINT REWEIGHT_BIAS CONVERT_TO_FES RMSD CONTACTMAP METAD HISTOGRAM RESTART DUMPGRID FLUSH CUSTOM	setup colvar gridtools generic bias function
25.017	Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity	bio	EMMIVox, cryo-EM, allostery, decamer, filament, ensemble refinement, glutamine synthetase	Samuel Hoff	PRINT MOLINFO WHOLEMOLECULES EMMIVOX BIASVALUE GROUP	generic core bias isdb
25.011	Chiral perovskite nucleation	chemistry	metadynamics, chiral perovskites, nucleation	Adriana Pietropaolo	PRINT MATHEVAL UPPER_WALLS PBMETAD MULTI_RMSD RESTART DISTANCE LOWER_WALLS UNITS	setup colvar generic bias function
25.003	Surrogate Model CV	methods	Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding	Sompriya Chatterjee	PRINT MATHEVAL ENDPLUMED TORSION MOLINFO ENERGY COMMITTOR WHOLEMOLECULES DISTANCE OPES_METAD GROUP CUSTOM PYTORCH_MODEL COMBINE	opes colvar core generic pytorch function
24.029	Combination of OPES and OPES-Explore	methods	OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin	Dhiman Ray	PRINT ENDPLUMED MOLINFO DISTANCE FLUSH PYTORCH_MODEL MATHEVAL COORDINATION LOWER_WALLS CUSTOM UNITS OPES_METAD_EXPLORE CONTACTMAP OPES_METAD CENTER GROUP INCLUDE POSITION FIT_TO_TEMPLATE ENERGY UPPER_WALLS RMSD WHOLEMOLECULES METAD FIXEDATOM BIASVALUE COMBINE	opes setup colvar core generic bias pytorch function vatom
24.009	Weighted Shape Gaussian Mixture Models	bio	metadynamics, clustering	Glen Hocky	PRINT TORSION METAD GROUP UNITS	setup colvar core generic bias
23.027	CmuMD simulations of NaCl(aq) at NaCl	chemistry	CmuMD, DFS, Q3, Pair Entropy	Aaron Finney	PRINT LOCAL_AVERAGE LOCAL_Q3 DENSITY CLUSTER_NATOMS RESTRAINT DFSCLUSTERING Q3 CONTACT_MATRIX HISTOGRAM COORDINATIONNUMBER FIXEDATOM AROUND DUMPGRID CLUSTER_DISTRIBUTION LOAD GROUP UNITS	setup adjmat clusters core gridtools generic volumes bias symfunc vatom
23.019	Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors	bio	binding pathway, binding energy, sketch-map, drug development	Raitis Bobrovs	VORONOI PRINT COM UPPER_WALLS COLLECT_FRAMES SKETCHMAP_PROJECTION WHOLEMOLECULES METAD SKETCHMAP DISTANCE TRANSPOSE DISSIMILARITIES VSTACK LANDMARK_SELECT_FPS CUSTOM PATHMSD	colvar valtools bias landmarks generic matrixtools dimred function vatom
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 PRINT ENDPLUMED ECV_MULTITHERMAL TORSION MOLINFO ENERGY OPES_EXPANDED METAD DISTANCE	opes colvar bias generic
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	PRINT ENDPLUMED MOLINFO DISTANCE PYTORCH_MODEL ANGLE MATHEVAL COMMITTOR COORDINATION LOWER_WALLS CUSTOM CONTACTMAP OPES_METAD CENTER GROUP INCLUDE FIT_TO_TEMPLATE ENERGY UPPER_WALLS RMSD WHOLEMOLECULES FIXEDATOM COMBINE	opes colvar core generic bias pytorch function vatom
22.030	Mixing physics across temperatures with generative artificial intelligence	methods	REMD, Generative AI, DDPM	Yihang Wang	WHOLEMOLECULES PRINT TORSION	generic colvar
22.016	Homogeneous ice nucleation in an ab initio machine learning model of water	chemistry	ice, water, nucleation, seeding, environment similarity, interfacial free energy, interfaces	Pablo Piaggi	PRINT ENERGY UPPER_WALLS VOLUME HISTOGRAM ENVIRONMENTSIMILARITY AROUND RESTART OPES_METAD DUMPGRID CUSTOM	opes envsim setup colvar gridtools generic bias volumes function
22.015	Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome	bio	photodynamics, bacteriophytochrome, variationally enhanced sampling	Jakub Rydzewski	PRINT OPT_AVERAGED_SGD VES_LINEAR_EXPANSION TORSION TD_UNIFORM BF_FOURIER	generic colvar ves
22.009	Glycosylation in calixarenes capsule	chemistry	Metadynamics, glycosylation, supramolecular catalysis	GiovanniMaria Piccini	PRINT ANGLE BRIDGE FIT_TO_TEMPLATE MATHEVAL UNITS UPPER_WALLS DISTANCES RMSD WHOLEMOLECULES COORDINATION METAD DISTANCE LOWER_WALLS FLUSH GROUP COMBINE	setup adjmat colvar core generic bias multicolvar function
22.006	Peptide framework for screening the effects of amino acids on assembly	bio	metadynamics, peptides	Andrew White	PRINT COM REWEIGHT_BIAS CONVERT_TO_FES DISTANCES GYRATION HISTOGRAM METAD DUMPGRID GROUP INCLUDE COMBINE	colvar core gridtools generic bias multicolvar function vatom
21.050	N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity	methods	bio	Isabell Louise Grothaus	PRINT DISTANCE CENTER	generic colvar vatom
21.038	Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics	materials	metadynamics, SGOOP, nucleation, urea	Ziyue Zou	PRINT ENERGY VOLUME COORDINATIONNUMBER METAD CENTER LOAD GROUP INCLUDE COMBINE	setup colvar core generic bias symfunc function vatom
21.011	CmuMD simulations of NaCl(aq) at graphite	chemistry	CmuMD, DFS clustering	Aaron Finney	PRINT RESTRAINT DENSITY CLUSTER_NATOMS DFSCLUSTERING MFILTER_MORE CONTACT_MATRIX COORDINATIONNUMBER FIXEDATOM AROUND MULTICOLVARDENS LOAD CLUSTER_DISTRIBUTION DUMPGRID GROUP	setup adjmat clusters core gridtools generic volumes bias multicolvar symfunc vatom
20.027	Allosteric Regulation of SARS-CoV-2 Protease. Towards Informed Structure-Based Drug Discovery	bio	SARS-CoV2, MPro, Covid-19, Molecular Dynamics, Metadynamics, Computer-Aided Drug Discovery	Khaled Abdel-Maksoud	METAD TORSION DISTANCE PRINT	bias colvar 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	PRINT BF_LEGENDRE OPT_AVERAGED_SGD MATHEVAL VES_LINEAR_EXPANSION OPT_DUMMY UPPER_WALLS VOLUME TD_WELLTEMPERED ENVIRONMENTSIMILARITY RESTART Q6	ves symfunc envsim setup colvar generic bias function
20.007	Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics	bio	metadynamics, loop movement, artificial intelligence	Pratyush Tiwary	PRINT TORSION UPPER_WALLS MOLINFO RMSD WHOLEMOLECULES METAD RESTART DISTANCE COMBINE	setup colvar generic bias function
20.002	Exploring conformational dynamics of the extracellular Venus flytrap domain of the GABAB receptor, a path-metadynamics study	bio	Metadynamics, path CVs	Riccardo Ocello	PRINT MOLINFO UPPER_WALLS WHOLEMOLECULES METAD RESTART GROUP PATHMSD	setup colvar core generic bias
19.076	Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones	bio	molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics	Salvatore Assenza	PRINT ENDPLUMED GYRATION MOVINGRESTRAINT UNITS	generic colvar setup bias
19.072	SINE hairpin MD+NMR	bio	metadynamics, RNA, NMR	Giovanni Bussi	PRINT COM MATHEVAL MAXENT TORSION MOLINFO WHOLEMOLECULES COORDINATION METAD DISTANCE SORT FLUSH INCLUDE	colvar generic bias function vatom
19.056	maze	methods	maze, ligand unbinding	Jakub Rydzewski	PRINT MAZE_LOSS MAZE_SIMULATED_ANNEALING MAZE_OPTIMIZER_BIAS POSITION UNITS	generic maze setup 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	PRINT COM ENERGY UPPER_WALLS METAD DISTANCE	generic colvar bias vatom
19.024	PT-MetaD-WTE	methods	metadynamics, WTE, trp cage, PT	Jim Pfaendtner	EXTERNAL ENERGY COORDINATION METAD GROUP	bias colvar core
19.020	PTMetaD-WTE simulation of the Ntail IDP	bio	metadynamics, IDPs, protein folding	Mattia Bernetti	PRINT ENDPLUMED MOLINFO ENERGY GYRATION WHOLEMOLECULES METAD ALPHARMSD	generic colvar bias secondarystructure
19.016	Succinnic acid gamma polymorph	materials	Succinnic acid, conformers, polymorphs, metadynamics	Matteo Salvalaglio	PRINT ENDPLUMED MATHEVAL TORSION ENERGY UPPER_WALLS VOLUME COMBINE METAD LOWER_WALLS CELL	generic function bias colvar
25.030	Committor Regularization	methods	metadynamics, enhanced sampling, mlcvs, committor, machine learning	Florian Dietrich	UNITS PRINT METAD MOVINGRESTRAINT	bias setup generic
24.031	DeepLNE	methods	PATHCV, OPES, OneOPES	Thorben Fröhlking	COORDINATION PYTORCH_MODEL PRINT OPES_METAD_EXPLORE ERMSD OPES_EXPANDED RESTART COMBINE ENERGY MOLINFO ECV_MULTITHERMAL VOLUME	generic colvar function setup pytorch opes
24.020	Graph Neural Network-State Predictive Information Bottleneck (GNN-SPIB) approach for learning molecular thermodynamics and kinetics	bio	LJ7, alanine, well-tempered metadynamics, infrequent metadynamics, machine learning	Ziyue Zou, Dedi Wang, Pratyush Tiwary	PRINT GROUP COMMITTOR METAD TORSION LOAD	generic colvar core setup bias
24.016	Cryo-EM guided simulations of ribozyme	bio	metainference, cryo-EM	Giovanni Bussi	PRINT GROUP RESTRAINT WHOLEMOLECULES ERMSD MOLINFO BIASVALUE INCLUDE EMMIVOX	isdb generic colvar core bias
24.010	Oxytocin metadynamics simulation	bio	metadynamics, oxytocin, peptide	Jan Beránek	PRINT WHOLEMOLECULES RESTART METAD FLUSH TORSION	colvar bias setup generic
24.007	SWISH-X	bio	swish-x, SWISH-X, swish, expanded SWISH	Alberto Borsatto	PRINT WHOLEMOLECULES UPPER_WALLS OPES_EXPANDED ENERGY MOLINFO ECV_MULTITHERMAL CONTACTMAP INCLUDE	colvar opes bias generic
24.002	Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes	chemistry	metadynamics, ligand design, solvent extraction	Xiaoyu Wang	PRINT RESTART METAD UNITS TORSION	colvar bias setup generic
23.044	Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition	materials	metadynamics, interlocked molecules	Luigi Leanza	COORDINATION PRINT GROUP HISTOGRAM CONVERT_TO_FES METAD COMMITTOR READ DUMPGRID ENDPLUMED	generic colvar gridtools core bias
23.039	Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation	chemistry	metadynamics, ligand dissociation	Eric Beyerle	PRINT RESTRAINT DISTANCE DUMPMASSCHARGE CENTER COMBINE MOLINFO METAD UPPER_WALLS FIXEDATOM	vatom generic colvar function bias
23.038	Determinants of Neutral Antagonism and Inverse Agonism in the β2-adrenergic receptor	bio	protein coupled receptor, beta-adrenergic, receptor activation, antagonism, inverse agonism, metadynamics	Timothy Clark	PRINT MATHEVAL WHOLEMOLECULES DISTANCE RMSD MOLINFO METAD	colvar bias function generic
23.032	Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics	bio	metadynamics, tSNE, neural network, machine learning, trp-cage, folding	Vojtech Spiwok	PRINT ALPHARMSD WHOLEMOLECULES FIT_TO_TEMPLATE COMBINE MOLINFO METAD POSITION ANN	secondarystructure generic colvar function annfunc bias
23.016	Activation/deactivation free-energy profiles for the β2-adrenergic receptor: Ligand modes of action	bio	G protein coupled receptor, beta-adrenergic, receptor activation, partial agonism, metadynamics	Timothy Clark	PRINT HISTOGRAM MATHEVAL WHOLEMOLECULES DISTANCE RMSD CONVERT_TO_FES MOLINFO METAD REWEIGHT_METAD READ DUMPGRID	generic colvar function gridtools bias
23.006	Transcription factor unbinding	bio	metadynamics, DNA, conformational changes	Malin Lüking	PRINT ALPHARMSD DISTANCE DUMPFORCES COM MOLINFO ANGLE METAD CONTACTMAP	vatom secondarystructure generic colvar bias
23.005	A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs	bio	metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A	Timothy Clark	PRINT HISTOGRAM MATHEVAL WHOLEMOLECULES DISTANCE RMSD CONVERT_TO_FES MOLINFO METAD REWEIGHT_METAD READ DUMPGRID	generic colvar function gridtools bias
23.002	Critical comparison of general-purpose collective variables for crystal nucleation	methods	metadynamics, umbrella sampling, commitor, entropy, PIV	Julien Lam	PIV PRINT LOCAL_AVERAGE RESTRAINT PAIRENTROPY Q4 CUSTOM ENERGY METAD Q6 UNITS UPPER_WALLS VOLUME FUNCPATHMSD	piv generic colvar gridtools function setup bias symfunc
22.040	From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure	bio	SARS-CoV-2, Spike, Omicron	Miłosz Wieczór	PRINT WHOLEMOLECULES LOWER_WALLS METAD PCAVARS UPPER_WALLS	bias mapping generic
22.036	Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction	bio	Well-tempered MetaDynamics with Hamiltonian Replica Exchange	Miroslav Krepl	COORDINATION PRINT GROUP CUSTOM GHBFIX COMBINE MOLINFO BIASVALUE METAD FLUSH UPPER_WALLS LOAD	generic colvar function core setup bias
22.019	Exploring aspartic protease inhibitor binding to design selective antimalarials	bio	ligand binding, loop opening, path CV, funnel metadynamics, drug development	Raitis Bobrovs	FUNNEL_PS PRINT WHOLEMOLECULES DISTANCE LOWER_WALLS FUNNEL COM METAD PATHMSD UPPER_WALLS	vatom generic colvar funnel bias
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 PYTORCH_MODEL PRINT FIXEDATOM GROUP MATHEVAL WHOLEMOLECULES DISTANCE RMSD CUSTOM CENTER LOWER_WALLS FIT_TO_TEMPLATE COMMITTOR UPPER_WALLS OPES_METAD	vatom generic colvar function core pytorch opes bias
22.002	GAMBES_SAMPL5_RATES	other	GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding	Jayashrita Debnath	COORDINATION PYTORCH_MODEL PRINT FIXEDATOM GROUP MATHEVAL WHOLEMOLECULES DISTANCE CENTER FIT_TO_TEMPLATE ENERGY COMMITTOR FLUSH UPPER_WALLS ANGLE LOAD ENDPLUMED	vatom generic colvar function core setup pytorch bias
21.052	On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets	materials	Ibuprofen, unbinding, WTmetaD	Matteo Salvalaglio	PRINT DISTANCE CENTER COMMITTOR METAD TORSION COORDINATIONNUMBER ENDPLUMED	vatom generic colvar bias symfunc
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	PRINT FIT_TO_TEMPLATE METAD TORSION FIXEDATOM	vatom colvar bias generic
21.042	Peptoid-mediated Au nanocrystal growth	materials	parallel-bias metadynamics, peptoid, Au	Xin Qi	GYRATION PRINT DISTANCE PBMETAD COM MOLINFO UPPER_WALLS	vatom colvar bias generic
21.032	Metal-coupled folding mechanism to metallothionein	bio	parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination	Manuel-Peris Diaz	COORDINATION GROUP WHOLEMOLECULES PBMETAD UNITS	generic colvar core setup bias
21.027	EGFR activating mutations mechanism	bio	metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA	Francesco Gervasio	PRINT ALPHARMSD MATHEVAL WHOLEMOLECULES DISTANCE LOWER_WALLS ENERGY MOLINFO METAD UPPER_WALLS CONTACTMAP INCLUDE	secondarystructure generic colvar function bias
21.026	Probing allosteric regulations with coevolution-driven molecular simulations	bio	metadynamics, coevolution, allostery, adenylate cyclase	Francesco Colizzi	PRINT WHOLEMOLECULES DISTANCE COM METAD PATHMSD UNITS UPPER_WALLS	vatom generic colvar setup bias
21.005	Crystallization Collective Variable	methods	Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA	Tarak Karmakar	PYTORCH_MODEL PRINT GROUP MATHEVAL LOWER_WALLS FLUSH UPPER_WALLS LOAD OPES_METAD	generic function core setup pytorch opes bias
20.015	Rational design of ASCT2 inhibitors using an integrated experimental-computational approach	bio	ASCT2 transporter, small-molecules, cryo-EM, metainference	Max Bonomi	PRINT GROUP WHOLEMOLECULES MOLINFO BIASVALUE DUMPATOMS LOAD EMMIVOX	isdb generic core setup 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	PRINT GROUP WHOLEMOLECULES ANTIBETARMSD PBMETAD LOWER_WALLS MOLINFO BIASVALUE ALPHABETA FLUSH UPPER_WALLS CS2BACKBONE ENDPLUMED	isdb secondarystructure generic core multicolvar bias
19.071	Time-independent free energies from metadynamics via Mean Force Integration	methods	metadynamics, mean force integration, MFI, thermodynamic integration	Matteo Salvalaglio	PRINT HISTOGRAM MATHEVAL DISTANCE CONVERT_TO_FES REWEIGHT_BIAS EXTERNAL BIASVALUE METAD COMMITTOR REWEIGHT_METAD TORSION READ DUMPGRID	generic colvar function gridtools bias
19.061	Diffusion in porous materials	materials	metadynamics, porous materials, diffusion	Kim E. Jelfs	PRINT GROUP DISTANCE CENTER RESTART LOWER_WALLS COM METAD UPPER_WALLS	vatom generic colvar core setup bias
19.051	Solid liquid interfacial free energy out of equilibrium	materials	metadynamics, nucleation, surface excess free energy	Gareth Tribello	PRINT AROUND LOWER_WALLS CELL METAD UNITS UPPER_WALLS FCCUBIC ENDPLUMED	generic colvar setup volumes bias symfunc
19.042	Harmonic Linear Discriminant Analysis (HLDA)	methods	metadynamics, chemistry, HLDA	GiovanniMaria Piccini	PRINT DISTANCE COMBINE ENERGY METAD FLUSH UNITS UPPER_WALLS	generic colvar function setup bias
19.038	native state dynamics of human and mouse b2m	bio	metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation	Carlo Camilloni	PRINT GROUP WHOLEMOLECULES ANTIBETARMSD PBMETAD RESTART LOWER_WALLS MOLINFO BIASVALUE ALPHABETA FLUSH UPPER_WALLS CS2BACKBONE ENDPLUMED	isdb secondarystructure generic core multicolvar setup bias
19.036	Thermodynamics and kinetics of G protein-coupled receptor activation	bio	metadynamics, allostery, receptor conformation, GPCR, pharmacology	Davide Provasi	PRINT WHOLEMOLECULES DISTANCE FUNCPATHMSD RMSD COM METAD CONTACTMAP ENDPLUMED	vatom generic colvar function bias
19.026	Ice Nucleation on Cholesterol Crystals	materials	forward flux sampling, crystal nucleation, water, ice, organic crystals	Gabriele Cesare Sosso	MFILTER_MORE CLUSTER_NATOMS DFSCLUSTERING LOCAL_Q6 CLUSTER_WITHSURFACE COMMITTOR FLUSH Q6 OUTPUT_CLUSTER CONTACT_MATRIX ENDPLUMED	generic clusters multicolvar adjmat symfunc
19.021	Coarse-Grained Directed Simulation	methods	experiment directed simulation, coarse-grain, bias	Glen Hocky	PRINT RESTRAINT DISTANCE COMBINE EDS TORSION	generic colvar function eds bias
19.000	VesDeltaF	methods	VES, convergence, suboptimal CVs	Michele Invernizzi	PRINT RESTART ENERGY VES_DELTA_F METAD POSITION UNITS TORSION LOAD ENDPLUMED	generic colvar ves setup 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	ANGLE WHOLEMOLECULES DISTANCE METAD PRINT	bias colvar generic
26.001	Molecular simulations Alx riboswitch	bio	RNA, riboswitch	Giovanni Bussi	ERMSD DISTANCE MOLINFO RESTRAINT MOVINGRESTRAINT PRINT MATHEVAL	function bias colvar generic
25.029	Energetic Constraints in the Enzymatic Depolymerization of Crystalline PET from enhanced molecular simulations	bio	HREX-Metadynamics, PETase, crystalline PET, amorphous PET, conformational ensembles, substrate binding, chain detachment	Ania Di Pede-Mattatelli and Francesco Colizzi	HISTOGRAM UPPER_WALLS WHOLEMOLECULES DUMPGRID DISTANCE COM FIXEDATOM REWEIGHT_BIAS MOLINFO METAD PRINT LOWER_WALLS CONVERT_TO_FES	bias vatom gridtools colvar generic
25.009	Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water	chemistry	metadynamics, nitrate photolysis	Kam-Tung Chan	HISTOGRAM GROUP FLUSH UPPER_WALLS CUSTOM DUMPGRID COORDINATION READ DISTANCE RESTART METAD REWEIGHT_METAD PRINT	function bias core gridtools colvar setup generic
24.026	Constant pH metadynamics of RNA oligomers	bio	metadynamics, pH, RNA	Giovanni Bussi	RESTART MOLINFO PUCKERING METAD TORSION PRINT	bias setup colvar generic
24.011	Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble	methods	committor, machine learning	Peilin Kang	CUSTOM POSITION TORSION GROUP DISTANCE BIASVALUE INCLUDE UNITS MATHEVAL UPPER_WALLS COORDINATION LOAD MOLINFO ENERGY PRINT ENDPLUMED CELL RMSD WHOLEMOLECULES LOWER_WALLS	function bias core colvar setup generic
24.006	Water vapor condensation	chemistry	metadynamics, homogeneous condensation, chemical potential	Shenghui Zhong	CONTACT_MATRIX CLUSTER_PROPERTIES UPPER_WALLS CLUSTER_NATOMS METAD PRINT UNITS DFSCLUSTERING COORDINATIONNUMBER	bias symfunc clusters adjmat setup generic
24.004	Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables	materials	metadynamics, nucleation, machine learning	Ziyue Zou	GROUP LOAD RESTART INCLUDE METAD PRINT	generic bias setup core
23.045	Minute-timescale simulations of G Protein Coupled Receptor A2A activation mechanism reveal a receptor pseudo-active state	bio	Path CVs Metadynamics, GPCRs activation transition	Vittorio Limongelli	ALPHARMSD CONTACTMAP UPPER_WALLS FUNCPATHMSD DISTANCE PATHMSD MOLINFO INCLUDE METAD PRINT LOWER_WALLS	function bias secondarystructure colvar generic
23.026	Machine Learning Nucleation Collective Variables with Graph Neural Networks	chemistry	Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks	Florian Dietrich	GROUP LOCAL_Q6 Q6 MFILTER_MORE COMBINE METAD MOVINGRESTRAINT PRINT LOWER_WALLS COORDINATIONNUMBER	multicolvar bias function core symfunc generic
22.028	N-glycan conformer distributions in atomistic simulation	bio	REST2, RECT, N-glycan, pucker	Isabell Grothaus	HISTOGRAM DUMPGRID READ MOLINFO PUCKERING METAD TORSION PRINT CONVERT_TO_FES	bias gridtools colvar generic
22.026	Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification	materials	Peptoid, silica	Jim Pfaendtner	PBMETAD UPPER_WALLS DISTANCE COM MOLINFO GYRATION PRINT	bias vatom colvar generic
22.013	Ligand dissociation from PreQ1 riboswitch	bio	ligand, RNA, metadynamics, pRAVE	Yihang Wang	COMMITTOR RMSD WHOLEMOLECULES DISTANCE COMBINE COM MOLINFO METAD PRINT COORDINATIONNUMBER	function bias symfunc vatom colvar generic
22.004	Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques	chemistry	reaction discovery, OPES, collective variables	Umberto Raucci	GROUP MATHEVAL UPPER_WALLS CUSTOM OPES_METAD COORDINATION DISTANCE LOAD COM PYTORCH_MODEL OPES_METAD_EXPLORE PRINT UNITS LOWER_WALLS	function bias opes core vatom colvar pytorch setup generic
22.001	Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials	methods	enhanced sampling, variationally enhanced sampling, ves, metadynamics, bias representation, wavelets, adam	Benjamin Pampel	BF_GAUSSIANS POSITION OPT_ADAM TD_WELLTEMPERED OPT_AVERAGED_SGD DISTANCE BF_CHEBYSHEV INCLUDE UNITS BF_WAVELETS BF_CUBIC_B_SPLINES FLUSH UPPER_WALLS COORDINATION ENERGY PRINT VES_LINEAR_EXPANSION TD_UNIFORM BF_LEGENDRE METAD VES_OUTPUT_BASISFUNCTIONS	bias ves colvar setup generic
21.047	Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations	materials	pair entropy, metadynamics, ves, solids, crystallization	Pablo Piaggi	VES_LINEAR_EXPANSION PAIRENTROPY VOLUME TD_WELLTEMPERED OPT_AVERAGED_SGD RESTART COMBINE LOAD BF_LEGENDRE METAD ENERGY PRINT	function bias ves gridtools colvar setup generic
21.046	Ubiquitin Interacting Motifs, Duality Between Structured and Disordered Motifs	bio	wt metadynamics, ubiquitin, ataxin-3, short linear motifs, ubiquitin binding motif, moonlight functions, intrinsic disorder	Elena Papaleo	GROUP LOWER_WALLS UPPER_WALLS WHOLEMOLECULES GYRATION METAD ALPHABETA PRINT ENDPLUMED	multicolvar bias core colvar generic
21.028	From Enhanced Sampling to Reaction Profiles	methods	collective variables, multi-state, machine learning, Deep-TDA	Enrico Trizio	TORSION GROUP CENTER DISTANCE FIXEDATOM UNITS MATHEVAL UPPER_WALLS COORDINATION LOAD PYTORCH_MODEL PRINT ENDPLUMED ANGLE WHOLEMOLECULES OPES_METAD FIT_TO_TEMPLATE DISTANCES LOWER_WALLS	function bias multicolvar opes core vatom colvar pytorch setup generic
21.023	Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling	methods	enhanced sampling, collective variables, machine learning	Jakub Rydzewski	CUSTOM CONSTANT DISTANCE BIASVALUE INCLUDE METAD ENERGY REWEIGHT_METAD PRINT UNITS TORSION	function bias colvar setup generic
21.020	Reweighted Jarzynski sampling	methods	free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions	Kristof Bal	CUSTOM TD_WELLTEMPERED ANN CONSTANT DISTANCE BIASVALUE OPT_AVERAGED_SGD BF_CHEBYSHEV MOVINGRESTRAINT UNITS FLUSH UPPER_WALLS DUMPGRID LOAD COMBINE PRINT COORDINATIONNUMBER HISTOGRAM VES_LINEAR_EXPANSION OPES_METAD REWEIGHT_BIAS RESTRAINT METAD REWEIGHT_METAD CONVERT_TO_FES	function bias opes ves symfunc annfunc gridtools colvar setup generic
20.022	Unified Approach to Enhanced Sampling	methods	OPES, expanded ensembles, importance sampling	Michele Invernizzi	CUSTOM POSITION ECV_LINEAR VOLUME TORSION ECV_UMBRELLAS_LINE Q6 MATHEVAL UNITS ECV_MULTITHERMAL_MULTIBARIC UPPER_WALLS LOAD MOLINFO ENERGY PRINT ENDPLUMED RMSD WHOLEMOLECULES OPES_EXPANDED ECV_MULTITHERMAL ENVIRONMENTSIMILARITY	function bias opes symfunc envsim colvar setup 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	WHOLEMOLECULES STATS COORDINATION MOLINFO RESTRAINT PRINT	function bias colvar generic
19.077	Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations	materials	metadynamics, peptide-surface binding	Jim Pfaendtner	UPPER_WALLS DISTANCE COM MOLINFO GYRATION METAD ENERGY PRINT	bias vatom colvar generic
19.031	Ice nucleation using PIV-based path coordinates	materials	phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics	Silvio Pipolo	UPPER_WALLS CELL FUNCPATHMSD METAD PIV PRINT LOWER_WALLS	function bias piv colvar generic
19.023	RECT	methods	metadynamics, replica exchange	Giovanni Bussi	WHOLEMOLECULES GYRATION METAD TORSION PRINT	bias colvar generic
19.007	EMMI Microtubules	bio	metainference, cryo-EM	Max Bonomi	GROUP EMMI WHOLEMOLECULES BIASVALUE MOLINFO PRINT	generic bias isdb core
25.019	The Arch from the Stones. Understanding Protein Folding Energy Landscapes via Bio-inspired Collective Variables	bio	protein folding, OPES, OneOPES, binding free energy	Valerio Rizzi	ENERGY PRINT OPES_EXPANDED MOLINFO CENTER COMBINE OPES_METAD_EXPLORE GROUP ECV_MULTITHERMAL GHOST CUSTOM COORDINATION DISTANCE RMSD	vatom opes colvar function core generic
25.008	Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting	methods	metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting	Dhiman Ray	ENERGY PRINT METAD MOLINFO DISTANCE TORSION LOWER_WALLS GROUP CUSTOM UPPER_WALLS BIASVALUE POSITION WHOLEMOLECULES OPES_METAD ENDPLUMED UNITS PYTORCH_MODEL RMSD	pytorch opes colvar function core setup bias generic
25.004	Machine Learning-Driven Molecular Dynamics Unveil a Bulk Phase Transformation Driving Ammonia Synthesis on Barium Hydride	chemistry	OPES, OPES flooding, Catalysis, Ammonia Synthesis	Axel Tosello Gardini	PRINT COORDINATIONNUMBER FLUSH FIXEDATOM GROUP COMMITTOR UPPER_WALLS UNITS ZDISTANCES CUSTOM OPES_METAD DISTANCES DISTANCE	vatom symfunc opes colvar function core setup bias generic multicolvar
25.001	RNA G-quadruplex folding with ST-metaD protocol	bio	RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD	Pavlína Pokorná	METAD MOLINFO COMBINE WHOLEMOLECULES ERMSD	bias function generic colvar
24.021	Ab initio machine learning simulation of calcium carbonate from aqueous solutions to the solid state	chemistry	ion pairing, caco3, opes, proton transfer, crystallization	Pablo Piaggi	ENERGY PRINT UPPER_WALLS OPES_METAD COORDINATION DISTANCE	bias generic 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	PRINT MOLINFO EMMIVOX GROUP UPPER_WALLS BIASVALUE WHOLEMOLECULES WRAPAROUND INCLUDE DISTANCE	isdb generic core bias colvar
23.036	Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water?	bio	NaCl, nucleation, metadynamics	Ruiyu Wang	ENERGY PRINT METAD COMBINE Q4 VOLUME COORDINATIONNUMBER MATHEVAL Q6	symfunc colvar function bias generic
23.031	Identifying small molecules binding sites in RNA conformational ensembles with SHAMAN	bio	RNA, metadynamics, probes, mixed-solvent MD, small molecules, binding sites	Max Bonomi	PRINT METAD MOLINFO CENTER GROUP UPPER_WALLS POSITION WHOLEMOLECULES WRAPAROUND SHADOW DISTANCES FIT_TO_TEMPLATE	vatom isdb generic core bias colvar multicolvar
23.015	MPCs aggregation	bio	opes_explore, dimerization, MPCs, self-assembly	Vikas Tiwari	PRINT METAD CENTER COM OPES_METAD_EXPLORE LOWER_WALLS GROUP UPPER_WALLS WHOLEMOLECULES CUSTOM COORDINATION DISTANCE	vatom opes colvar function core bias generic
22.044	Colloid Crystallisation Analyses	materials	Q4, Q6, Pair Entropy, DFS	Aaron Finney	MFILTER_LESS PRINT MFILTER_MORE COMBINE GROUP Q4 LOCAL_Q4 CLUSTER_NATOMS LOCAL_AVERAGE LOCAL_Q6 COORDINATIONNUMBER DFSCLUSTERING CONTACT_MATRIX Q6	symfunc clusters function core adjmat generic multicolvar
22.037	Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site	chemistry	metadynamics, DNA, abasic	Mike Jones	DISTANCES METAD DISTANCE PRINT	generic bias colvar multicolvar
22.029	Angiotensin-1-7_Metadynamics	bio	Metadynamics, Angiotensin-(1-7), peptide	L.-América Chi	PRINT METAD FLUSH LOWER_WALLS GROUP GYRATION UPPER_WALLS WHOLEMOLECULES COORDINATION	bias colvar generic core
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 WHOLEMOLECULES LOAD	bias generic setup
21.051	Automatic learning of hydrogen-bond fixes in an AMBER RNA force field	methods	force field, RNA	Giovanni Bussi	PRINT METAD MOLINFO COMBINE BIASVALUE WHOLEMOLECULES ERMSD COORDINATION	bias function generic colvar
21.029	Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs	bio	metadynamics, small peptide, machine learning	Pratyush Tiwary	ENERGY EXTERNAL PRINT MOLINFO FLUSH TORSION RESTART	generic bias colvar setup
21.018	Localized Volume-based Metadynamics	bio	LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification	Riccardo Capelli	PRINT COM HISTOGRAM MATHEVAL METAD FLUSH FIXEDATOM READ ENDPLUMED RMSD REWEIGHT_METAD CONVERT_TO_FES WHOLEMOLECULES GROUP DUMPGRID UPPER_WALLS POSITION COORDINATION DISTANCE	vatom colvar function gridtools core bias generic
20.011	Uremic toxin analysis	bio	metadynamics, uremic toxin, serum albumin	Jim Pfaendtner	PRINT CENTER GROUP WHOLEMOLECULES COORDINATION DISTANCES RESTART DISTANCE	vatom core setup generic colvar multicolvar
19.075	PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python	other	Python, automatic differentiation	Toni Giorgino	RESTRAINT PRINT CENTER COMBINE TORSION GROUP DUMPDERIVATIVES ENDPLUMED CUSTOM ANGLE DISTANCE	vatom colvar function core bias generic
19.073	On the role of enthalpic and entropic contributions on the conformational free energy landscape of MIL-101(Cr) building units	materials	metadynamics, MOF, MIL101Cr, conformational	Matteo Salvalaglio	ENERGY PRINT METAD LOWER_WALLS GYRATION UPPER_WALLS ENDPLUMED COORDINATIONNUMBER DISTANCES	symfunc colvar bias generic multicolvar
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	PRINT METAD FLUSH LOWER_WALLS GROUP UPPER_WALLS POSITION COORDINATION UNITS RESTART	generic core setup bias colvar
19.032	Chemical reaction in solution using path collective variables based on coordination patterns	chemistry	chemical reactions, solutions, metadynamics, coordination patterns	Fabio Pietrucci	PRINT PATH METAD FLUSH UPPER_WALLS DISTANCES RESTART	mapping setup bias generic multicolvar
19.013	RNA FF FITTING	methods	force field, RNA	Giovanni Bussi	PUCKERING MOLINFO TORSION BIASVALUE INCLUDE MATHEVAL CONSTANT	bias generic function colvar
26.006	Metadynamics simulations of buried phosphorylation sites and proline isomerisation	bio	metadynamics	Julian Streit	TORSION WHOLEMOLECULES METAD COORDINATION MOLINFO PRINT	bias generic colvar
26.000	OPES simulations of disordered proteins	bio	OPES, IDPs	Julian Streit	ENERGY OPES_EXPANDED RESTART ECV_MULTITHERMAL PRINT	generic opes setup colvar
25.026	Deciphering the Molecular Mechanisms of Startle Disease - the Role of the Asn46Lys Mutation in the Glycine Receptor	bio	metadynamics, glycine receptors, funnel metadynamics	Jacob Adam Clark	METAD FUNNEL_PS COM FUNNEL UPPER_WALLS PRINT LOWER_WALLS	bias generic funnel vatom
24.030	NMR guided simulation of dsRBD	bio	Metainference, NMR, protein dynamics	Debadutta Patra	WHOLEMOLECULES STATS FLUSH METAINFERENCE ALPHABETA DISTANCE ENSEMBLE MOLINFO PRINT GROUP RDC	generic multicolvar function colvar isdb core
24.025	Correlating Enzymatic Reactivity for Different Substrates using Transferable Data-Driven Collective Variables	bio	enzymatic reactivity, k_cat, transfer learning, data-driven CVs, catalysis, ligand-binding modes, water, alpha-amylase, sugar, classical MD, OPES, machine learning, Deep TDA CV, path CV	Sudip Das	TORSION CENTER WHOLEMOLECULES GROUP FIT_TO_TEMPLATE CUSTOM PYTORCH_MODEL COORDINATION OPES_METAD RESTART DISTANCE FIXEDATOM PATH UPPER_WALLS PRINT LOWER_WALLS	opes pytorch vatom mapping bias generic function colvar core 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	DISTANCE PRINT	generic colvar
24.014	Learning Collective Variables with Synthetic Data Augmentation through Physics-inspired Geodesic Interpolation	methods	data augmentation, geodesic interpolation, collective variables, protein folding	Juno Nam	DRR WHOLEMOLECULES METAD FLUSH PYTORCH_MODEL COORDINATION RMSD MOLINFO UPPER_WALLS PRINT LOWER_WALLS	pytorch bias generic colvar drr
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	TORSION BIASVALUE METAD ENERGY FLUSH COORDINATIONNUMBER MATHEVAL DISTANCE RESTART COMMITTOR MOLINFO PRINT RESTRAINT	bias generic function colvar symfunc setup
24.003	Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations	chemistry	steered molecular dynamics, foldamers, peptoids, bio-inspired	Kaylyn Torkelson	TORSION WHOLEMOLECULES GYRATION COORDINATION INCLUDE ALPHABETA COM DISTANCE PRINT MOVINGRESTRAINT	vatom bias generic multicolvar colvar
23.046	Lasso Peptides - HLDA CV	bio	metadynamics, protein folding, HLDA, harmonic	Gabriel da Hora	WHOLEMOLECULES METAD DISTANCE UNITS COMBINE PRINT	bias generic function 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 FLUSH TRANSPOSE MATHEVAL SUM INCLUDE SELECT_COMPONENTS PRINT	matrixtools bias generic function valtools
23.034	Urea nucleation in water: do long-range forces matter?	materials	LMF theory, Metadynamics, Nucleation	Ziyue Zou	CENTER METAD INCLUDE PRINT GROUP LOAD COORDINATIONNUMBER	vatom bias generic symfunc core setup
23.030	Data Driven Classification of Ligand Unbinding Pathways	bio	OPES Explore, OPES Flooding, Benzene T4 Lysozyme, Ligand unbinding, Pathway classification, Kinetics, Residence time	Dhiman Ray	TORSION POSITION OPES_METAD COM DISTANCE PRINT WRAPAROUND ENERGY CUSTOM ENDPLUMED MATHEVAL LOWER_WALLS COMMITTOR OPES_METAD_EXPLORE CENTER WHOLEMOLECULES BIASVALUE FIT_TO_TEMPLATE FLUSH UNITS MOLINFO COORDINATION UPPER_WALLS GROUP	opes vatom bias generic function colvar core setup
23.028	Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process	chemistry	Ammonia decomposition; Dynamics;OPES; Neural Network potential	Manyi Yang	ZDISTANCES DISTANCES ENERGY FLUSH CUSTOM MATHEVAL OPES_METAD COM DISTANCE UNITS LOWER_WALLS FIXEDATOM COMMITTOR UPPER_WALLS PRINT GROUP COORDINATIONNUMBER	opes vatom bias generic multicolvar function colvar symfunc core setup
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	TORSION CENTER WHOLEMOLECULES GROUP FIT_TO_TEMPLATE CUSTOM PYTORCH_MODEL COORDINATION OPES_METAD DISTANCE UNITS FIXEDATOM PATH UPPER_WALLS PRINT LOWER_WALLS OPES_METAD_EXPLORE	opes pytorch vatom mapping bias generic function colvar core setup
23.004	Melting curves of ice polymorphs in the vicinity of the liquid-liquid critical point	chemistry	water, liquid-liquid transition, second critical point, ice, polymorphs, melting curves, environment similarity, opes, density-functional theory, scan, machine learning potential	Pablo Piaggi	ECV_UMBRELLAS_LINE OPES_EXPANDED RESTART ENVIRONMENTSIMILARITY DUMPGRID UPPER_WALLS PRINT LOWER_WALLS HISTOGRAM	opes envsim bias generic gridtools setup
23.001	Quantum phase diagram of water	chemistry	Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella	Sigbjørn-Løland Bore	ECV_UMBRELLAS_LINE INCLUDE OPES_EXPANDED RESTART ENVIRONMENTSIMILARITY UPPER_WALLS PRINT LOWER_WALLS	opes envsim bias generic setup
22.033	Reciprocal barrier restraint. Application to PROTAC passive permeability prediction	methods	PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR	Istvan Kolossvary	DRR BIASVALUE METAD FLUSH CUSTOM COM DISTANCE UNITS PRINT	vatom bias generic setup function colvar drr
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	TORSION WHOLEMOLECULES METAD COM DISTANCE PRINT GROUP	vatom bias generic colvar core
21.049	Multiple-path-metadynamics and PathMaps	methods	path-CV, metadynamics, multiple-walker, multiple paths, pathmap	Alberto Pérez-de-Alba-Ortíz	TORSION METAD CONSTANT CUSTOM MOVINGRESTRAINT UNITS COMBINE ENSEMBLE UPPER_WALLS PRINT LOWER_WALLS LOAD RESTRAINT	bias generic function colvar 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	TORSION METAD CUSTOM COM DISTANCE UNITS UPPER_WALLS PRINT LOWER_WALLS	vatom bias generic function colvar setup
21.040	A structural ensemble of a tau-microtubule complex reveals regulatory tau phosphorylation and acetylation mechanisms	bio	EMMI, CryoEM, tau-microtubules, post-translational modifications, chemical mutagenesis, structural ensemble, Metainference	Faidon Brotzakis	GROUP BIASVALUE WHOLEMOLECULES COM RESTART DISTANCE MOLINFO UPPER_WALLS PRINT EMMI	vatom bias generic colvar isdb core setup
21.037	Molecular Dynamics simulations of RBD/hACE2 complexes	bio	SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain	Max Bonomi	DISTANCE PRINT RMSD	generic colvar
21.036	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	RANDOM_EXCHANGES GROUP WHOLEMOLECULES METAD ALPHARMSD ENERGY GYRATION COORDINATION PARABETARMSD DIHCOR ANTIBETARMSD MOLINFO UPPER_WALLS PRINT LOWER_WALLS	bias generic multicolvar colvar secondarystructure core
21.035	CmuMD simulations of NaCl(aq) at NaCl	chemistry	CmuMD, interface	Aaron Finney	DISTANCE FIXEDATOM PRINT GROUP LOAD RESTRAINT	vatom bias generic colvar core setup
21.003	aSYN SAXS metainference	bio	metainference, SAXS	Kresten Lindorff-Larsen	BIASVALUE WHOLEMOLECULES CENTER ALPHARMSD SAXS FLUSH GYRATION METAINFERENCE PBMETAD MOLINFO EEFSOLV PRINT GROUP	vatom bias generic colvar isdb secondarystructure core
20.033	COVID-19 Spike protein opening transition mechanism	bio	EMMI, CryoEM, COVID-19, Spike, Metainference	Faidon Brotzakis	GROUP BIASVALUE WHOLEMOLECULES DISTANCES RMSD CONVERT_TO_FES MOLINFO DUMPGRID PRINT EMMI READ HISTOGRAM	bias generic multicolvar colvar isdb gridtools core
20.024	Gaussian Mixture Based Enhanced Sampling (GAMBES)	methods	enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias	Jayashrita Debnath	TORSION GROUP DISTANCES ENERGY DISTANCE UNITS COMBINE UPPER_WALLS PRINT LOWER_WALLS LOAD	bias generic multicolvar function colvar core setup
20.023	metadynminer and metadynminer3d	methods	metadynamics, visualization, R	Vojtech Spiwok	TORSION PRINT METAD	bias generic colvar
19.083	Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis	chemistry	metadynamics, chemical reactions, reaction discovery	Valerio Rizzi	METAD DISTANCES FLUSH ENDPLUMED RESTART UNITS COMBINE UPPER_WALLS PRINT GROUP COORDINATIONNUMBER	bias generic multicolvar function symfunc core setup
19.067	Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways	bio	metadynamics, ligand unbinding	Jakub Rydzewski	METAD PATHMSD RESTART UNITS UPPER_WALLS PRINT LOWER_WALLS	bias generic setup colvar
19.059	cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide	bio	bias-exchange metadynamics, cis-trans isomerization	Fabrizio Marinelli	RANDOM_EXCHANGES TORSION METAD INCLUDE PRINT	bias generic colvar
19.058	Constrained MD for maintaining a cavity in a calculation	chemistry	constrained MD, porous molecules, porosity, cavity	Kim Jelfs	DISTANCES FLUSH COM RESTART INPLANEDISTANCES PRINT MOVINGRESTRAINT	vatom bias generic multicolvar setup
19.057	SAXS ensembles using Martini-Beads multi-scale SAXS	methods	metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics	Cristina Paissoni	BIASVALUE CENTER WHOLEMOLECULES ANGLE SAXS STATS ENDPLUMED COORDINATION INCLUDE MATHEVAL ALPHABETA PBMETAD ENSEMBLE COMBINE MOLINFO PRINT GROUP	vatom bias generic multicolvar function colvar isdb core
19.052	Gibbs free energy of homogeneous nucleation	materials	nucleation, surface excess free energy	Gareth Tribello	METAD ENDPLUMED UNITS CELL UPPER_WALLS PRINT FCCUBIC	bias generic colvar symfunc setup
19.048	Understanding Ligand Binding Selectivity in a Prototypical GPCR Family	bio	metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding	Francesco Gervasio	BIASVALUE WHOLEMOLECULES METAD CONSTANT MATHEVAL COM DISTANCE UPPER_WALLS PRINT LOWER_WALLS	vatom bias generic function colvar
19.029	WTE-metaD of FF domain of URNF1 C57D variant	bio	metadynamics, mutations, post-translational modification, ff domain	Elena Papaleo	GROUP WHOLEMOLECULES METAD GYRATION ALPHABETA MOLINFO UPPER_WALLS PRINT LOWER_WALLS	bias generic multicolvar colvar core
19.010	Multi-domain protein dynamics	bio	metainference, NMR, protein dynamics	Carlo Camilloni	TORSION CENTER WHOLEMOLECULES STATS ENDPLUMED METAINFERENCE ALPHABETA DISTANCE DHENERGY PBMETAD DIHCOR ENSEMBLE UPPER_WALLS MOLINFO PRINT GROUP RDC RESTRAINT	vatom bias generic multicolvar function colvar isdb core
19.005	Cmyc small molecule interaction	bio	metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP	Gabriella Heller	GROUP CENTER WHOLEMOLECULES GYRATION COORDINATION INCLUDE ALPHABETA METAINFERENCE DISTANCE PBMETAD MOLINFO PRINT CS2BACKBONE	vatom bias generic multicolvar colvar isdb core
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	MATHEVAL WHOLEMOLECULES COORDINATION GROUP CENTER GYRATION DISTANCE PRINT METAD COMBINE LOWER_WALLS UPPER_WALLS	core colvar generic bias function 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	OPES_METAD MATHEVAL WHOLEMOLECULES GROUP CENTER TORSION COORDINATION CUSTOM PRINT COMMITTOR FUNNEL FUNNEL_PS LOWER_WALLS METAD COM UPPER_WALLS WRAPAROUND RMSD	funnel core colvar generic bias opes function vatom
25.022	Imidazole Diffusion in SALEM-2 MOF	materials	OPES, Diffusion, Ring opening, MOFs, Machine Learning Potentials	Sudheesh Kumar Ethirajan	PROJECTION_ON_AXIS OPES_METAD ENDPLUMED WHOLEMOLECULES CENTER GROUP UNITS DISTANCE PRINT DISTANCES MOLINFO	core colvar generic setup opes vatom multicolvar
25.013	Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices	bio	umbrella sampling, temperature ramping	Alexander Berlaga	PYTORCH_MODEL RESTRAINT PRINT GYRATION DISTANCE	bias colvar generic pytorch
25.006	Characterizing the conformational ensemble of PROTAC degraders in solutions via atomistic simulations	methods	Enhanced sampling, Atomistic simulations, Conformational ensemble, PROTACs, Targeted Protein Degradation, Chamelonic molecules	Shikshya Bhusal, Omar Valsson	INCLUDE VOLUME PBMETAD UPDATE_IF WHOLEMOLECULES ENERGY CENTER DUMPATOMS DISTANCE GYRATION PRINT READ TORSION RESTART MOLINFO	colvar generic setup vatom bias
25.005	Mechanism of Nanocluster Formation from Machine-Learned Potential-based Simulations	chemistry	WT-metadynamics, metal nanoclusters, nucleation, neural network potential, deepMD	Vikas Tiwari, Tarak Karmakar	FLUSH FIXEDATOM RESTRAINT GROUP COORDINATION UNITS DISTANCE ANGLE PRINT METAD COMBINE DISTANCES LOWER_WALLS COM COORDINATIONNUMBER UPPER_WALLS	core colvar generic setup symfunc bias function vatom multicolvar
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 CENTER COORDINATION DISTANCE DEBUG PRINT METAD COMBINE GHBFIX BIASVALUE LOWER_WALLS COM UPPER_WALLS MOLINFO	core colvar generic bias function vatom
22.038	Enhanced Sampling Aided Design of Molecular Photoswitches	chemistry	reaction discovery, OPES explore, graph CV	Umberto Raucci	PYTORCH_MODEL OPES_METAD_EXPLORE COORDINATION PRINT UNITS CUSTOM	colvar generic pytorch setup opes function
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	INCLUDE PBMETAD ENDPLUMED PRINT TORSION METAD RANDOM_EXCHANGES	bias colvar generic
21.016	MD SAXS GTPase associated center	bio	metadynamics, RNA, folding, SAXS	Giovanni Bussi	INCLUDE WHOLEMOLECULES GROUP SAXS GYRATION PRINT ERMSD CUSTOM METAD LOWER_WALLS UPPER_WALLS MOLINFO	core colvar generic isdb function bias
21.013	Role of vibrational excitation in heterogeneous catalysis	chemistry	catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption	Kristof Bal	REWEIGHT_BIAS RESTRAINT BF_CHEBYSHEV OPT_AVERAGED_SGD METAD COORDINATIONNUMBER TD_GRID ANGLES FLUSH COORDINATION LOAD UWALLS CONVERT_TO_FES DISTANCES DUMPGRID LOWER_WALLS REWEIGHT_METAD HISTOGRAM VES_LINEAR_EXPANSION PRINT DISTANCE UNITS EXTERNAL COMBINE UPPER_WALLS	colvar generic symfunc setup gridtools function bias ves multicolvar
21.006	OPES, On-the-fly Probability Enhanced Sampling Method	methods	opes, alanine dipeptide, well-tempered, multithermal, multiumbrella	Michele Invernizzi	OPES_METAD ENDPLUMED ENERGY PRINT ECV_UMBRELLAS_LINE TORSION ECV_MULTITHERMAL OPES_EXPANDED	opes colvar generic
20.034	Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations	bio	RNA, SARS-CoV-2, partial tempering	Sandro Bottaro	ABMD CENTER PRINT DISTANCE TORSION ERMSD RESTART MOLINFO	colvar generic setup vatom bias
20.028	Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane	bio	metadynamics, KRas-4B, anionic membrane	Huixia Lu	PRINT FIT_TO_TEMPLATE CENTER DISTANCE METAD RESTART	colvar generic setup bias vatom
20.019	Systematic finite-temperature reduction of crystal energy landscapes	materials	crystals, organics, structure prediction	Matteo Salvalaglio	MATHEVAL VOLUME ENERGY PRINT METAD LOWER_WALLS CELL UPPER_WALLS	colvar bias function generic
20.014	amyloid beta small molecule interaction	bio	intrinsically disordered proteins, disordered proteins, IDPs, fuzzy binding, small molecule, drugs, entropy, binding, Alzheimer’s disease, amyloid beta	Gabriella Heller	INCLUDE ALPHARMSD PBMETAD WHOLEMOLECULES DIHCOR ENSEMBLE METAINFERENCE FLUSH COORDINATION GYRATION STATS MOLINFO ENDPLUMED PARABETARMSD ANTIBETARMSD CS2BACKBONE GROUP PRINT TORSION COMBINE	core colvar generic isdb secondarystructure function bias multicolvar
20.006	Class B GPCR activation mechanism	bio	metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding	Francesco Gervasio	MATHEVAL ENERGY WHOLEMOLECULES PRINT CENTER DISTANCE METAD COMBINE LOWER_WALLS RMSD UPPER_WALLS MOLINFO	colvar generic function vatom bias
20.000	Muscarinic M2 receptor-ligand funnel metadynamics	bio	multiple walker metadynamics, well-tempered metadynamics, funnel metadynamics, MC-HLDA, GPCR, receptor, Adiabatic Bias MD	Riccardo Capelli	REWEIGHT_METAD MATHEVAL HISTOGRAM ENDPLUMED PRINT DISTANCE READ CONVERT_TO_FES METAD COMBINE LOWER_WALLS DUMPGRID COM UPPER_WALLS ABMD	colvar generic function gridtools vatom bias
19.080	Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium	methods	ves, variationally enhanced sampling, vibrational excitation, chemical reactions	Kristof Bal	HISTOGRAM FLUSH VES_LINEAR_EXPANSION COORDINATION ANGLE UNITS DISTANCE EXTERNAL BF_CHEBYSHEV OPT_AVERAGED_SGD PRINT CONVERT_TO_FES COMBINE DUMPGRID LOWER_WALLS UPPER_WALLS TD_GRID TD_WELLTEMPERED	colvar generic setup gridtools function bias ves
19.035	Dimerization of GPCRs from coarse-grained umbrella sampling	bio	Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization	Davide Provasi	RESTRAINT GROUP PRINT TORSION DISTANCE COM	core colvar generic vatom bias
19.003	EMMI ClpP	bio	metainference, cryo-EM	Max Bonomi	GROUP PRINT EMMI BIASVALUE MOLINFO	isdb bias generic core
25.014	Atomic resolution ensembles of intrinsically disordered proteins with Alphafold	bio	bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement	Vincent Schnapka	PRINT BAIES GROUP BIASVALUE	bias generic isdb core
25.010	Kinetic rates calculation with Ratchet&Pawl MD	methods	kinetics, ligand binding, ABMD, ratchet&pawl MD	Riccardo Capelli	ABMD DISTANCE FLUSH PRINT GROUP COM WHOLEMOLECULES COMMITTOR	bias generic colvar vatom core
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 CUSTOM DISTANCE OPES_METAD RESTART UPPER_WALLS PRINT GROUP COORDINATION COMMITTOR UNITS	opes function bias setup generic colvar core
24.033	Transient interactions between the fuzzy coat and the cross-b core of brain-derived Ab42 filaments	bio	CryoEM, MEMMI, Metadynamics, Metainference, Ab42 Fibrils, structural ensemble	Maria Milanesi	DUMPATOMS PBMETAD BIASVALUE DISTANCE EMMI DUMPMASSCHARGE UPPER_WALLS ALPHARMSD PRINT MOLINFO GROUP CENTER COORDINATION COM PARABETARMSD WHOLEMOLECULES RMSD	core bias generic colvar vatom isdb secondarystructure
24.032	DeepLNE++	methods	PATHCV, OPES	Thorben Fröhlking	TORSION CUSTOM ENERGY LOAD DISTANCE PRINT GROUP COORDINATION COMBINE OPES_METAD	opes function setup generic colvar core
24.027	Proline cis and trans subensembles of a disordered peptide	bio	intrinsically disordered proteins, proline cis trans isomerisation, metadynamics, collective variables	Alice Pettitt	TORSION INCLUDE DIHCOR PBMETAD ANTIBETARMSD DISTANCE FLUSH ENDPLUMED ALPHARMSD PRINT GROUP WHOLEMOLECULES MOLINFO GYRATION PARABETARMSD COORDINATION COMBINE	multicolvar core function bias generic colvar secondarystructure
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	UPPER_WALLS PRINT ANGLE OPES_METAD WHOLEMOLECULES METAD FIXEDATOM CUSTOM DISTANCE GROUP MOLINFO RMSD COMMITTOR MATHEVAL FIT_TO_TEMPLATE CONTACTMAP CENTER COMBINE TORSION ENDPLUMED COORDINATION	opes function bias generic colvar vatom core
24.019	Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning	bio	OPES, machine learning, protein folding, adaptive sampling	Mingyuan Zhang	TORSION CUSTOM DISTANCE ALPHARMSD PRINT WHOLEMOLECULES COORDINATION MOLINFO GYRATION OPES_METAD COMBINE	opes function generic colvar secondarystructure
23.040	Supramolecular capsules assembly dynamics	chemistry	Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics	Riccardo Capelli	METAD CUSTOM COM DISTANCE FLUSH DISTANCES PRINT GROUP CENTER POSITION WHOLEMOLECULES UNITS	multicolvar function bias generic setup colvar vatom core
23.037	Estimating binding free energy of solid binding peptides without extensive sampling	bio	metadynamics, solid binding peptides	Xin Qi	LOWER_WALLS PBMETAD DISTANCE UPPER_WALLS PRINT MOLINFO COM GYRATION	vatom bias generic colvar
23.025	Probing ion binding to G-quadruplexes and related events	chemistry	metadynamics, repulsive potential, nucleic acids, G-quadruplexes	Marcelo Poleto	METAD WRAPAROUND LOWER_WALLS MATHEVAL COM DISTANCE FLUSH FIT_TO_TEMPLATE POSITION DISTANCES UPPER_WALLS RESTART PRINT GROUP DUMPATOMS WHOLEMOLECULES UNITS	multicolvar function bias generic setup colvar vatom core
23.024	Permutationally Invariant Networks for Enhanced Sampling (PINES)	methods	collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent	Nicholas Herringer	LOAD PRINT PBMETAD	bias setup generic
23.022	A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar	methods	collective variables, machine learning, toy model	Enrico Trizio	LOWER_WALLS CUSTOM BIASVALUE PYTORCH_MODEL ENDPLUMED UPPER_WALLS PRINT POSITION OPES_METAD UNITS	pytorch opes function bias generic setup colvar
23.020	FEP simulations of ATOX1 homodimer	chemistry	parallel bias metadynamics, FEP, free-energy of metal ion dissociation	Adriana Pietropaolo	MATHEVAL PBMETAD BIASVALUE DISTANCE PRINT ANGLE WHOLEMOLECULES CONSTANT	bias generic function colvar
23.014	Structural basis of dimerization of chemokine receptors CCR5 and CXCR4	bio	metadynamics, oligomerization, chemokine receptors, GPCR, membrane	Vittorio Limongelli	METAD TORSION DISTANCE FLUSH UPPER_WALLS PRINT COM WHOLEMOLECULES COMBINE	function bias generic 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	METAD CUSTOM PATHMSD BIASVALUE FLUSH PRINT DRR	function bias generic colvar drr
22.031	Rare Event Kinetics from Adaptive Bias Enhanced Sampling	methods	OPES Flooding, Kinetics, Rate, OPES, Machine Learning	Dhiman Ray	PRINT WHOLEMOLECULES OPES_METAD CUSTOM ENERGY DISTANCE GROUP MOLINFO RMSD COMMITTOR BIASVALUE CONTACTMAP COMBINE CONSTANT TORSION INCLUDE PYTORCH_MODEL ENDPLUMED POSITION UNITS	pytorch opes function bias generic setup colvar core
22.022	Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir	bio	RMSD, protein-ligand interactions	Isabell Grothaus	PRINT RMSD	generic colvar
21.045	QM/MM metadynamics of thiol-disulfide exchange between methylthiolate and dimethyldisulfide in water with an imposed external electrostatic potential (ESP)	chemistry	metadynamics, QM/MM, electrostatic potential, thiol-disulfide exchange	Denis Maag	METAD LOWER_WALLS COORDINATIONNUMBER DISTANCE UPPER_WALLS PRINT COMBINE COORDINATION	function bias generic colvar symfunc
21.039	Deep learning the slow modes for rare events sampling	methods	collective variables, machine learning, slow modes, deep-tica, opes	Luigi Bonati	FLUSH PRINT ECV_MULTITHERMAL OPES_METAD WHOLEMOLECULES ENERGY DISTANCE LOAD Q6 GROUP MOLINFO RMSD ENVIRONMENTSIMILARITY CONTACTMAP COMBINE VOLUME TORSION INCLUDE OPES_EXPANDED PYTORCH_MODEL ENDPLUMED UNITS	pytorch opes function setup generic envsim colvar symfunc core
21.033	Multiple-path-metadynamics applied to DNA base-pairing transitions	bio	path-CV, metadynamics, multiple-walker, dna	Alberto Pérez-de-Alba-Ortíz	METAD INCLUDE MOVINGRESTRAINT UPPER_WALLS PRINT RESTRAINT COMBINE CONSTANT	bias generic function
21.031	Photo-switchable sulfonulureas in KATP channel	bio	metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels	Katarzyna Walczewska-Szewc	METAD LOWER_WALLS DISTANCE UPPER_WALLS PRINT COM WHOLEMOLECULES UNITS	bias generic setup colvar vatom
21.004	Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy	bio	machine learning, well-tempered metadynamics, path collective variable, potential of mean force, standard binding free energy calculations, host-guest, protein-ligand unbinding	Dorothea Gobbo	METAD LOWER_WALLS PATHMSD RESTART UPPER_WALLS PRINT WHOLEMOLECULES	generic bias setup colvar
21.001	Substrate recognition and catalysis by glycosaminoglycan sulfotransferases	bio	metadynamics, well-tempered metadynamics, puckering, coordination	Tarsis Ferreira	METAD PUCKERING LOWER_WALLS INCLUDE ENERGY DUMPGRID DISTANCE RANDOM_EXCHANGES HISTOGRAM UPPER_WALLS REWEIGHT_METAD PRINT GROUP WHOLEMOLECULES MOLINFO COORDINATION	bias generic gridtools colvar core
20.032	Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil	materials	clustering, conformational isomers	Matteo Salvalaglio	TORSION PRINT ENDPLUMED	generic colvar
20.018	Free energy barriers from biased molecular dynamics simulations	methods	kinetics, free energy barriers, chemical reactions, nucleation, metadynamics	Kristof Bal	LOWER_WALLS FLUSH PAIRENTROPY UPPER_WALLS PRINT REWEIGHT_BIAS CONTACT_MATRIX METAD ENERGY LOAD DISTANCE Q6 DUMPGRID HISTOGRAM CENTER COMBINE DENSITY VOLUME COORDINATIONNUMBER LOCAL_AVERAGE REWEIGHT_METAD CONVERT_TO_FES SPRINT COORDINATION UNITS	volumes function bias generic gridtools setup adjmat colvar vatom symfunc sprint
20.017	FISST	methods	FISST, force, peptide, sampling, tempering	Glen Hocky	MATHEVAL ENERGY BIASVALUE DISTANCE PRINT RESTRAINT GROUP GYRATION UNITS FISST	fisst function bias generic setup colvar core
20.004	Data-driven collective variables for enhanced sampling	methods	collective variables, machine learning, deep-lda	Luigi Bonati	MATHEVAL TORSION LOWER_WALLS DISTANCE LOAD FLUSH PYTORCH_MODEL ENDPLUMED UPPER_WALLS PRINT GROUP COM OPES_METAD UNITS	pytorch opes function bias generic setup colvar vatom core
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	LOWER_WALLS CELL RESTART OPT_DUMMY UPPER_WALLS TD_WELLTEMPERED PRINT REWEIGHT_BIAS ENERGY REWEIGHT_TEMP_PRESS LOAD Q6 READ MATHEVAL DUMPGRID HISTOGRAM OPT_AVERAGED_SGD COMBINE BF_LEGENDRE VOLUME TD_MULTITHERMAL_MULTIBARIC VES_LINEAR_EXPANSION CONVERT_TO_FES	function bias generic setup gridtools colvar ves symfunc
19.063	Protein-ligand binding through metadynamics with path CVs	bio	metadynamics, path CVs, ligand binding	Mattia Bernetti	METAD LOWER_WALLS PATHMSD UPPER_WALLS PRINT WHOLEMOLECULES	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	FUNNEL ALPHABETA LOWER_WALLS TORSION METAD DISTANCE DISTANCES UPPER_WALLS REWEIGHT_METAD PRINT MOLINFO GROUP BRIDGE COM WHOLEMOLECULES RMSD COMBINE	multicolvar function bias generic adjmat colvar vatom core funnel
19.014	MIL101(Cr) SBUs assembly	materials	MOFs, nucleation, self-assembly, metadynamics	Matteo Salvalaglio	METAD COORDINATIONNUMBER RESTART ENDPLUMED DISTANCES PRINT GYRATION	multicolvar bias generic setup colvar symfunc
19.004	MI Ubiquitin	bio	metainference, NMR	Max Bonomi	METAINFERENCE CS2BACKBONE PRINT GROUP MOLINFO WHOLEMOLECULES RDC	generic isdb core
19.002	EMMI STRA6	bio	metainference, cryo-EM	Max Bonomi	BIASVALUE EMMI PRINT GROUP MOLINFO	bias generic isdb core
19.001	RNA SHAPE	bio	metadynamics, RNA, ligand binding	Giovanni Bussi	METAD ERMSD INCLUDE LOWER_WALLS DISTANCE FLUSH RANDOM_EXCHANGES DISTANCES UPPER_WALLS PRINT ANGLE MOLINFO COMBINE	multicolvar function bias generic colvar
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	ECV_MULTITHERMAL CUSTOM DISTANCE COORDINATION OPES_EXPANDED PRINT UPPER_WALLS CENTER PATH LOWER_WALLS GROUP VOLUME PATHMSD OPES_METAD_EXPLORE ENERGY RMSD	colvar generic vatom mapping opes function bias core
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	INCLUDE CUSTOM COMBINE COORDINATION DISTANCE PRINT OPES_METAD FLUSH POSITION MATHEVAL UNITS TORSION CELL LOAD ENERGY BIASVALUE	colvar generic opes function bias setup
25.002	M3_PCV-ABMD	chemistry	Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor	Gian Marco Elisi	ENDPLUMED PRINT UPPER_WALLS ABMD UNITS PATHMSD	colvar setup generic bias
24.034	Umbrella sampling of ion in transporter SLC26A7	bio	umbrella sampling, transporter, ions	Xiaoli Lu	RESTRAINT PRINT UNITS POSITION	colvar setup generic bias
24.028	All-atom simulations of RNA-membrane interactions	bio	metadynamics, membrane, RNA	Giovanni Bussi	GYRATION DISTANCE COMBINE SORT MOLINFO PRINT PUCKERING GHOST CENTER POSITION DISTANCES LOWER_WALLS WHOLEMOLECULES GROUP UPPER_WALLS MATHEVAL METAD	colvar generic vatom function multicolvar bias core
24.005	Learning Markovian Dynamics with Spectral Maps	methods	spectral map, collective variables, machine learning	Jakub Rydzewski	DISTANCE CUSTOM PRINT UNITS BIASVALUE	colvar generic function bias setup
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 WHOLEMOLECULES DISTANCE PRINT UPPER_WALLS CENTER LOWER_WALLS MATHEVAL METAD BIASVALUE	colvar generic vatom function bias
23.021	Into the Dynamics of Rotaxanes at Atomistic Resolution	materials	metadynamics, rotaxanes, molecular shuttles, molecular machines	Luigi Leanza	DISTANCE CUSTOM PRINT UPPER_WALLS CENTER MATHEVAL TORSION FIXEDATOM METAD	colvar generic vatom function bias
23.012	JAK2 2D meta-eABF PMF with statistical analysis	bio	2D meta-eABF, path CV, PMF	Istvan Kolossvary	CUSTOM DRR UPPER_WALLS PRINT FLUSH LOWER_WALLS PATHMSD METAD BIASVALUE	colvar generic drr function bias
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	PRINT TORSION METAD EXTRACV READ	colvar generic bias
23.000	Atomistic simulations of RNA tetraloop folding via PTWTE-WTM	bio	parallel tempering, well-tempered metadynamics, well-tempered ensemble, RNA, Tetraloop, Folding	Gül Zerze	WHOLEMOLECULES PRINT UPPER_WALLS CONTACTMAP LOWER_WALLS METAD ENERGY	colvar generic bias
22.043	Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES	bio	OPES, RNA, Tetraloop, Folding	Gül Zerze	ECV_MULTITHERMAL WHOLEMOLECULES OPES_EXPANDED PRINT ECV_UMBRELLAS_LINE CONTACTMAP ENERGY	opes colvar generic
22.042	Metadynamics of NSP10 and variants	bio	metadynamics, NSP10, crystal structure, variants	Shozeb Haider	METAD PRINT TORSION	colvar generic bias
22.035	Deciphering the alphabet of disorder — Glu and Asp act differently on local but not global properties	bio	intrinsically disordered proteins, parallel bias metadynamics, protein	Kresten Lindorff-Larsen	GYRATION WHOLEMOLECULES MOLINFO TORSION PBMETAD	colvar generic 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	COMMITTOR CUSTOM PRINT UPPER_WALLS LOWER_WALLS DRMSD MATHEVAL CELL METAD	colvar generic function bias
22.003	Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling	methods	opes, metadynamics, reweighting, alanine, muller	Michele Invernizzi	ECV_MULTITHERMAL CUSTOM ENDPLUMED OPES_EXPANDED ECV_UMBRELLAS_FILE PRINT UPPER_WALLS OPES_METAD POSITION LOWER_WALLS UNITS TORSION PBMETAD OPES_METAD_EXPLORE METAD ENERGY BIASVALUE	colvar generic opes function bias setup
21.010	Step by Step Strecker Amino Acid Synthesis from Ab Initio Prebiotic Chemistry	chemistry	Strecker reaction, free energy landscape, ab initio molecular dynamics, glycine, prebiotic synthesis	Théo Magrino	PRINT	generic
21.009	Nucleation rates from small scale atomistic simulations and transition state theory	materials	kinetics, free energy barriers, nucleation, droplets, metadynamics	Kristof Bal	HISTOGRAM CONVERT_TO_FES COMMITTOR MOVINGRESTRAINT PRINT UPPER_WALLS FLUSH UNITS COORDINATIONNUMBER REWEIGHT_METAD LOAD METAD DUMPGRID	generic gridtools bias setup symfunc
21.008	Multi-replica biased sampling for photoisomerization processes in conjugated polymers	methods	metadynamics, FEP, replica-exchange	Adriana Pietropaolo	CONSTANT WHOLEMOLECULES PRINT RESTART MATHEVAL TORSION PBMETAD BIASVALUE	colvar generic function bias setup
21.000	Uremic toxin time scale dynamics	bio	uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs)	Jim Pfaendtner	WHOLEMOLECULES DISTANCE PRINT COM GROUP	colvar core generic vatom
19.082	Ammonia Borane Dehydrogenation	chemistry	metadynamics, reaction discovery, hydrogen production, chemistry	Valerio Rizzi	ENDPLUMED COMBINE PRINT FLUSH RESTART GROUP UNITS COORDINATIONNUMBER EXTERNAL METAD	generic core function bias setup symfunc
19.068	Rethinking Metadynamics	methods	metadynamics, opes, convergence	Michele Invernizzi	ENDPLUMED PRINT OPES_METAD POSITION UNITS TORSION EXTERNAL METAD	colvar generic opes bias setup
19.065	Molecular Enhanced Sampling with Autoencoders	methods	enhanced sampling, collective variables, deep learning	Wei Chen	RESTRAINT COMBINE POSITION COM ANN	colvar vatom annfunc function bias
19.062	Elucidating molecular design principles for charge-alternating peptides	bio	peptide folding, metadynamics, well-tempered ensemble, parallel tempering	Jim Pfaendtner	GYRATION WHOLEMOLECULES PRINT METAD ENERGY	colvar generic bias
19.049	Determining the sizes of solid/liquid clusters in MD trajectories of nucleation	methods	nucleation, metadynamics, clustering, Steinhardt order parameters	Gareth Tribello	CONTACT_MATRIX METAD DFSCLUSTERING MATRIX_VECTOR_PRODUCT CUSTOM CLUSTER_NATOMS Q6 SMAC PRINT CLUSTER_PROPERTIES MORE_THAN OUTPUT_CLUSTER CLUSTER_DISTRIBUTION DISTANCES COORDINATIONNUMBER LOCAL_Q6 OUTER_PRODUCT ONES	generic matrixtools adjmat function bias multicolvar symfunc clusters
19.030	Coarse-Grained MetaDynamics (CG-MetaD)	bio	Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy	Vittorio Limongelli	WHOLEMOLECULES DISTANCE PRINT UPPER_WALLS LOWER_WALLS COM METAD	colvar generic vatom bias
19.017	Ligand binding pathways exploration	bio	metadynamics, ligand binding	Riccardo Capelli	HISTOGRAM WRAPAROUND CONVERT_TO_FES WHOLEMOLECULES ENDPLUMED COORDINATION PRINT UPPER_WALLS POSITION FLUSH FIT_TO_TEMPLATE GROUP COM MATHEVAL DUMPGRID METAD READ REWEIGHT_METAD	colvar generic vatom gridtools function bias core
19.011	Automatic Gradient Computation for Collective Variables	other	gradient, differentiation, curvature	Toni Giorgino	ENDPLUMED	generic
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	UPPER_WALLS GROUP OPES_METAD_EXPLORE COORDINATION WHOLEMOLECULES FIXEDATOM PRINT ANGLE DISTANCE MATHEVAL CENTER FIT_TO_TEMPLATE ENERGY	core bias generic vatom opes colvar function
25.018	Metainference simulation for dimerization of RNA binding protein	bio	Metainference, Metadynamics, SAXS, protein dimer	Debadutta Patra	UPPER_WALLS STATS MOLINFO SAXS TORSION PBMETAD WHOLEMOLECULES PRINT DISTANCE ENSEMBLE CENTER GYRATION FLUSH METAINFERENCE	generic bias vatom isdb colvar function
25.016	Advancing in silico drug design with Bayesian refinement of AlphaFold models	bio	bAIes, AlphaFold, Bayesian refinement, virtual screening, docking, small-molecule, enrichment	Samiran Sen	BAIES PRINT GROUP BIASVALUE	isdb bias core generic
25.007	Shaping the glycan landscape. Hidden relationships between linkage and ring distortion induced by carbohydrate-active enzmyes	bio	REST-RECT, REST2, glycan, enzyme, CAZyme, steered	Isabell Grothaus	MOLINFO PUCKERING RESTART MOVINGRESTRAINT PRINT RESTRAINT DISTANCE METAD TORSION	bias setup colvar generic
25.000	Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer	bio	metadynamics, pathCV	Sahithya Sridharan Iyer	UPPER_WALLS MOLINFO RESTART GROUP WHOLEMOLECULES COM PRINT DISTANCE METAD FUNCPATHGENERAL	core generic bias vatom colvar function setup
24.024	Host-Guest binding free energies à la carte, an automated OneOPES protocol	bio	OneOPES, ligand binding, binding free energy,SAMPL challenge, host-guest	Valerio Rizzi	UPPER_WALLS ENERGY GROUP OPES_EXPANDED OPES_METAD_EXPLORE COORDINATION ECV_MULTITHERMAL WHOLEMOLECULES FIXEDATOM PRINT ENDPLUMED ANGLE DISTANCE MATHEVAL FIT_TO_TEMPLATE TORSION LOWER_WALLS CENTER	core bias generic vatom opes colvar function
24.008	yCD Metadynamics	bio	volume-based MetaD, path CVs, infrequent MetaD, product release	James McCarty	HISTOGRAM COMMITTOR COORDINATION FIT_TO_TEMPLATE WHOLEMOLECULES FIXEDATOM ENDPLUMED DISTANCE CONVERT_TO_FES UPPER_WALLS DUMPGRID CONTACTMAP COM METAD FLUSH MOLINFO INCLUDE REWEIGHT_METAD MATHEVAL GROUP WRAPAROUND RMSD PRINT PATH READ	core bias generic mapping vatom colvar function gridtools
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	UPPER_WALLS CUSTOM COMMITTOR UNITS OPES_METAD PRINT COMBINE DISTANCE TORSION LOWER_WALLS FLUSH	generic bias opes colvar function setup
24.000	Ammonia Decomposition on Non-stoichiometric Lithium Imide	chemistry	ammonia decomposition, non-stoichiometric lithium imide, machine learning interatomic potentials, enhanced sampling, heterogeneous catalysis	Francesco Mambretti	UPPER_WALLS GROUP UNITS ZDISTANCES OPES_METAD FIXEDATOM PRINT COORDINATIONNUMBER DISTANCE FLUSH	core bias generic vatom opes symfunc colvar multicolvar setup
23.010	An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G‑Protein-Coupled Receptor Ligands	bio	GPCR, binding free energy, free energy surface	Timothy Clark	UPPER_WALLS CONSTANT WHOLEMOLECULES PRINT DISTANCE MATHEVAL METAD LOWER_WALLS BIASVALUE	generic colvar function bias
23.008	PBMetaD simulations of Histatin5	bio	metadynamics, IDP, Rg, PPII	Francesco Pesce	MOLINFO GROUP GYRATION WHOLEMOLECULES PRINT TORSION PBMETAD	bias core colvar generic
22.041	Skipping the Replica Exchange Ladder with Normalizing Flows	methods	OPES, alanine, normalizing flows, replica exchange	Michele Invernizzi	POSITION OPES_EXPANDED UNITS ECV_MULTITHERMAL OPES_METAD PRINT ENDPLUMED TORSION ENERGY	opes colvar generic setup
22.039	Driving and characterizing nucleation of urea and glycine polymorphs in water	bio	metadynamics, nucleation, amino acids, polymorphism	Eric Beyerle	PAIRENTROPY GROUP Q6 INCLUDE Q4 PRINT COORDINATIONNUMBER COMBINE LOAD MATHEVAL METAD CENTER	core generic bias vatom symfunc function gridtools setup
22.027	Molecular Dynamics simulations of BANAL-236 RBD-hACE2 complexes	bio	SARS-CoV-2, COVID-19, MD, human-ACE2, spike, BANAL-236, receptor-binding domain	Max Bonomi	RMSD PRINT	colvar generic
22.025	Bubble nucleation rate predictions in a Lennard-Jones fluid	materials	free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation	Kristof Bal	UPPER_WALLS CUSTOM DUMPGRID VOLUME REWEIGHT_BIAS HISTOGRAM COMMITTOR UNITS MOVINGRESTRAINT ANN PRINT COORDINATIONNUMBER RESTRAINT LOAD CONVERT_TO_FES FLUSH BIASVALUE	bias generic annfunc colvar function gridtools symfunc setup
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	UPPER_WALLS XANGLES MOLINFO CUSTOM ZANGLES YANGLES ALPHABETA WHOLEMOLECULES COM PRINT COMBINE DISTANCE MATHEVAL METAD TORSION LOWER_WALLS	generic bias vatom colvar function multicolvar
21.044	NaCl nucleation	chemistry	metadynamics, DFS clustering	Aaron Finney	LOCAL_Q6 MFILTER_MORE GROUP DUMPGRID HISTOGRAM Q6 CONTACT_MATRIX CLUSTER_DISTRIBUTION DFSCLUSTERING CLUSTER_NATOMS FIXEDATOM PRINT COORDINATIONNUMBER COMBINE INSPHERE METAD	core generic bias vatom clusters symfunc function gridtools adjmat volumes multicolvar
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 MOLINFO COM PRINT DISTANCE GYRATION LOWER_WALLS ENERGY PBMETAD	vatom generic colvar bias
21.014	how to determine statistically accurate conformational ensembles	bio	metadynamics, metainference, errors, cv, SAXS, ensemble determination	Cristina Paissoni	ANTIBETARMSD TORSION MOLINFO STATS SAXS ALPHABETA BIASVALUE WHOLEMOLECULES CONTACTMAP PRINT ENSEMBLE METAD GYRATION CENTER PBMETAD	generic bias vatom isdb colvar function multicolvar secondarystructure
21.012	NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition	bio	funnel metadynamics	Jim Pfaendtner	UPPER_WALLS FUNNEL_PS COM FUNNEL PRINT DISTANCE METAD LOWER_WALLS	generic bias vatom colvar funnel
20.031	Soft fluorescent nanoshuttles targeting receptors	chemistry	polymers, receptors, nanoparticles, fluorescent probes	Adriana Pietropaolo	COORDINATION WHOLEMOLECULES PRINT CENTER PBMETAD	vatom bias colvar generic
20.030	Converging experimental and computational views of the knotting mechanism of the smallest knotted protein	bio	phi-values, transition state, knotted proteins	Cristina Paissoni	STATS MOLINFO COORDINATION WHOLEMOLECULES PRINT RESTRAINT COMBINE	bias colvar function generic
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 INCLUDE PRINT LOAD METAD VOLUME CENTER	core generic bias vatom colvar setup
20.005	Muscarinic M2 receptor/ligand Frequency-Adaptive Metadynamics and QM/MM calculations	bio	Frequency-adaptive metadynamics, multiple-walkers metadynamics, well-tempered metadynamics, GPCR, receptor, Adiabatic Bias MD	Riccardo Capelli	HISTOGRAM WHOLEMOLECULES ENDPLUMED DISTANCE CONVERT_TO_FES UPPER_WALLS DUMPGRID CONTACTMAP COM METAD FLUSH MOLINFO REWEIGHT_METAD COMBINE LOWER_WALLS FUNCPATHMSD PRINT READ ABMD	bias generic vatom colvar function gridtools
19.074	Asymmetric base pair opening in nucleic acids	bio	double helix, DNA, RNA, unwindability	Giovanni Bussi	COORDINATION WHOLEMOLECULES ENDPLUMED RESTRAINT DISTANCE LOWER_WALLS	bias colvar generic
19.070	Unexpected Dynamics in the UUCG RNA Tetraloop	bio	well-tempered metadynamics, RNA, UUCG, maximum entropy	Sandro Bottaro	ERMSD MOLINFO WHOLEMOLECULES RMSD PRINT DISTANCE METAD TORSION	bias colvar generic
19.069	Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen	materials	ibuprofen, crystal, solvent, surface	Matteo Salvalaglio	GROUP INCLUDE PRINT ENDPLUMED DISTANCE CENTER	vatom core colvar generic
19.064	Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations	materials	metadynamics, peptide-surface binding	Jim Pfaendtner	UPPER_WALLS MOLINFO COM PRINT DISTANCE METAD GYRATION ENERGY	vatom generic colvar bias
19.053	Capillary fluctuations with PLUMED	methods	nucleation, surface tension, capillary fluctuations	Gareth Tribello	MULTICOLVARDENS DUMPGRID MORE_THAN GROUP UNITS FIND_CONTOUR_SURFACE FOURIER_TRANSFORM FCCUBIC CENTER	core vatom symfunc function gridtools fourier contour setup
19.050	Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes	chemistry	metadynamics, membranes, Willard Chandler surface	Gareth Tribello	UPPER_WALLS DUMPGRID RESTART REWEIGHT_BIAS HISTOGRAM PRINT COMBINE DISTANCE_FROM_CONTOUR METAD CONVERT_TO_FES READ	bias generic function gridtools contour setup
19.040	Optimal Metric for Path Collective Variables	bio	metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path	Francesco Luigi Gervasio	MATHEVAL PRINT ENDPLUMED METAD TORSION	bias colvar function generic
19.039	Funnel Metadynamics	bio	funnel-metadynamics, absolute binding free energy, ligand-receptor complexes	Vittorio Limongelli	UPPER_WALLS FUNNEL_PS WHOLEMOLECULES RMSD COM FUNNEL PRINT DISTANCE METAD LOWER_WALLS	generic bias vatom colvar funnel
19.037	Scission free energy of organic dyes	chemistry	metadynamics, multiple walkers, matheval/lepton	Paolo Raiteri	UPPER_WALLS RESTART UNITS PRINT DISTANCE MATHEVAL METAD FLUSH	generic bias colvar function setup
19.028	pRAVE	methods	RAVE, reaction coordinate, deep learning, metadynamics, kinetics	Pratyush Tiwary	RESTART EXTERNAL COMMITTOR ALPHABETA WHOLEMOLECULES COM PRINT COMBINE DISTANCE TORSION	generic bias vatom colvar function multicolvar setup
19.025	Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide	bio	metainference, NMR, protein dynamics, force-fields	Carlo Camilloni	STATS TORSION MOLINFO PBMETAD BIASVALUE WHOLEMOLECULES JCOUPLING RDC PRINT ENDPLUMED ENSEMBLE CS2BACKBONE GYRATION FLUSH METAINFERENCE	bias generic isdb colvar function
19.018	Excited state FEP/Metadynamics simulations	chemistry	metadynamics, FEP, excited states, conjugated polymers, torsional potential	Adriana Pietropaolo	CONSTANT WHOLEMOLECULES MATHEVAL PRINT METAD TORSION BIASVALUE	bias colvar function generic
19.009	RNA tetraloops folding	bio	metadynamics, RNA, folding	Giovanni Bussi	ERMSD MOLINFO WHOLEMOLECULES RMSD PRINT ENDPLUMED METAD	bias colvar generic
26.004	Resolving the ambiguous binding site of quercetin at the calcineurin subunit junction using funnel metadynamics with deep learning collective variables	bio	metadynamics, funnel metadynamics, DeepTICA	Jason Loo	PYTORCH_MODEL GROUP LOWER_WALLS COORDINATION FUNNEL METAD ENERGY WRAPAROUND UPPER_WALLS COM RMSD WHOLEMOLECULES FUNNEL_PS MATHEVAL PRINT DISTANCE	generic colvar core funnel function pytorch vatom bias
25.024	Sampling glycan-glycan interactions for B22 calculations	bio	B22, glycan, carbohydrates, distance, REST2, metadynamics, RECT, replica exchange	Isabell Louise Grothaus	COMBINE METAD RESTRAINT POSITION COM PRINT DISTANCE	generic colvar function vatom bias
25.020	Revealing Water-Mediated Activation Mechanisms in the Beta 1-Adrenergic Receptor via OneOPES-Enhanced Free Energy Landscapes	bio	OneOPES, GPCR, ADRB1, activation, microswitches, conformational changes, allostery	Valerio Rizzi	OPES_METAD_EXPLORE GROUP LOWER_WALLS COORDINATION OPES_EXPANDED CENTER ECV_MULTITHERMAL CUSTOM ENERGY PATHMSD DISTANCES GHOST UPPER_WALLS RMSD PRINT DISTANCE	opes generic colvar core multicolvar function vatom bias
25.015	Assessment of Force Fields for Describing Conformational Polymorphic Crystals of ROY	materials	Molecular crystal, Force Field, Collective Variable	Pradip Si and Omar Valsson	TORSIONS DUMPMULTICOLVAR DISTANCES PRINT SMAC	symfunc generic multicolvar
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	GROUP COORDINATION ANGLE HISTOGRAM DUMPGRID TORSION CONVERT_TO_FES WHOLEMOLECULES PRINT DISTANCE	core gridtools generic colvar
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	OPES_METAD_EXPLORE GROUP COORDINATION OPES_EXPANDED COMBINE RESTART ECV_MULTITHERMAL CUSTOM ENERGY TORSION PRINT DISTANCE	opes generic colvar core setup function
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	COORDINATION COMBINE METAD MOLINFO BIASVALUE GHBFIX ERMSD WHOLEMOLECULES PRINT	generic function bias colvar
23.023	Rational design of novel biomimetic sequence-defined polymers for mineralization applications	methods	metadynamics, surface binding, biomimetic mineralization	Kaylyn Torkelson	COORDINATION GYRATION PBMETAD UPPER_WALLS COM PRINT DISTANCE	vatom bias generic colvar
22.045	Binding mode and mechanism of enzymatic polyethylene terephthalate degradation	bio	metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation	Francesco Colizzi	LOWER_WALLS ANGLE MOVINGRESTRAINT METAD UPPER_WALLS COM WHOLEMOLECULES PRINT DISTANCE	vatom bias generic colvar
22.024	Conformational Entropy as a Potential Liability of Computationally Designed Antibodies	bio	metadynamics, conformational entropy, antibody, nanobody	Thomas Löhr	ANTIBETARMSD WHOLEMOLECULES ALPHARMSD RESTART MOLINFO PBMETAD TORSION COM ALPHABETA PRINT	generic secondarystructure colvar setup multicolvar vatom bias
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	GROUP COORDINATION RESTART MOLINFO EMMI BIASVALUE PBMETAD TORSION UPPER_WALLS COM RMSD WHOLEMOLECULES PRINT	isdb generic colvar core setup vatom bias
22.021	Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations	chemistry	Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella	Sigbjørn Løland Bore	INCLUDE LOWER_WALLS OPES_EXPANDED ECV_UMBRELLAS_LINE UPPER_WALLS ENVIRONMENTSIMILARITY PRINT	opes bias generic envsim
22.018	Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations	bio	ligand binding, docking, EMMI, LAT1	Max Bonomi	GROUP MOLINFO EMMIVOX BIASVALUE WHOLEMOLECULES PRINT LOAD	isdb generic core setup bias
22.012	Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT	bio	contact maps, protein-protein interactions	Isabell-Louise Grothaus	CONTACTMAP CENTER PRINT DISTANCE	vatom generic 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	COORDINATION LOWER_WALLS COMBINE UNITS GYRATION METAD COORDINATIONNUMBER UPPER_WALLS COM FLUSH DISTANCE	generic colvar setup symfunc function vatom bias
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	COORDINATION WHOLEMOLECULES ANGLE ALPHARMSD MOLINFO METAD TORSION UPPER_WALLS FLUSH ALPHABETA PRINT DISTANCE	generic secondarystructure colvar multicolvar bias
22.000	Amyloid precursor protein processing by human γ-secretase	bio	Bias Exchange Metadynamics, Helix unfolding, coupled binding	Xiaoli Lu	INCLUDE ANTIBETARMSD COORDINATION RANDOM_EXCHANGES ALPHARMSD CENTER UNITS MOLINFO METAD CONTACTMAP PRINT DISTANCE	generic secondarystructure colvar setup vatom bias
21.019	Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations	materials	Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen	Matteo Salvalaglio	TORSIONS KDE COM MATHEVAL PRINT DISTANCE	generic gridtools colvar multicolvar function vatom
21.015	Coarse-grained metadynamics and umbrella sampling simulations to investigate interactions of carbohydrate-binding modules with chitin	bio	metadynamics, umbrella sampling, coarse-grained, MARTINI, chitin, carbohydrate-binding module	Gaston Courtade	COORDINATION MATHEVAL CENTER RESTART METAD RESTRAINT POSITION WHOLEMOLECULES REWEIGHT_BIAS PRINT	generic colvar setup function vatom bias
21.002	Phase equilibrium of water with hexagonal and cubic ice using the SCAN functional	materials	ice, water, SCAN, OPES, VES, multithermal, crystallization, environment similarity, refcv, reweighting	Pablo Piaggi	OPES_EXPANDED TD_UNIFORM MATHEVAL OPT_AVERAGED_SGD VES_LINEAR_EXPANSION RESTART ENERGY Q6 ECV_UMBRELLAS_LINE ECV_MULTITHERMAL_MULTIBARIC UPPER_WALLS VOLUME ENVIRONMENTSIMILARITY PRINT BF_LEGENDRE	opes generic colvar setup envsim symfunc function ves bias
20.025	The role of water in host-guest interaction	bio	ligand binding, water, opes, SAMPL5	Valerio Rizzi	PYTORCH_MODEL GROUP COORDINATION ANGLE CENTER FIXEDATOM ENERGY ENDPLUMED OPES_METAD FIT_TO_TEMPLATE UPPER_WALLS WHOLEMOLECULES MATHEVAL PRINT DISTANCE	opes generic colvar core function pytorch vatom bias
20.020	Parallel Bias Metadynamics	methods	pbmetad, trp-cage, folding	Max Bonomi	INCLUDE COORDINATION WHOLEMOLECULES MOLINFO GYRATION PBMETAD ALPHABETA DIHCOR PRINT	bias generic multicolvar colvar
20.012	Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies	bio	metadynamics, well-tempered ensemble, ligand binding, binding affinity calculations, novel COLVAR, funnel restraints, Hamiltonian replica-exchange, PathCV, COMetPath, SWISH	Francesco Gervasio	INCLUDE GROUP LOWER_WALLS MATHEVAL PROJECTION_ON_AXIS METAD MOLINFO CONTACTMAP BIASVALUE CONSTANT UPPER_WALLS COM DISTANCE WHOLEMOLECULES PRINT LOAD FUNCPATHGENERAL	generic colvar core setup function vatom bias
20.009	The dynamics of linear polyubiquitin	bio	saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics	Carlo Camilloni	ENSEMBLE WHOLEMOLECULES CENTER MOLINFO GYRATION METAINFERENCE PBMETAD TORSION FLUSH ALPHABETA STATS PRINT SAXS DISTANCE	isdb generic colvar multicolvar function vatom 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	COORDINATION UNITS METAD CUSTOM DISTANCES PRINT	generic colvar setup multicolvar function bias
19.066	Finding ligand unbinding reaction pathways	methods	maze, ligand unbinding	Jakub Rydzewski	MAZE_OPTIMIZER_BIAS UNITS POSITION MAZE_LOSS MAZE_SIMULATED_ANNEALING PRINT	setup maze generic colvar
19.060	Neural networks-based variationally enhanced sampling	methods	ves, neural networks	Luigi Bonati	UNITS POSITION ENERGY ENDPLUMED TORSION Q6 ENVIRONMENTSIMILARITY PRINT LOAD	generic colvar setup envsim symfunc
19.054	MetaFEP	methods	metadynamics, chemistry, free energy perturbation	GiovanniMaria Piccini	LOWER_WALLS COMBINE UNITS METAD ENERGY UPPER_WALLS FLUSH PRINT DISTANCE	generic colvar setup function bias
19.022	eABF simulation of NANMA (alanine dipeptide)	methods	eABF, DRR, alanine dipeptide	Haochuan Chen	DRR TORSION PRINT	drr generic colvar
19.019	FA-MetaD-JCP-Wang-et-al	bio	Frequency adaptive metadynamics; peptide	Kresten Lindorff-Larsen	COMBINE METAD MOLINFO COMMITTOR FLUSH ALPHABETA PRINT	generic function bias multicolvar
19.015	Ibuprofen conformational dynamics and thermodynamics surface	materials	Ibuprofen, crystal, surface, solvents, conformers, metadynamics	Matteo Salvalaglio	LOWER_WALLS CENTER METAD COMMITTOR TORSION UPPER_WALLS PRINT DISTANCE	vatom bias generic colvar

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