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
25.029	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 CONVERT_TO_FES DISTANCE PRINT HISTOGRAM FIXEDATOM REWEIGHT_BIAS MOLINFO WHOLEMOLECULES DUMPGRID LOWER_WALLS	generic gridtools vatom bias colvar
25.022	Imidazole Diffusion in SALEM-2 MOF	materials	OPES, Diffusion, Ring opening, MOFs, Machine Learning Potentials	Sudheesh Kumar Ethirajan	UNITS DISTANCE PRINT ENDPLUMED MOLINFO GROUP DISTANCES WHOLEMOLECULES OPES_METAD PROJECTION_ON_AXIS CENTER	core setup generic multicolvar opes vatom colvar
25.000	Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer	bio	metadynamics, pathCV	Sahithya Sridharan Iyer	UPPER_WALLS METAD COM DISTANCE PRINT FUNCPATHGENERAL MOLINFO GROUP WHOLEMOLECULES RESTART	core setup generic vatom function bias colvar
24.034	Umbrella sampling of ion in transporter SLC26A7	bio	umbrella sampling, transporter, ions	Xiaoli Lu	POSITION UNITS RESTRAINT PRINT	generic bias colvar setup
24.031	DeepLNE	methods	PATHCV, OPES, OneOPES	Thorben Fröhlking	PYTORCH_MODEL PRINT ENERGY OPES_EXPANDED COORDINATION ERMSD ECV_MULTITHERMAL COMBINE MOLINFO RESTART VOLUME OPES_METAD_EXPLORE	pytorch setup generic opes function colvar
24.026	Constant pH metadynamics of RNA oligomers	bio	metadynamics, pH, RNA	Giovanni Bussi	TORSION PUCKERING METAD PRINT MOLINFO RESTART	generic bias colvar setup
24.008	yCD Metadynamics	bio	volume-based MetaD, path CVs, infrequent MetaD, product release	James McCarty	INCLUDE UPPER_WALLS COM FIXEDATOM WRAPAROUND MOLINFO DUMPGRID REWEIGHT_METAD METAD DISTANCE CONTACTMAP GROUP MATHEVAL FIT_TO_TEMPLATE COMMITTOR ENDPLUMED PATH FLUSH READ CONVERT_TO_FES PRINT HISTOGRAM COORDINATION RMSD WHOLEMOLECULES	core generic gridtools mapping vatom function bias colvar
23.029	An accurate and efficient SAXS/SANS implementation including solvation layer effects suitable for restrained Molecular Dynamics simulations	bio	SAXS, SANS, SAS, metainference, proteins, nucleic-acid	Federico Ballabio	UPPER_WALLS STATS DISTANCE PRINT BIASVALUE RMSD MOLINFO WRAPAROUND SAXS GROUP ENSEMBLE CENTER	core isdb generic vatom function bias colvar
23.027	CmuMD simulations of NaCl(aq) at NaCl	chemistry	CmuMD, DFS, Q3, Pair Entropy	Aaron Finney	UNITS Q3 COORDINATIONNUMBER RESTRAINT LOCAL_AVERAGE DFSCLUSTERING PRINT HISTOGRAM FIXEDATOM CONTACT_MATRIX LOCAL_Q3 AROUND CLUSTER_NATOMS GROUP DENSITY DUMPGRID CLUSTER_DISTRIBUTION LOAD	adjmat core setup generic gridtools volumes vatom bias symfunc clusters
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	FLUSH UNITS UPPER_WALLS METAD PRINT BIASVALUE DRR PATHMSD CUSTOM TIME LOWER_WALLS	setup generic function bias colvar drr
23.007	Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains	bio	metadynamics, peptoids, parallel-bias metadynamics	Jim Pfaendtner	TORSION INCLUDE RESTRAINT COM PBMETAD PRINT COORDINATION GYRATION WHOLEMOLECULES	generic bias colvar vatom
23.003	Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations	methods	metadynamics, alchemical variable, alchemical free energy calculations	Wei-Tse Hsu	TORSION READ METAD EXTRACV PRINT	generic bias colvar
22.041	Skipping the Replica Exchange Ladder with Normalizing Flows	methods	OPES, alanine, normalizing flows, replica exchange	Michele Invernizzi	TORSION UNITS OPES_EXPANDED ENERGY PRINT ECV_MULTITHERMAL ENDPLUMED POSITION OPES_METAD	opes generic colvar setup
22.040	From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure	bio	SARS-CoV-2, Spike, Omicron	Miłosz Wieczór	UPPER_WALLS METAD PCAVARS PRINT WHOLEMOLECULES LOWER_WALLS	mapping generic bias
22.034	Rationalising the difference in crystallisability of two Sulflowers using efficient in silico methods	materials	metadynamics, crystallizability, crystal structure prediction, sulflower, persulforated coronene	Matteo Salvalaglio	UPPER_WALLS DRMSD METAD MATHEVAL CELL PRINT COMMITTOR CUSTOM LOWER_WALLS	function generic bias colvar
22.024	Conformational Entropy as a Potential Liability of Computationally Designed Antibodies	bio	metadynamics, conformational entropy, antibody, nanobody	Thomas Löhr	TORSION ALPHABETA ANTIBETARMSD COM PBMETAD PRINT ALPHARMSD MOLINFO WHOLEMOLECULES RESTART	secondarystructure setup generic multicolvar vatom bias colvar
22.020	Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix–Junction–Helix RNA	bio	RNA force field, Helix-Junction-Helix RNA, SAXS, Well tempered metadynamics	Weiwei He	TORSION METAD COM DISTANCE PRINT GROUP WHOLEMOLECULES	core generic vatom bias colvar
21.052	On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets	materials	Ibuprofen, unbinding, WTmetaD	Matteo Salvalaglio	TORSION COORDINATIONNUMBER METAD DISTANCE PRINT COMMITTOR ENDPLUMED CENTER	generic vatom bias colvar symfunc
21.020	Reweighted Jarzynski sampling	methods	free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions	Kristof Bal	UPPER_WALLS REWEIGHT_BIAS CUSTOM OPES_METAD DUMPGRID ANN BF_CHEBYSHEV REWEIGHT_METAD COORDINATIONNUMBER METAD CONSTANT DISTANCE TD_WELLTEMPERED VES_LINEAR_EXPANSION BIASVALUE COMBINE LOAD FLUSH UNITS RESTRAINT OPT_AVERAGED_SGD CONVERT_TO_FES PRINT HISTOGRAM MOVINGRESTRAINT	setup generic gridtools opes annfunc ves function bias colvar symfunc
21.019	Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations	materials	Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen	Matteo Salvalaglio	COM MATHEVAL DISTANCE KDE PRINT TORSIONS	generic gridtools multicolvar vatom function colvar
21.010	Step by Step Strecker Amino Acid Synthesis from Ab Initio Prebiotic Chemistry	chemistry	Strecker reaction, free energy landscape, ab initio molecular dynamics, glycine, prebiotic synthesis	Théo Magrino	PRINT	generic
21.001	Substrate recognition and catalysis by glycosaminoglycan sulfotransferases	bio	metadynamics, well-tempered metadynamics, puckering, coordination	Tarsis Ferreira	INCLUDE PUCKERING UPPER_WALLS RANDOM_EXCHANGES METAD REWEIGHT_METAD DISTANCE PRINT ENERGY HISTOGRAM COORDINATION MOLINFO GROUP WHOLEMOLECULES DUMPGRID LOWER_WALLS	core generic gridtools bias colvar
20.023	metadynminer and metadynminer3d	methods	metadynamics, visualization, R	Vojtech Spiwok	TORSION PRINT METAD	generic bias colvar
20.018	Free energy barriers from biased molecular dynamics simulations	methods	kinetics, free energy barriers, chemical reactions, nucleation, metadynamics	Kristof Bal	UPPER_WALLS SPRINT REWEIGHT_BIAS DUMPGRID REWEIGHT_METAD COORDINATIONNUMBER METAD DISTANCE ENERGY PAIRENTROPY VOLUME CENTER LOCAL_AVERAGE CONTACT_MATRIX COMBINE Q6 DENSITY LOWER_WALLS LOAD FLUSH UNITS CONVERT_TO_FES PRINT HISTOGRAM COORDINATION	sprint adjmat setup generic gridtools volumes vatom function bias colvar symfunc
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	UNITS METAD PRINT COORDINATION DISTANCES CUSTOM	setup generic multicolvar function bias colvar
20.007	Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics	bio	metadynamics, loop movement, artificial intelligence	Pratyush Tiwary	TORSION UPPER_WALLS METAD DISTANCE PRINT RMSD COMBINE MOLINFO WHOLEMOLECULES RESTART	setup generic function bias colvar
20.005	Muscarinic M2 receptor/ligand Frequency-Adaptive Metadynamics and QM/MM calculations	bio	Frequency-adaptive metadynamics, multiple-walkers metadynamics, well-tempered metadynamics, GPCR, receptor, Adiabatic Bias MD	Riccardo Capelli	UPPER_WALLS COM MOLINFO DUMPGRID REWEIGHT_METAD METAD DISTANCE CONTACTMAP ABMD FUNCPATHMSD ENDPLUMED COMBINE LOWER_WALLS FLUSH READ CONVERT_TO_FES PRINT HISTOGRAM WHOLEMOLECULES	generic gridtools vatom function bias colvar
19.082	Ammonia Borane Dehydrogenation	chemistry	metadynamics, reaction discovery, hydrogen production, chemistry	Valerio Rizzi	FLUSH UNITS COORDINATIONNUMBER METAD PRINT ENDPLUMED EXTERNAL COMBINE GROUP RESTART	core setup generic function bias symfunc
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	UPPER_WALLS REWEIGHT_TEMP_PRESS REWEIGHT_BIAS DUMPGRID CELL TD_WELLTEMPERED ENERGY TD_MULTITHERMAL_MULTIBARIC VES_LINEAR_EXPANSION OPT_DUMMY RESTART VOLUME MATHEVAL BF_LEGENDRE COMBINE Q6 LOWER_WALLS LOAD OPT_AVERAGED_SGD READ CONVERT_TO_FES PRINT HISTOGRAM	setup generic gridtools ves function bias colvar symfunc
19.076	Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones	bio	molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics	Salvatore Assenza	UNITS PRINT MOVINGRESTRAINT ENDPLUMED GYRATION	generic bias colvar setup
19.067	Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways	bio	metadynamics, ligand unbinding	Jakub Rydzewski	UNITS UPPER_WALLS METAD PRINT PATHMSD RESTART LOWER_WALLS	generic bias colvar setup
19.051	Solid liquid interfacial free energy out of equilibrium	materials	metadynamics, nucleation, surface excess free energy	Gareth Tribello	FCCUBIC UNITS UPPER_WALLS METAD CELL PRINT ENDPLUMED AROUND LOWER_WALLS	setup generic volumes bias colvar symfunc
19.050	Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes	chemistry	metadynamics, membranes, Willard Chandler surface	Gareth Tribello	UPPER_WALLS READ CONVERT_TO_FES METAD PRINT HISTOGRAM REWEIGHT_BIAS COMBINE RESTART DUMPGRID DISTANCE_FROM_CONTOUR	setup generic gridtools function contour bias
19.036	Thermodynamics and kinetics of G protein-coupled receptor activation	bio	metadynamics, allostery, receptor conformation, GPCR, pharmacology	Davide Provasi	METAD COM DISTANCE FUNCPATHMSD PRINT CONTACTMAP RMSD ENDPLUMED WHOLEMOLECULES	generic vatom function bias colvar
19.003	EMMI ClpP	bio	metainference, cryo-EM	Max Bonomi	PRINT EMMI BIASVALUE MOLINFO GROUP	generic bias core isdb
19.000	VesDeltaF	methods	VES, convergence, suboptimal CVs	Michele Invernizzi	TORSION UNITS METAD PRINT ENERGY VES_DELTA_F ENDPLUMED POSITION RESTART LOAD	setup generic bias ves colvar
26.001	Molecular simulations Alx riboswitch	bio	RNA, riboswitch	Giovanni Bussi	RESTRAINT DISTANCE ERMSD MOLINFO PRINT MOVINGRESTRAINT MATHEVAL	bias colvar generic function
25.005	Mechanism of Nanocluster Formation from Machine-Learned Potential-based Simulations	chemistry	WT-metadynamics, metal nanoclusters, nucleation, neural network potential, deepMD	Vikas Tiwari, Tarak Karmakar	ANGLE RESTRAINT COORDINATIONNUMBER COORDINATION DISTANCE COM METAD UPPER_WALLS UNITS GROUP PRINT FIXEDATOM DISTANCES FLUSH COMBINE LOWER_WALLS	bias symfunc multicolvar function colvar core vatom generic setup
24.009	Weighted Shape Gaussian Mixture Models	bio	metadynamics, clustering	Glen Hocky	TORSION METAD UNITS GROUP PRINT	bias colvar core generic setup
24.005	Learning Markovian Dynamics with Spectral Maps	methods	spectral map, collective variables, machine learning	Jakub Rydzewski	BIASVALUE CUSTOM DISTANCE UNITS PRINT	bias function colvar generic setup
23.004	Melting curves of ice polymorphs in the vicinity of the liquid-liquid critical point	chemistry	water, liquid-liquid transition, second critical point, ice, polymorphs, melting curves, environment similarity, opes, density-functional theory, scan, machine learning potential	Pablo Piaggi	DUMPGRID RESTART UPPER_WALLS HISTOGRAM PRINT ENVIRONMENTSIMILARITY ECV_UMBRELLAS_LINE OPES_EXPANDED LOWER_WALLS	bias envsim gridtools generic setup opes
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	BIASVALUE CUSTOM METAD PATHMSD PRINT FLUSH DRR	bias function colvar drr 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	FUNNEL FUNNEL_PS DISTANCE COM METAD UPPER_WALLS PRINT PATHMSD WHOLEMOLECULES LOWER_WALLS	bias funnel colvar vatom generic
22.004	Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques	chemistry	reaction discovery, OPES, collective variables	Umberto Raucci	OPES_METAD_EXPLORE CUSTOM COORDINATION PYTORCH_MODEL COM DISTANCE UPPER_WALLS OPES_METAD UNITS GROUP PRINT MATHEVAL LOAD LOWER_WALLS	bias function colvar core vatom generic pytorch opes setup
21.049	Multiple-path-metadynamics and PathMaps	methods	path-CV, metadynamics, multiple-walker, multiple paths, pathmap	Alberto Pérez-de-Alba-Ortíz	TORSION CUSTOM RESTRAINT METAD UPPER_WALLS ENSEMBLE UNITS PRINT MOVINGRESTRAINT CONSTANT COMBINE LOAD LOWER_WALLS	bias function colvar generic setup
21.037	Molecular Dynamics simulations of RBD/hACE2 complexes	bio	SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain	Max Bonomi	DISTANCE PRINT RMSD	colvar generic
21.005	Crystallization Collective Variable	methods	Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA	Tarak Karmakar	PYTORCH_MODEL OPES_METAD UPPER_WALLS GROUP PRINT LOWER_WALLS FLUSH LOAD MATHEVAL	bias function core generic pytorch opes setup
20.028	Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane	bio	metadynamics, KRas-4B, anionic membrane	Huixia Lu	DISTANCE METAD CENTER RESTART FIT_TO_TEMPLATE PRINT	bias colvar vatom generic setup
20.022	Unified Approach to Enhanced Sampling	methods	OPES, expanded ensembles, importance sampling	Michele Invernizzi	TORSION POSITION UNITS ECV_UMBRELLAS_LINE MATHEVAL LOAD VOLUME UPPER_WALLS ENERGY CUSTOM ECV_LINEAR Q6 PRINT OPES_EXPANDED WHOLEMOLECULES ECV_MULTITHERMAL_MULTIBARIC MOLINFO ECV_MULTITHERMAL RMSD ENDPLUMED ENVIRONMENTSIMILARITY	bias symfunc function colvar envsim generic setup opes
20.004	Data-driven collective variables for enhanced sampling	methods	collective variables, machine learning, deep-lda	Luigi Bonati	TORSION DISTANCE PYTORCH_MODEL OPES_METAD COM UPPER_WALLS UNITS GROUP PRINT LOWER_WALLS ENDPLUMED FLUSH LOAD MATHEVAL	bias function colvar core vatom generic pytorch opes setup
19.048	Understanding Ligand Binding Selectivity in a Prototypical GPCR Family	bio	metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding	Francesco Gervasio	BIASVALUE DISTANCE COM METAD UPPER_WALLS PRINT MATHEVAL WHOLEMOLECULES CONSTANT LOWER_WALLS	bias function colvar vatom generic
19.017	Ligand binding pathways exploration	bio	metadynamics, ligand binding	Riccardo Capelli	DUMPGRID COORDINATION COM METAD UPPER_WALLS FIT_TO_TEMPLATE WRAPAROUND POSITION GROUP PRINT HISTOGRAM REWEIGHT_METAD ENDPLUMED CONVERT_TO_FES FLUSH WHOLEMOLECULES READ MATHEVAL	bias function colvar core vatom gridtools generic
26.000	OPES simulations of disordered proteins	bio	OPES, IDPs	Julian Streit	PRINT RESTART ECV_MULTITHERMAL OPES_EXPANDED ENERGY	colvar generic opes setup
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	GYRATION INCLUDE CENTER PRINT SAXS DISTANCE UPPER_WALLS WHOLEMOLECULES MOLINFO MOVINGRESTRAINT METAD GROUP	core generic colvar bias isdb vatom
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	PRINT UPPER_WALLS LOWER_WALLS COM FUNNEL_PS METAD FUNNEL	vatom generic funnel bias
25.021	All You Need Is Water. Converging Ligand Binding Simulations with Hydration Collective Variables	bio	OPES Explore, ligand binding, binding free energy, water, hydration CVs, SAMPL challenge, host-guest	Valerio Rizzi	CENTER PRINT ANGLE FIT_TO_TEMPLATE DISTANCE UPPER_WALLS WHOLEMOLECULES FIXEDATOM COORDINATION ENERGY GROUP MATHEVAL OPES_METAD_EXPLORE	core function generic colvar bias vatom opes
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 GHOST PRINT DISTANCE CUSTOM RMSD ECV_MULTITHERMAL MOLINFO COORDINATION OPES_EXPANDED ENERGY GROUP COMBINE OPES_METAD_EXPLORE	core function generic colvar vatom opes
25.008	Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting	methods	metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting	Dhiman Ray	TORSION PRINT ENDPLUMED BIASVALUE UNITS DISTANCE CUSTOM RMSD WHOLEMOLECULES UPPER_WALLS LOWER_WALLS MOLINFO POSITION OPES_METAD METAD ENERGY GROUP PYTORCH_MODEL	core function generic pytorch colvar bias setup opes
24.029	Combination of OPES and OPES-Explore	methods	OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin	Dhiman Ray	BIASVALUE FLUSH WHOLEMOLECULES RMSD LOWER_WALLS FIT_TO_TEMPLATE PYTORCH_MODEL CENTER ENDPLUMED CONTACTMAP UNITS UPPER_WALLS MOLINFO POSITION ENERGY COMBINE PRINT DISTANCE CUSTOM FIXEDATOM OPES_METAD COORDINATION GROUP INCLUDE METAD MATHEVAL OPES_METAD_EXPLORE	core function generic pytorch colvar bias vatom setup opes
24.027	Proline cis and trans subensembles of a disordered peptide	bio	intrinsically disordered proteins, proline cis trans isomerisation, metadynamics, collective variables	Alice Pettitt	PARABETARMSD TORSION GYRATION PRINT ANTIBETARMSD ALPHARMSD ENDPLUMED INCLUDE FLUSH DISTANCE WHOLEMOLECULES MOLINFO COORDINATION DIHCOR PBMETAD GROUP COMBINE	core function generic multicolvar secondarystructure colvar bias
24.024	Host-Guest binding free energies à la carte, an automated OneOPES protocol	bio	OneOPES, ligand binding, binding free energy,SAMPL challenge, host-guest	Valerio Rizzi	ENERGY CENTER TORSION PRINT ENDPLUMED ANGLE DISTANCE UPPER_WALLS WHOLEMOLECULES LOWER_WALLS ECV_MULTITHERMAL FIXEDATOM COORDINATION OPES_EXPANDED FIT_TO_TEMPLATE GROUP MATHEVAL OPES_METAD_EXPLORE	core function generic colvar bias vatom opes
24.018	A new route to the prebiotic synthesis of glycine via ab initio-based machine learning calculations	chemistry	prebiotic chemistry, glycine, Strecker synthesis, ab initio calculations, machine learning	Léon HUET	DISTANCE PRINT	generic colvar
24.004	Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables	materials	metadynamics, nucleation, machine learning	Ziyue Zou	INCLUDE PRINT RESTART LOAD METAD GROUP	core generic bias setup
23.040	Supramolecular capsules assembly dynamics	chemistry	Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics	Riccardo Capelli	CENTER PRINT DISTANCES UNITS DISTANCE CUSTOM WHOLEMOLECULES FLUSH COM POSITION METAD GROUP	core function generic multicolvar colvar bias vatom setup
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	BIASVALUE PRINT WHOLEMOLECULES MOLINFO GHBFIX ERMSD COORDINATION METAD COMBINE	function generic colvar bias
23.031	Identifying small molecules binding sites in RNA conformational ensembles with SHAMAN	bio	RNA, metadynamics, probes, mixed-solvent MD, small molecules, binding sites	Max Bonomi	CENTER WRAPAROUND PRINT DISTANCES SHADOW UPPER_WALLS WHOLEMOLECULES MOLINFO POSITION METAD FIT_TO_TEMPLATE GROUP	core generic multicolvar colvar bias isdb vatom
23.016	Activation/deactivation free-energy profiles for the β2-adrenergic receptor: Ligand modes of action	bio	G protein coupled receptor, beta-adrenergic, receptor activation, partial agonism, metadynamics	Timothy Clark	PRINT REWEIGHT_METAD DISTANCE RMSD WHOLEMOLECULES DUMPGRID MOLINFO HISTOGRAM CONVERT_TO_FES METAD READ MATHEVAL	function generic colvar bias gridtools
22.027	Molecular Dynamics simulations of BANAL-236 RBD-hACE2 complexes	bio	SARS-CoV-2, COVID-19, MD, human-ACE2, spike, BANAL-236, receptor-binding domain	Max Bonomi	RMSD PRINT	generic colvar
22.015	Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome	bio	photodynamics, bacteriophytochrome, variationally enhanced sampling	Jakub Rydzewski	TORSION PRINT TD_UNIFORM BF_FOURIER VES_LINEAR_EXPANSION OPT_AVERAGED_SGD	ves generic colvar
22.008	Ab initio metadynamics determination of temperature-dependent free-energy landscape in ultrasmall silver clusters	materials	Well tempered metadynamics, ab-initio, ase	Daniel Sucerquia	GYRATION UNITS FLUSH UPPER_WALLS DISTANCE LOWER_WALLS COM COORDINATION COORDINATIONNUMBER METAD COMBINE	symfunc function generic colvar bias vatom setup
22.001	Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials	methods	enhanced sampling, variationally enhanced sampling, ves, metadynamics, bias representation, wavelets, adam	Benjamin Pampel	TD_WELLTEMPERED BF_WAVELETS FLUSH BF_LEGENDRE VES_LINEAR_EXPANSION VES_OUTPUT_BASISFUNCTIONS BF_CHEBYSHEV OPT_AVERAGED_SGD UNITS TD_UNIFORM UPPER_WALLS POSITION BF_CUBIC_B_SPLINES ENERGY BF_GAUSSIANS PRINT DISTANCE COORDINATION INCLUDE OPT_ADAM METAD	ves generic colvar bias setup
22.000	Amyloid precursor protein processing by human γ-secretase	bio	Bias Exchange Metadynamics, Helix unfolding, coupled binding	Xiaoli Lu	CENTER ANTIBETARMSD PRINT RANDOM_EXCHANGES CONTACTMAP UNITS ALPHARMSD DISTANCE MOLINFO COORDINATION METAD INCLUDE	generic secondarystructure colvar bias vatom setup
21.042	Peptoid-mediated Au nanocrystal growth	materials	parallel-bias metadynamics, peptoid, Au	Xin Qi	GYRATION PRINT DISTANCE UPPER_WALLS COM MOLINFO PBMETAD	vatom generic colvar bias
21.040	A structural ensemble of a tau-microtubule complex reveals regulatory tau phosphorylation and acetylation mechanisms	bio	EMMI, CryoEM, tau-microtubules, post-translational modifications, chemical mutagenesis, structural ensemble, Metainference	Faidon Brotzakis	BIASVALUE PRINT RESTART DISTANCE UPPER_WALLS WHOLEMOLECULES COM MOLINFO EMMI GROUP	core generic colvar bias isdb vatom setup
21.017	All-atom simulations of the Vav1 AD construct	bio	metadynamics, parallel-bias, well-tempered	Simone Orioli	PRINT ALPHARMSD RESTART CONTACTMAP WHOLEMOLECULES MOLINFO PBMETAD ALPHABETA METAD GROUP REWEIGHT_BIAS	core generic multicolvar secondarystructure colvar bias setup
21.013	Role of vibrational excitation in heterogeneous catalysis	chemistry	catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption	Kristof Bal	DISTANCES REWEIGHT_METAD TD_GRID FLUSH DUMPGRID VES_LINEAR_EXPANSION LOWER_WALLS ANGLES OPT_AVERAGED_SGD BF_CHEBYSHEV UNITS UPPER_WALLS RESTRAINT UWALLS HISTOGRAM COMBINE EXTERNAL PRINT DISTANCE LOAD COORDINATION COORDINATIONNUMBER CONVERT_TO_FES METAD REWEIGHT_BIAS	symfunc ves function generic multicolvar colvar bias setup gridtools
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	PRINT RESTART UPPER_WALLS WHOLEMOLECULES PATHMSD LOWER_WALLS METAD	generic colvar bias setup
20.006	Class B GPCR activation mechanism	bio	metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding	Francesco Gervasio	CENTER PRINT MATHEVAL DISTANCE UPPER_WALLS RMSD WHOLEMOLECULES LOWER_WALLS MOLINFO METAD ENERGY COMBINE	function generic colvar bias vatom
20.002	Exploring conformational dynamics of the extracellular Venus flytrap domain of the GABAB receptor, a path-metadynamics study	bio	Metadynamics, path CVs	Riccardo Ocello	PRINT RESTART UPPER_WALLS WHOLEMOLECULES PATHMSD MOLINFO METAD GROUP	core generic colvar bias setup
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	PRINT ENDPLUMED MATHEVAL REWEIGHT_METAD DISTANCE UPPER_WALLS LOWER_WALLS DUMPGRID COM HISTOGRAM ABMD CONVERT_TO_FES METAD READ COMBINE	function generic colvar bias vatom gridtools
19.064	Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations	materials	metadynamics, peptide-surface binding	Jim Pfaendtner	GYRATION PRINT DISTANCE UPPER_WALLS COM MOLINFO METAD ENERGY	vatom generic colvar bias
19.039	Funnel Metadynamics	bio	funnel-metadynamics, absolute binding free energy, ligand-receptor complexes	Vittorio Limongelli	PRINT DISTANCE UPPER_WALLS WHOLEMOLECULES RMSD LOWER_WALLS COM FUNNEL_PS METAD FUNNEL	generic colvar bias vatom funnel
19.032	Chemical reaction in solution using path collective variables based on coordination patterns	chemistry	chemical reactions, solutions, metadynamics, coordination patterns	Fabio Pietrucci	PRINT DISTANCES RESTART FLUSH UPPER_WALLS PATH METAD	mapping generic multicolvar bias setup
19.021	Coarse-Grained Directed Simulation	methods	experiment directed simulation, coarse-grain, bias	Glen Hocky	TORSION PRINT DISTANCE EDS RESTRAINT COMBINE	function generic colvar bias eds
19.019	FA-MetaD-JCP-Wang-et-al	bio	Frequency adaptive metadynamics; peptide	Kresten Lindorff-Larsen	PRINT METAD FLUSH MOLINFO ALPHABETA COMMITTOR COMBINE	function generic multicolvar bias
19.016	Succinnic acid gamma polymorph	materials	Succinnic acid, conformers, polymorphs, metadynamics	Matteo Salvalaglio	VOLUME TORSION PRINT ENDPLUMED UPPER_WALLS LOWER_WALLS COMBINE METAD ENERGY CELL MATHEVAL	function generic colvar bias
25.023	Molecular simulations of Tau-protein oligomers	bio	metadynamics, proteins, aggregation	Giovanni Bussi	CUSTOM CONTACTMAP RMSD RESTART RESTRAINT METAD FLUSH PRINT	bias function generic colvar setup
25.013	Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices	bio	umbrella sampling, temperature ramping	Alexander Berlaga	PYTORCH_MODEL GYRATION DISTANCE RESTRAINT PRINT	pytorch generic colvar bias
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	CUSTOM BIASVALUE POSITION TORSION INCLUDE COORDINATION CELL OPES_METAD DISTANCE LOAD FLUSH ENERGY UNITS PRINT MATHEVAL COMBINE	opes bias function setup generic colvar
25.011	Chiral perovskite nucleation	chemistry	metadynamics, chiral perovskites, nucleation	Adriana Pietropaolo	PBMETAD RESTART DISTANCE MULTI_RMSD UPPER_WALLS LOWER_WALLS UNITS PRINT MATHEVAL	bias function setup generic colvar
24.030	NMR guided simulation of dsRBD	bio	Metainference, NMR, protein dynamics	Debadutta Patra	RDC STATS GROUP METAINFERENCE ENSEMBLE DISTANCE ALPHABETA MOLINFO WHOLEMOLECULES FLUSH PRINT	core multicolvar isdb function generic colvar
24.016	Cryo-EM guided simulations of ribozyme	bio	metainference, cryo-EM	Giovanni Bussi	BIASVALUE EMMIVOX INCLUDE GROUP ERMSD RESTRAINT MOLINFO WHOLEMOLECULES PRINT	core bias isdb generic colvar
24.010	Oxytocin metadynamics simulation	bio	metadynamics, oxytocin, peptide	Jan Beránek	TORSION RESTART WHOLEMOLECULES METAD FLUSH PRINT	bias generic colvar 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 COMBINE OPES_METAD DISTANCE UPPER_WALLS FLUSH LOWER_WALLS UNITS PRINT COMMITTOR	opes function setup generic colvar bias
23.045	Minute-timescale simulations of G Protein Coupled Receptor A2A activation mechanism reveal a receptor pseudo-active state	bio	Path CVs Metadynamics, GPCRs activation transition	Vittorio Limongelli	ALPHARMSD CONTACTMAP INCLUDE PATHMSD DISTANCE UPPER_WALLS FUNCPATHMSD MOLINFO METAD LOWER_WALLS PRINT	bias function secondarystructure generic colvar
23.039	Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation	chemistry	metadynamics, ligand dissociation	Eric Beyerle	FIXEDATOM DUMPMASSCHARGE DISTANCE UPPER_WALLS RESTRAINT MOLINFO METAD CENTER PRINT COMBINE	vatom bias function generic colvar
23.036	Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water?	bio	NaCl, nucleation, metadynamics	Ruiyu Wang	Q6 Q4 COORDINATIONNUMBER VOLUME ENERGY METAD MATHEVAL PRINT COMBINE	function symfunc generic colvar bias
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	CUSTOM FIT_TO_TEMPLATE GROUP COM UPPER_WALLS CENTER WRAPAROUND TORSION ENDPLUMED OPES_METAD_EXPLORE MOLINFO FLUSH ENERGY COMMITTOR COORDINATION OPES_METAD DISTANCE WHOLEMOLECULES LOWER_WALLS PRINT BIASVALUE POSITION MATHEVAL UNITS	opes core vatom function setup generic colvar bias
23.023	Rational design of novel biomimetic sequence-defined polymers for mineralization applications	methods	metadynamics, surface binding, biomimetic mineralization	Kaylyn Torkelson	PBMETAD COORDINATION GYRATION COM DISTANCE UPPER_WALLS PRINT	generic vatom colvar bias
23.021	Into the Dynamics of Rotaxanes at Atomistic Resolution	materials	metadynamics, rotaxanes, molecular shuttles, molecular machines	Luigi Leanza	CUSTOM FIXEDATOM TORSION DISTANCE UPPER_WALLS METAD CENTER PRINT MATHEVAL	vatom function generic colvar bias
23.020	FEP simulations of ATOX1 homodimer	chemistry	parallel bias metadynamics, FEP, free-energy of metal ion dissociation	Adriana Pietropaolo	BIASVALUE PBMETAD ANGLE DISTANCE WHOLEMOLECULES MATHEVAL CONSTANT PRINT	generic colvar bias function
23.011	OneOPES, a combined enhanced sampling method to rule them all	bio	OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding	Valerio Rizzi	ECV_MULTITHERMAL TORSION ENDPLUMED OPES_METAD_EXPLORE DISTANCE MOLINFO METAD ENERGY PRINT OPES_EXPANDED	opes generic colvar bias
23.008	PBMetaD simulations of Histatin5	bio	metadynamics, IDP, Rg, PPII	Francesco Pesce	TORSION PBMETAD GYRATION GROUP MOLINFO WHOLEMOLECULES PRINT	core generic colvar bias
23.006	Transcription factor unbinding	bio	metadynamics, DNA, conformational changes	Malin Lüking	ALPHARMSD CONTACTMAP COM DISTANCE ANGLE MOLINFO METAD DUMPFORCES PRINT	vatom bias secondarystructure generic colvar
22.038	Enhanced Sampling Aided Design of Molecular Photoswitches	chemistry	reaction discovery, OPES explore, graph CV	Umberto Raucci	CUSTOM COORDINATION PYTORCH_MODEL OPES_METAD_EXPLORE UNITS PRINT	opes function pytorch generic colvar setup
22.036	Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction	bio	Well-tempered MetaDynamics with Hamiltonian Replica Exchange	Miroslav Krepl	CUSTOM BIASVALUE COORDINATION GHBFIX GROUP UPPER_WALLS MOLINFO LOAD METAD FLUSH PRINT COMBINE	core bias function setup generic colvar
22.023	Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy	bio	CryoEM, MEMMI,EMMI, Metadynamics, Metainference, IAPP, structural ensemble	Faidon Brotzakis	EMMI BIASVALUE TORSION PBMETAD COORDINATION RMSD GROUP COM RESTART UPPER_WALLS MOLINFO WHOLEMOLECULES PRINT	core vatom bias isdb setup generic colvar
22.021	Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations	chemistry	Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella	Sigbjørn Løland Bore	INCLUDE ENVIRONMENTSIMILARITY UPPER_WALLS ECV_UMBRELLAS_LINE LOWER_WALLS PRINT OPES_EXPANDED	opes generic bias envsim
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	CUSTOM FIXEDATOM FIT_TO_TEMPLATE COMMITTOR COORDINATION RMSD PYTORCH_MODEL GROUP OPES_METAD CENTER DISTANCE UPPER_WALLS WHOLEMOLECULES LOWER_WALLS PRINT MATHEVAL	opes core vatom bias function pytorch generic colvar
22.005	Collective Variable for Metadynamics Derived from AlphaFold Output	bio	AlphaFold, protein folding, protein structure prediction, metadynamics, deep learning, free energy simulation, collective variable	Vojtech Spiwok	LOAD PRINT WHOLEMOLECULES METAD	generic setup bias
22.003	Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling	methods	opes, metadynamics, reweighting, alanine, muller	Michele Invernizzi	CUSTOM OPES_EXPANDED BIASVALUE POSITION TORSION ENDPLUMED PBMETAD OPES_METAD OPES_METAD_EXPLORE LOWER_WALLS UPPER_WALLS METAD ENERGY UNITS PRINT ECV_UMBRELLAS_FILE ECV_MULTITHERMAL	opes bias function setup generic colvar
21.051	Automatic learning of hydrogen-bond fixes in an AMBER RNA force field	methods	force field, RNA	Giovanni Bussi	BIASVALUE COORDINATION ERMSD MOLINFO WHOLEMOLECULES METAD PRINT COMBINE	generic colvar bias function
21.030	Thermodynamic Basis for Stabilization of Helical Peptoids by Chiral Sidechains	bio	parallel bias parallel tempered metadynamics in WTE, synthetic foldamers, self-assembly, peptoid secondary structure	Jim Pfaendtner	TORSION PBMETAD COORDINATION INCLUDE GYRATION COM DISTANCE ALPHABETA METAD ENERGY PRINT	vatom multicolvar bias generic colvar
21.023	Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling	methods	enhanced sampling, collective variables, machine learning	Jakub Rydzewski	CUSTOM REWEIGHT_METAD BIASVALUE TORSION INCLUDE CONSTANT DISTANCE METAD ENERGY UNITS PRINT	bias function generic colvar 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	core vatom colvar generic
20.033	COVID-19 Spike protein opening transition mechanism	bio	EMMI, CryoEM, COVID-19, Spike, Metainference	Faidon Brotzakis	HISTOGRAM EMMI BIASVALUE RMSD GROUP READ MOLINFO WHOLEMOLECULES DISTANCES CONVERT_TO_FES PRINT DUMPGRID	core bias isdb multicolvar gridtools generic colvar
20.024	Gaussian Mixture Based Enhanced Sampling (GAMBES)	methods	enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias	Jayashrita Debnath	TORSION GROUP DISTANCE UPPER_WALLS LOAD ENERGY DISTANCES LOWER_WALLS UNITS PRINT COMBINE	core multicolvar bias function generic colvar setup
20.019	Systematic finite-temperature reduction of crystal energy landscapes	materials	crystals, organics, structure prediction	Matteo Salvalaglio	CELL UPPER_WALLS VOLUME ENERGY METAD LOWER_WALLS PRINT MATHEVAL	generic function colvar bias
20.017	FISST	methods	FISST, force, peptide, sampling, tempering	Glen Hocky	BIASVALUE FISST GYRATION GROUP DISTANCE RESTRAINT ENERGY UNITS PRINT MATHEVAL	core bias function setup generic fisst colvar
20.016	Predicting polymorphism in molecular crystals using orientational entropy	materials	metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy	Pablo Piaggi	INCLUDE GROUP VOLUME UPPER_WALLS LOAD METAD CENTER PRINT	core vatom bias setup generic colvar
20.015	Rational design of ASCT2 inhibitors using an integrated experimental-computational approach	bio	ASCT2 transporter, small-molecules, cryo-EM, metainference	Max Bonomi	BIASVALUE EMMIVOX DUMPATOMS GROUP MOLINFO WHOLEMOLECULES LOAD PRINT	core isdb setup generic bias
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	PROJECTION_ON_AXIS BIASVALUE CONTACTMAP INCLUDE GROUP COM DISTANCE UPPER_WALLS FUNCPATHGENERAL MOLINFO WHOLEMOLECULES METAD LOAD LOWER_WALLS CONSTANT PRINT MATHEVAL	core vatom bias function setup generic colvar
19.077	Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations	materials	metadynamics, peptide-surface binding	Jim Pfaendtner	GYRATION COM DISTANCE UPPER_WALLS MOLINFO METAD ENERGY PRINT	generic vatom colvar bias
19.063	Protein-ligand binding through metadynamics with path CVs	bio	metadynamics, path CVs, ligand binding	Mattia Bernetti	PATHMSD UPPER_WALLS WHOLEMOLECULES METAD LOWER_WALLS PRINT	generic colvar bias
19.062	Elucidating molecular design principles for charge-alternating peptides	bio	peptide folding, metadynamics, well-tempered ensemble, parallel tempering	Jim Pfaendtner	GYRATION WHOLEMOLECULES METAD ENERGY PRINT	generic colvar 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	TORSION INCLUDE METAD PRINT RANDOM_EXCHANGES	generic colvar bias
19.012	Martini-Beads multi-scale SAXS	methods	metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex	Carlo Camilloni	BIASVALUE ENDPLUMED INCLUDE RMSD STATS GROUP DISTANCE UPPER_WALLS SAXS MOLINFO WHOLEMOLECULES RESTRAINT CENTER PRINT	core vatom bias isdb function generic colvar
19.010	Multi-domain protein dynamics	bio	metainference, NMR, protein dynamics	Carlo Camilloni	TORSION PBMETAD ENDPLUMED STATS RDC DHENERGY GROUP METAINFERENCE ENSEMBLE DISTANCE ALPHABETA DIHCOR MOLINFO WHOLEMOLECULES UPPER_WALLS RESTRAINT CENTER PRINT	core vatom isdb bias multicolvar function generic colvar
26.002	A Transferable and Robust Computational Framework for Class A GPCR Activation Free Energies	bio	OneOPES, GPCR, ADRB1, activation, euclidean path, microswitches, conformational changes, allostery	Valerio Rizzi	VOLUME DISTANCE PATHMSD PRINT COORDINATION PATH ECV_MULTITHERMAL CUSTOM OPES_METAD_EXPLORE UPPER_WALLS RMSD OPES_EXPANDED GROUP ENERGY LOWER_WALLS CENTER	colvar vatom function bias opes core generic mapping
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	DISTANCE PATHMSD PRINT DISTANCES COORDINATION GHOST OPES_EXPANDED ECV_MULTITHERMAL CUSTOM OPES_METAD_EXPLORE UPPER_WALLS RMSD GROUP ENERGY LOWER_WALLS CENTER	colvar vatom function bias multicolvar opes core generic
25.003	Surrogate Model CV	methods	Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding	Sompriya Chatterjee	COMMITTOR DISTANCE MOLINFO PRINT COMBINE ENDPLUMED PYTORCH_MODEL CUSTOM WHOLEMOLECULES GROUP OPES_METAD ENERGY MATHEVAL TORSION	colvar function pytorch opes core generic
24.021	Ab initio machine learning simulation of calcium carbonate from aqueous solutions to the solid state	chemistry	ion pairing, caco3, opes, proton transfer, crystallization	Pablo Piaggi	DISTANCE PRINT COORDINATION UPPER_WALLS OPES_METAD ENERGY	colvar bias generic opes
24.007	SWISH-X	bio	swish-x, SWISH-X, swish, expanded SWISH	Alberto Borsatto	PRINT CONTACTMAP ECV_MULTITHERMAL WHOLEMOLECULES UPPER_WALLS INCLUDE ENERGY OPES_EXPANDED MOLINFO	colvar opes generic bias
24.006	Water vapor condensation	chemistry	metadynamics, homogeneous condensation, chemical potential	Shenghui Zhong	CLUSTER_PROPERTIES METAD PRINT COORDINATIONNUMBER UPPER_WALLS UNITS CONTACT_MATRIX DFSCLUSTERING CLUSTER_NATOMS	clusters adjmat setup bias symfunc 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	HISTOGRAM REWEIGHT_METAD DISTANCE READ PRINT METAD WHOLEMOLECULES RMSD CONVERT_TO_FES DUMPGRID MATHEVAL MOLINFO	colvar gridtools bias function generic
22.043	Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES	bio	OPES, RNA, Tetraloop, Folding	Gül Zerze	PRINT ECV_MULTITHERMAL WHOLEMOLECULES ENERGY ECV_UMBRELLAS_LINE CONTACTMAP OPES_EXPANDED	colvar opes generic
22.029	Angiotensin-1-7_Metadynamics	bio	Metadynamics, Angiotensin-(1-7), peptide	L.-América Chi	PRINT METAD COORDINATION FLUSH GYRATION WHOLEMOLECULES UPPER_WALLS GROUP LOWER_WALLS	colvar core bias generic
22.026	Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification	materials	Peptoid, silica	Jim Pfaendtner	DISTANCE PRINT GYRATION UPPER_WALLS COM PBMETAD MOLINFO	colvar bias generic vatom
22.022	Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir	bio	RMSD, protein-ligand interactions	Isabell Grothaus	RMSD PRINT	colvar generic
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	VOLUME PRINT COMBINE METAD COORDINATION ENDPLUMED CUSTOM	colvar function generic bias
21.026	Probing allosteric regulations with coevolution-driven molecular simulations	bio	metadynamics, coevolution, allostery, adenylate cyclase	Francesco Colizzi	DISTANCE PATHMSD PRINT METAD WHOLEMOLECULES UPPER_WALLS UNITS COM	colvar vatom setup bias generic
21.022	Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly	materials	parallel bias metadynamics, adsorption, peptide	Xin Qi	DISTANCE PRINT COM GYRATION UPPER_WALLS ENERGY LOWER_WALLS PBMETAD MOLINFO	colvar vatom generic bias
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	RESTRAINT STATS PRINT COMBINE COORDINATION WHOLEMOLECULES MOLINFO	colvar bias generic function
20.009	The dynamics of linear polyubiquitin	bio	saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics	Carlo Camilloni	DISTANCE SAXS STATS PRINT MOLINFO FLUSH GYRATION WHOLEMOLECULES ALPHABETA METAINFERENCE PBMETAD CENTER TORSION ENSEMBLE	colvar vatom function bias isdb multicolvar generic
19.074	Asymmetric base pair opening in nucleic acids	bio	double helix, DNA, RNA, unwindability	Giovanni Bussi	RESTRAINT DISTANCE COORDINATION ENDPLUMED WHOLEMOLECULES LOWER_WALLS	colvar bias generic
19.071	Time-independent free energies from metadynamics via Mean Force Integration	methods	metadynamics, mean force integration, MFI, thermodynamic integration	Matteo Salvalaglio	HISTOGRAM COMMITTOR DISTANCE READ REWEIGHT_METAD METAD PRINT REWEIGHT_BIAS EXTERNAL BIASVALUE CONVERT_TO_FES DUMPGRID MATHEVAL TORSION	colvar gridtools bias function generic
19.070	Unexpected Dynamics in the UUCG RNA Tetraloop	bio	well-tempered metadynamics, RNA, UUCG, maximum entropy	Sandro Bottaro	DISTANCE TORSION PRINT METAD WHOLEMOLECULES RMSD ERMSD MOLINFO	colvar bias generic
19.069	Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen	materials	ibuprofen, crystal, solvent, surface	Matteo Salvalaglio	DISTANCE PRINT ENDPLUMED GROUP INCLUDE CENTER	colvar core vatom generic
19.068	Rethinking Metadynamics	methods	metadynamics, opes, convergence	Michele Invernizzi	METAD PRINT ENDPLUMED POSITION OPES_METAD UNITS EXTERNAL TORSION	colvar setup bias opes generic
19.060	Neural networks-based variationally enhanced sampling	methods	ves, neural networks	Luigi Bonati	Q6 PRINT ENVIRONMENTSIMILARITY POSITION ENDPLUMED LOAD UNITS ENERGY TORSION	colvar setup symfunc generic envsim
19.058	Constrained MD for maintaining a cavity in a calculation	chemistry	constrained MD, porous molecules, porosity, cavity	Kim Jelfs	INPLANEDISTANCES PRINT DISTANCES FLUSH MOVINGRESTRAINT RESTART COM	vatom setup bias multicolvar generic
19.054	MetaFEP	methods	metadynamics, chemistry, free energy perturbation	GiovanniMaria Piccini	DISTANCE PRINT METAD COMBINE FLUSH UPPER_WALLS UNITS ENERGY LOWER_WALLS	colvar setup bias function generic
19.053	Capillary fluctuations with PLUMED	methods	nucleation, surface tension, capillary fluctuations	Gareth Tribello	MULTICOLVARDENS FIND_CONTOUR_SURFACE GROUP UNITS DUMPGRID FOURIER_TRANSFORM CENTER MORE_THAN FCCUBIC	vatom setup gridtools function symfunc contour core fourier
19.052	Gibbs free energy of homogeneous nucleation	materials	nucleation, surface excess free energy	Gareth Tribello	PRINT METAD ENDPLUMED CELL UPPER_WALLS UNITS FCCUBIC	colvar setup bias symfunc generic
19.042	Harmonic Linear Discriminant Analysis (HLDA)	methods	metadynamics, chemistry, HLDA	GiovanniMaria Piccini	DISTANCE PRINT METAD COMBINE FLUSH UPPER_WALLS UNITS ENERGY	colvar setup bias function generic
19.038	native state dynamics of human and mouse b2m	bio	metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation	Carlo Camilloni	PRINT ENDPLUMED FLUSH ALPHABETA WHOLEMOLECULES CS2BACKBONE UPPER_WALLS RESTART BIASVALUE GROUP LOWER_WALLS PBMETAD MOLINFO ANTIBETARMSD	setup bias isdb secondarystructure multicolvar core generic
19.026	Ice Nucleation on Cholesterol Crystals	materials	forward flux sampling, crystal nucleation, water, ice, organic crystals	Gabriele Cesare Sosso	COMMITTOR Q6 LOCAL_Q6 OUTPUT_CLUSTER ENDPLUMED FLUSH CLUSTER_WITHSURFACE MFILTER_MORE CONTACT_MATRIX DFSCLUSTERING CLUSTER_NATOMS	clusters adjmat symfunc multicolvar generic
19.022	eABF simulation of NANMA (alanine dipeptide)	methods	eABF, DRR, alanine dipeptide	Haochuan Chen	TORSION PRINT DRR	colvar generic drr
19.015	Ibuprofen conformational dynamics and thermodynamics surface	materials	Ibuprofen, crystal, surface, solvents, conformers, metadynamics	Matteo Salvalaglio	COMMITTOR DISTANCE PRINT METAD UPPER_WALLS LOWER_WALLS CENTER TORSION	colvar bias generic vatom
19.013	RNA FF FITTING	methods	force field, RNA	Giovanni Bussi	MOLINFO CONSTANT BIASVALUE PUCKERING INCLUDE MATHEVAL TORSION	colvar bias generic function
19.009	RNA tetraloops folding	bio	metadynamics, RNA, folding	Giovanni Bussi	PRINT METAD ENDPLUMED WHOLEMOLECULES RMSD ERMSD MOLINFO	colvar bias generic
19.007	EMMI Microtubules	bio	metainference, cryo-EM	Max Bonomi	PRINT BIASVALUE WHOLEMOLECULES GROUP EMMI MOLINFO	core bias generic isdb
25.024	Sampling glycan-glycan interactions for B22 calculations	bio	B22, glycan, carbohydrates, distance, REST2, metadynamics, RECT, replica exchange	Isabell Louise Grothaus	PRINT METAD RESTRAINT COM COMBINE DISTANCE POSITION	colvar generic bias vatom function
25.016	Advancing in silico drug design with Bayesian refinement of AlphaFold models	bio	bAIes, AlphaFold, Bayesian refinement, virtual screening, docking, small-molecule, enrichment	Samiran Sen	PRINT BIASVALUE BAIES GROUP	generic core isdb bias
25.010	Kinetic rates calculation with Ratchet&Pawl MD	methods	kinetics, ligand binding, ABMD, ratchet&pawl MD	Riccardo Capelli	PRINT COM FLUSH GROUP DISTANCE ABMD WHOLEMOLECULES COMMITTOR	colvar generic core bias vatom
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	PRINT METAD PUCKERING MOLINFO RESTRAINT DISTANCE RESTART TORSION MOVINGRESTRAINT	colvar generic setup bias
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	PRINT VOLUME READ MOLINFO ENERGY INCLUDE GYRATION UPDATE_IF TORSION CENTER DISTANCE RESTART PBMETAD DUMPATOMS WHOLEMOLECULES	colvar generic setup bias vatom
24.036	Leveraging cryptic ligand envelopes through enhanced molecular simulations	bio	HREX, conformational heterogeneity, drug discovery, ligand binding, plitidepsin, aplidin, ligand-target complexes, cryptic ligand envelope	Francesco Colizzi	PRINT ANGLE DUMPGRID CONVERT_TO_FES GROUP WHOLEMOLECULES DISTANCE HISTOGRAM TORSION COORDINATION	colvar generic core gridtools
24.028	All-atom simulations of RNA-membrane interactions	bio	metadynamics, membrane, RNA	Giovanni Bussi	PRINT SORT METAD DISTANCES PUCKERING MOLINFO MATHEVAL GHOST GYRATION LOWER_WALLS COMBINE CENTER DISTANCE WHOLEMOLECULES UPPER_WALLS POSITION GROUP	multicolvar colvar generic core bias vatom function
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	PRINT FIXEDATOM CUSTOM COORDINATION LOWER_WALLS PYTORCH_MODEL PATH TORSION CENTER FIT_TO_TEMPLATE DISTANCE RESTART UPPER_WALLS WHOLEMOLECULES GROUP OPES_METAD	colvar generic setup pytorch core opes bias mapping vatom function
24.013	Estimating Free Energy Surfaces and their Convergence from multiple, independent static and history-dependent biased molecular-dynamics simulations with Mean Force Integration	methods	Mean Force Integration, Convergence, FES, Umbrella Sampling	Matteo Salvalaglio	PRINT METAD MATHEVAL MOLINFO ENERGY RESTRAINT FLUSH BIASVALUE DISTANCE RESTART COORDINATIONNUMBER TORSION COMMITTOR	colvar generic setup bias symfunc function
24.012	Molecular simulations to investigate the impact of N6-methylation in RNA recognition	bio	metadynamics, alchemistry, RNA modification, RNA:protein interactions	Giovanni Bussi	PRINT METAD MOLINFO DEBUG COM LOWER_WALLS COMBINE BIASVALUE GROUP CENTER DISTANCE UPPER_WALLS GHBFIX COORDINATION	generic colvar core bias vatom function
24.003	Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations	chemistry	steered molecular dynamics, foldamers, peptoids, bio-inspired	Kaylyn Torkelson	PRINT COM INCLUDE GYRATION WHOLEMOLECULES DISTANCE ALPHABETA TORSION COORDINATION MOVINGRESTRAINT	multicolvar colvar generic bias vatom
23.035	An Extended Metadynamics Protocol for Binding/Unbinding of Peptide Ligands to Class A G-Protein Coupled Receptors	bio	G protein coupled receptor, peptide ligands, metadynamics, multiple-walker	Timothy Clark	PRINT METAD CONSTANT MATHEVAL LOWER_WALLS BIASVALUE CENTER DISTANCE WHOLEMOLECULES UPPER_WALLS	colvar generic bias vatom function
23.018	Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention	materials	metadynamics, surface binding, peptide adsorption	Kaylyn Torkelson	PRINT COM DISTANCE PBMETAD GYRATION UPPER_WALLS	colvar generic vatom bias
23.015	MPCs aggregation	bio	opes_explore, dimerization, MPCs, self-assembly	Vikas Tiwari	PRINT METAD COORDINATION COM LOWER_WALLS OPES_METAD_EXPLORE GROUP CENTER DISTANCE UPPER_WALLS WHOLEMOLECULES CUSTOM	colvar generic core opes bias vatom function
23.012	JAK2 2D meta-eABF PMF with statistical analysis	bio	2D meta-eABF, path CV, PMF	Istvan Kolossvary	PRINT PATHMSD METAD DRR CUSTOM LOWER_WALLS FLUSH BIASVALUE UPPER_WALLS	colvar generic bias drr function
23.001	Quantum phase diagram of water	chemistry	Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella	Sigbjørn-Løland Bore	PRINT INCLUDE LOWER_WALLS ENVIRONMENTSIMILARITY OPES_EXPANDED ECV_UMBRELLAS_LINE RESTART UPPER_WALLS	generic setup opes bias envsim
22.044	Colloid Crystallisation Analyses	materials	Q4, Q6, Pair Entropy, DFS	Aaron Finney	PRINT Q6 LOCAL_AVERAGE DFSCLUSTERING CONTACT_MATRIX Q4 MFILTER_LESS LOCAL_Q4 CLUSTER_NATOMS COMBINE LOCAL_Q6 COORDINATIONNUMBER MFILTER_MORE GROUP	multicolvar generic core adjmat clusters symfunc function
22.042	Metadynamics of NSP10 and variants	bio	metadynamics, NSP10, crystal structure, variants	Shozeb Haider	PRINT METAD TORSION	colvar 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	PRINT METAD DISTANCES DISTANCE	multicolvar colvar generic bias
22.018	Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations	bio	ligand binding, docking, EMMI, LAT1	Max Bonomi	PRINT MOLINFO BIASVALUE WHOLEMOLECULES EMMIVOX LOAD GROUP	generic setup core isdb bias
22.016	Homogeneous ice nucleation in an ab initio machine learning model of water	chemistry	ice, water, nucleation, seeding, environment similarity, interfacial free energy, interfaces	Pablo Piaggi	PRINT DUMPGRID VOLUME OPES_METAD ENERGY ENVIRONMENTSIMILARITY UPPER_WALLS RESTART AROUND HISTOGRAM CUSTOM	colvar generic volumes setup gridtools opes bias envsim function
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	PRINT METAD MOLINFO COORDINATION FLUSH TORSION WHOLEMOLECULES ALPHARMSD DISTANCE ALPHABETA ANGLE UPPER_WALLS	multicolvar colvar generic secondarystructure bias
21.038	Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics	materials	metadynamics, SGOOP, nucleation, urea	Ziyue Zou	PRINT METAD VOLUME ENERGY INCLUDE COMBINE CENTER COORDINATIONNUMBER LOAD GROUP	colvar generic setup core bias symfunc vatom function
21.036	Modelling the structure and interactions of intrinsically disordered peptides with multiple-replica, metadynamics-based sampling methods and force-field combinations	bio	Bias Exchange Metadynamics, PTWTE-metaD	Matteo Salvalaglio	PRINT ANTIBETARMSD METAD MOLINFO DIHCOR COORDINATION ENERGY LOWER_WALLS GYRATION RANDOM_EXCHANGES PARABETARMSD UPPER_WALLS ALPHARMSD WHOLEMOLECULES GROUP	multicolvar colvar generic secondarystructure core bias
21.033	Multiple-path-metadynamics applied to DNA base-pairing transitions	bio	path-CV, metadynamics, multiple-walker, dna	Alberto Pérez-de-Alba-Ortíz	PRINT METAD CONSTANT RESTRAINT INCLUDE COMBINE UPPER_WALLS MOVINGRESTRAINT	generic function bias
21.028	From Enhanced Sampling to Reaction Profiles	methods	collective variables, multi-state, machine learning, Deep-TDA	Enrico Trizio	UNITS LOAD PYTORCH_MODEL LOWER_WALLS WHOLEMOLECULES FIT_TO_TEMPLATE OPES_METAD PRINT MATHEVAL CENTER ENDPLUMED TORSION GROUP UPPER_WALLS COORDINATION FIXEDATOM DISTANCES DISTANCE ANGLE	multicolvar generic colvar setup pytorch core opes bias vatom function
21.009	Nucleation rates from small scale atomistic simulations and transition state theory	materials	kinetics, free energy barriers, nucleation, droplets, metadynamics	Kristof Bal	PRINT REWEIGHT_METAD METAD DUMPGRID LOAD FLUSH CONVERT_TO_FES UNITS UPPER_WALLS COORDINATIONNUMBER HISTOGRAM COMMITTOR MOVINGRESTRAINT	generic setup gridtools bias symfunc
21.006	OPES, On-the-fly Probability Enhanced Sampling Method	methods	opes, alanine dipeptide, well-tempered, multithermal, multiumbrella	Michele Invernizzi	PRINT ENERGY OPES_EXPANDED ECV_UMBRELLAS_LINE ECV_MULTITHERMAL ENDPLUMED TORSION OPES_METAD	colvar generic opes
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	ANTIBETARMSD MOLINFO FLUSH COMBINE ALPHARMSD METAINFERENCE CS2BACKBONE INCLUDE WHOLEMOLECULES PRINT STATS ENDPLUMED PARABETARMSD GROUP COORDINATION TORSION ENSEMBLE DIHCOR PBMETAD GYRATION	multicolvar generic colvar secondarystructure core isdb bias function
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 ANTIBETARMSD CS2BACKBONE MOLINFO ALPHABETA LOWER_WALLS FLUSH GROUP BIASVALUE PBMETAD ENDPLUMED WHOLEMOLECULES UPPER_WALLS	multicolvar generic secondarystructure core bias isdb
19.066	Finding ligand unbinding reaction pathways	methods	maze, ligand unbinding	Jakub Rydzewski	PRINT MAZE_OPTIMIZER_BIAS MAZE_SIMULATED_ANNEALING MAZE_LOSS UNITS POSITION	colvar generic maze setup
19.061	Diffusion in porous materials	materials	metadynamics, porous materials, diffusion	Kim E. Jelfs	PRINT METAD COM LOWER_WALLS CENTER DISTANCE RESTART GROUP UPPER_WALLS	colvar generic setup core bias vatom
19.031	Ice nucleation using PIV-based path coordinates	materials	phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics	Silvio Pipolo	PRINT METAD CELL FUNCPATHMSD LOWER_WALLS UPPER_WALLS PIV	colvar generic bias piv function
19.029	WTE-metaD of FF domain of URNF1 C57D variant	bio	metadynamics, mutations, post-translational modification, ff domain	Elena Papaleo	PRINT METAD MOLINFO LOWER_WALLS GYRATION GROUP ALPHABETA WHOLEMOLECULES UPPER_WALLS	multicolvar colvar generic core bias
19.028	pRAVE	methods	RAVE, reaction coordinate, deep learning, metadynamics, kinetics	Pratyush Tiwary	PRINT EXTERNAL COM COMBINE TORSION DISTANCE RESTART ALPHABETA WHOLEMOLECULES COMMITTOR	multicolvar colvar generic setup bias vatom function
19.023	RECT	methods	metadynamics, replica exchange	Giovanni Bussi	PRINT METAD TORSION WHOLEMOLECULES GYRATION	colvar generic bias
19.005	Cmyc small molecule interaction	bio	metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP	Gabriella Heller	PRINT CS2BACKBONE METAINFERENCE MOLINFO ALPHABETA INCLUDE GROUP WHOLEMOLECULES CENTER DISTANCE PBMETAD GYRATION COORDINATION	multicolvar generic colvar core isdb bias vatom
19.002	EMMI STRA6	bio	metainference, cryo-EM	Max Bonomi	PRINT EMMI MOLINFO BIASVALUE GROUP	generic core bias isdb
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	GROUP GYRATION LOWER_WALLS WHOLEMOLECULES COORDINATION MATHEVAL PRINT METAD CENTER DISTANCE COMBINE UPPER_WALLS	bias function core generic colvar vatom
25.025	Enhanced Sampling of Ligand Binding Coupled to RNA Conformational Dynamics	bio	OPES, OPES Flooding , Metadynamics, RNA, Ligand binding, Free Energy, Kinetics, Funnel	Revanth Elangovan and Dhiman Ray	GROUP WRAPAROUND FUNNEL CUSTOM OPES_METAD TORSION COM WHOLEMOLECULES RMSD COMMITTOR COORDINATION CENTER MATHEVAL PRINT METAD LOWER_WALLS FUNNEL_PS UPPER_WALLS	opes funnel function bias core generic colvar vatom
25.018	Metainference simulation for dimerization of RNA binding protein	bio	Metainference, Metadynamics, SAXS, protein dimer	Debadutta Patra	SAXS DISTANCE PBMETAD ENSEMBLE TORSION WHOLEMOLECULES MOLINFO STATS FLUSH PRINT METAINFERENCE CENTER GYRATION UPPER_WALLS	isdb bias function generic colvar vatom
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	GROUP BIASVALUE WHOLEMOLECULES MOLINFO EMMIVOX PRINT	isdb bias core generic
24.032	DeepLNE++	methods	PATHCV, OPES	Thorben Fröhlking	GROUP CUSTOM OPES_METAD TORSION LOAD ENERGY COORDINATION PRINT DISTANCE COMBINE	opes function setup core generic colvar
24.020	Graph Neural Network-State Predictive Information Bottleneck (GNN-SPIB) approach for learning molecular thermodynamics and kinetics	bio	LJ7, alanine, well-tempered metadynamics, infrequent metadynamics, machine learning	Ziyue Zou, Dedi Wang, Pratyush Tiwary	GROUP TORSION LOAD COMMITTOR PRINT METAD	bias setup core generic colvar
24.019	Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning	bio	OPES, machine learning, protein folding, adaptive sampling	Mingyuan Zhang	CUSTOM OPES_METAD ALPHARMSD TORSION WHOLEMOLECULES MOLINFO COORDINATION PRINT DISTANCE GYRATION COMBINE	opes function secondarystructure generic colvar
24.002	Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes	chemistry	metadynamics, ligand design, solvent extraction	Xiaoyu Wang	UNITS TORSION PRINT METAD RESTART	bias colvar generic setup
24.000	Ammonia Decomposition on Non-stoichiometric Lithium Imide	chemistry	ammonia decomposition, non-stoichiometric lithium imide, machine learning interatomic potentials, enhanced sampling, heterogeneous catalysis	Francesco Mambretti	GROUP UNITS OPES_METAD COORDINATIONNUMBER ZDISTANCES PRINT FIXEDATOM FLUSH DISTANCE UPPER_WALLS	opes bias setup symfunc core multicolvar generic colvar vatom
23.037	Estimating binding free energy of solid binding peptides without extensive sampling	bio	metadynamics, solid binding peptides	Xin Qi	PBMETAD GYRATION COM MOLINFO PRINT LOWER_WALLS DISTANCE UPPER_WALLS	bias generic colvar vatom
23.019	Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors	bio	binding pathway, binding energy, sketch-map, drug development	Raitis Bobrovs	COLLECT_FRAMES CUSTOM PATHMSD VSTACK WHOLEMOLECULES COM LANDMARK_SELECT_FPS SKETCHMAP DISSIMILARITIES VORONOI PRINT SKETCHMAP_PROJECTION METAD TRANSPOSE DISTANCE UPPER_WALLS	landmarks dimred function bias valtools generic colvar matrixtools vatom
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 WHOLEMOLECULES MATHEVAL UPPER_WALLS PRINT METAD LOWER_WALLS DISTANCE CONSTANT	bias generic colvar function
23.009	Deep Learning Collective Variables from Transition Path Ensemble	methods	TPI-Deep-TDA, Deep-TDA, Transition Path, OPES, OPES Flooding, Machine Learning, Protein folding, Ligand binding	Dhiman Ray	PYTORCH_MODEL INCLUDE FIT_TO_TEMPLATE COMMITTOR MATHEVAL LOWER_WALLS UPPER_WALLS GROUP FIXEDATOM ENDPLUMED DISTANCE CUSTOM OPES_METAD MOLINFO ENERGY CENTER RMSD COMBINE CONTACTMAP ANGLE WHOLEMOLECULES COORDINATION PRINT	opes pytorch bias function core generic colvar vatom
22.035	Deciphering the alphabet of disorder — Glu and Asp act differently on local but not global properties	bio	intrinsically disordered proteins, parallel bias metadynamics, protein	Kresten Lindorff-Larsen	PBMETAD TORSION WHOLEMOLECULES MOLINFO GYRATION	bias generic colvar
22.033	Reciprocal barrier restraint. Application to PROTAC passive permeability prediction	methods	PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR	Istvan Kolossvary	DRR CUSTOM BIASVALUE UNITS COM PRINT FLUSH METAD DISTANCE	bias drr function setup generic colvar vatom
22.013	Ligand dissociation from PreQ1 riboswitch	bio	ligand, RNA, metadynamics, pRAVE	Yihang Wang	COORDINATIONNUMBER COM WHOLEMOLECULES MOLINFO RMSD COMMITTOR PRINT METAD DISTANCE COMBINE	bias function symfunc generic colvar vatom
22.012	Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT	bio	contact maps, protein-protein interactions	Isabell-Louise Grothaus	CONTACTMAP CENTER DISTANCE PRINT	generic colvar vatom
21.046	Ubiquitin Interacting Motifs, Duality Between Structured and Disordered Motifs	bio	wt metadynamics, ubiquitin, ataxin-3, short linear motifs, ubiquitin binding motif, moonlight functions, intrinsic disorder	Elena Papaleo	GROUP ALPHABETA WHOLEMOLECULES PRINT METAD ENDPLUMED LOWER_WALLS GYRATION UPPER_WALLS	bias core generic multicolvar colvar
21.011	CmuMD simulations of NaCl(aq) at graphite	chemistry	CmuMD, DFS clustering	Aaron Finney	GROUP AROUND RESTRAINT COORDINATIONNUMBER MULTICOLVARDENS CLUSTER_NATOMS LOAD DUMPGRID MFILTER_MORE PRINT FIXEDATOM DFSCLUSTERING CLUSTER_DISTRIBUTION DENSITY CONTACT_MATRIX	adjmat bias clusters setup volumes symfunc core multicolvar generic vatom gridtools
21.008	Multi-replica biased sampling for photoisomerization processes in conjugated polymers	methods	metadynamics, FEP, replica-exchange	Adriana Pietropaolo	PBMETAD BIASVALUE TORSION WHOLEMOLECULES MATHEVAL PRINT RESTART CONSTANT	bias function setup generic colvar
20.031	Soft fluorescent nanoshuttles targeting receptors	chemistry	polymers, receptors, nanoparticles, fluorescent probes	Adriana Pietropaolo	PBMETAD WHOLEMOLECULES COORDINATION PRINT CENTER	bias generic colvar vatom
20.027	Allosteric Regulation of SARS-CoV-2 Protease. Towards Informed Structure-Based Drug Discovery	bio	SARS-CoV2, MPro, Covid-19, Molecular Dynamics, Metadynamics, Computer-Aided Drug Discovery	Khaled Abdel-Maksoud	METAD TORSION DISTANCE PRINT	bias generic colvar
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	RESTRAINT WHOLEMOLECULES MOLINFO COORDINATION PRINT STATS	bias generic colvar function
20.011	Uremic toxin analysis	bio	metadynamics, uremic toxin, serum albumin	Jim Pfaendtner	GROUP DISTANCES WHOLEMOLECULES RESTART COORDINATION PRINT CENTER DISTANCE	setup core generic colvar multicolvar 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	VOLUME Q6 TD_WELLTEMPERED OPT_DUMMY OPT_AVERAGED_SGD VES_LINEAR_EXPANSION ENVIRONMENTSIMILARITY BF_LEGENDRE MATHEVAL PRINT RESTART UPPER_WALLS	function bias setup symfunc generic envsim ves colvar
19.073	On the role of enthalpic and entropic contributions on the conformational free energy landscape of MIL-101(Cr) building units	materials	metadynamics, MOF, MIL101Cr, conformational	Matteo Salvalaglio	DISTANCES COORDINATIONNUMBER ENERGY PRINT METAD ENDPLUMED LOWER_WALLS GYRATION UPPER_WALLS	bias symfunc generic multicolvar colvar
19.072	SINE hairpin MD+NMR	bio	metadynamics, RNA, NMR	Giovanni Bussi	MAXENT SORT COM TORSION WHOLEMOLECULES INCLUDE MOLINFO COORDINATION MATHEVAL PRINT FLUSH METAD DISTANCE	bias function generic colvar vatom
19.065	Molecular Enhanced Sampling with Autoencoders	methods	enhanced sampling, collective variables, deep learning	Wei Chen	ANN RESTRAINT COM POSITION COMBINE	bias function annfunc colvar vatom
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	GROUP REWEIGHT_METAD DISTANCES ALPHABETA COM TORSION WHOLEMOLECULES MOLINFO BRIDGE RMSD UPPER_WALLS PRINT METAD LOWER_WALLS DISTANCE COMBINE FUNNEL	adjmat funnel bias function core multicolvar colvar generic vatom
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	COM ENERGY PRINT METAD DISTANCE UPPER_WALLS	bias generic colvar vatom
19.011	Automatic Gradient Computation for Collective Variables	other	gradient, differentiation, curvature	Toni Giorgino	ENDPLUMED	generic
25.014	Atomic resolution ensembles of intrinsically disordered proteins with Alphafold	bio	bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement	Vincent Schnapka	PRINT GROUP BIASVALUE BAIES	isdb core generic bias
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	COM DISTANCE UPPER_WALLS EMMI COORDINATION DUMPATOMS CENTER WHOLEMOLECULES GROUP PRINT RMSD MOLINFO DUMPMASSCHARGE ALPHARMSD PARABETARMSD PBMETAD BIASVALUE	generic bias secondarystructure colvar vatom isdb core
24.014	Learning Collective Variables with Synthetic Data Augmentation through Physics-inspired Geodesic Interpolation	methods	data augmentation, geodesic interpolation, collective variables, protein folding	Juno Nam	UPPER_WALLS DRR WHOLEMOLECULES PRINT RMSD MOLINFO LOWER_WALLS PYTORCH_MODEL METAD FLUSH COORDINATION	generic bias pytorch colvar drr
24.011	Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble	methods	committor, machine learning	Peilin Kang	POSITION LOAD UNITS UPPER_WALLS INCLUDE GROUP CELL LOWER_WALLS CUSTOM WHOLEMOLECULES PRINT MOLINFO TORSION DISTANCE ENERGY BIASVALUE RMSD MATHEVAL ENDPLUMED COORDINATION	generic setup bias colvar core function
23.046	Lasso Peptides - HLDA CV	bio	metadynamics, protein folding, HLDA, harmonic	Gabriel da Hora	UNITS WHOLEMOLECULES PRINT METAD DISTANCE COMBINE	generic setup bias colvar function
23.034	Urea nucleation in water: do long-range forces matter?	materials	LMF theory, Metadynamics, Nucleation	Ziyue Zou	LOAD INCLUDE CENTER GROUP PRINT METAD COORDINATIONNUMBER	generic setup bias symfunc vatom core
23.026	Machine Learning Nucleation Collective Variables with Graph Neural Networks	chemistry	Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks	Florian Dietrich	MFILTER_MORE MOVINGRESTRAINT Q6 GROUP PRINT LOCAL_Q6 COMBINE LOWER_WALLS METAD COORDINATIONNUMBER	generic bias symfunc core multicolvar function
23.025	Probing ion binding to G-quadruplexes and related events	chemistry	metadynamics, repulsive potential, nucleic acids, G-quadruplexes	Marcelo Poleto	COM UNITS UPPER_WALLS POSITION DISTANCES DUMPATOMS WRAPAROUND GROUP WHOLEMOLECULES FIT_TO_TEMPLATE PRINT LOWER_WALLS MATHEVAL METAD FLUSH RESTART DISTANCE	generic setup bias colvar vatom core multicolvar function
23.002	Critical comparison of general-purpose collective variables for crystal nucleation	methods	metadynamics, umbrella sampling, commitor, entropy, PIV	Julien Lam	UNITS PAIRENTROPY UPPER_WALLS PIV Q6 CUSTOM LOCAL_AVERAGE VOLUME PRINT RESTRAINT FUNCPATHMSD Q4 METAD ENERGY	piv generic gridtools setup bias colvar symfunc function
22.045	Binding mode and mechanism of enzymatic polyethylene terephthalate degradation	bio	metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation	Francesco Colizzi	COM UPPER_WALLS MOVINGRESTRAINT WHOLEMOLECULES PRINT LOWER_WALLS METAD ANGLE DISTANCE	colvar vatom generic bias
22.031	Rare Event Kinetics from Adaptive Bias Enhanced Sampling	methods	OPES Flooding, Kinetics, Rate, OPES, Machine Learning	Dhiman Ray	CONSTANT UNITS POSITION INCLUDE GROUP COMBINE CUSTOM WHOLEMOLECULES PRINT MOLINFO OPES_METAD TORSION DISTANCE ENERGY BIASVALUE CONTACTMAP RMSD PYTORCH_MODEL ENDPLUMED COMMITTOR	generic setup bias pytorch colvar core opes function
22.025	Bubble nucleation rate predictions in a Lennard-Jones fluid	materials	free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation	Kristof Bal	UNITS LOAD UPPER_WALLS MOVINGRESTRAINT ANN CUSTOM HISTOGRAM CONVERT_TO_FES REWEIGHT_BIAS VOLUME DUMPGRID PRINT RESTRAINT FLUSH COMMITTOR COORDINATIONNUMBER BIASVALUE	generic gridtools setup bias colvar annfunc symfunc function
22.009	Glycosylation in calixarenes capsule	chemistry	Metadynamics, glycosylation, supramolecular catalysis	GiovanniMaria Piccini	DISTANCE UNITS UPPER_WALLS DISTANCES WHOLEMOLECULES GROUP FIT_TO_TEMPLATE RMSD BRIDGE LOWER_WALLS PRINT MATHEVAL METAD FLUSH ANGLE COMBINE COORDINATION	generic setup bias colvar core multicolvar function adjmat
21.039	Deep learning the slow modes for rare events sampling	methods	collective variables, machine learning, slow modes, deep-tica, opes	Luigi Bonati	UNITS LOAD INCLUDE Q6 GROUP ENVIRONMENTSIMILARITY FLUSH COMBINE WHOLEMOLECULES PRINT MOLINFO OPES_EXPANDED OPES_METAD TORSION DISTANCE ENERGY CONTACTMAP VOLUME ECV_MULTITHERMAL RMSD PYTORCH_MODEL ENDPLUMED	generic setup pytorch envsim colvar symfunc core opes function
21.029	Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs	bio	metadynamics, small peptide, machine learning	Pratyush Tiwary	PRINT MOLINFO TORSION FLUSH RESTART ENERGY EXTERNAL	colvar generic setup bias
21.025	Computational and biochemical analysis of type IV pilus dynamics and stability	bio	molecular dynamics, calcium binding, Type IV pilus	Yasaman Karami	LOWER_WALLS DISTANCE UPPER_WALLS PRINT	colvar generic bias
21.012	NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition	bio	funnel metadynamics	Jim Pfaendtner	COM UPPER_WALLS FUNNEL_PS FUNNEL PRINT LOWER_WALLS METAD DISTANCE	funnel generic bias colvar vatom
20.032	Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil	materials	clustering, conformational isomers	Matteo Salvalaglio	PRINT TORSION ENDPLUMED	colvar generic
19.057	SAXS ensembles using Martini-Beads multi-scale SAXS	methods	metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics	Cristina Paissoni	ENSEMBLE SAXS ALPHABETA COORDINATION INCLUDE CENTER WHOLEMOLECULES GROUP PRINT MOLINFO STATS MATHEVAL ENDPLUMED ANGLE PBMETAD COMBINE BIASVALUE	generic bias colvar isdb vatom multicolvar core function
19.030	Coarse-Grained MetaDynamics (CG-MetaD)	bio	Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy	Vittorio Limongelli	COM UPPER_WALLS WHOLEMOLECULES PRINT LOWER_WALLS METAD DISTANCE	colvar vatom generic bias
19.024	PT-MetaD-WTE	methods	metadynamics, WTE, trp cage, PT	Jim Pfaendtner	GROUP METAD ENERGY EXTERNAL COORDINATION	colvar core bias
19.001	RNA SHAPE	bio	metadynamics, RNA, ligand binding	Giovanni Bussi	DISTANCE UPPER_WALLS INCLUDE DISTANCES ERMSD PRINT MOLINFO LOWER_WALLS FLUSH METAD ANGLE COMBINE RANDOM_EXCHANGES	generic bias colvar multicolvar function
25.004	Machine Learning-Driven Molecular Dynamics Unveil a Bulk Phase Transformation Driving Ammonia Synthesis on Barium Hydride	chemistry	OPES, OPES flooding, Catalysis, Ammonia Synthesis	Axel Tosello Gardini	ZDISTANCES DISTANCE FLUSH GROUP COMMITTOR CUSTOM UPPER_WALLS PRINT FIXEDATOM DISTANCES COORDINATIONNUMBER OPES_METAD UNITS	core symfunc multicolvar generic opes function vatom bias colvar setup
25.002	M3_PCV-ABMD	chemistry	Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor	Gian Marco Elisi	ABMD ENDPLUMED UPPER_WALLS PATHMSD PRINT UNITS	bias colvar generic setup
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	DISTANCE COORDINATION COMMITTOR CUSTOM UPPER_WALLS OPES_METAD LOWER_WALLS RESTART PRINT GROUP UNITS	core generic opes function bias colvar setup
24.017	Absolute Binding Free Energies with OneOPES	methods	protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy	Francesco Gervasio	TORSION CONTACTMAP INCLUDE RESTART LOWER_WALLS WHOLEMOLECULES MATHEVAL PROJECTION_ON_AXIS WRAPAROUND PRINT OPES_EXPANDED COM ENERGY COORDINATION CONSTANT GROUP RMSD OPES_METAD_EXPLORE CUSTOM MOLINFO UPPER_WALLS ECV_MULTITHERMAL BIASVALUE METAD	core generic opes function vatom bias colvar setup
23.044	Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition	materials	metadynamics, interlocked molecules	Luigi Leanza	CONVERT_TO_FES DUMPGRID COORDINATION ENDPLUMED COMMITTOR PRINT HISTOGRAM METAD READ GROUP	gridtools core generic bias colvar
23.041	Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference	methods	EMMIVox, cryo-EM, single-structure refinement, ensemble refinement, Bayesian inference, B-factors, structural ensembles	Samuel Hoff	DISTANCE WRAPAROUND MOLINFO EMMIVOX UPPER_WALLS INCLUDE PRINT BIASVALUE WHOLEMOLECULES GROUP	core generic isdb bias colvar
23.038	Determinants of Neutral Antagonism and Inverse Agonism in the β2-adrenergic receptor	bio	protein coupled receptor, beta-adrenergic, receptor activation, antagonism, inverse agonism, metadynamics	Timothy Clark	WHOLEMOLECULES DISTANCE RMSD MOLINFO PRINT METAD MATHEVAL	generic function bias colvar
23.028	Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process	chemistry	Ammonia decomposition; Dynamics;OPES; Neural Network potential	Manyi Yang	ZDISTANCES ENERGY DISTANCE FLUSH GROUP COMMITTOR CUSTOM UPPER_WALLS COORDINATIONNUMBER UNITS LOWER_WALLS PRINT FIXEDATOM DISTANCES MATHEVAL OPES_METAD COM	core symfunc multicolvar generic opes function vatom bias colvar setup
23.024	Permutationally Invariant Networks for Enhanced Sampling (PINES)	methods	collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent	Nicholas Herringer	LOAD PBMETAD PRINT	bias generic setup
23.014	Structural basis of dimerization of chemokine receptors CCR5 and CXCR4	bio	metadynamics, oligomerization, chemokine receptors, GPCR, membrane	Vittorio Limongelli	COMBINE WHOLEMOLECULES DISTANCE TORSION FLUSH UPPER_WALLS PRINT METAD COM	generic function vatom bias colvar
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 CONTACTMAP LOWER_WALLS PRINT WHOLEMOLECULES	bias colvar generic
22.039	Driving and characterizing nucleation of urea and glycine polymorphs in water	bio	metadynamics, nucleation, amino acids, polymorphism	Eric Beyerle	CENTER COMBINE LOAD Q6 INCLUDE COORDINATIONNUMBER Q4 PRINT METAD MATHEVAL GROUP PAIRENTROPY	core gridtools generic function vatom bias symfunc setup
22.030	Mixing physics across temperatures with generative artificial intelligence	methods	REMD, Generative AI, DDPM	Yihang Wang	PRINT TORSION WHOLEMOLECULES	generic colvar
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	COMBINE WHOLEMOLECULES DISTANCE TORSION ALPHABETA METAD CUSTOM MOLINFO UPPER_WALLS LOWER_WALLS ZANGLES PRINT YANGLES MATHEVAL XANGLES COM	multicolvar generic function vatom bias colvar
22.002	GAMBES_SAMPL5_RATES	other	GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding	Jayashrita Debnath	CENTER ENERGY DISTANCE FIT_TO_TEMPLATE COORDINATION FLUSH LOAD ENDPLUMED PYTORCH_MODEL MATHEVAL COMMITTOR UPPER_WALLS PRINT ANGLE WHOLEMOLECULES FIXEDATOM GROUP	core generic pytorch function vatom bias colvar setup
21.048	Enhancing ligand exploration within a channel pore and fenestrations using metadynamics	bio	well-tempered metadynamics, protein-ligand enhanced sampling, sodium channel, Nav, small molecule drug	Elaine Tao	COM DISTANCE TORSION CUSTOM UPPER_WALLS LOWER_WALLS PRINT METAD UNITS	generic function vatom bias colvar 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	COMBINE DISTANCE COORDINATION UPPER_WALLS LOWER_WALLS PRINT METAD COORDINATIONNUMBER	symfunc generic function bias colvar
21.035	CmuMD simulations of NaCl(aq) at NaCl	chemistry	CmuMD, interface	Aaron Finney	DISTANCE RESTRAINT LOAD PRINT FIXEDATOM GROUP	core generic vatom bias colvar setup
21.032	Metal-coupled folding mechanism to metallothionein	bio	parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination	Manuel-Peris Diaz	COORDINATION PBMETAD WHOLEMOLECULES GROUP UNITS	core generic bias colvar setup
21.031	Photo-switchable sulfonulureas in KATP channel	bio	metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels	Katarzyna Walczewska-Szewc	WHOLEMOLECULES COM DISTANCE UPPER_WALLS LOWER_WALLS PRINT METAD UNITS	generic vatom bias colvar setup
21.027	EGFR activating mutations mechanism	bio	metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA	Francesco Gervasio	ENERGY WHOLEMOLECULES DISTANCE ALPHARMSD MOLINFO UPPER_WALLS CONTACTMAP INCLUDE LOWER_WALLS PRINT METAD MATHEVAL	generic function bias colvar secondarystructure
21.016	MD SAXS GTPase associated center	bio	metadynamics, RNA, folding, SAXS	Giovanni Bussi	WHOLEMOLECULES SAXS GYRATION CUSTOM ERMSD MOLINFO UPPER_WALLS INCLUDE LOWER_WALLS PRINT METAD GROUP	core generic function isdb bias colvar
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	CENTER POSITION COORDINATION RESTRAINT METAD REWEIGHT_BIAS RESTART PRINT WHOLEMOLECULES MATHEVAL	generic function vatom bias colvar setup
21.002	Phase equilibrium of water with hexagonal and cubic ice using the SCAN functional	materials	ice, water, SCAN, OPES, VES, multithermal, crystallization, environment similarity, refcv, reweighting	Pablo Piaggi	ENERGY ECV_UMBRELLAS_LINE VES_LINEAR_EXPANSION Q6 UPPER_WALLS BF_LEGENDRE VOLUME RESTART ENVIRONMENTSIMILARITY ECV_MULTITHERMAL_MULTIBARIC PRINT TD_UNIFORM OPES_EXPANDED MATHEVAL OPT_AVERAGED_SGD	ves colvar generic opes function bias envsim symfunc setup
20.025	The role of water in host-guest interaction	bio	ligand binding, water, opes, SAMPL5	Valerio Rizzi	CENTER ENERGY DISTANCE FIT_TO_TEMPLATE COORDINATION ENDPLUMED MATHEVAL PYTORCH_MODEL GROUP UPPER_WALLS PRINT ANGLE WHOLEMOLECULES FIXEDATOM OPES_METAD	core generic pytorch opes function vatom bias colvar
19.083	Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis	chemistry	metadynamics, chemical reactions, reaction discovery	Valerio Rizzi	COMBINE DISTANCES FLUSH ENDPLUMED UPPER_WALLS RESTART PRINT METAD COORDINATIONNUMBER GROUP UNITS	core multicolvar generic function bias symfunc setup
19.080	Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium	methods	ves, variationally enhanced sampling, vibrational excitation, chemical reactions	Kristof Bal	COMBINE CONVERT_TO_FES DISTANCE EXTERNAL VES_LINEAR_EXPANSION COORDINATION FLUSH TD_WELLTEMPERED UPPER_WALLS TD_GRID UNITS LOWER_WALLS PRINT HISTOGRAM ANGLE DUMPGRID OPT_AVERAGED_SGD BF_CHEBYSHEV	ves gridtools generic function bias colvar setup
19.075	PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python	other	Python, automatic differentiation	Toni Giorgino	COMBINE CENTER DISTANCE TORSION RESTRAINT ENDPLUMED CUSTOM ANGLE PRINT DUMPDERIVATIVES GROUP	core generic function vatom bias colvar
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	POSITION COORDINATION FLUSH UPPER_WALLS RESTART LOWER_WALLS PRINT METAD GROUP UNITS	core generic bias colvar setup
19.043	Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA)	methods	metadynamics, chemistry, HLDA	GiovanniMaria Piccini	COMBINE DISTANCE DISTANCES FLUSH UPPER_WALLS RESTART PRINT METAD UNITS	multicolvar generic function bias colvar setup
19.040	Optimal Metric for Path Collective Variables	bio	metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path	Francesco Luigi Gervasio	TORSION ENDPLUMED PRINT METAD MATHEVAL	generic function bias colvar
19.035	Dimerization of GPCRs from coarse-grained umbrella sampling	bio	Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization	Davide Provasi	DISTANCE TORSION RESTRAINT PRINT GROUP COM	core generic vatom bias colvar
19.025	Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide	bio	metainference, NMR, protein dynamics, force-fields	Carlo Camilloni	WHOLEMOLECULES TORSION ENSEMBLE CS2BACKBONE FLUSH METAINFERENCE ENDPLUMED JCOUPLING GYRATION MOLINFO PBMETAD STATS PRINT BIASVALUE RDC	generic function isdb bias colvar
19.020	PTMetaD-WTE simulation of the Ntail IDP	bio	metadynamics, IDPs, protein folding	Mattia Bernetti	ENERGY ALPHARMSD WHOLEMOLECULES ENDPLUMED GYRATION MOLINFO PRINT METAD	generic bias colvar secondarystructure
19.014	MIL101(Cr) SBUs assembly	materials	MOFs, nucleation, self-assembly, metadynamics	Matteo Salvalaglio	DISTANCES ENDPLUMED GYRATION RESTART PRINT METAD COORDINATIONNUMBER	symfunc multicolvar generic bias colvar setup
25.030	Committor Regularization	methods	metadynamics, enhanced sampling, mlcvs, committor, machine learning	Florian Dietrich	MOVINGRESTRAINT METAD UNITS PRINT	setup generic bias
25.015	Assessment of Force Fields for Describing Conformational Polymorphic Crystals of ROY	materials	Molecular crystal, Force Field, Collective Variable	Pradip Si and Omar Valsson	TORSIONS PRINT SMAC DUMPMULTICOLVAR DISTANCES	symfunc multicolvar generic
25.009	Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water	chemistry	metadynamics, nitrate photolysis	Kam-Tung Chan	DISTANCE DUMPGRID UPPER_WALLS GROUP FLUSH CUSTOM RESTART METAD HISTOGRAM REWEIGHT_METAD PRINT READ COORDINATION	setup gridtools colvar function core generic bias
25.001	RNA G-quadruplex folding with ST-metaD protocol	bio	RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD	Pavlína Pokorná	METAD WHOLEMOLECULES ERMSD COMBINE MOLINFO	function colvar generic bias
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	DISTANCE ECV_MULTITHERMAL GROUP CUSTOM RESTART OPES_EXPANDED OPES_METAD_EXPLORE PRINT TORSION ENERGY COORDINATION COMBINE	setup function colvar opes core 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	GROUP UPPER_WALLS ANGLE OPES_METAD CONTACTMAP CENTER FIXEDATOM WHOLEMOLECULES COMMITTOR RMSD MOLINFO DISTANCE FIT_TO_TEMPLATE PRINT COMBINE CUSTOM METAD MATHEVAL TORSION ENDPLUMED COORDINATION	vatom colvar function opes core generic bias
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 FLUSH INCLUDE METAD SELECT_COMPONENTS PRINT MATHEVAL SUM	function matrixtools generic bias valtools
23.032	Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics	bio	metadynamics, tSNE, neural network, machine learning, trp-cage, folding	Vojtech Spiwok	FIT_TO_TEMPLATE ANN POSITION METAD WHOLEMOLECULES PRINT ALPHARMSD COMBINE MOLINFO	annfunc colvar function generic bias secondarystructure
23.022	A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar	methods	collective variables, machine learning, toy model	Enrico Trizio	LOWER_WALLS PYTORCH_MODEL UPPER_WALLS OPES_METAD POSITION UNITS PRINT BIASVALUE ENDPLUMED CUSTOM	setup colvar function opes pytorch generic bias
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	DISTANCE PYTORCH_MODEL CUSTOM GROUP FIT_TO_TEMPLATE UPPER_WALLS OPES_METAD_EXPLORE OPES_METAD UNITS PRINT WHOLEMOLECULES CENTER FIXEDATOM TORSION PATH LOWER_WALLS COORDINATION	setup function colvar vatom opes core pytorch generic bias mapping
22.028	N-glycan conformer distributions in atomistic simulation	bio	REST2, RECT, N-glycan, pucker	Isabell Grothaus	DUMPGRID METAD HISTOGRAM PRINT PUCKERING TORSION CONVERT_TO_FES READ MOLINFO	generic gridtools bias colvar
22.006	Peptide framework for screening the effects of amino acids on assembly	bio	metadynamics, peptides	Andrew White	DUMPGRID GROUP INCLUDE METAD HISTOGRAM PRINT DISTANCES GYRATION CONVERT_TO_FES REWEIGHT_BIAS COM COMBINE	gridtools colvar vatom function multicolvar core generic bias
21.050	N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity	methods	bio	Isabell Louise Grothaus	DISTANCE CENTER PRINT	vatom generic colvar
21.047	Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations	materials	pair entropy, metadynamics, ves, solids, crystallization	Pablo Piaggi	LOAD RESTART METAD BF_LEGENDRE PRINT TD_WELLTEMPERED PAIRENTROPY VOLUME ENERGY VES_LINEAR_EXPANSION COMBINE OPT_AVERAGED_SGD	setup gridtools colvar function ves generic bias
21.044	NaCl nucleation	chemistry	metadynamics, DFS clustering	Aaron Finney	LOCAL_Q6 DUMPGRID CLUSTER_DISTRIBUTION GROUP DFSCLUSTERING INSPHERE COORDINATIONNUMBER METAD FIXEDATOM PRINT HISTOGRAM CLUSTER_NATOMS MFILTER_MORE Q6 COMBINE CONTACT_MATRIX	gridtools vatom function symfunc volumes multicolvar adjmat core generic bias clusters
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	FIT_TO_TEMPLATE METAD PRINT FIXEDATOM TORSION	vatom colvar generic bias
21.034	Efficient sampling of high-dimensional free energy landscapes using adaptive reinforced dynamics	bio	reinforced dynamics, bias-exchange metadynamics, parallel-bias metadynamics	Dongdong Wang	RANDOM_EXCHANGES INCLUDE PBMETAD METAD PRINT TORSION ENDPLUMED	colvar generic bias
21.018	Localized Volume-based Metadynamics	bio	LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification	Riccardo Capelli	DUMPGRID GROUP UPPER_WALLS POSITION CONVERT_TO_FES FLUSH WHOLEMOLECULES FIXEDATOM COM RMSD DISTANCE HISTOGRAM PRINT METAD REWEIGHT_METAD MATHEVAL ENDPLUMED COORDINATION READ	gridtools colvar vatom function core generic bias
21.014	how to determine statistically accurate conformational ensembles	bio	metadynamics, metainference, errors, cv, SAXS, ensemble determination	Cristina Paissoni	ALPHABETA CONTACTMAP SAXS PBMETAD METAD WHOLEMOLECULES CENTER PRINT STATS ANTIBETARMSD GYRATION TORSION ENSEMBLE BIASVALUE MOLINFO	isdb colvar vatom function multicolvar generic bias secondarystructure
21.003	aSYN SAXS metainference	bio	metainference, SAXS	Kresten Lindorff-Larsen	GROUP FLUSH SAXS PBMETAD WHOLEMOLECULES EEFSOLV PRINT CENTER ALPHARMSD GYRATION METAINFERENCE BIASVALUE MOLINFO	isdb colvar vatom core generic bias secondarystructure
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	DISTANCE RESTART PRINT CENTER ERMSD TORSION ABMD MOLINFO	setup vatom colvar generic bias
20.029	High Conformational Flexibility of the E2F1/DP1/DNA complex	bio	SAXS, protein-DNA complex, hySAXS, ensemble determination	Cristina Paissoni	DISTANCE GROUP SAXS INCLUDE CENTER WHOLEMOLECULES PRINT STATS RESTRAINT ENSEMBLE BIASVALUE MOLINFO	isdb vatom colvar function core generic bias
20.026	Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor	bio	Metadynamics, Umbrella sampling	Brandon Peters	DUMPGRID METAD HISTOGRAM PRINT REWEIGHT_METAD RESTRAINT CONVERT_TO_FES MULTI_RMSD	generic gridtools bias colvar
20.020	Parallel Bias Metadynamics	methods	pbmetad, trp-cage, folding	Max Bonomi	ALPHABETA INCLUDE PBMETAD PRINT WHOLEMOLECULES GYRATION DIHCOR COORDINATION MOLINFO	multicolvar generic bias colvar
19.056	maze	methods	maze, ligand unbinding	Jakub Rydzewski	POSITION MAZE_OPTIMIZER_BIAS UNITS PRINT MAZE_SIMULATED_ANNEALING MAZE_LOSS	maze generic setup colvar
19.049	Determining the sizes of solid/liquid clusters in MD trajectories of nucleation	methods	nucleation, metadynamics, clustering, Steinhardt order parameters	Gareth Tribello	LOCAL_Q6 CLUSTER_DISTRIBUTION CLUSTER_PROPERTIES MORE_THAN DFSCLUSTERING MATRIX_VECTOR_PRODUCT METAD COORDINATIONNUMBER OUTER_PRODUCT ONES PRINT OUTPUT_CLUSTER CLUSTER_NATOMS SMAC DISTANCES Q6 CUSTOM CONTACT_MATRIX	function matrixtools symfunc multicolvar adjmat generic bias clusters
19.037	Scission free energy of organic dyes	chemistry	metadynamics, multiple walkers, matheval/lepton	Paolo Raiteri	DISTANCE UPPER_WALLS FLUSH RESTART METAD UNITS PRINT MATHEVAL	setup function colvar generic bias
19.018	Excited state FEP/Metadynamics simulations	chemistry	metadynamics, FEP, excited states, conjugated polymers, torsional potential	Adriana Pietropaolo	METAD PRINT WHOLEMOLECULES CONSTANT MATHEVAL TORSION BIASVALUE	function generic bias colvar
19.004	MI Ubiquitin	bio	metainference, NMR	Max Bonomi	GROUP CS2BACKBONE PRINT WHOLEMOLECULES METAINFERENCE RDC MOLINFO	core generic isdb

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