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
25.030	Committor Regularization	methods	metadynamics, enhanced sampling, mlcvs, committor, machine learning	Florian Dietrich	METAD MOVINGRESTRAINT UNITS PRINT	bias generic setup
25.021	All You Need Is Water. Converging Ligand Binding Simulations with Hydration Collective Variables	bio	OPES Explore, ligand binding, binding free energy, water, hydration CVs, SAMPL challenge, host-guest	Valerio Rizzi	OPES_METAD_EXPLORE UPPER_WALLS ENERGY MATHEVAL GROUP COORDINATION FIXEDATOM FIT_TO_TEMPLATE DISTANCE CENTER WHOLEMOLECULES ANGLE PRINT	colvar vatom bias core function generic opes
25.003	Surrogate Model CV	methods	Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding	Sompriya Chatterjee	TORSION CUSTOM WHOLEMOLECULES ENERGY OPES_METAD MATHEVAL GROUP MOLINFO ENDPLUMED DISTANCE COMMITTOR PYTORCH_MODEL COMBINE PRINT	colvar core function generic opes pytorch
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 ANTIBETARMSD ALPHARMSD PBMETAD FLUSH GROUP DIHCOR MOLINFO COORDINATION ENDPLUMED DISTANCE INCLUDE WHOLEMOLECULES COMBINE PARABETARMSD PRINT GYRATION	colvar multicolvar bias secondarystructure core function 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	TORSION CUSTOM LOWER_WALLS UPPER_WALLS OPES_METAD GROUP COORDINATION FIXEDATOM PATH FIT_TO_TEMPLATE DISTANCE RESTART CENTER WHOLEMOLECULES PYTORCH_MODEL PRINT	colvar vatom bias setup core mapping function generic opes pytorch
24.016	Cryo-EM guided simulations of ribozyme	bio	metainference, cryo-EM	Giovanni Bussi	GROUP BIASVALUE MOLINFO EMMIVOX RESTRAINT INCLUDE ERMSD WHOLEMOLECULES PRINT	colvar bias core generic isdb
24.010	Oxytocin metadynamics simulation	bio	metadynamics, oxytocin, peptide	Jan Beránek	TORSION FLUSH RESTART METAD WHOLEMOLECULES PRINT	colvar bias generic setup
24.009	Weighted Shape Gaussian Mixture Models	bio	metadynamics, clustering	Glen Hocky	TORSION GROUP UNITS METAD PRINT	colvar bias core generic setup
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	CUSTOM TORSION LOWER_WALLS UPPER_WALLS OPES_METAD FLUSH DISTANCE UNITS COMMITTOR COMBINE PRINT	colvar setup bias function generic opes
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	LOWER_WALLS UPPER_WALLS MATHEVAL BIASVALUE CONSTANT DISTANCE CENTER METAD WHOLEMOLECULES PRINT	colvar vatom bias function generic
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	OPES_METAD POSITION FIT_TO_TEMPLATE PRINT MATHEVAL CUSTOM TORSION OPES_METAD_EXPLORE FLUSH COM ENDPLUMED DISTANCE COMMITTOR LOWER_WALLS UPPER_WALLS ENERGY GROUP BIASVALUE WRAPAROUND COORDINATION MOLINFO UNITS CENTER WHOLEMOLECULES	colvar vatom bias setup core function generic opes
23.025	Probing ion binding to G-quadruplexes and related events	chemistry	metadynamics, repulsive potential, nucleic acids, G-quadruplexes	Marcelo Poleto	LOWER_WALLS UPPER_WALLS DUMPATOMS MATHEVAL GROUP FLUSH POSITION WRAPAROUND COM FIT_TO_TEMPLATE DISTANCE UNITS RESTART METAD WHOLEMOLECULES DISTANCES PRINT	colvar multicolvar vatom bias core function generic setup
23.014	Structural basis of dimerization of chemokine receptors CCR5 and CXCR4	bio	metadynamics, oligomerization, chemokine receptors, GPCR, membrane	Vittorio Limongelli	TORSION UPPER_WALLS FLUSH COM DISTANCE METAD WHOLEMOLECULES COMBINE PRINT	colvar vatom bias function generic
23.005	A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs	bio	metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A	Timothy Clark	DUMPGRID MATHEVAL MOLINFO CONVERT_TO_FES HISTOGRAM DISTANCE RMSD REWEIGHT_METAD METAD WHOLEMOLECULES READ PRINT	colvar bias gridtools function generic
23.001	Quantum phase diagram of water	chemistry	Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella	Sigbjørn-Løland Bore	LOWER_WALLS ENVIRONMENTSIMILARITY UPPER_WALLS ECV_UMBRELLAS_LINE OPES_EXPANDED INCLUDE RESTART PRINT	bias opes envsim generic setup
22.036	Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction	bio	Well-tempered MetaDynamics with Hamiltonian Replica Exchange	Miroslav Krepl	CUSTOM UPPER_WALLS FLUSH GROUP BIASVALUE MOLINFO COORDINATION LOAD GHBFIX METAD COMBINE PRINT	colvar bias core function generic setup
22.016	Homogeneous ice nucleation in an ab initio machine learning model of water	chemistry	ice, water, nucleation, seeding, environment similarity, interfacial free energy, interfaces	Pablo Piaggi	CUSTOM ENVIRONMENTSIMILARITY UPPER_WALLS ENERGY OPES_METAD DUMPGRID HISTOGRAM AROUND RESTART VOLUME PRINT	colvar volumes setup bias gridtools envsim function generic opes
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_CUBIC_B_SPLINES POSITION OPT_AVERAGED_SGD BF_GAUSSIANS TD_WELLTEMPERED PRINT BF_LEGENDRE VES_OUTPUT_BASISFUNCTIONS BF_WAVELETS VES_LINEAR_EXPANSION BF_CHEBYSHEV FLUSH DISTANCE INCLUDE METAD UPPER_WALLS ENERGY COORDINATION TD_UNIFORM OPT_ADAM UNITS	colvar ves 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	CUSTOM TORSION LOWER_WALLS UPPER_WALLS COM DISTANCE UNITS METAD PRINT	colvar vatom bias function generic setup
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	LOWER_WALLS UPPER_WALLS COORDINATIONNUMBER COORDINATION DISTANCE METAD COMBINE PRINT	colvar symfunc bias function generic
21.039	Deep learning the slow modes for rare events sampling	methods	collective variables, machine learning, slow modes, deep-tica, opes	Luigi Bonati	OPES_METAD LOAD OPES_EXPANDED PRINT PYTORCH_MODEL ENVIRONMENTSIMILARITY Q6 VOLUME TORSION CONTACTMAP FLUSH ENDPLUMED DISTANCE RMSD ECV_MULTITHERMAL INCLUDE COMBINE ENERGY GROUP MOLINFO UNITS WHOLEMOLECULES	colvar symfunc opes core envsim function generic setup pytorch
21.038	Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics	materials	metadynamics, SGOOP, nucleation, urea	Ziyue Zou	ENERGY COORDINATIONNUMBER VOLUME GROUP LOAD INCLUDE CENTER METAD COMBINE PRINT	colvar symfunc vatom bias core function generic setup
21.026	Probing allosteric regulations with coevolution-driven molecular simulations	bio	metadynamics, coevolution, allostery, adenylate cyclase	Francesco Colizzi	PATHMSD UPPER_WALLS COM DISTANCE UNITS METAD WHOLEMOLECULES PRINT	colvar vatom bias generic setup
21.013	Role of vibrational excitation in heterogeneous catalysis	chemistry	catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption	Kristof Bal	REWEIGHT_BIAS EXTERNAL ANGLES LOAD OPT_AVERAGED_SGD DISTANCES PRINT DUMPGRID COORDINATIONNUMBER REWEIGHT_METAD VES_LINEAR_EXPANSION BF_CHEBYSHEV FLUSH DISTANCE UWALLS METAD COMBINE LOWER_WALLS UPPER_WALLS CONVERT_TO_FES COORDINATION HISTOGRAM TD_GRID RESTRAINT UNITS	multicolvar colvar symfunc ves bias gridtools function generic 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	GROUP COM DISTANCE WHOLEMOLECULES PRINT	colvar core vatom generic
19.063	Protein-ligand binding through metadynamics with path CVs	bio	metadynamics, path CVs, ligand binding	Mattia Bernetti	LOWER_WALLS PATHMSD UPPER_WALLS METAD WHOLEMOLECULES PRINT	colvar bias generic
19.060	Neural networks-based variationally enhanced sampling	methods	ves, neural networks	Luigi Bonati	TORSION ENVIRONMENTSIMILARITY ENERGY POSITION Q6 LOAD ENDPLUMED UNITS PRINT	colvar symfunc envsim generic setup
19.049	Determining the sizes of solid/liquid clusters in MD trajectories of nucleation	methods	nucleation, metadynamics, clustering, Steinhardt order parameters	Gareth Tribello	CUSTOM CLUSTER_DISTRIBUTION DFSCLUSTERING COORDINATIONNUMBER CLUSTER_NATOMS MATRIX_VECTOR_PRODUCT Q6 METAD CLUSTER_PROPERTIES CONTACT_MATRIX ONES LOCAL_Q6 OUTER_PRODUCT SMAC OUTPUT_CLUSTER DISTANCES MORE_THAN PRINT	multicolvar clusters generic bias matrixtools adjmat function symfunc
19.048	Understanding Ligand Binding Selectivity in a Prototypical GPCR Family	bio	metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding	Francesco Gervasio	LOWER_WALLS UPPER_WALLS MATHEVAL BIASVALUE CONSTANT COM DISTANCE METAD WHOLEMOLECULES PRINT	colvar vatom bias function generic
19.038	native state dynamics of human and mouse b2m	bio	metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation	Carlo Camilloni	ANTIBETARMSD LOWER_WALLS UPPER_WALLS PBMETAD FLUSH GROUP BIASVALUE MOLINFO ALPHABETA ENDPLUMED CS2BACKBONE RESTART WHOLEMOLECULES PRINT	multicolvar bias secondarystructure core generic isdb setup
19.026	Ice Nucleation on Cholesterol Crystals	materials	forward flux sampling, crystal nucleation, water, ice, organic crystals	Gabriele Cesare Sosso	DFSCLUSTERING CLUSTER_NATOMS FLUSH CLUSTER_WITHSURFACE Q6 MFILTER_MORE ENDPLUMED LOCAL_Q6 COMMITTOR OUTPUT_CLUSTER CONTACT_MATRIX	multicolvar clusters generic adjmat symfunc
19.019	FA-MetaD-JCP-Wang-et-al	bio	Frequency adaptive metadynamics; peptide	Kresten Lindorff-Larsen	FLUSH MOLINFO ALPHABETA METAD COMMITTOR COMBINE PRINT	multicolvar bias generic function
19.017	Ligand binding pathways exploration	bio	metadynamics, ligand binding	Riccardo Capelli	UPPER_WALLS DUMPGRID FLUSH GROUP MATHEVAL POSITION WRAPAROUND COORDINATION CONVERT_TO_FES COM HISTOGRAM FIT_TO_TEMPLATE ENDPLUMED REWEIGHT_METAD METAD WHOLEMOLECULES READ PRINT	colvar vatom bias core gridtools function generic
19.013	RNA FF FITTING	methods	force field, RNA	Giovanni Bussi	TORSION MATHEVAL BIASVALUE CONSTANT MOLINFO PUCKERING INCLUDE	colvar bias generic function
19.007	EMMI Microtubules	bio	metainference, cryo-EM	Max Bonomi	GROUP BIASVALUE MOLINFO WHOLEMOLECULES EMMI PRINT	core bias generic isdb
19.002	EMMI STRA6	bio	metainference, cryo-EM	Max Bonomi	GROUP BIASVALUE MOLINFO EMMI PRINT	core bias generic isdb
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	UPPER_WALLS METAD COM PRINT REWEIGHT_BIAS DUMPGRID CONVERT_TO_FES MOLINFO LOWER_WALLS FIXEDATOM WHOLEMOLECULES DISTANCE HISTOGRAM	vatom gridtools colvar generic bias
25.024	Sampling glycan-glycan interactions for B22 calculations	bio	B22, glycan, carbohydrates, distance, REST2, metadynamics, RECT, replica exchange	Isabell Louise Grothaus	METAD POSITION COM PRINT COMBINE RESTRAINT DISTANCE	vatom function colvar generic bias
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	CENTER OPES_METAD_EXPLORE PRINT COMBINE ECV_MULTITHERMAL RMSD MOLINFO GHOST CUSTOM GROUP COORDINATION DISTANCE ENERGY OPES_EXPANDED	core function colvar generic vatom opes
25.017	Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity	bio	EMMIVox, cryo-EM, allostery, decamer, filament, ensemble refinement, glutamine synthetase	Samuel Hoff	PRINT EMMIVOX MOLINFO WHOLEMOLECULES GROUP BIASVALUE	core bias isdb generic
25.009	Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water	chemistry	metadynamics, nitrate photolysis	Kam-Tung Chan	UPPER_WALLS METAD COORDINATION PRINT RESTART DUMPGRID FLUSH REWEIGHT_METAD CUSTOM GROUP HISTOGRAM DISTANCE READ	core function gridtools setup colvar generic bias
24.030	NMR guided simulation of dsRBD	bio	Metainference, NMR, protein dynamics	Debadutta Patra	STATS ALPHABETA PRINT RDC ENSEMBLE MOLINFO FLUSH WHOLEMOLECULES GROUP DISTANCE METAINFERENCE	core function colvar generic multicolvar isdb
24.012	Molecular simulations to investigate the impact of N6-methylation in RNA recognition	bio	metadynamics, alchemistry, RNA modification, RNA:protein interactions	Giovanni Bussi	CENTER UPPER_WALLS METAD COM PRINT COMBINE GHBFIX MOLINFO LOWER_WALLS GROUP COORDINATION DISTANCE DEBUG BIASVALUE	core function colvar bias generic vatom
24.008	yCD Metadynamics	bio	volume-based MetaD, path CVs, infrequent MetaD, product release	James McCarty	UPPER_WALLS MATHEVAL CONVERT_TO_FES WHOLEMOLECULES ENDPLUMED COORDINATION HISTOGRAM PRINT CONTACTMAP FIXEDATOM FLUSH FIT_TO_TEMPLATE DISTANCE INCLUDE DUMPGRID RMSD PATH COMMITTOR WRAPAROUND METAD COM MOLINFO REWEIGHT_METAD GROUP READ	mapping vatom core function gridtools colvar 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	UPPER_WALLS PRINT ZDISTANCES FIXEDATOM FLUSH COORDINATIONNUMBER UNITS GROUP OPES_METAD DISTANCE	vatom core setup colvar bias generic symfunc opes multicolvar
23.033	DNA G-quadruplex and G-hairpin folding with ST-metaD protocol	bio	DNA, G4, GQ, quadruplex, hairpin, folding, metadynamics, REST2, ST-metaD	Pavlína Pokorná	METAD PRINT COMBINE ERMSD GHBFIX MOLINFO WHOLEMOLECULES COORDINATION BIASVALUE	function bias colvar generic
23.028	Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process	chemistry	Ammonia decomposition; Dynamics;OPES; Neural Network potential	Manyi Yang	UPPER_WALLS COM DISTANCES PRINT ZDISTANCES MATHEVAL CUSTOM FIXEDATOM FLUSH LOWER_WALLS COORDINATIONNUMBER UNITS COMMITTOR GROUP OPES_METAD DISTANCE ENERGY	vatom core function setup colvar bias symfunc generic multicolvar opes
23.027	CmuMD simulations of NaCl(aq) at NaCl	chemistry	CmuMD, DFS, Q3, Pair Entropy	Aaron Finney	LOCAL_AVERAGE PRINT Q3 CLUSTER_NATOMS DUMPGRID DFSCLUSTERING RESTRAINT LOAD FIXEDATOM CLUSTER_DISTRIBUTION LOCAL_Q3 UNITS COORDINATIONNUMBER CONTACT_MATRIX GROUP HISTOGRAM DENSITY AROUND	adjmat clusters vatom core gridtools setup bias volumes generic symfunc
23.022	A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar	methods	collective variables, machine learning, toy model	Enrico Trizio	UPPER_WALLS POSITION PRINT LOWER_WALLS PYTORCH_MODEL UNITS ENDPLUMED OPES_METAD CUSTOM BIASVALUE	function setup colvar pytorch generic bias opes
23.008	PBMetaD simulations of Histatin5	bio	metadynamics, IDP, Rg, PPII	Francesco Pesce	PRINT TORSION MOLINFO GYRATION WHOLEMOLECULES PBMETAD GROUP	core bias colvar generic
22.041	Skipping the Replica Exchange Ladder with Normalizing Flows	methods	OPES, alanine, normalizing flows, replica exchange	Michele Invernizzi	POSITION PRINT ECV_MULTITHERMAL TORSION ENDPLUMED UNITS OPES_METAD ENERGY OPES_EXPANDED	setup colvar opes generic
22.038	Enhanced Sampling Aided Design of Molecular Photoswitches	chemistry	reaction discovery, OPES explore, graph CV	Umberto Raucci	OPES_METAD_EXPLORE PRINT PYTORCH_MODEL UNITS COORDINATION CUSTOM	function setup colvar pytorch generic opes
22.024	Conformational Entropy as a Potential Liability of Computationally Designed Antibodies	bio	metadynamics, conformational entropy, antibody, nanobody	Thomas Löhr	ALPHABETA COM PRINT TORSION MOLINFO WHOLEMOLECULES ALPHARMSD PBMETAD RESTART ANTIBETARMSD	secondarystructure vatom setup colvar bias generic 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	UPPER_WALLS PRINT ECV_UMBRELLAS_LINE ENVIRONMENTSIMILARITY LOWER_WALLS INCLUDE OPES_EXPANDED	envsim bias opes generic
22.013	Ligand dissociation from PreQ1 riboswitch	bio	ligand, RNA, metadynamics, pRAVE	Yihang Wang	METAD COM PRINT COMBINE RMSD MOLINFO COMMITTOR WHOLEMOLECULES COORDINATIONNUMBER DISTANCE	vatom function colvar symfunc generic bias
22.005	Collective Variable for Metadynamics Derived from AlphaFold Output	bio	AlphaFold, protein folding, protein structure prediction, metadynamics, deep learning, free energy simulation, collective variable	Vojtech Spiwok	METAD LOAD WHOLEMOLECULES PRINT	setup bias generic
21.051	Automatic learning of hydrogen-bond fixes in an AMBER RNA force field	methods	force field, RNA	Giovanni Bussi	METAD PRINT COMBINE ERMSD MOLINFO WHOLEMOLECULES COORDINATION BIASVALUE	function bias colvar 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	UPPER_WALLS METAD ALPHABETA PRINT LOWER_WALLS GYRATION WHOLEMOLECULES ENDPLUMED GROUP	core colvar generic bias multicolvar
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 PRINT COMBINE VOLUME ENDPLUMED COORDINATION CUSTOM	function bias colvar generic
21.040	A structural ensemble of a tau-microtubule complex reveals regulatory tau phosphorylation and acetylation mechanisms	bio	EMMI, CryoEM, tau-microtubules, post-translational modifications, chemical mutagenesis, structural ensemble, Metainference	Faidon Brotzakis	UPPER_WALLS COM PRINT MOLINFO GROUP WHOLEMOLECULES DISTANCE RESTART EMMI BIASVALUE	core vatom setup colvar generic bias isdb
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 METAD PRINT DIHCOR RANDOM_EXCHANGES ENERGY MOLINFO LOWER_WALLS PARABETARMSD GYRATION WHOLEMOLECULES ALPHARMSD GROUP COORDINATION ANTIBETARMSD	secondarystructure core colvar bias generic multicolvar
21.023	Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling	methods	enhanced sampling, collective variables, machine learning	Jakub Rydzewski	METAD PRINT TORSION REWEIGHT_METAD UNITS CONSTANT ENERGY DISTANCE INCLUDE CUSTOM BIASVALUE	function setup colvar generic bias
21.012	NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition	bio	funnel metadynamics	Jim Pfaendtner	UPPER_WALLS METAD COM PRINT FUNNEL_PS FUNNEL LOWER_WALLS DISTANCE	vatom colvar generic funnel bias
21.005	Crystallization Collective Variable	methods	Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA	Tarak Karmakar	UPPER_WALLS PRINT MATHEVAL LOWER_WALLS FLUSH PYTORCH_MODEL GROUP OPES_METAD LOAD	core function setup pytorch generic bias opes
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 PRINT COMBINE RESTRAINT MOLINFO WHOLEMOLECULES COORDINATION	function bias colvar generic
20.019	Systematic finite-temperature reduction of crystal energy landscapes	materials	crystals, organics, structure prediction	Matteo Salvalaglio	UPPER_WALLS METAD PRINT VOLUME MATHEVAL CELL LOWER_WALLS ENERGY	function bias colvar generic
19.075	PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python	other	Python, automatic differentiation	Toni Giorgino	DUMPDERIVATIVES CENTER PRINT COMBINE TORSION RESTRAINT GROUP ANGLE ENDPLUMED DISTANCE CUSTOM	core function colvar bias generic vatom
19.072	SINE hairpin MD+NMR	bio	metadynamics, RNA, NMR	Giovanni Bussi	METAD COM PRINT MATHEVAL TORSION MOLINFO MAXENT FLUSH SORT WHOLEMOLECULES DISTANCE COORDINATION INCLUDE	vatom function colvar generic bias
19.020	PTMetaD-WTE simulation of the Ntail IDP	bio	metadynamics, IDPs, protein folding	Mattia Bernetti	METAD PRINT MOLINFO GYRATION WHOLEMOLECULES ALPHARMSD ENDPLUMED ENERGY	secondarystructure bias colvar generic
19.003	EMMI ClpP	bio	metainference, cryo-EM	Max Bonomi	PRINT MOLINFO GROUP EMMI BIASVALUE	core bias isdb generic
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 RESTART UPDATE_IF GYRATION PBMETAD WHOLEMOLECULES MOLINFO DUMPATOMS PRINT DISTANCE TORSION READ CENTER ENERGY VOLUME	generic vatom bias colvar setup
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	RESTRAINT FIXEDATOM ANGLE COMBINE LOWER_WALLS COORDINATION UPPER_WALLS PRINT DISTANCE COORDINATIONNUMBER FLUSH DISTANCES UNITS GROUP COM METAD	function generic core vatom bias colvar multicolvar symfunc setup
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 DRR WHOLEMOLECULES MOLINFO RMSD COORDINATION UPPER_WALLS PRINT FLUSH METAD PYTORCH_MODEL	generic bias colvar drr pytorch
24.007	SWISH-X	bio	swish-x, SWISH-X, swish, expanded SWISH	Alberto Borsatto	INCLUDE WHOLEMOLECULES MOLINFO PRINT UPPER_WALLS ENERGY ECV_MULTITHERMAL OPES_EXPANDED CONTACTMAP	generic colvar opes bias
24.004	Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables	materials	metadynamics, nucleation, machine learning	Ziyue Zou	INCLUDE RESTART LOAD PRINT GROUP METAD	generic core bias setup
23.045	Minute-timescale simulations of G Protein Coupled Receptor A2A activation mechanism reveal a receptor pseudo-active state	bio	Path CVs Metadynamics, GPCRs activation transition	Vittorio Limongelli	INCLUDE LOWER_WALLS MOLINFO ALPHARMSD UPPER_WALLS PRINT DISTANCE FUNCPATHMSD PATHMSD METAD CONTACTMAP	function generic bias colvar secondarystructure
23.021	Into the Dynamics of Rotaxanes at Atomistic Resolution	materials	metadynamics, rotaxanes, molecular shuttles, molecular machines	Luigi Leanza	FIXEDATOM UPPER_WALLS PRINT DISTANCE MATHEVAL TORSION CUSTOM CENTER METAD	function generic vatom bias colvar
23.018	Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention	materials	metadynamics, surface binding, peptide adsorption	Kaylyn Torkelson	PBMETAD GYRATION UPPER_WALLS PRINT DISTANCE COM	generic colvar vatom bias
23.007	Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains	bio	metadynamics, peptoids, parallel-bias metadynamics	Jim Pfaendtner	INCLUDE RESTRAINT PBMETAD GYRATION WHOLEMOLECULES COORDINATION PRINT TORSION COM	generic colvar vatom bias
22.044	Colloid Crystallisation Analyses	materials	Q4, Q6, Pair Entropy, DFS	Aaron Finney	MFILTER_MORE COMBINE CONTACT_MATRIX MFILTER_LESS Q4 LOCAL_AVERAGE LOCAL_Q6 CLUSTER_NATOMS COORDINATIONNUMBER PRINT LOCAL_Q4 GROUP Q6 DFSCLUSTERING	function generic core clusters adjmat multicolvar symfunc
22.035	Deciphering the alphabet of disorder — Glu and Asp act differently on local but not global properties	bio	intrinsically disordered proteins, parallel bias metadynamics, protein	Kresten Lindorff-Larsen	PBMETAD GYRATION WHOLEMOLECULES MOLINFO TORSION	generic colvar bias
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 PRINT FLUSH CUSTOM PATHMSD BIASVALUE METAD	function generic bias colvar drr
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	RESTART PBMETAD WHOLEMOLECULES MOLINFO RMSD COORDINATION EMMI UPPER_WALLS PRINT TORSION GROUP COM BIASVALUE	isdb generic core vatom bias colvar setup
22.015	Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome	bio	photodynamics, bacteriophytochrome, variationally enhanced sampling	Jakub Rydzewski	BF_FOURIER PRINT TD_UNIFORM TORSION OPT_AVERAGED_SGD VES_LINEAR_EXPANSION	generic colvar ves
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	FIXEDATOM PRINT TORSION FIT_TO_TEMPLATE METAD	generic colvar vatom bias
21.037	Molecular Dynamics simulations of RBD/hACE2 complexes	bio	SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain	Max Bonomi	RMSD PRINT DISTANCE	generic colvar
21.035	CmuMD simulations of NaCl(aq) at NaCl	chemistry	CmuMD, interface	Aaron Finney	RESTRAINT FIXEDATOM LOAD PRINT DISTANCE GROUP	generic core vatom bias colvar setup
20.020	Parallel Bias Metadynamics	methods	pbmetad, trp-cage, folding	Max Bonomi	INCLUDE ALPHABETA PBMETAD GYRATION DIHCOR WHOLEMOLECULES MOLINFO COORDINATION PRINT	generic colvar multicolvar bias
20.006	Class B GPCR activation mechanism	bio	metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding	Francesco Gervasio	LOWER_WALLS COMBINE WHOLEMOLECULES MOLINFO RMSD UPPER_WALLS PRINT DISTANCE MATHEVAL ENERGY CENTER METAD	function generic vatom bias colvar
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 MATHEVAL TORSION METAD	generic colvar function bias
19.015	Ibuprofen conformational dynamics and thermodynamics surface	materials	Ibuprofen, crystal, surface, solvents, conformers, metadynamics	Matteo Salvalaglio	COMMITTOR LOWER_WALLS UPPER_WALLS PRINT DISTANCE TORSION CENTER METAD	generic colvar 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	PRINT SMAC TORSIONS DISTANCES DUMPMULTICOLVAR	multicolvar generic symfunc
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	ENERGY PRINT INCLUDE COORDINATION DISTANCE UNITS LOAD CUSTOM FLUSH TORSION OPES_METAD CELL POSITION COMBINE MATHEVAL BIASVALUE	colvar bias opes setup function generic
25.000	Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer	bio	metadynamics, pathCV	Sahithya Sridharan Iyer	DISTANCE PRINT MOLINFO METAD WHOLEMOLECULES GROUP FUNCPATHGENERAL UPPER_WALLS RESTART COM	colvar bias vatom setup function generic core
24.029	Combination of OPES and OPES-Explore	methods	OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin	Dhiman Ray	PRINT CONTACTMAP CENTER WHOLEMOLECULES POSITION UPPER_WALLS ENERGY UNITS FLUSH GROUP ENDPLUMED COMBINE OPES_METAD_EXPLORE PYTORCH_MODEL FIXEDATOM LOWER_WALLS COORDINATION CUSTOM MATHEVAL RMSD FIT_TO_TEMPLATE BIASVALUE DISTANCE INCLUDE MOLINFO METAD OPES_METAD	colvar bias opes vatom setup function pytorch generic core
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 COMMITTOR LOAD TORSION METAD GROUP	colvar bias setup generic core
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	DISTANCE PRINT ENERGY RESTRAINT MOLINFO COMMITTOR FLUSH TORSION METAD COORDINATIONNUMBER RESTART MATHEVAL BIASVALUE	colvar bias symfunc setup function generic
23.044	Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition	materials	metadynamics, interlocked molecules	Luigi Leanza	COORDINATION PRINT READ COMMITTOR METAD GROUP ENDPLUMED DUMPGRID CONVERT_TO_FES HISTOGRAM	gridtools colvar bias generic core
23.023	Rational design of novel biomimetic sequence-defined polymers for mineralization applications	methods	metadynamics, surface binding, biomimetic mineralization	Kaylyn Torkelson	DISTANCE PRINT COORDINATION GYRATION UPPER_WALLS PBMETAD COM	generic vatom colvar bias
23.020	FEP simulations of ATOX1 homodimer	chemistry	parallel bias metadynamics, FEP, free-energy of metal ion dissociation	Adriana Pietropaolo	DISTANCE PRINT ANGLE WHOLEMOLECULES MATHEVAL PBMETAD CONSTANT BIASVALUE	generic bias colvar function
23.015	MPCs aggregation	bio	opes_explore, dimerization, MPCs, self-assembly	Vikas Tiwari	DISTANCE PRINT COORDINATION CENTER CUSTOM METAD WHOLEMOLECULES GROUP UPPER_WALLS OPES_METAD_EXPLORE COM LOWER_WALLS	bias colvar opes vatom function generic core
22.030	Mixing physics across temperatures with generative artificial intelligence	methods	REMD, Generative AI, DDPM	Yihang Wang	PRINT TORSION WHOLEMOLECULES	colvar generic
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	DISTANCE PRINT TORSION METAD WHOLEMOLECULES GROUP COM	colvar bias vatom generic core
22.018	Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations	bio	ligand binding, docking, EMMI, LAT1	Max Bonomi	PRINT EMMIVOX MOLINFO LOAD WHOLEMOLECULES GROUP BIASVALUE	bias setup generic core isdb
22.012	Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT	bio	contact maps, protein-protein interactions	Isabell-Louise Grothaus	DISTANCE PRINT CONTACTMAP CENTER	generic vatom colvar
22.003	Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling	methods	opes, metadynamics, reweighting, alanine, muller	Michele Invernizzi	ENERGY PRINT ECV_MULTITHERMAL UNITS CUSTOM TORSION METAD OPES_EXPANDED OPES_METAD ENDPLUMED POSITION UPPER_WALLS OPES_METAD_EXPLORE PBMETAD ECV_UMBRELLAS_FILE BIASVALUE LOWER_WALLS	colvar bias opes setup function generic
21.049	Multiple-path-metadynamics and PathMaps	methods	path-CV, metadynamics, multiple-walker, multiple paths, pathmap	Alberto Pérez-de-Alba-Ortíz	PRINT RESTRAINT UNITS LOAD CUSTOM TORSION METAD MOVINGRESTRAINT UPPER_WALLS ENSEMBLE COMBINE CONSTANT LOWER_WALLS	colvar bias setup function generic
21.047	Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations	materials	pair entropy, metadynamics, ves, solids, crystallization	Pablo Piaggi	ENERGY PRINT BF_LEGENDRE VOLUME OPT_AVERAGED_SGD VES_LINEAR_EXPANSION LOAD TD_WELLTEMPERED METAD COMBINE RESTART PAIRENTROPY	gridtools bias colvar setup function generic ves
21.044	NaCl nucleation	chemistry	metadynamics, DFS clustering	Aaron Finney	INSPHERE PRINT CLUSTER_DISTRIBUTION MFILTER_MORE CONTACT_MATRIX CLUSTER_NATOMS Q6 METAD GROUP COORDINATIONNUMBER COMBINE LOCAL_Q6 DUMPGRID DFSCLUSTERING HISTOGRAM FIXEDATOM	core gridtools bias clusters volumes adjmat vatom symfunc function generic multicolvar
21.042	Peptoid-mediated Au nanocrystal growth	materials	parallel-bias metadynamics, peptoid, Au	Xin Qi	DISTANCE PRINT MOLINFO GYRATION UPPER_WALLS PBMETAD COM	generic vatom colvar bias
21.027	EGFR activating mutations mechanism	bio	metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA	Francesco Gervasio	DISTANCE ENERGY INCLUDE CONTACTMAP PRINT MOLINFO METAD WHOLEMOLECULES UPPER_WALLS MATHEVAL LOWER_WALLS ALPHARMSD	colvar bias secondarystructure function generic
21.014	how to determine statistically accurate conformational ensembles	bio	metadynamics, metainference, errors, cv, SAXS, ensemble determination	Cristina Paissoni	PRINT CONTACTMAP SAXS MOLINFO CENTER STATS TORSION METAD WHOLEMOLECULES GYRATION ANTIBETARMSD ALPHABETA ENSEMBLE PBMETAD BIASVALUE	colvar bias vatom secondarystructure function generic multicolvar isdb
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
21.008	Multi-replica biased sampling for photoisomerization processes in conjugated polymers	methods	metadynamics, FEP, replica-exchange	Adriana Pietropaolo	PRINT TORSION WHOLEMOLECULES RESTART MATHEVAL PBMETAD CONSTANT BIASVALUE	colvar bias setup function generic
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	DISTANCE PRINT TORSION METAD	generic colvar bias
20.009	The dynamics of linear polyubiquitin	bio	saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics	Carlo Camilloni	DISTANCE PRINT SAXS MOLINFO CENTER STATS METAINFERENCE TORSION FLUSH WHOLEMOLECULES GYRATION ALPHABETA ENSEMBLE PBMETAD	colvar bias vatom function generic multicolvar isdb
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 MOLINFO FLUSH ANTIBETARMSD WHOLEMOLECULES GROUP ALPHABETA UPPER_WALLS CS2BACKBONE ENDPLUMED PBMETAD BIASVALUE LOWER_WALLS	core bias secondarystructure generic multicolvar isdb
19.069	Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen	materials	ibuprofen, crystal, solvent, surface	Matteo Salvalaglio	DISTANCE PRINT INCLUDE CENTER GROUP ENDPLUMED	generic vatom colvar core
19.053	Capillary fluctuations with PLUMED	methods	nucleation, surface tension, capillary fluctuations	Gareth Tribello	FIND_CONTOUR_SURFACE MULTICOLVARDENS FOURIER_TRANSFORM UNITS CENTER FCCUBIC GROUP DUMPGRID MORE_THAN	contour gridtools fourier vatom setup function symfunc core
19.050	Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes	chemistry	metadynamics, membranes, Willard Chandler surface	Gareth Tribello	DISTANCE_FROM_CONTOUR READ PRINT METAD UPPER_WALLS COMBINE RESTART DUMPGRID REWEIGHT_BIAS CONVERT_TO_FES HISTOGRAM	contour gridtools bias setup function generic
19.037	Scission free energy of organic dyes	chemistry	metadynamics, multiple walkers, matheval/lepton	Paolo Raiteri	DISTANCE PRINT UNITS FLUSH METAD UPPER_WALLS RESTART MATHEVAL	colvar bias setup function generic
19.036	Thermodynamics and kinetics of G protein-coupled receptor activation	bio	metadynamics, allostery, receptor conformation, GPCR, pharmacology	Davide Provasi	DISTANCE PRINT CONTACTMAP METAD WHOLEMOLECULES ENDPLUMED RMSD COM FUNCPATHMSD	colvar bias vatom function generic
19.018	Excited state FEP/Metadynamics simulations	chemistry	metadynamics, FEP, excited states, conjugated polymers, torsional potential	Adriana Pietropaolo	PRINT TORSION METAD WHOLEMOLECULES MATHEVAL CONSTANT BIASVALUE	colvar generic function bias
19.016	Succinnic acid gamma polymorph	materials	Succinnic acid, conformers, polymorphs, metadynamics	Matteo Salvalaglio	ENERGY PRINT VOLUME TORSION METAD ENDPLUMED CELL UPPER_WALLS COMBINE MATHEVAL LOWER_WALLS	generic colvar function bias
25.023	Molecular simulations of Tau-protein oligomers	bio	metadynamics, proteins, aggregation	Giovanni Bussi	RESTRAINT PRINT METAD RMSD RESTART FLUSH CUSTOM CONTACTMAP	function setup bias colvar generic
25.011	Chiral perovskite nucleation	chemistry	metadynamics, chiral perovskites, nucleation	Adriana Pietropaolo	MULTI_RMSD DISTANCE MATHEVAL UPPER_WALLS LOWER_WALLS PRINT RESTART PBMETAD UNITS	function setup bias colvar 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	DISTANCES FIXEDATOM DISTANCE UPPER_WALLS COORDINATIONNUMBER PRINT FLUSH ZDISTANCES OPES_METAD COMMITTOR CUSTOM UNITS GROUP	function core setup bias colvar opes vatom multicolvar symfunc generic
24.028	All-atom simulations of RNA-membrane interactions	bio	metadynamics, membrane, RNA	Giovanni Bussi	DISTANCE COMBINE DISTANCES SORT PUCKERING MATHEVAL GYRATION POSITION UPPER_WALLS LOWER_WALLS PRINT METAD GHOST WHOLEMOLECULES CENTER MOLINFO GROUP	function core bias colvar vatom multicolvar generic
24.022	Integrating Path Sampling with Enhanced Sampling for Rare-event Kinetics	methods	OPES Flooding, Weighted Ensemble, Metadynamics, Kinetics, Infrequent Metadynamics, Integrated Sampling	Dhiman Ray	FIT_TO_TEMPLATE FIXEDATOM MATHEVAL PRINT OPES_METAD COMMITTOR ANGLE MOLINFO DISTANCE UPPER_WALLS RMSD GROUP COMBINE METAD CUSTOM WHOLEMOLECULES COORDINATION ENDPLUMED CONTACTMAP TORSION CENTER	function core bias colvar opes vatom generic
24.002	Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes	chemistry	metadynamics, ligand design, solvent extraction	Xiaoyu Wang	TORSION PRINT METAD RESTART UNITS	generic setup bias colvar
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	TRANSPOSE INCLUDE MATHEVAL PRINT METAD FLUSH SELECT_COMPONENTS SUM	function bias matrixtools valtools 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	MOVINGRESTRAINT COMBINE COORDINATIONNUMBER LOWER_WALLS PRINT METAD Q6 LOCAL_Q6 MFILTER_MORE GROUP	function core bias multicolvar symfunc 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	FIT_TO_TEMPLATE FIXEDATOM INCLUDE MATHEVAL PRINT OPES_METAD COMMITTOR ANGLE MOLINFO DISTANCE UPPER_WALLS LOWER_WALLS RMSD GROUP COMBINE PYTORCH_MODEL CUSTOM WHOLEMOLECULES COORDINATION ENDPLUMED CONTACTMAP ENERGY CENTER	function core bias colvar opes vatom generic pytorch
22.042	Metadynamics of NSP10 and variants	bio	metadynamics, NSP10, crystal structure, variants	Shozeb Haider	METAD TORSION PRINT	generic bias colvar
22.026	Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification	materials	Peptoid, silica	Jim Pfaendtner	DISTANCE GYRATION UPPER_WALLS PRINT COM PBMETAD MOLINFO	generic bias vatom colvar
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	generic colvar
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	COORDINATION DISTANCE INCLUDE TORSION GYRATION PRINT ALPHABETA METAD ENERGY PBMETAD COM	bias colvar vatom multicolvar generic
21.028	From Enhanced Sampling to Reaction Profiles	methods	collective variables, multi-state, machine learning, Deep-TDA	Enrico Trizio	FIT_TO_TEMPLATE FIXEDATOM DISTANCES MATHEVAL PRINT OPES_METAD ANGLE DISTANCE LOAD UPPER_WALLS LOWER_WALLS GROUP PYTORCH_MODEL WHOLEMOLECULES COORDINATION ENDPLUMED TORSION CENTER UNITS	function core setup bias colvar opes vatom multicolvar generic pytorch
21.017	All-atom simulations of the Vav1 AD construct	bio	metadynamics, parallel-bias, well-tempered	Simone Orioli	CONTACTMAP REWEIGHT_BIAS PRINT ALPHABETA METAD WHOLEMOLECULES RESTART ALPHARMSD PBMETAD MOLINFO GROUP	secondarystructure core setup bias colvar multicolvar generic
21.011	CmuMD simulations of NaCl(aq) at graphite	chemistry	CmuMD, DFS clustering	Aaron Finney	CONTACT_MATRIX FIXEDATOM DENSITY RESTRAINT DUMPGRID MULTICOLVARDENS LOAD MFILTER_MORE COORDINATIONNUMBER AROUND PRINT CLUSTER_NATOMS CLUSTER_DISTRIBUTION DFSCLUSTERING GROUP	core setup bias adjmat vatom multicolvar gridtools clusters symfunc generic volumes
21.009	Nucleation rates from small scale atomistic simulations and transition state theory	materials	kinetics, free energy barriers, nucleation, droplets, metadynamics	Kristof Bal	MOVINGRESTRAINT DUMPGRID LOAD UPPER_WALLS COORDINATIONNUMBER HISTOGRAM PRINT METAD FLUSH COMMITTOR CONVERT_TO_FES UNITS REWEIGHT_METAD	setup bias gridtools symfunc generic
21.006	OPES, On-the-fly Probability Enhanced Sampling Method	methods	opes, alanine dipeptide, well-tempered, multithermal, multiumbrella	Michele Invernizzi	ENDPLUMED TORSION ECV_UMBRELLAS_LINE ECV_MULTITHERMAL PRINT ENERGY OPES_METAD OPES_EXPANDED	opes generic colvar
21.001	Substrate recognition and catalysis by glycosaminoglycan sulfotransferases	bio	metadynamics, well-tempered metadynamics, puckering, coordination	Tarsis Ferreira	COORDINATION DISTANCE INCLUDE DUMPGRID PUCKERING REWEIGHT_METAD UPPER_WALLS LOWER_WALLS PRINT METAD WHOLEMOLECULES ENERGY RANDOM_EXCHANGES MOLINFO HISTOGRAM GROUP	core bias colvar gridtools generic
20.033	COVID-19 Spike protein opening transition mechanism	bio	EMMI, CryoEM, COVID-19, Spike, Metainference	Faidon Brotzakis	DISTANCES DUMPGRID READ HISTOGRAM PRINT BIASVALUE WHOLEMOLECULES RMSD MOLINFO EMMI CONVERT_TO_FES GROUP	core isdb bias colvar multicolvar gridtools generic
20.032	Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil	materials	clustering, conformational isomers	Matteo Salvalaglio	ENDPLUMED TORSION PRINT	generic colvar
20.024	Gaussian Mixture Based Enhanced Sampling (GAMBES)	methods	enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias	Jayashrita Debnath	DISTANCE COMBINE DISTANCES TORSION LOAD UPPER_WALLS LOWER_WALLS PRINT ENERGY UNITS GROUP	function core setup bias colvar multicolvar generic
19.067	Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways	bio	metadynamics, ligand unbinding	Jakub Rydzewski	UPPER_WALLS PATHMSD LOWER_WALLS PRINT METAD RESTART UNITS	generic setup bias colvar
19.054	MetaFEP	methods	metadynamics, chemistry, free energy perturbation	GiovanniMaria Piccini	DISTANCE COMBINE UPPER_WALLS LOWER_WALLS PRINT METAD ENERGY FLUSH UNITS	function setup bias colvar generic
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	DISTANCE COMBINE DISTANCES TORSION UPPER_WALLS LOWER_WALLS PRINT BRIDGE ALPHABETA METAD COM WHOLEMOLECULES RMSD GROUP FUNNEL MOLINFO REWEIGHT_METAD	function core bias colvar adjmat funnel vatom multicolvar generic
19.023	RECT	methods	metadynamics, replica exchange	Giovanni Bussi	TORSION GYRATION PRINT METAD WHOLEMOLECULES	generic bias colvar
19.021	Coarse-Grained Directed Simulation	methods	experiment directed simulation, coarse-grain, bias	Glen Hocky	DISTANCE COMBINE TORSION RESTRAINT EDS PRINT	function bias colvar generic eds
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	CUSTOM CENTER METAD UPPER_WALLS LOWER_WALLS COORDINATION FUNNEL_PS WRAPAROUND GROUP OPES_METAD PRINT MATHEVAL FUNNEL WHOLEMOLECULES COMMITTOR RMSD COM TORSION	vatom core funnel colvar function opes generic bias
25.014	Atomic resolution ensembles of intrinsically disordered proteins with Alphafold	bio	bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement	Vincent Schnapka	BAIES PRINT GROUP BIASVALUE	isdb generic bias core
24.034	Umbrella sampling of ion in transporter SLC26A7	bio	umbrella sampling, transporter, ions	Xiaoli Lu	UNITS PRINT POSITION RESTRAINT	generic bias setup colvar
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	FIT_TO_TEMPLATE CENTER OPES_EXPANDED UPPER_WALLS LOWER_WALLS COORDINATION FIXEDATOM ECV_MULTITHERMAL GROUP DISTANCE MATHEVAL ANGLE PRINT ENERGY TORSION WHOLEMOLECULES OPES_METAD_EXPLORE ENDPLUMED	vatom opes core colvar function generic bias
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	CUSTOM COMBINE COORDINATION DISTANCE GYRATION MOLINFO OPES_METAD PRINT ALPHARMSD WHOLEMOLECULES TORSION	opes colvar function secondarystructure generic
23.046	Lasso Peptides - HLDA CV	bio	metadynamics, protein folding, HLDA, harmonic	Gabriel da Hora	COMBINE METAD DISTANCE PRINT UNITS WHOLEMOLECULES	colvar function generic setup bias
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	PATHMSD BIASVALUE CUSTOM FLUSH METAD UPPER_WALLS LOWER_WALLS DRR PRINT UNITS TIME	function colvar drr generic setup bias
23.010	An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G‑Protein-Coupled Receptor Ligands	bio	GPCR, binding free energy, free energy surface	Timothy Clark	BIASVALUE CONSTANT METAD UPPER_WALLS LOWER_WALLS DISTANCE MATHEVAL PRINT WHOLEMOLECULES	generic bias function colvar
23.006	Transcription factor unbinding	bio	metadynamics, DNA, conformational changes	Malin Lüking	METAD DUMPFORCES DISTANCE CONTACTMAP MOLINFO ANGLE PRINT ALPHARMSD COM	bias colvar secondarystructure generic vatom
22.045	Binding mode and mechanism of enzymatic polyethylene terephthalate degradation	bio	metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation	Francesco Colizzi	METAD UPPER_WALLS LOWER_WALLS MOVINGRESTRAINT DISTANCE PRINT ANGLE WHOLEMOLECULES COM	vatom generic bias colvar
21.025	Computational and biochemical analysis of type IV pilus dynamics and stability	bio	molecular dynamics, calcium binding, Type IV pilus	Yasaman Karami	PRINT DISTANCE UPPER_WALLS LOWER_WALLS	generic bias colvar
21.020	Reweighted Jarzynski sampling	methods	free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions	Kristof Bal	FLUSH MOVINGRESTRAINT TD_WELLTEMPERED OPT_AVERAGED_SGD ANN PRINT UNITS BIASVALUE UPPER_WALLS OPES_METAD BF_CHEBYSHEV CONSTANT DISTANCE RESTRAINT REWEIGHT_BIAS CONVERT_TO_FES DUMPGRID REWEIGHT_METAD CUSTOM COMBINE METAD HISTOGRAM VES_LINEAR_EXPANSION COORDINATIONNUMBER LOAD	gridtools opes colvar function annfunc ves generic setup symfunc bias
21.003	aSYN SAXS metainference	bio	metainference, SAXS	Kresten Lindorff-Larsen	METAINFERENCE BIASVALUE CENTER FLUSH EEFSOLV GROUP GYRATION MOLINFO PRINT PBMETAD SAXS ALPHARMSD WHOLEMOLECULES	isdb bias core colvar secondarystructure generic vatom
20.029	High Conformational Flexibility of the E2F1/DP1/DNA complex	bio	SAXS, protein-DNA complex, hySAXS, ensemble determination	Cristina Paissoni	BIASVALUE CENTER STATS GROUP DISTANCE RESTRAINT MOLINFO PRINT INCLUDE SAXS WHOLEMOLECULES ENSEMBLE	isdb bias core colvar function generic vatom
20.025	The role of water in host-guest interaction	bio	ligand binding, water, opes, SAMPL5	Valerio Rizzi	FIT_TO_TEMPLATE CENTER UPPER_WALLS COORDINATION FIXEDATOM GROUP DISTANCE MATHEVAL ANGLE OPES_METAD ENERGY PRINT PYTORCH_MODEL WHOLEMOLECULES ENDPLUMED	vatom core opes colvar function generic bias pytorch
20.023	metadynminer and metadynminer3d	methods	metadynamics, visualization, R	Vojtech Spiwok	PRINT METAD TORSION	generic bias colvar
20.018	Free energy barriers from biased molecular dynamics simulations	methods	kinetics, free energy barriers, chemical reactions, nucleation, metadynamics	Kristof Bal	FLUSH CONTACT_MATRIX COORDINATION LOCAL_AVERAGE PRINT VOLUME UNITS CENTER UPPER_WALLS SPRINT Q6 LOWER_WALLS DISTANCE REWEIGHT_BIAS CONVERT_TO_FES DUMPGRID REWEIGHT_METAD DENSITY METAD COMBINE PAIRENTROPY HISTOGRAM COORDINATIONNUMBER ENERGY LOAD	gridtools bias colvar function adjmat volumes sprint generic setup symfunc vatom
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	FLUSH COORDINATION GROUP PRINT TORSION STATS GYRATION PARABETARMSD PBMETAD WHOLEMOLECULES ENSEMBLE METAINFERENCE CS2BACKBONE MOLINFO INCLUDE ALPHARMSD DIHCOR COMBINE ANTIBETARMSD ENDPLUMED	isdb core function colvar multicolvar secondarystructure generic bias
20.007	Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics	bio	metadynamics, loop movement, artificial intelligence	Pratyush Tiwary	COMBINE METAD RESTART UPPER_WALLS DISTANCE MOLINFO PRINT WHOLEMOLECULES RMSD TORSION	colvar function generic setup bias
19.071	Time-independent free energies from metadynamics via Mean Force Integration	methods	metadynamics, mean force integration, MFI, thermodynamic integration	Matteo Salvalaglio	BIASVALUE READ METAD DISTANCE REWEIGHT_BIAS EXTERNAL HISTOGRAM CONVERT_TO_FES MATHEVAL PRINT DUMPGRID REWEIGHT_METAD COMMITTOR TORSION	gridtools function colvar generic bias
19.068	Rethinking Metadynamics	methods	metadynamics, opes, convergence	Michele Invernizzi	METAD ENDPLUMED EXTERNAL OPES_METAD PRINT POSITION UNITS TORSION	opes colvar generic setup bias
19.059	cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide	bio	bias-exchange metadynamics, cis-trans isomerization	Fabrizio Marinelli	METAD RANDOM_EXCHANGES PRINT INCLUDE TORSION	generic bias colvar
19.058	Constrained MD for maintaining a cavity in a calculation	chemistry	constrained MD, porous molecules, porosity, cavity	Kim Jelfs	FLUSH RESTART MOVINGRESTRAINT PRINT INPLANEDISTANCES DISTANCES COM	bias multicolvar generic setup vatom
19.039	Funnel Metadynamics	bio	funnel-metadynamics, absolute binding free energy, ligand-receptor complexes	Vittorio Limongelli	METAD UPPER_WALLS LOWER_WALLS FUNNEL_PS DISTANCE PRINT FUNNEL WHOLEMOLECULES RMSD COM	bias funnel colvar generic vatom
19.009	RNA tetraloops folding	bio	metadynamics, RNA, folding	Giovanni Bussi	METAD ERMSD MOLINFO PRINT WHOLEMOLECULES RMSD ENDPLUMED	generic bias colvar
25.028	Designing transferable transition state guided collective variable via interpretable machine learning model for enhanced sampling. A case study on polymer collapse transition	bio	metadynamics, polymer collapse transition, transferable CV,interpretable ML-model	Saikat Dhibar and Biman Jana	LOWER_WALLS WHOLEMOLECULES METAD COORDINATION PRINT GYRATION CENTER UPPER_WALLS COMBINE GROUP MATHEVAL DISTANCE	vatom colvar bias core function generic
25.020	Revealing Water-Mediated Activation Mechanisms in the Beta 1-Adrenergic Receptor via OneOPES-Enhanced Free Energy Landscapes	bio	OneOPES, GPCR, ADRB1, activation, microswitches, conformational changes, allostery	Valerio Rizzi	ECV_MULTITHERMAL LOWER_WALLS COORDINATION PRINT DISTANCES GHOST CENTER UPPER_WALLS GROUP OPES_METAD_EXPLORE ENERGY OPES_EXPANDED PATHMSD RMSD DISTANCE CUSTOM	colvar multicolvar vatom bias core function generic opes
25.018	Metainference simulation for dimerization of RNA binding protein	bio	Metainference, Metadynamics, SAXS, protein dimer	Debadutta Patra	PBMETAD STATS WHOLEMOLECULES GYRATION PRINT FLUSH CENTER UPPER_WALLS MOLINFO SAXS METAINFERENCE DISTANCE ENSEMBLE TORSION	vatom colvar bias function generic isdb
25.013	Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices	bio	umbrella sampling, temperature ramping	Alexander Berlaga	GYRATION PRINT PYTORCH_MODEL RESTRAINT DISTANCE	bias colvar pytorch 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	PUCKERING RESTART METAD PRINT RESTRAINT MOLINFO MOVINGRESTRAINT DISTANCE TORSION	bias colvar setup generic
24.036	Leveraging cryptic ligand envelopes through enhanced molecular simulations	bio	HREX, conformational heterogeneity, drug discovery, ligand binding, plitidepsin, aplidin, ligand-target complexes, cryptic ligand envelope	Francesco Colizzi	WHOLEMOLECULES COORDINATION PRINT ANGLE HISTOGRAM GROUP DUMPGRID CONVERT_TO_FES DISTANCE TORSION	core generic gridtools 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	COORDINATION PRINT UPPER_WALLS ENERGY OPES_METAD DISTANCE	bias colvar generic opes
24.011	Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble	methods	committor, machine learning	Peilin Kang	UPPER_WALLS ENERGY RMSD TORSION BIASVALUE LOWER_WALLS WHOLEMOLECULES MOLINFO MATHEVAL UNITS PRINT ENDPLUMED LOAD CUSTOM CELL INCLUDE COORDINATION GROUP POSITION DISTANCE	colvar bias setup core function generic
24.006	Water vapor condensation	chemistry	metadynamics, homogeneous condensation, chemical potential	Shenghui Zhong	COORDINATIONNUMBER CLUSTER_NATOMS CONTACT_MATRIX METAD DFSCLUSTERING PRINT UPPER_WALLS UNITS CLUSTER_PROPERTIES	bias clusters setup adjmat symfunc generic
24.003	Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations	chemistry	steered molecular dynamics, foldamers, peptoids, bio-inspired	Kaylyn Torkelson	WHOLEMOLECULES INCLUDE GYRATION PRINT COORDINATION ALPHABETA MOVINGRESTRAINT COM DISTANCE TORSION	vatom multicolvar colvar bias generic
23.041	Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference	methods	EMMIVox, cryo-EM, single-structure refinement, ensemble refinement, Bayesian inference, B-factors, structural ensembles	Samuel Hoff	BIASVALUE EMMIVOX WHOLEMOLECULES PRINT UPPER_WALLS MOLINFO GROUP DISTANCE INCLUDE WRAPAROUND	colvar bias core generic isdb
23.039	Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation	chemistry	metadynamics, ligand dissociation	Eric Beyerle	DUMPMASSCHARGE METAD PRINT RESTRAINT CENTER UPPER_WALLS MOLINFO COMBINE FIXEDATOM DISTANCE	vatom colvar bias function generic
23.034	Urea nucleation in water: do long-range forces matter?	materials	LMF theory, Metadynamics, Nucleation	Ziyue Zou	COORDINATIONNUMBER METAD PRINT CENTER GROUP LOAD INCLUDE	vatom bias setup core symfunc generic
23.024	Permutationally Invariant Networks for Enhanced Sampling (PINES)	methods	collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent	Nicholas Herringer	PRINT LOAD PBMETAD	bias generic 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	LOWER_WALLS WHOLEMOLECULES COORDINATION PRINT PYTORCH_MODEL CENTER UPPER_WALLS PATH OPES_METAD_EXPLORE GROUP FIXEDATOM UNITS OPES_METAD DISTANCE CUSTOM FIT_TO_TEMPLATE TORSION	vatom colvar bias setup core mapping function generic pytorch opes
23.012	JAK2 2D meta-eABF PMF with statistical analysis	bio	2D meta-eABF, path CV, PMF	Istvan Kolossvary	BIASVALUE LOWER_WALLS METAD PRINT FLUSH UPPER_WALLS DRR CUSTOM PATHMSD	colvar bias function drr generic
22.034	Rationalising the difference in crystallisability of two Sulflowers using efficient in silico methods	materials	metadynamics, crystallizability, crystal structure prediction, sulflower, persulforated coronene	Matteo Salvalaglio	LOWER_WALLS METAD PRINT UPPER_WALLS MATHEVAL CELL DRMSD COMMITTOR CUSTOM	bias generic function colvar
22.033	Reciprocal barrier restraint. Application to PROTAC passive permeability prediction	methods	PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR	Istvan Kolossvary	BIASVALUE METAD PRINT FLUSH UNITS DRR COM DISTANCE CUSTOM	vatom colvar bias setup drr function generic
22.011	Accelerating all-atom simulations and gaining mechanistic understanding of biophysical systems through State Predictive Information Bottleneck	methods	metadynamics, membrane permeation, protein folding	Shams Mehdi	LOWER_WALLS WHOLEMOLECULES METAD PRINT TORSION YANGLES ALPHABETA UPPER_WALLS MOLINFO COMBINE MATHEVAL XANGLES COM DISTANCE CUSTOM ZANGLES	colvar multicolvar vatom bias function generic
22.002	GAMBES_SAMPL5_RATES	other	GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding	Jayashrita Debnath	WHOLEMOLECULES COORDINATION PRINT PYTORCH_MODEL FLUSH ENDPLUMED CENTER LOAD UPPER_WALLS ANGLE GROUP FIXEDATOM MATHEVAL ENERGY COMMITTOR DISTANCE FIT_TO_TEMPLATE	vatom colvar bias setup core function generic pytorch
21.050	N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity	methods	bio	Isabell Louise Grothaus	PRINT DISTANCE CENTER	generic vatom colvar
21.032	Metal-coupled folding mechanism to metallothionein	bio	parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination	Manuel-Peris Diaz	PBMETAD WHOLEMOLECULES COORDINATION GROUP UNITS	colvar bias setup core generic
21.031	Photo-switchable sulfonulureas in KATP channel	bio	metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels	Katarzyna Walczewska-Szewc	LOWER_WALLS WHOLEMOLECULES METAD PRINT UPPER_WALLS UNITS COM DISTANCE	vatom colvar bias setup generic
21.022	Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly	materials	parallel bias metadynamics, adsorption, peptide	Xin Qi	LOWER_WALLS PBMETAD GYRATION PRINT UPPER_WALLS MOLINFO ENERGY COM DISTANCE	bias colvar vatom generic
21.018	Localized Volume-based Metadynamics	bio	LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification	Riccardo Capelli	READ UPPER_WALLS HISTOGRAM COM RMSD WHOLEMOLECULES FLUSH REWEIGHT_METAD MATHEVAL DUMPGRID CONVERT_TO_FES PRINT ENDPLUMED FIXEDATOM METAD COORDINATION GROUP POSITION DISTANCE	vatom colvar gridtools bias core function generic
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	LOWER_WALLS RESTART WHOLEMOLECULES METAD PRINT UPPER_WALLS PATHMSD	bias generic setup colvar
20.031	Soft fluorescent nanoshuttles targeting receptors	chemistry	polymers, receptors, nanoparticles, fluorescent probes	Adriana Pietropaolo	PBMETAD WHOLEMOLECULES COORDINATION PRINT CENTER	bias generic vatom colvar
20.022	Unified Approach to Enhanced Sampling	methods	OPES, expanded ensembles, importance sampling	Michele Invernizzi	ECV_MULTITHERMAL Q6 UPPER_WALLS ENERGY RMSD TORSION VOLUME WHOLEMOLECULES MOLINFO ECV_MULTITHERMAL_MULTIBARIC MATHEVAL ECV_UMBRELLAS_LINE OPES_EXPANDED UNITS ENVIRONMENTSIMILARITY ECV_LINEAR PRINT ENDPLUMED LOAD CUSTOM POSITION	colvar envsim bias setup symfunc function generic opes
20.017	FISST	methods	FISST, force, peptide, sampling, tempering	Glen Hocky	BIASVALUE GYRATION PRINT FISST RESTRAINT GROUP MATHEVAL ENERGY UNITS DISTANCE	colvar bias setup core function generic fisst
20.004	Data-driven collective variables for enhanced sampling	methods	collective variables, machine learning, deep-lda	Luigi Bonati	LOWER_WALLS PRINT PYTORCH_MODEL ENDPLUMED FLUSH LOAD UPPER_WALLS GROUP MATHEVAL UNITS OPES_METAD COM DISTANCE TORSION	vatom colvar bias setup core function generic pytorch opes
20.002	Exploring conformational dynamics of the extracellular Venus flytrap domain of the GABAB receptor, a path-metadynamics study	bio	Metadynamics, path CVs	Riccardo Ocello	RESTART WHOLEMOLECULES METAD PRINT UPPER_WALLS MOLINFO GROUP PATHMSD	colvar bias setup core generic
19.080	Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium	methods	ves, variationally enhanced sampling, vibrational excitation, chemical reactions	Kristof Bal	LOWER_WALLS OPT_AVERAGED_SGD COORDINATION PRINT EXTERNAL BF_CHEBYSHEV VES_LINEAR_EXPANSION FLUSH UPPER_WALLS ANGLE HISTOGRAM COMBINE DUMPGRID TD_GRID UNITS CONVERT_TO_FES DISTANCE TD_WELLTEMPERED	colvar gridtools bias setup function generic ves
19.073	On the role of enthalpic and entropic contributions on the conformational free energy landscape of MIL-101(Cr) building units	materials	metadynamics, MOF, MIL101Cr, conformational	Matteo Salvalaglio	COORDINATIONNUMBER LOWER_WALLS METAD GYRATION PRINT ENDPLUMED UPPER_WALLS ENERGY DISTANCES	colvar multicolvar bias symfunc generic
19.061	Diffusion in porous materials	materials	metadynamics, porous materials, diffusion	Kim E. Jelfs	LOWER_WALLS RESTART METAD PRINT CENTER UPPER_WALLS GROUP COM DISTANCE	vatom colvar bias setup core generic
19.057	SAXS ensembles using Martini-Beads multi-scale SAXS	methods	metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics	Cristina Paissoni	BIASVALUE PBMETAD WHOLEMOLECULES STATS COORDINATION PRINT ENDPLUMED CENTER ALPHABETA ANGLE MOLINFO COMBINE GROUP MATHEVAL SAXS ENSEMBLE INCLUDE	vatom colvar multicolvar bias core function generic isdb
19.052	Gibbs free energy of homogeneous nucleation	materials	nucleation, surface excess free energy	Gareth Tribello	FCCUBIC METAD PRINT ENDPLUMED UPPER_WALLS UNITS CELL	colvar bias setup symfunc generic
19.043	Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA)	methods	metadynamics, chemistry, HLDA	GiovanniMaria Piccini	RESTART METAD PRINT DISTANCES FLUSH UPPER_WALLS COMBINE UNITS DISTANCE	colvar multicolvar bias setup function generic
19.032	Chemical reaction in solution using path collective variables based on coordination patterns	chemistry	chemical reactions, solutions, metadynamics, coordination patterns	Fabio Pietrucci	RESTART METAD PRINT FLUSH UPPER_WALLS PATH DISTANCES	multicolvar bias setup mapping generic
19.031	Ice nucleation using PIV-based path coordinates	materials	phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics	Silvio Pipolo	LOWER_WALLS METAD PRINT FUNCPATHMSD UPPER_WALLS PIV CELL	colvar bias function generic piv
19.022	eABF simulation of NANMA (alanine dipeptide)	methods	eABF, DRR, alanine dipeptide	Haochuan Chen	PRINT TORSION DRR	generic drr colvar
19.004	MI Ubiquitin	bio	metainference, NMR	Max Bonomi	WHOLEMOLECULES PRINT MOLINFO GROUP METAINFERENCE CS2BACKBONE RDC	core generic isdb
19.001	RNA SHAPE	bio	metadynamics, RNA, ligand binding	Giovanni Bussi	LOWER_WALLS METAD PRINT RANDOM_EXCHANGES FLUSH UPPER_WALLS ANGLE MOLINFO COMBINE DISTANCE ERMSD DISTANCES INCLUDE	colvar multicolvar bias function generic
25.008	Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting	methods	metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting	Dhiman Ray	CUSTOM LOWER_WALLS METAD UPPER_WALLS RMSD ENERGY OPES_METAD MOLINFO ENDPLUMED DISTANCE PRINT PYTORCH_MODEL WHOLEMOLECULES POSITION UNITS TORSION BIASVALUE GROUP	setup colvar bias generic function core opes pytorch
25.002	M3_PCV-ABMD	chemistry	Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor	Gian Marco Elisi	UPPER_WALLS ENDPLUMED PRINT UNITS ABMD PATHMSD	colvar bias setup generic
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	function bias colvar generic
23.040	Supramolecular capsules assembly dynamics	chemistry	Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics	Riccardo Capelli	CUSTOM COM DISTANCES METAD GROUP CENTER DISTANCE PRINT WHOLEMOLECULES UNITS POSITION FLUSH	setup bias colvar generic multicolvar function core 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	METAD RMSD MOLINFO DISTANCE PRINT MATHEVAL WHOLEMOLECULES	colvar bias function generic
23.037	Estimating binding free energy of solid binding peptides without extensive sampling	bio	metadynamics, solid binding peptides	Xin Qi	LOWER_WALLS UPPER_WALLS COM PBMETAD GYRATION MOLINFO DISTANCE PRINT	colvar vatom bias generic
23.019	Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors	bio	binding pathway, binding energy, sketch-map, drug development	Raitis Bobrovs	DISSIMILARITIES CUSTOM UPPER_WALLS METAD COM TRANSPOSE SKETCHMAP_PROJECTION SKETCHMAP VSTACK COLLECT_FRAMES LANDMARK_SELECT_FPS VORONOI DISTANCE PRINT WHOLEMOLECULES PATHMSD	bias colvar landmarks generic matrixtools valtools function vatom dimred
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	DUMPGRID METAD READ RMSD MOLINFO REWEIGHT_METAD DISTANCE HISTOGRAM PRINT MATHEVAL CONVERT_TO_FES WHOLEMOLECULES	colvar bias gridtools generic 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	DUMPGRID LOWER_WALLS UPPER_WALLS ECV_UMBRELLAS_LINE ENVIRONMENTSIMILARITY HISTOGRAM PRINT OPES_EXPANDED RESTART	envsim setup bias gridtools generic opes
23.002	Critical comparison of general-purpose collective variables for crystal nucleation	methods	metadynamics, umbrella sampling, commitor, entropy, PIV	Julien Lam	CUSTOM UPPER_WALLS METAD ENERGY FUNCPATHMSD LOCAL_AVERAGE Q4 PIV RESTRAINT VOLUME PRINT Q6 UNITS PAIRENTROPY	setup piv colvar bias gridtools generic symfunc function
22.031	Rare Event Kinetics from Adaptive Bias Enhanced Sampling	methods	OPES Flooding, Kinetics, Rate, OPES, Machine Learning	Dhiman Ray	COMMITTOR ENDPLUMED DISTANCE CONTACTMAP PRINT TORSION BIASVALUE MOLINFO PYTORCH_MODEL WHOLEMOLECULES POSITION ENERGY INCLUDE UNITS CUSTOM RMSD OPES_METAD COMBINE CONSTANT GROUP	setup bias colvar generic function core opes pytorch
22.028	N-glycan conformer distributions in atomistic simulation	bio	REST2, RECT, N-glycan, pucker	Isabell Grothaus	DUMPGRID PUCKERING METAD READ MOLINFO HISTOGRAM PRINT CONVERT_TO_FES TORSION	bias colvar gridtools generic
22.025	Bubble nucleation rate predictions in a Lennard-Jones fluid	materials	free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation	Kristof Bal	DUMPGRID CUSTOM ANN UPPER_WALLS COMMITTOR HISTOGRAM RESTRAINT VOLUME PRINT COORDINATIONNUMBER CONVERT_TO_FES MOVINGRESTRAINT REWEIGHT_BIAS UNITS BIASVALUE LOAD FLUSH	setup bias gridtools colvar generic symfunc function annfunc
22.008	Ab initio metadynamics determination of temperature-dependent free-energy landscape in ultrasmall silver clusters	materials	Well tempered metadynamics, ab-initio, ase	Daniel Sucerquia	LOWER_WALLS UPPER_WALLS METAD COORDINATION COM GYRATION COMBINE DISTANCE COORDINATIONNUMBER UNITS FLUSH	setup colvar bias generic symfunc function vatom
22.004	Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques	chemistry	reaction discovery, OPES, collective variables	Umberto Raucci	CUSTOM UPPER_WALLS COM COORDINATION LOWER_WALLS OPES_METAD OPES_METAD_EXPLORE DISTANCE PRINT MATHEVAL PYTORCH_MODEL LOAD UNITS GROUP	setup colvar bias generic function core vatom opes pytorch
22.000	Amyloid precursor protein processing by human γ-secretase	bio	Bias Exchange Metadynamics, Helix unfolding, coupled binding	Xiaoli Lu	ANTIBETARMSD METAD COORDINATION INCLUDE MOLINFO ALPHARMSD CENTER CONTACTMAP DISTANCE PRINT UNITS RANDOM_EXCHANGES	setup colvar bias generic secondarystructure vatom
21.033	Multiple-path-metadynamics applied to DNA base-pairing transitions	bio	path-CV, metadynamics, multiple-walker, dna	Alberto Pérez-de-Alba-Ortíz	UPPER_WALLS METAD INCLUDE COMBINE MOVINGRESTRAINT RESTRAINT PRINT CONSTANT	function bias generic
21.016	MD SAXS GTPase associated center	bio	metadynamics, RNA, folding, SAXS	Giovanni Bussi	LOWER_WALLS CUSTOM UPPER_WALLS METAD GYRATION INCLUDE SAXS MOLINFO PRINT WHOLEMOLECULES ERMSD GROUP	colvar bias generic isdb function core
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	TD_UNIFORM UPPER_WALLS VES_LINEAR_EXPANSION ECV_UMBRELLAS_LINE ENERGY BF_LEGENDRE OPT_AVERAGED_SGD ENVIRONMENTSIMILARITY VOLUME PRINT Q6 MATHEVAL ECV_MULTITHERMAL_MULTIBARIC OPES_EXPANDED RESTART	envsim setup colvar bias generic symfunc ves function opes
20.028	Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane	bio	metadynamics, KRas-4B, anionic membrane	Huixia Lu	METAD CENTER DISTANCE PRINT FIT_TO_TEMPLATE RESTART	setup colvar bias generic vatom
20.021	Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins.	bio	phi-values, restrained MD, transition-state, protein folding, disordered proteins, protein evolution	Cristina Paissoni	COORDINATION STATS MOLINFO RESTRAINT PRINT WHOLEMOLECULES	generic colvar bias function
20.011	Uremic toxin analysis	bio	metadynamics, uremic toxin, serum albumin	Jim Pfaendtner	COORDINATION DISTANCES CENTER DISTANCE PRINT WHOLEMOLECULES RESTART GROUP	setup colvar generic multicolvar core vatom
20.010	Phase equilibrium of liquid water and hexagonal ice from enhanced sampling molecular dynamics simulations	materials	water, ice, TIP4P, crystallization, EnvironmentSimilarity, RefCV, kernel, VES, variationally enhanced sampling	Pablo Piaggi	TD_WELLTEMPERED UPPER_WALLS VES_LINEAR_EXPANSION OPT_DUMMY BF_LEGENDRE OPT_AVERAGED_SGD ENVIRONMENTSIMILARITY VOLUME Q6 MATHEVAL PRINT RESTART	envsim setup colvar bias generic symfunc ves function
20.008	Simulating solvation and acidity in complex mixtures with first-principles accuracy. The case of CH3SO3H and H2O2 in phenol	chemistry	proton trasfer, metadynamics	Kevin Rossi	CUSTOM METAD COORDINATION DISTANCES PRINT UNITS	setup colvar bias generic function multicolvar
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 LOWER_WALLS UPPER_WALLS COM METAD READ COMBINE ENDPLUMED REWEIGHT_METAD DISTANCE HISTOGRAM PRINT MATHEVAL CONVERT_TO_FES ABMD	bias gridtools colvar generic function vatom
19.076	Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones	bio	molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics	Salvatore Assenza	GYRATION ENDPLUMED MOVINGRESTRAINT PRINT UNITS	bias colvar setup generic
19.074	Asymmetric base pair opening in nucleic acids	bio	double helix, DNA, RNA, unwindability	Giovanni Bussi	LOWER_WALLS COORDINATION ENDPLUMED DISTANCE RESTRAINT WHOLEMOLECULES	colvar bias generic
19.066	Finding ligand unbinding reaction pathways	methods	maze, ligand unbinding	Jakub Rydzewski	MAZE_OPTIMIZER_BIAS MAZE_LOSS PRINT UNITS POSITION MAZE_SIMULATED_ANNEALING	colvar maze setup generic
19.051	Solid liquid interfacial free energy out of equilibrium	materials	metadynamics, nucleation, surface excess free energy	Gareth Tribello	FCCUBIC LOWER_WALLS UPPER_WALLS METAD ENDPLUMED PRINT UNITS AROUND CELL	setup volumes bias colvar generic symfunc
19.035	Dimerization of GPCRs from coarse-grained umbrella sampling	bio	Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization	Davide Provasi	COM DISTANCE RESTRAINT PRINT TORSION GROUP	bias colvar generic core vatom
19.030	Coarse-Grained MetaDynamics (CG-MetaD)	bio	Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy	Vittorio Limongelli	LOWER_WALLS UPPER_WALLS METAD COM DISTANCE PRINT WHOLEMOLECULES	colvar vatom bias generic
19.024	PT-MetaD-WTE	methods	metadynamics, WTE, trp cage, PT	Jim Pfaendtner	METAD COORDINATION ENERGY EXTERNAL GROUP	colvar bias core
19.000	VesDeltaF	methods	VES, convergence, suboptimal CVs	Michele Invernizzi	METAD ENERGY VES_DELTA_F ENDPLUMED PRINT LOAD UNITS TORSION POSITION RESTART	setup colvar bias generic ves
25.022	Imidazole Diffusion in SALEM-2 MOF	materials	OPES, Diffusion, Ring opening, MOFs, Machine Learning Potentials	Sudheesh Kumar Ethirajan	OPES_METAD MOLINFO PRINT DISTANCE CENTER GROUP DISTANCES WHOLEMOLECULES ENDPLUMED PROJECTION_ON_AXIS UNITS	setup generic core vatom colvar multicolvar opes
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	COORDINATION BIASVALUE PARABETARMSD EMMI MOLINFO UPPER_WALLS COM ALPHARMSD DISTANCE PRINT CENTER GROUP PBMETAD RMSD WHOLEMOLECULES DUMPATOMS DUMPMASSCHARGE	secondarystructure generic core vatom colvar isdb bias
24.032	DeepLNE++	methods	PATHCV, OPES	Thorben Fröhlking	COORDINATION ENERGY COMBINE CUSTOM LOAD OPES_METAD PRINT DISTANCE GROUP TORSION	function setup generic core colvar opes
24.031	DeepLNE	methods	PATHCV, OPES, OneOPES	Thorben Fröhlking	COORDINATION ENERGY COMBINE PYTORCH_MODEL MOLINFO PRINT ECV_MULTITHERMAL OPES_METAD_EXPLORE VOLUME ERMSD OPES_EXPANDED RESTART	function setup generic colvar opes pytorch
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	COORDINATION ENERGY COMBINE CUSTOM PRINT ECV_MULTITHERMAL DISTANCE OPES_METAD_EXPLORE GROUP TORSION OPES_EXPANDED RESTART	function setup generic core colvar opes
24.005	Learning Markovian Dynamics with Spectral Maps	methods	spectral map, collective variables, machine learning	Jakub Rydzewski	BIASVALUE CUSTOM PRINT DISTANCE UNITS	function setup generic colvar bias
23.036	Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water?	bio	NaCl, nucleation, metadynamics	Ruiyu Wang	ENERGY COMBINE MATHEVAL Q4 COORDINATIONNUMBER METAD PRINT VOLUME Q6	function generic symfunc colvar bias
23.032	Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics	bio	metadynamics, tSNE, neural network, machine learning, trp-cage, folding	Vojtech Spiwok	COMBINE ANN MOLINFO METAD PRINT POSITION FIT_TO_TEMPLATE ALPHARMSD WHOLEMOLECULES	function secondarystructure generic colvar annfunc 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	MOLINFO METAD PRINT UPPER_WALLS FIT_TO_TEMPLATE POSITION WRAPAROUND CENTER GROUP DISTANCES WHOLEMOLECULES SHADOW	generic core vatom colvar isdb multicolvar 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	READ METAD PRINT EXTRACV TORSION	generic colvar 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	ENERGY METAD UPPER_WALLS PRINT LOWER_WALLS WHOLEMOLECULES CONTACTMAP	generic colvar bias
22.043	Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES	bio	OPES, RNA, Tetraloop, Folding	Gül Zerze	ENERGY PRINT ECV_MULTITHERMAL WHOLEMOLECULES OPES_EXPANDED CONTACTMAP ECV_UMBRELLAS_LINE	generic colvar opes
22.040	From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure	bio	SARS-CoV-2, Spike, Omicron	Miłosz Wieczór	METAD PRINT UPPER_WALLS LOWER_WALLS PCAVARS WHOLEMOLECULES	generic bias mapping
22.039	Driving and characterizing nucleation of urea and glycine polymorphs in water	bio	metadynamics, nucleation, amino acids, polymorphism	Eric Beyerle	COMBINE MATHEVAL LOAD Q4 COORDINATIONNUMBER METAD PRINT CENTER GROUP Q6 PAIRENTROPY INCLUDE	function setup generic symfunc core gridtools vatom bias
22.029	Angiotensin-1-7_Metadynamics	bio	Metadynamics, Angiotensin-(1-7), peptide	L.-América Chi	COORDINATION GYRATION METAD PRINT UPPER_WALLS FLUSH GROUP LOWER_WALLS WHOLEMOLECULES	generic colvar bias core
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	PRINT RMSD	generic colvar
22.009	Glycosylation in calixarenes capsule	chemistry	Metadynamics, glycosylation, supramolecular catalysis	GiovanniMaria Piccini	COORDINATION COMBINE MATHEVAL METAD UPPER_WALLS FIT_TO_TEMPLATE PRINT DISTANCE FLUSH BRIDGE GROUP ANGLE DISTANCES LOWER_WALLS RMSD WHOLEMOLECULES UNITS	function setup generic core colvar adjmat multicolvar bias
21.052	On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets	materials	Ibuprofen, unbinding, WTmetaD	Matteo Salvalaglio	COORDINATIONNUMBER METAD PRINT DISTANCE CENTER TORSION ENDPLUMED COMMITTOR	generic symfunc vatom colvar bias
21.029	Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs	bio	metadynamics, small peptide, machine learning	Pratyush Tiwary	ENERGY MOLINFO PRINT FLUSH TORSION EXTERNAL RESTART	setup generic colvar 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 MATHEVAL KDE PRINT COM DISTANCE	function generic gridtools vatom colvar multicolvar
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 METAD PRINT POSITION RESTRAINT CENTER REWEIGHT_BIAS WHOLEMOLECULES RESTART	function setup generic vatom colvar bias
20.015	Rational design of ASCT2 inhibitors using an integrated experimental-computational approach	bio	ASCT2 transporter, small-molecules, cryo-EM, metainference	Max Bonomi	BIASVALUE LOAD MOLINFO PRINT EMMIVOX GROUP WHOLEMOLECULES DUMPATOMS	setup generic core isdb bias
19.065	Molecular Enhanced Sampling with Autoencoders	methods	enhanced sampling, collective variables, deep learning	Wei Chen	COMBINE ANN COM POSITION RESTRAINT	function vatom colvar annfunc bias
19.062	Elucidating molecular design principles for charge-alternating peptides	bio	peptide folding, metadynamics, well-tempered ensemble, parallel tempering	Jim Pfaendtner	ENERGY GYRATION METAD PRINT WHOLEMOLECULES	generic colvar bias
19.056	maze	methods	maze, ligand unbinding	Jakub Rydzewski	MAZE_SIMULATED_ANNEALING PRINT MAZE_OPTIMIZER_BIAS POSITION MAZE_LOSS UNITS	setup generic maze colvar
19.042	Harmonic Linear Discriminant Analysis (HLDA)	methods	metadynamics, chemistry, HLDA	GiovanniMaria Piccini	ENERGY COMBINE METAD UPPER_WALLS FLUSH PRINT DISTANCE UNITS	function setup generic colvar bias
19.029	WTE-metaD of FF domain of URNF1 C57D variant	bio	metadynamics, mutations, post-translational modification, ff domain	Elena Papaleo	ALPHABETA GYRATION MOLINFO METAD UPPER_WALLS PRINT GROUP LOWER_WALLS WHOLEMOLECULES	generic core colvar multicolvar bias
19.028	pRAVE	methods	RAVE, reaction coordinate, deep learning, metadynamics, kinetics	Pratyush Tiwary	COMBINE ALPHABETA PRINT COM DISTANCE TORSION WHOLEMOLECULES EXTERNAL RESTART COMMITTOR	function setup generic vatom colvar multicolvar bias
19.025	Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide	bio	metainference, NMR, protein dynamics, force-fields	Carlo Camilloni	BIASVALUE RDC METAINFERENCE GYRATION MOLINFO PRINT FLUSH ENSEMBLE WHOLEMOLECULES PBMETAD TORSION JCOUPLING ENDPLUMED STATS CS2BACKBONE	function generic colvar isdb bias
19.011	Automatic Gradient Computation for Collective Variables	other	gradient, differentiation, curvature	Toni Giorgino	ENDPLUMED	generic
19.010	Multi-domain protein dynamics	bio	metainference, NMR, protein dynamics	Carlo Camilloni	ALPHABETA DIHCOR RDC METAINFERENCE MOLINFO UPPER_WALLS PRINT DISTANCE ENSEMBLE CENTER GROUP RESTRAINT WHOLEMOLECULES PBMETAD TORSION ENDPLUMED STATS DHENERGY	function generic core vatom colvar isdb multicolvar bias
25.027	Enhanced-sampling MD simulations of a protein-peptide complex integrating SAXS and XL-MS experimental information	bio	steered MD, metadynamics, SAXS, XL-MS, ensemble reconstruction	Mattia Bernetti	CENTER WHOLEMOLECULES UPPER_WALLS GYRATION INCLUDE GROUP DISTANCE MOVINGRESTRAINT SAXS MOLINFO PRINT METAD	bias colvar vatom isdb generic core
25.026	Deciphering the Molecular Mechanisms of Startle Disease - the Role of the Asn46Lys Mutation in the Glycine Receptor	bio	metadynamics, glycine receptors, funnel metadynamics	Jacob Adam Clark	FUNNEL UPPER_WALLS FUNNEL_PS LOWER_WALLS METAD COM PRINT	funnel vatom generic bias
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 BAIES PRINT GROUP	bias core generic isdb
25.010	Kinetic rates calculation with Ratchet&Pawl MD	methods	kinetics, ligand binding, ABMD, ratchet&pawl MD	Riccardo Capelli	ABMD WHOLEMOLECULES COMMITTOR GROUP DISTANCE FLUSH COM PRINT	bias colvar vatom generic 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	RESTART UPPER_WALLS COMMITTOR LOWER_WALLS GROUP CUSTOM DISTANCE OPES_METAD UNITS COORDINATION PRINT	bias colvar opes function generic core setup
24.026	Constant pH metadynamics of RNA oligomers	bio	metadynamics, pH, RNA	Giovanni Bussi	TORSION RESTART PUCKERING MOLINFO PRINT METAD	colvar setup generic bias
24.018	A new route to the prebiotic synthesis of glycine via ab initio-based machine learning calculations	chemistry	prebiotic chemistry, glycine, Strecker synthesis, ab initio calculations, machine learning	Léon HUET	PRINT DISTANCE	generic colvar
24.017	Absolute Binding Free Energies with OneOPES	methods	protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy	Francesco Gervasio	RMSD TORSION ECV_MULTITHERMAL OPES_METAD_EXPLORE METAD COORDINATION PRINT OPES_EXPANDED ENERGY GROUP CONSTANT MATHEVAL RESTART UPPER_WALLS INCLUDE LOWER_WALLS CUSTOM BIASVALUE MOLINFO WHOLEMOLECULES PROJECTION_ON_AXIS WRAPAROUND COM CONTACTMAP	bias colvar opes vatom function generic core setup
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	CENTER RMSD UPPER_WALLS STATS WRAPAROUND DISTANCE GROUP SAXS BIASVALUE ENSEMBLE MOLINFO PRINT	bias colvar vatom isdb function generic core
23.011	OneOPES, a combined enhanced sampling method to rule them all	bio	OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding	Valerio Rizzi	TORSION OPES_EXPANDED ENDPLUMED ENERGY ECV_MULTITHERMAL DISTANCE OPES_METAD_EXPLORE MOLINFO PRINT METAD	colvar opes generic bias
22.037	Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site	chemistry	metadynamics, DNA, abasic	Mike Jones	METAD DISTANCES PRINT DISTANCE	bias colvar multicolvar 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	WHOLEMOLECULES FUNNEL UPPER_WALLS FUNNEL_PS LOWER_WALLS DISTANCE PATHMSD METAD COM PRINT	bias colvar vatom generic funnel
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	CENTER RMSD WHOLEMOLECULES PYTORCH_MODEL UPPER_WALLS COMMITTOR FIXEDATOM LOWER_WALLS GROUP DISTANCE OPES_METAD FIT_TO_TEMPLATE MATHEVAL CUSTOM COORDINATION PRINT	bias colvar vatom opes function generic core pytorch
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	ALPHARMSD TORSION WHOLEMOLECULES UPPER_WALLS DISTANCE PRINT ANGLE FLUSH MOLINFO COORDINATION ALPHABETA METAD	bias multicolvar secondarystructure colvar generic
22.006	Peptide framework for screening the effects of amino acids on assembly	bio	metadynamics, peptides	Andrew White	COM DISTANCES GYRATION INCLUDE GROUP HISTOGRAM PRINT COMBINE CONVERT_TO_FES METAD REWEIGHT_BIAS DUMPGRID	bias gridtools multicolvar colvar vatom function generic core
21.034	Efficient sampling of high-dimensional free energy landscapes using adaptive reinforced dynamics	bio	reinforced dynamics, bias-exchange metadynamics, parallel-bias metadynamics	Dongdong Wang	TORSION RANDOM_EXCHANGES ENDPLUMED INCLUDE PBMETAD METAD PRINT	colvar generic bias
20.034	Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations	bio	RNA, SARS-CoV-2, partial tempering	Sandro Bottaro	CENTER TORSION ABMD RESTART DISTANCE MOLINFO ERMSD PRINT	bias colvar vatom generic 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	MULTI_RMSD HISTOGRAM RESTRAINT REWEIGHT_METAD CONVERT_TO_FES METAD DUMPGRID PRINT	colvar gridtools generic bias
20.016	Predicting polymorphism in molecular crystals using orientational entropy	materials	metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy	Pablo Piaggi	CENTER LOAD VOLUME UPPER_WALLS INCLUDE GROUP METAD PRINT	bias colvar vatom generic core setup
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	LOAD WHOLEMOLECULES PROJECTION_ON_AXIS CONTACTMAP UPPER_WALLS INCLUDE LOWER_WALLS GROUP DISTANCE CONSTANT MATHEVAL BIASVALUE MOLINFO FUNCPATHGENERAL METAD COM PRINT	bias colvar vatom function generic core 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	READ FLUSH COMBINE METAD DUMPGRID PRINT ABMD CONVERT_TO_FES FUNCPATHMSD UPPER_WALLS LOWER_WALLS HISTOGRAM MOLINFO WHOLEMOLECULES ENDPLUMED DISTANCE REWEIGHT_METAD COM CONTACTMAP	bias gridtools colvar vatom function generic
19.083	Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis	chemistry	metadynamics, chemical reactions, reaction discovery	Valerio Rizzi	COORDINATIONNUMBER DISTANCES RESTART ENDPLUMED UPPER_WALLS GROUP UNITS FLUSH METAD COMBINE PRINT	bias multicolvar symfunc function generic core setup
19.082	Ammonia Borane Dehydrogenation	chemistry	metadynamics, reaction discovery, hydrogen production, chemistry	Valerio Rizzi	COORDINATIONNUMBER RESTART ENDPLUMED EXTERNAL GROUP UNITS FLUSH METAD COMBINE PRINT	bias symfunc function generic core setup
19.081	Calculation of phase diagrams in the multithermal-multibaric ensemble	methods	VES, variationally enhanced sampling, multithermal-multibaric, energy, Wang Landau, RefCV, kernel, bcc, fcc, sodium, aluminum	Pablo Piaggi	LOAD READ OPT_DUMMY COMBINE REWEIGHT_BIAS DUMPGRID PRINT OPT_AVERAGED_SGD REWEIGHT_TEMP_PRESS ENERGY MATHEVAL VES_LINEAR_EXPANSION TD_WELLTEMPERED TD_MULTITHERMAL_MULTIBARIC CONVERT_TO_FES RESTART UPPER_WALLS LOWER_WALLS HISTOGRAM BF_LEGENDRE VOLUME Q6 CELL	bias gridtools ves symfunc colvar function generic setup
19.077	Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations	materials	metadynamics, peptide-surface binding	Jim Pfaendtner	UPPER_WALLS ENERGY GYRATION DISTANCE MOLINFO COM PRINT METAD	bias vatom colvar generic
19.070	Unexpected Dynamics in the UUCG RNA Tetraloop	bio	well-tempered metadynamics, RNA, UUCG, maximum entropy	Sandro Bottaro	RMSD TORSION WHOLEMOLECULES DISTANCE MOLINFO ERMSD PRINT METAD	colvar generic bias
19.064	Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations	materials	metadynamics, peptide-surface binding	Jim Pfaendtner	UPPER_WALLS ENERGY GYRATION DISTANCE MOLINFO COM PRINT METAD	bias vatom colvar generic
19.045	Adsorption free energy of Ca/CO3 ions on calcite steps in contact with water	materials	metadynamics, well-tempered, multiple walkers, LAMMPS	Marco De La Pierre	RESTART UPPER_WALLS LOWER_WALLS GROUP UNITS POSITION FLUSH METAD COORDINATION PRINT	bias colvar generic core setup
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 ENERGY DISTANCE METAD COM PRINT	bias vatom colvar generic
19.014	MIL101(Cr) SBUs assembly	materials	MOFs, nucleation, self-assembly, metadynamics	Matteo Salvalaglio	COORDINATIONNUMBER DISTANCES RESTART ENDPLUMED GYRATION METAD PRINT	bias multicolvar symfunc colvar generic setup
19.012	Martini-Beads multi-scale SAXS	methods	metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex	Carlo Camilloni	CENTER RMSD WHOLEMOLECULES ENDPLUMED UPPER_WALLS INCLUDE STATS GROUP DISTANCE SAXS BIASVALUE RESTRAINT MOLINFO PRINT	bias colvar vatom isdb function generic core
19.005	Cmyc small molecule interaction	bio	metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP	Gabriella Heller	CENTER WHOLEMOLECULES INCLUDE GYRATION GROUP DISTANCE CS2BACKBONE PBMETAD ALPHABETA MOLINFO COORDINATION PRINT METAINFERENCE	bias multicolvar colvar vatom isdb generic core

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