Browse the eggs in PLUMED-NEST

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

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

plumID	Name	Category	Keywords	Contributor	Actions	Modules
26.000	OPES simulations of disordered proteins	bio	OPES, IDPs	Julian Streit	PRINT ENERGY ECV_MULTITHERMAL OPES_EXPANDED RESTART	colvar setup generic opes
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	TORSION LOWER_WALLS PRINT COORDINATION OPES_METAD UPPER_WALLS FUNNEL RMSD WHOLEMOLECULES CENTER COM METAD FUNNEL_PS MATHEVAL CUSTOM GROUP COMMITTOR WRAPAROUND	colvar core vatom opes function bias funnel generic
25.006	Characterizing the conformational ensemble of PROTAC degraders in solutions via atomistic simulations	methods	Enhanced sampling, Atomistic simulations, Conformational ensemble, PROTACs, Targeted Protein Degradation, Chamelonic molecules	Shikshya Bhusal, Omar Valsson	TORSION PRINT ENERGY DISTANCE MOLINFO PBMETAD WHOLEMOLECULES CENTER UPDATE_IF VOLUME INCLUDE GYRATION DUMPATOMS RESTART READ	colvar vatom bias setup generic
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	PRINT DUMPATOMS COORDINATION DISTANCE MOLINFO ALPHARMSD RMSD WHOLEMOLECULES COM PARABETARMSD PBMETAD UPPER_WALLS CENTER EMMI DUMPMASSCHARGE GROUP BIASVALUE	colvar isdb core vatom bias secondarystructure generic
24.026	Constant pH metadynamics of RNA oligomers	bio	metadynamics, pH, RNA	Giovanni Bussi	TORSION PRINT MOLINFO METAD PUCKERING RESTART	colvar setup generic bias
23.038	Determinants of Neutral Antagonism and Inverse Agonism in the β2-adrenergic receptor	bio	protein coupled receptor, beta-adrenergic, receptor activation, antagonism, inverse agonism, metadynamics	Timothy Clark	PRINT DISTANCE MATHEVAL MOLINFO RMSD WHOLEMOLECULES METAD	colvar function generic bias
23.023	Rational design of novel biomimetic sequence-defined polymers for mineralization applications	methods	metadynamics, surface binding, biomimetic mineralization	Kaylyn Torkelson	PRINT COORDINATION DISTANCE PBMETAD COM GYRATION UPPER_WALLS	colvar vatom generic bias
23.022	A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar	methods	collective variables, machine learning, toy model	Enrico Trizio	POSITION LOWER_WALLS PRINT ENDPLUMED UNITS OPES_METAD BIASVALUE CUSTOM PYTORCH_MODEL UPPER_WALLS	colvar opes function bias pytorch setup generic
23.008	PBMetaD simulations of Histatin5	bio	metadynamics, IDP, Rg, PPII	Francesco Pesce	TORSION PRINT PBMETAD MOLINFO WHOLEMOLECULES GYRATION GROUP	colvar core generic bias
23.006	Transcription factor unbinding	bio	metadynamics, DNA, conformational changes	Malin Lüking	PRINT DISTANCE MOLINFO ALPHARMSD METAD COM ANGLE CONTACTMAP DUMPFORCES	colvar vatom bias secondarystructure generic
22.043	Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES	bio	OPES, RNA, Tetraloop, Folding	Gül Zerze	PRINT ENERGY WHOLEMOLECULES ECV_UMBRELLAS_LINE ECV_MULTITHERMAL CONTACTMAP OPES_EXPANDED	colvar generic opes
22.015	Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome	bio	photodynamics, bacteriophytochrome, variationally enhanced sampling	Jakub Rydzewski	TORSION PRINT TD_UNIFORM VES_LINEAR_EXPANSION OPT_AVERAGED_SGD BF_FOURIER	colvar generic ves
22.008	Ab initio metadynamics determination of temperature-dependent free-energy landscape in ultrasmall silver clusters	materials	Well tempered metadynamics, ab-initio, ase	Daniel Sucerquia	LOWER_WALLS UNITS COORDINATION FLUSH DISTANCE METAD COMBINE COM GYRATION COORDINATIONNUMBER UPPER_WALLS	colvar vatom symfunc function bias setup generic
22.000	Amyloid precursor protein processing by human γ-secretase	bio	Bias Exchange Metadynamics, Helix unfolding, coupled binding	Xiaoli Lu	PRINT COORDINATION UNITS RANDOM_EXCHANGES MOLINFO ALPHARMSD ANTIBETARMSD CENTER DISTANCE METAD CONTACTMAP INCLUDE	colvar vatom bias secondarystructure setup generic
21.048	Enhancing ligand exploration within a channel pore and fenestrations using metadynamics	bio	well-tempered metadynamics, protein-ligand enhanced sampling, sodium channel, Nav, small molecule drug	Elaine Tao	TORSION LOWER_WALLS PRINT UNITS DISTANCE METAD COM CUSTOM UPPER_WALLS	colvar vatom function bias setup generic
21.042	Peptoid-mediated Au nanocrystal growth	materials	parallel-bias metadynamics, peptoid, Au	Xin Qi	PRINT DISTANCE PBMETAD MOLINFO COM GYRATION UPPER_WALLS	colvar vatom generic bias
21.028	From Enhanced Sampling to Reaction Profiles	methods	collective variables, multi-state, machine learning, Deep-TDA	Enrico Trizio	PRINT LOWER_WALLS DISTANCE WHOLEMOLECULES DISTANCES PYTORCH_MODEL UPPER_WALLS TORSION ENDPLUMED MATHEVAL COORDINATION FIXEDATOM ANGLE FIT_TO_TEMPLATE OPES_METAD UNITS CENTER LOAD GROUP	colvar core multicolvar vatom opes function bias pytorch setup generic
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	POSITION PRINT COORDINATION MATHEVAL METAD WHOLEMOLECULES CENTER REWEIGHT_BIAS RESTRAINT RESTART	colvar vatom function bias setup generic
20.033	COVID-19 Spike protein opening transition mechanism	bio	EMMI, CryoEM, COVID-19, Spike, Metainference	Faidon Brotzakis	DUMPGRID PRINT HISTOGRAM MOLINFO RMSD WHOLEMOLECULES EMMI DISTANCES CONVERT_TO_FES GROUP BIASVALUE READ	colvar isdb multicolvar core gridtools bias generic
20.031	Soft fluorescent nanoshuttles targeting receptors	chemistry	polymers, receptors, nanoparticles, fluorescent probes	Adriana Pietropaolo	PRINT COORDINATION PBMETAD WHOLEMOLECULES CENTER	colvar vatom generic bias
20.024	Gaussian Mixture Based Enhanced Sampling (GAMBES)	methods	enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias	Jayashrita Debnath	TORSION PRINT LOWER_WALLS ENERGY UNITS DISTANCE COMBINE LOAD DISTANCES GROUP UPPER_WALLS	colvar core multicolvar function bias setup generic
20.017	FISST	methods	FISST, force, peptide, sampling, tempering	Glen Hocky	PRINT FISST UNITS DISTANCE ENERGY MATHEVAL RESTRAINT GYRATION GROUP BIASVALUE	colvar core fisst function bias setup generic
20.007	Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics	bio	metadynamics, loop movement, artificial intelligence	Pratyush Tiwary	TORSION PRINT DISTANCE MOLINFO RMSD WHOLEMOLECULES COMBINE METAD RESTART UPPER_WALLS	colvar function bias setup generic
19.060	Neural networks-based variationally enhanced sampling	methods	ves, neural networks	Luigi Bonati	POSITION TORSION PRINT ENVIRONMENTSIMILARITY ENDPLUMED UNITS ENERGY LOAD Q6	colvar envsim symfunc setup generic
19.056	maze	methods	maze, ligand unbinding	Jakub Rydzewski	POSITION PRINT UNITS MAZE_SIMULATED_ANNEALING MAZE_LOSS MAZE_OPTIMIZER_BIAS	colvar maze setup generic
19.045	Adsorption free energy of Ca/CO3 ions on calcite steps in contact with water	materials	metadynamics, well-tempered, multiple walkers, LAMMPS	Marco De La Pierre	POSITION LOWER_WALLS PRINT UNITS COORDINATION FLUSH METAD GROUP RESTART UPPER_WALLS	colvar core bias setup generic
19.031	Ice nucleation using PIV-based path coordinates	materials	phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics	Silvio Pipolo	LOWER_WALLS PRINT CELL METAD FUNCPATHMSD PIV UPPER_WALLS	colvar piv function bias generic
19.021	Coarse-Grained Directed Simulation	methods	experiment directed simulation, coarse-grain, bias	Glen Hocky	TORSION PRINT DISTANCE COMBINE RESTRAINT EDS	colvar function bias generic eds
19.016	Succinnic acid gamma polymorph	materials	Succinnic acid, conformers, polymorphs, metadynamics	Matteo Salvalaglio	TORSION PRINT LOWER_WALLS ENDPLUMED CELL ENERGY MATHEVAL METAD COMBINE VOLUME UPPER_WALLS	colvar function generic bias
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	DISTANCE GROUP DISTANCES ZDISTANCES COMMITTOR FIXEDATOM PRINT UPPER_WALLS OPES_METAD FLUSH CUSTOM UNITS COORDINATIONNUMBER	function symfunc multicolvar generic colvar setup vatom opes bias core
24.032	DeepLNE++	methods	PATHCV, OPES	Thorben Fröhlking	DISTANCE COORDINATION GROUP TORSION LOAD COMBINE PRINT OPES_METAD CUSTOM ENERGY	function generic colvar opes setup core
24.018	A new route to the prebiotic synthesis of glycine via ab initio-based machine learning calculations	chemistry	prebiotic chemistry, glycine, Strecker synthesis, ab initio calculations, machine learning	Léon HUET	DISTANCE PRINT	colvar generic
24.016	Cryo-EM guided simulations of ribozyme	bio	metainference, cryo-EM	Giovanni Bussi	ERMSD MOLINFO GROUP EMMIVOX INCLUDE PRINT BIASVALUE WHOLEMOLECULES RESTRAINT	generic isdb colvar bias core
24.005	Learning Markovian Dynamics with Spectral Maps	methods	spectral map, collective variables, machine learning	Jakub Rydzewski	DISTANCE PRINT BIASVALUE CUSTOM UNITS	function generic colvar setup bias
23.010	An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G‑Protein-Coupled Receptor Ligands	bio	GPCR, binding free energy, free energy surface	Timothy Clark	DISTANCE CONSTANT PRINT UPPER_WALLS BIASVALUE WHOLEMOLECULES LOWER_WALLS METAD MATHEVAL	bias function colvar generic
23.007	Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains	bio	metadynamics, peptoids, parallel-bias metadynamics	Jim Pfaendtner	PBMETAD COORDINATION TORSION INCLUDE PRINT COM WHOLEMOLECULES GYRATION RESTRAINT	bias vatom colvar generic
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	HISTOGRAM ECV_UMBRELLAS_LINE ENVIRONMENTSIMILARITY PRINT RESTART OPES_EXPANDED UPPER_WALLS LOWER_WALLS DUMPGRID	generic bias opes setup envsim gridtools
22.041	Skipping the Replica Exchange Ladder with Normalizing Flows	methods	OPES, alanine, normalizing flows, replica exchange	Michele Invernizzi	POSITION ENERGY TORSION PRINT OPES_METAD ENDPLUMED UNITS ECV_MULTITHERMAL OPES_EXPANDED	setup opes colvar generic
22.040	From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure	bio	SARS-CoV-2, Spike, Omicron	Miłosz Wieczór	PRINT UPPER_WALLS WHOLEMOLECULES LOWER_WALLS METAD PCAVARS	bias mapping generic
22.039	Driving and characterizing nucleation of urea and glycine polymorphs in water	bio	metadynamics, nucleation, amino acids, polymorphism	Eric Beyerle	Q4 Q6 GROUP CENTER LOAD INCLUDE COMBINE PRINT METAD PAIRENTROPY MATHEVAL COORDINATIONNUMBER	symfunc function generic bias vatom setup gridtools core
22.032	Reciprocal barrier restraint. Application to path-meta-eABF	methods	restraint, upper wall, lower wall, path colvar, meta-eABF, metadynamics, DRR, protein conformational transition, PROTAC	Istvan Kolossvary	DRR PRINT BIASVALUE FLUSH METAD CUSTOM PATHMSD	function generic colvar drr bias
21.052	On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets	materials	Ibuprofen, unbinding, WTmetaD	Matteo Salvalaglio	DISTANCE CENTER COMMITTOR TORSION PRINT METAD ENDPLUMED COORDINATIONNUMBER	symfunc generic colvar vatom bias
21.050	N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity	methods	bio	Isabell Louise Grothaus	DISTANCE PRINT CENTER	vatom colvar generic
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	TORSION FIXEDATOM FIT_TO_TEMPLATE PRINT METAD	bias vatom colvar generic
21.027	EGFR activating mutations mechanism	bio	metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA	Francesco Gervasio	DISTANCE MOLINFO INCLUDE ALPHARMSD PRINT UPPER_WALLS WHOLEMOLECULES LOWER_WALLS METAD MATHEVAL CONTACTMAP ENERGY	function generic colvar bias secondarystructure
21.016	MD SAXS GTPase associated center	bio	metadynamics, RNA, folding, SAXS	Giovanni Bussi	ERMSD MOLINFO GROUP SAXS INCLUDE PRINT UPPER_WALLS WHOLEMOLECULES LOWER_WALLS METAD GYRATION CUSTOM	function generic isdb colvar bias core
21.014	how to determine statistically accurate conformational ensembles	bio	metadynamics, metainference, errors, cv, SAXS, ensemble determination	Cristina Paissoni	PBMETAD MOLINFO ALPHABETA CENTER SAXS TORSION ENSEMBLE PRINT BIASVALUE WHOLEMOLECULES METAD ANTIBETARMSD STATS GYRATION CONTACTMAP	function multicolvar generic isdb colvar vatom bias secondarystructure
21.012	NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition	bio	funnel metadynamics	Jim Pfaendtner	DISTANCE FUNNEL PRINT COM UPPER_WALLS METAD LOWER_WALLS FUNNEL_PS	generic colvar vatom bias funnel
21.009	Nucleation rates from small scale atomistic simulations and transition state theory	materials	kinetics, free energy barriers, nucleation, droplets, metadynamics	Kristof Bal	MOVINGRESTRAINT REWEIGHT_METAD COMMITTOR LOAD HISTOGRAM PRINT UPPER_WALLS FLUSH METAD CONVERT_TO_FES UNITS COORDINATIONNUMBER DUMPGRID	symfunc generic setup bias gridtools
20.022	Unified Approach to Enhanced Sampling	methods	OPES, expanded ensembles, importance sampling	Michele Invernizzi	POSITION ECV_MULTITHERMAL_MULTIBARIC LOAD UPPER_WALLS ENERGY OPES_EXPANDED MOLINFO Q6 TORSION VOLUME PRINT UNITS ECV_LINEAR RMSD ENVIRONMENTSIMILARITY WHOLEMOLECULES ENDPLUMED MATHEVAL ECV_MULTITHERMAL ECV_UMBRELLAS_LINE CUSTOM	symfunc function generic colvar bias opes setup envsim
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	DISTANCE MOLINFO CONSTANT GROUP FUNCPATHGENERAL LOAD INCLUDE PRINT COM UPPER_WALLS BIASVALUE WHOLEMOLECULES LOWER_WALLS METAD MATHEVAL PROJECTION_ON_AXIS CONTACTMAP	function generic colvar bias vatom setup core
20.010	Phase equilibrium of liquid water and hexagonal ice from enhanced sampling molecular dynamics simulations	materials	water, ice, TIP4P, crystallization, EnvironmentSimilarity, RefCV, kernel, VES, variationally enhanced sampling	Pablo Piaggi	Q6 OPT_DUMMY VES_LINEAR_EXPANSION VOLUME ENVIRONMENTSIMILARITY UPPER_WALLS RESTART BF_LEGENDRE PRINT OPT_AVERAGED_SGD MATHEVAL TD_WELLTEMPERED	symfunc function generic colvar envsim setup bias ves
20.009	The dynamics of linear polyubiquitin	bio	saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics	Carlo Camilloni	DISTANCE PBMETAD MOLINFO ALPHABETA METAINFERENCE CENTER SAXS TORSION ENSEMBLE PRINT FLUSH WHOLEMOLECULES GYRATION STATS	function multicolvar generic isdb colvar vatom bias
20.001	Conformational stability and dynamics in solution and in crystals report similarly on unfolding and aggregation propensity of amyloidogenic proteins	bio	metainference, metadynamics, NMR, protein dynamics, b2m, protein crystals	Carlo Camilloni	PBMETAD MOLINFO GROUP ALPHABETA PRINT UPPER_WALLS BIASVALUE FLUSH WHOLEMOLECULES LOWER_WALLS ENDPLUMED ANTIBETARMSD CS2BACKBONE	multicolvar generic isdb bias secondarystructure core
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 PRINT UPPER_WALLS METAD LOWER_WALLS ENDPLUMED GYRATION COORDINATIONNUMBER ENERGY	symfunc multicolvar generic colvar bias
19.064	Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations	materials	metadynamics, peptide-surface binding	Jim Pfaendtner	DISTANCE MOLINFO PRINT COM UPPER_WALLS METAD GYRATION ENERGY	bias vatom colvar generic
19.059	cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide	bio	bias-exchange metadynamics, cis-trans isomerization	Fabrizio Marinelli	RANDOM_EXCHANGES TORSION INCLUDE PRINT METAD	bias colvar generic
19.057	SAXS ensembles using Martini-Beads multi-scale SAXS	methods	metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics	Cristina Paissoni	PBMETAD COORDINATION ANGLE MOLINFO GROUP ALPHABETA CENTER SAXS ENSEMBLE INCLUDE COMBINE PRINT BIASVALUE WHOLEMOLECULES ENDPLUMED MATHEVAL STATS	function multicolvar generic isdb colvar vatom bias core
19.040	Optimal Metric for Path Collective Variables	bio	metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path	Francesco Luigi Gervasio	TORSION PRINT METAD ENDPLUMED MATHEVAL	bias function colvar generic
19.035	Dimerization of GPCRs from coarse-grained umbrella sampling	bio	Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization	Davide Provasi	DISTANCE GROUP TORSION PRINT COM RESTRAINT	generic colvar vatom bias core
25.030	Committor Regularization	methods	metadynamics, enhanced sampling, mlcvs, committor, machine learning	Florian Dietrich	METAD PRINT MOVINGRESTRAINT UNITS	setup generic bias
25.017	Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity	bio	EMMIVox, cryo-EM, allostery, decamer, filament, ensemble refinement, glutamine synthetase	Samuel Hoff	EMMIVOX WHOLEMOLECULES GROUP PRINT BIASVALUE MOLINFO	generic core isdb bias
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	RESTART DISTANCE RESTRAINT PRINT METAD PUCKERING MOVINGRESTRAINT MOLINFO TORSION	setup generic colvar bias
25.005	Mechanism of Nanocluster Formation from Machine-Learned Potential-based Simulations	chemistry	WT-metadynamics, metal nanoclusters, nucleation, neural network potential, deepMD	Vikas Tiwari, Tarak Karmakar	FIXEDATOM COMBINE DISTANCE RESTRAINT GROUP METAD PRINT UNITS ANGLE UPPER_WALLS COORDINATION COM DISTANCES LOWER_WALLS COORDINATIONNUMBER FLUSH	vatom core function symfunc bias generic setup colvar multicolvar
24.019	Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning	bio	OPES, machine learning, protein folding, adaptive sampling	Mingyuan Zhang	CUSTOM COMBINE WHOLEMOLECULES DISTANCE GYRATION PRINT OPES_METAD ALPHARMSD COORDINATION MOLINFO TORSION	function generic secondarystructure opes colvar
23.039	Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation	chemistry	metadynamics, ligand dissociation	Eric Beyerle	FIXEDATOM COMBINE DISTANCE DUMPMASSCHARGE RESTRAINT METAD PRINT UPPER_WALLS CENTER MOLINFO	vatom function bias generic colvar
23.024	Permutationally Invariant Networks for Enhanced Sampling (PINES)	methods	collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent	Nicholas Herringer	LOAD PRINT PBMETAD	setup generic bias
22.004	Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques	chemistry	reaction discovery, OPES, collective variables	Umberto Raucci	MATHEVAL CUSTOM DISTANCE GROUP PRINT OPES_METAD UNITS PYTORCH_MODEL UPPER_WALLS COM LOAD LOWER_WALLS COORDINATION OPES_METAD_EXPLORE	pytorch vatom core function bias generic setup opes colvar
22.003	Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling	methods	opes, metadynamics, reweighting, alanine, muller	Michele Invernizzi	CUSTOM OPES_EXPANDED PBMETAD PRINT OPES_METAD METAD ECV_MULTITHERMAL UNITS ECV_UMBRELLAS_FILE BIASVALUE UPPER_WALLS ENDPLUMED LOWER_WALLS ENERGY POSITION OPES_METAD_EXPLORE TORSION	function bias generic setup opes colvar
20.025	The role of water in host-guest interaction	bio	ligand binding, water, opes, SAMPL5	Valerio Rizzi	FIT_TO_TEMPLATE MATHEVAL FIXEDATOM DISTANCE WHOLEMOLECULES GROUP PRINT OPES_METAD PYTORCH_MODEL ANGLE UPPER_WALLS ENDPLUMED ENERGY COORDINATION CENTER	vatom pytorch core function bias generic opes colvar
19.082	Ammonia Borane Dehydrogenation	chemistry	metadynamics, reaction discovery, hydrogen production, chemistry	Valerio Rizzi	RESTART COMBINE GROUP PRINT METAD UNITS ENDPLUMED EXTERNAL COORDINATIONNUMBER FLUSH	core function symfunc bias generic setup
26.001	Molecular simulations Alx riboswitch	bio	RNA, riboswitch	Giovanni Bussi	PRINT MATHEVAL MOLINFO ERMSD RESTRAINT MOVINGRESTRAINT DISTANCE	function colvar bias generic
25.023	Molecular simulations of Tau-protein oligomers	bio	metadynamics, proteins, aggregation	Giovanni Bussi	RMSD PRINT CONTACTMAP METAD CUSTOM RESTART FLUSH RESTRAINT	bias colvar function setup generic
25.015	Assessment of Force Fields for Describing Conformational Polymorphic Crystals of ROY	materials	Molecular crystal, Force Field, Collective Variable	Pradip Si and Omar Valsson	PRINT SMAC DUMPMULTICOLVAR DISTANCES TORSIONS	symfunc generic multicolvar
25.011	Chiral perovskite nucleation	chemistry	metadynamics, chiral perovskites, nucleation	Adriana Pietropaolo	MULTI_RMSD PRINT MATHEVAL PBMETAD UNITS LOWER_WALLS RESTART UPPER_WALLS DISTANCE	function colvar bias setup generic
25.001	RNA G-quadruplex folding with ST-metaD protocol	bio	RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD	Pavlína Pokorná	METAD MOLINFO COMBINE ERMSD WHOLEMOLECULES	bias colvar function generic
24.036	Leveraging cryptic ligand envelopes through enhanced molecular simulations	bio	HREX, conformational heterogeneity, drug discovery, ligand binding, plitidepsin, aplidin, ligand-target complexes, cryptic ligand envelope	Francesco Colizzi	PRINT CONVERT_TO_FES TORSION HISTOGRAM GROUP WHOLEMOLECULES ANGLE DUMPGRID COORDINATION DISTANCE	colvar core generic gridtools
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	COMMITTOR MOLINFO WHOLEMOLECULES CONTACTMAP UPPER_WALLS FIXEDATOM MATHEVAL ENDPLUMED GROUP OPES_METAD DISTANCE RMSD METAD CENTER CUSTOM ANGLE COORDINATION FIT_TO_TEMPLATE PRINT TORSION COMBINE	bias colvar function opes generic vatom core
24.009	Weighted Shape Gaussian Mixture Models	bio	metadynamics, clustering	Glen Hocky	PRINT METAD TORSION UNITS GROUP	bias colvar setup generic core
24.002	Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes	chemistry	metadynamics, ligand design, solvent extraction	Xiaoyu Wang	PRINT METAD TORSION UNITS RESTART	bias colvar generic setup
23.041	Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference	methods	EMMIVox, cryo-EM, single-structure refinement, ensemble refinement, Bayesian inference, B-factors, structural ensembles	Samuel Hoff	PRINT MOLINFO INCLUDE GROUP EMMIVOX WHOLEMOLECULES BIASVALUE UPPER_WALLS WRAPAROUND DISTANCE	bias colvar generic isdb core
23.036	Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water?	bio	NaCl, nucleation, metadynamics	Ruiyu Wang	PRINT VOLUME MATHEVAL METAD Q4 COMBINE Q6 ENERGY COORDINATIONNUMBER	function colvar bias symfunc generic
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	RMSD PRINT ENSEMBLE STATS CENTER MOLINFO GROUP BIASVALUE SAXS UPPER_WALLS WRAPAROUND DISTANCE	function colvar bias generic isdb 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	PRINT METAD GROUP Q6 MFILTER_MORE LOCAL_Q6 COMBINE LOWER_WALLS MOVINGRESTRAINT COORDINATIONNUMBER	bias function symfunc generic multicolvar core
23.015	MPCs aggregation	bio	opes_explore, dimerization, MPCs, self-assembly	Vikas Tiwari	OPES_METAD_EXPLORE PRINT METAD CENTER CUSTOM GROUP LOWER_WALLS COM COORDINATION WHOLEMOLECULES UPPER_WALLS DISTANCE	bias function colvar opes generic vatom core
22.038	Enhanced Sampling Aided Design of Molecular Photoswitches	chemistry	reaction discovery, OPES explore, graph CV	Umberto Raucci	OPES_METAD_EXPLORE PRINT CUSTOM UNITS PYTORCH_MODEL COORDINATION	function colvar setup pytorch opes generic
22.037	Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site	chemistry	metadynamics, DNA, abasic	Mike Jones	DISTANCES METAD PRINT DISTANCE	bias colvar generic multicolvar
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	TORSION MOLINFO PBMETAD GYRATION WHOLEMOLECULES	bias colvar generic
22.033	Reciprocal barrier restraint. Application to PROTAC passive permeability prediction	methods	PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR	Istvan Kolossvary	PRINT METAD CUSTOM UNITS COM FLUSH DRR BIASVALUE DISTANCE	bias function colvar setup drr generic vatom
22.029	Angiotensin-1-7_Metadynamics	bio	Metadynamics, Angiotensin-(1-7), peptide	L.-América Chi	PRINT METAD GROUP LOWER_WALLS GYRATION WHOLEMOLECULES UPPER_WALLS FLUSH COORDINATION	bias colvar generic core
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 TORSION MOLINFO ALPHABETA COORDINATION WHOLEMOLECULES ANGLE FLUSH ALPHARMSD UPPER_WALLS DISTANCE	secondarystructure bias colvar generic multicolvar
21.051	Automatic learning of hydrogen-bond fixes in an AMBER RNA force field	methods	force field, RNA	Giovanni Bussi	PRINT METAD MOLINFO COMBINE ERMSD WHOLEMOLECULES BIASVALUE COORDINATION	bias colvar function generic
21.030	Thermodynamic Basis for Stabilization of Helical Peptoids by Chiral Sidechains	bio	parallel bias parallel tempered metadynamics in WTE, synthetic foldamers, self-assembly, peptoid secondary structure	Jim Pfaendtner	PRINT METAD TORSION INCLUDE ALPHABETA PBMETAD COM GYRATION ENERGY COORDINATION DISTANCE	bias colvar generic multicolvar vatom
21.005	Crystallization Collective Variable	methods	Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA	Tarak Karmakar	PRINT MATHEVAL LOWER_WALLS PYTORCH_MODEL GROUP OPES_METAD FLUSH LOAD UPPER_WALLS	function bias setup pytorch opes generic core
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	PRINT STATS MOLINFO COMBINE WHOLEMOLECULES RESTRAINT COORDINATION	function colvar bias generic
20.027	Allosteric Regulation of SARS-CoV-2 Protease. Towards Informed Structure-Based Drug Discovery	bio	SARS-CoV2, MPro, Covid-19, Molecular Dynamics, Metadynamics, Computer-Aided Drug Discovery	Khaled Abdel-Maksoud	METAD TORSION PRINT DISTANCE	bias colvar generic
20.023	metadynminer and metadynminer3d	methods	metadynamics, visualization, R	Vojtech Spiwok	METAD TORSION PRINT	bias colvar generic
20.014	amyloid beta small molecule interaction	bio	intrinsically disordered proteins, disordered proteins, IDPs, fuzzy binding, small molecule, drugs, entropy, binding, Alzheimer’s disease, amyloid beta	Gabriella Heller	ENSEMBLE MOLINFO INCLUDE WHOLEMOLECULES FLUSH METAINFERENCE ENDPLUMED GROUP PARABETARMSD CS2BACKBONE ALPHARMSD STATS GYRATION COORDINATION ANTIBETARMSD PRINT TORSION PBMETAD COMBINE DIHCOR	secondarystructure function colvar bias generic isdb multicolvar core
20.008	Simulating solvation and acidity in complex mixtures with first-principles accuracy. The case of CH3SO3H and H2O2 in phenol	chemistry	proton trasfer, metadynamics	Kevin Rossi	PRINT METAD CUSTOM UNITS DISTANCES COORDINATION	bias function colvar setup generic multicolvar
19.072	SINE hairpin MD+NMR	bio	metadynamics, RNA, NMR	Giovanni Bussi	SORT PRINT MATHEVAL METAD TORSION MOLINFO INCLUDE COM WHOLEMOLECULES MAXENT FLUSH COORDINATION DISTANCE	function colvar bias generic vatom
19.038	native state dynamics of human and mouse b2m	bio	metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation	Carlo Camilloni	ANTIBETARMSD PRINT ENDPLUMED MOLINFO ALPHABETA PBMETAD GROUP LOWER_WALLS RESTART WHOLEMOLECULES FLUSH CS2BACKBONE UPPER_WALLS BIASVALUE	secondarystructure bias setup generic isdb multicolvar core
19.029	WTE-metaD of FF domain of URNF1 C57D variant	bio	metadynamics, mutations, post-translational modification, ff domain	Elena Papaleo	PRINT METAD MOLINFO ALPHABETA GROUP LOWER_WALLS GYRATION WHOLEMOLECULES UPPER_WALLS	bias colvar generic multicolvar core
19.028	pRAVE	methods	RAVE, reaction coordinate, deep learning, metadynamics, kinetics	Pratyush Tiwary	PRINT TORSION COMMITTOR ALPHABETA COM COMBINE RESTART WHOLEMOLECULES EXTERNAL DISTANCE	function colvar bias setup generic multicolvar vatom
19.025	Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide	bio	metainference, NMR, protein dynamics, force-fields	Carlo Camilloni	PRINT ENSEMBLE STATS METAINFERENCE RDC JCOUPLING TORSION MOLINFO PBMETAD ENDPLUMED GYRATION WHOLEMOLECULES FLUSH CS2BACKBONE BIASVALUE	function colvar bias generic isdb
19.019	FA-MetaD-JCP-Wang-et-al	bio	Frequency adaptive metadynamics; peptide	Kresten Lindorff-Larsen	PRINT METAD MOLINFO ALPHABETA COMMITTOR COMBINE FLUSH	bias function generic multicolvar
19.005	Cmyc small molecule interaction	bio	metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP	Gabriella Heller	PRINT CENTER MOLINFO ALPHABETA INCLUDE PBMETAD GROUP GYRATION WHOLEMOLECULES CS2BACKBONE COORDINATION METAINFERENCE DISTANCE	bias colvar generic isdb multicolvar vatom core
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	SAXS PRINT UPPER_WALLS GYRATION CENTER INCLUDE METAD MOLINFO WHOLEMOLECULES GROUP DISTANCE MOVINGRESTRAINT	isdb core bias generic colvar vatom
25.024	Sampling glycan-glycan interactions for B22 calculations	bio	B22, glycan, carbohydrates, distance, REST2, metadynamics, RECT, replica exchange	Isabell Louise Grothaus	COMBINE PRINT RESTRAINT METAD DISTANCE POSITION COM	function bias generic colvar vatom
25.022	Imidazole Diffusion in SALEM-2 MOF	materials	OPES, Diffusion, Ring opening, MOFs, Machine Learning Potentials	Sudheesh Kumar Ethirajan	UNITS PROJECTION_ON_AXIS PRINT DISTANCES CENTER MOLINFO WHOLEMOLECULES GROUP DISTANCE OPES_METAD ENDPLUMED	core opes generic colvar multicolvar vatom setup
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	RMSD GHOST LOWER_WALLS CUSTOM OPES_METAD_EXPLORE PRINT UPPER_WALLS OPES_EXPANDED DISTANCES CENTER ECV_MULTITHERMAL ENERGY GROUP DISTANCE PATHMSD COORDINATION	function core bias opes generic colvar multicolvar vatom
25.014	Atomic resolution ensembles of intrinsically disordered proteins with Alphafold	bio	bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement	Vincent Schnapka	GROUP BIASVALUE BAIES PRINT	bias isdb core generic
25.012	A Machine Learning-Driven, Probability-Based Approach to Enzyme Catalysis	bio	enzyme catalysis, transition state, structure-activity relationship, free energy surface, reaction mechanism, water, alpha-amylase, sugar, QM/MM MD, OPES, committor function, machine learning	Sudip Das	COMBINE CELL UNITS TORSION CUSTOM PRINT LOAD INCLUDE ENERGY MATHEVAL FLUSH BIASVALUE OPES_METAD COORDINATION DISTANCE POSITION	function bias opes generic colvar setup
25.010	Kinetic rates calculation with Ratchet&Pawl MD	methods	kinetics, ligand binding, ABMD, ratchet&pawl MD	Riccardo Capelli	ABMD PRINT WHOLEMOLECULES FLUSH GROUP DISTANCE COMMITTOR COM	core bias generic colvar vatom
25.003	Surrogate Model CV	methods	Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding	Sompriya Chatterjee	COMBINE TORSION CUSTOM PRINT PYTORCH_MODEL ENERGY MOLINFO MATHEVAL WHOLEMOLECULES GROUP DISTANCE OPES_METAD ENDPLUMED COMMITTOR	function core opes generic colvar pytorch
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	LOWER_WALLS TORSION CUSTOM FIXEDATOM PRINT FIT_TO_TEMPLATE UPPER_WALLS COORDINATION RESTART CENTER PYTORCH_MODEL WHOLEMOLECULES PATH GROUP DISTANCE OPES_METAD	function core bias opes generic pytorch colvar mapping vatom setup
24.021	Ab initio machine learning simulation of calcium carbonate from aqueous solutions to the solid state	chemistry	ion pairing, caco3, opes, proton transfer, crystallization	Pablo Piaggi	COORDINATION PRINT UPPER_WALLS ENERGY DISTANCE OPES_METAD	generic bias opes colvar
24.003	Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations	chemistry	steered molecular dynamics, foldamers, peptoids, bio-inspired	Kaylyn Torkelson	TORSION ALPHABETA PRINT GYRATION COM INCLUDE WHOLEMOLECULES DISTANCE COORDINATION MOVINGRESTRAINT	bias generic colvar multicolvar vatom
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	LOWER_WALLS PRINT FUNCPATHMSD ALPHARMSD UPPER_WALLS CONTACTMAP INCLUDE METAD MOLINFO DISTANCE PATHMSD	function bias generic secondarystructure colvar
23.034	Urea nucleation in water: do long-range forces matter?	materials	LMF theory, Metadynamics, Nucleation	Ziyue Zou	COORDINATIONNUMBER PRINT LOAD CENTER INCLUDE METAD GROUP	core bias generic symfunc vatom setup
22.031	Rare Event Kinetics from Adaptive Bias Enhanced Sampling	methods	OPES Flooding, Kinetics, Rate, OPES, Machine Learning	Dhiman Ray	CUSTOM CONTACTMAP PYTORCH_MODEL MOLINFO COMMITTOR ENDPLUMED INCLUDE ENERGY BIASVALUE OPES_METAD POSITION RMSD COMBINE UNITS TORSION PRINT GROUP DISTANCE CONSTANT WHOLEMOLECULES	function core bias opes generic setup colvar pytorch
22.025	Bubble nucleation rate predictions in a Lennard-Jones fluid	materials	free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation	Kristof Bal	COORDINATIONNUMBER UNITS CUSTOM HISTOGRAM PRINT UPPER_WALLS DUMPGRID LOAD REWEIGHT_BIAS ANN VOLUME FLUSH BIASVALUE RESTRAINT COMMITTOR CONVERT_TO_FES MOVINGRESTRAINT	function bias generic annfunc colvar symfunc gridtools setup
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	RMSD LOWER_WALLS FIXEDATOM COORDINATION PRINT FIT_TO_TEMPLATE UPPER_WALLS CUSTOM CENTER PYTORCH_MODEL MATHEVAL WHOLEMOLECULES GROUP DISTANCE COMMITTOR OPES_METAD	function core bias opes generic colvar vatom pytorch
22.002	GAMBES_SAMPL5_RATES	other	GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding	Jayashrita Debnath	FIXEDATOM COORDINATION PRINT FIT_TO_TEMPLATE UPPER_WALLS LOAD CENTER PYTORCH_MODEL MATHEVAL ENERGY WHOLEMOLECULES FLUSH GROUP DISTANCE COMMITTOR ENDPLUMED ANGLE	function core bias generic pytorch colvar vatom setup
21.047	Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations	materials	pair entropy, metadynamics, ves, solids, crystallization	Pablo Piaggi	COMBINE BF_LEGENDRE TD_WELLTEMPERED PRINT PAIRENTROPY LOAD RESTART VES_LINEAR_EXPANSION VOLUME METAD ENERGY OPT_AVERAGED_SGD	function ves bias generic colvar gridtools setup
21.033	Multiple-path-metadynamics applied to DNA base-pairing transitions	bio	path-CV, metadynamics, multiple-walker, dna	Alberto Pérez-de-Alba-Ortíz	COMBINE PRINT UPPER_WALLS CONSTANT INCLUDE METAD RESTRAINT MOVINGRESTRAINT	bias function generic
21.023	Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling	methods	enhanced sampling, collective variables, machine learning	Jakub Rydzewski	UNITS TORSION CUSTOM PRINT CONSTANT INCLUDE METAD ENERGY REWEIGHT_METAD BIASVALUE DISTANCE	function bias generic colvar setup
21.019	Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations	materials	Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen	Matteo Salvalaglio	PRINT TORSIONS KDE MATHEVAL DISTANCE COM	function generic colvar multicolvar gridtools vatom
21.003	aSYN SAXS metainference	bio	metainference, SAXS	Kresten Lindorff-Larsen	SAXS PRINT PBMETAD ALPHARMSD GYRATION EEFSOLV METAINFERENCE CENTER MOLINFO WHOLEMOLECULES FLUSH GROUP BIASVALUE	isdb core bias generic secondarystructure colvar vatom
20.034	Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations	bio	RNA, SARS-CoV-2, partial tempering	Sandro Bottaro	ABMD ERMSD TORSION PRINT RESTART CENTER MOLINFO DISTANCE	bias generic colvar vatom setup
20.019	Systematic finite-temperature reduction of crystal energy landscapes	materials	crystals, organics, structure prediction	Matteo Salvalaglio	LOWER_WALLS PRINT UPPER_WALLS VOLUME METAD MATHEVAL ENERGY CELL	bias function colvar generic
20.011	Uremic toxin analysis	bio	metadynamics, uremic toxin, serum albumin	Jim Pfaendtner	PRINT RESTART DISTANCES CENTER WHOLEMOLECULES GROUP DISTANCE COORDINATION	core generic colvar multicolvar vatom setup
19.067	Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways	bio	metadynamics, ligand unbinding	Jakub Rydzewski	UNITS LOWER_WALLS PRINT UPPER_WALLS RESTART METAD PATHMSD	bias colvar setup generic
19.054	MetaFEP	methods	metadynamics, chemistry, free energy perturbation	GiovanniMaria Piccini	COMBINE UNITS LOWER_WALLS PRINT UPPER_WALLS METAD ENERGY FLUSH DISTANCE	function bias generic colvar setup
19.024	PT-MetaD-WTE	methods	metadynamics, WTE, trp cage, PT	Jim Pfaendtner	EXTERNAL METAD ENERGY GROUP COORDINATION	bias core colvar
19.012	Martini-Beads multi-scale SAXS	methods	metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex	Carlo Camilloni	RMSD SAXS PRINT UPPER_WALLS RESTRAINT ENDPLUMED CENTER INCLUDE MOLINFO WHOLEMOLECULES GROUP DISTANCE BIASVALUE STATS	isdb core function bias generic colvar vatom
25.029	Energetic Constraints in the Enzymatic Depolymerization of Crystalline PET from enhanced molecular simulations	bio	HREX-Metadynamics, PETase, crystalline PET, amorphous PET, conformational ensembles, substrate binding, chain detachment	Ania Di Pede-Mattatelli and Francesco Colizzi	METAD REWEIGHT_BIAS LOWER_WALLS MOLINFO DISTANCE UPPER_WALLS DUMPGRID CONVERT_TO_FES PRINT HISTOGRAM FIXEDATOM COM WHOLEMOLECULES	gridtools colvar vatom generic bias
25.028	Designing transferable transition state guided collective variable via interpretable machine learning model for enhanced sampling. A case study on polymer collapse transition	bio	metadynamics, polymer collapse transition, transferable CV,interpretable ML-model	Saikat Dhibar and Biman Jana	METAD GYRATION LOWER_WALLS DISTANCE MATHEVAL UPPER_WALLS GROUP PRINT COORDINATION CENTER COMBINE WHOLEMOLECULES	core colvar function vatom generic bias
25.016	Advancing in silico drug design with Bayesian refinement of AlphaFold models	bio	bAIes, AlphaFold, Bayesian refinement, virtual screening, docking, small-molecule, enrichment	Samiran Sen	GROUP BAIES BIASVALUE PRINT	core generic isdb bias
24.020	Graph Neural Network-State Predictive Information Bottleneck (GNN-SPIB) approach for learning molecular thermodynamics and kinetics	bio	LJ7, alanine, well-tempered metadynamics, infrequent metadynamics, machine learning	Ziyue Zou, Dedi Wang, Pratyush Tiwary	METAD COMMITTOR GROUP PRINT TORSION LOAD	core colvar setup generic bias
24.017	Absolute Binding Free Energies with OneOPES	methods	protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy	Francesco Gervasio	WRAPAROUND METAD MOLINFO OPES_EXPANDED INCLUDE CUSTOM COM OPES_METAD_EXPLORE RMSD LOWER_WALLS UPPER_WALLS PRINT CONSTANT TORSION BIASVALUE MATHEVAL ENERGY GROUP COORDINATION PROJECTION_ON_AXIS RESTART ECV_MULTITHERMAL CONTACTMAP WHOLEMOLECULES	core colvar opes vatom function setup generic bias
24.013	Estimating Free Energy Surfaces and their Convergence from multiple, independent static and history-dependent biased molecular-dynamics simulations with Mean Force Integration	methods	Mean Force Integration, Convergence, FES, Umbrella Sampling	Matteo Salvalaglio	METAD COMMITTOR RESTRAINT BIASVALUE RESTART COORDINATIONNUMBER MOLINFO DISTANCE MATHEVAL ENERGY PRINT TORSION FLUSH	colvar function setup symfunc generic bias
24.004	Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables	materials	metadynamics, nucleation, machine learning	Ziyue Zou	METAD RESTART INCLUDE GROUP PRINT LOAD	core setup generic bias
23.044	Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition	materials	metadynamics, interlocked molecules	Luigi Leanza	METAD COMMITTOR READ DUMPGRID GROUP CONVERT_TO_FES PRINT ENDPLUMED COORDINATION HISTOGRAM	core gridtools colvar 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 METAD INCLUDE SUM MATHEVAL PRINT SELECT_COMPONENTS FLUSH	valtools matrixtools function generic bias
23.037	Estimating binding free energy of solid binding peptides without extensive sampling	bio	metadynamics, solid binding peptides	Xin Qi	GYRATION MOLINFO LOWER_WALLS DISTANCE PBMETAD UPPER_WALLS PRINT COM	vatom generic bias colvar
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	METAD BIASVALUE LOWER_WALLS DISTANCE MATHEVAL UPPER_WALLS PRINT CONSTANT CENTER WHOLEMOLECULES	colvar vatom function generic 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	WRAPAROUND MOLINFO OPES_METAD CUSTOM CENTER COM OPES_METAD_EXPLORE LOWER_WALLS UPPER_WALLS PRINT ENDPLUMED TORSION FLUSH COMMITTOR BIASVALUE MATHEVAL ENERGY GROUP POSITION UNITS COORDINATION DISTANCE FIT_TO_TEMPLATE WHOLEMOLECULES	core colvar opes function vatom setup 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	PYTORCH_MODEL TORSION OPES_METAD_EXPLORE PATH LOWER_WALLS DISTANCE FIT_TO_TEMPLATE OPES_METAD UPPER_WALLS GROUP CUSTOM PRINT CENTER FIXEDATOM UNITS COORDINATION WHOLEMOLECULES	core colvar mapping pytorch opes function vatom setup generic bias
23.014	Structural basis of dimerization of chemokine receptors CCR5 and CXCR4	bio	metadynamics, oligomerization, chemokine receptors, GPCR, membrane	Vittorio Limongelli	METAD COM DISTANCE UPPER_WALLS PRINT TORSION COMBINE FLUSH WHOLEMOLECULES	colvar vatom function generic bias
23.012	JAK2 2D meta-eABF PMF with statistical analysis	bio	2D meta-eABF, path CV, PMF	Istvan Kolossvary	METAD PATHMSD BIASVALUE LOWER_WALLS UPPER_WALLS DRR CUSTOM PRINT FLUSH	colvar function drr generic 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	VOLUME RESTART OPES_METAD ENERGY UPPER_WALLS DUMPGRID CUSTOM PRINT ENVIRONMENTSIMILARITY AROUND HISTOGRAM	gridtools colvar volumes opes function envsim setup generic bias
21.044	NaCl nucleation	chemistry	metadynamics, DFS clustering	Aaron Finney	METAD INSPHERE Q6 COORDINATIONNUMBER CLUSTER_DISTRIBUTION DUMPGRID GROUP CLUSTER_NATOMS PRINT LOCAL_Q6 FIXEDATOM DFSCLUSTERING COMBINE CONTACT_MATRIX HISTOGRAM MFILTER_MORE	core gridtools volumes multicolvar vatom function adjmat symfunc clusters generic bias
21.038	Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics	materials	metadynamics, SGOOP, nucleation, urea	Ziyue Zou	VOLUME METAD COORDINATIONNUMBER COMBINE INCLUDE ENERGY GROUP PRINT CENTER LOAD	core colvar function vatom setup symfunc generic bias
21.037	Molecular Dynamics simulations of RBD/hACE2 complexes	bio	SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain	Max Bonomi	RMSD DISTANCE PRINT	generic colvar
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 METAD INCLUDE PBMETAD PRINT ENDPLUMED TORSION	generic bias colvar
21.025	Computational and biochemical analysis of type IV pilus dynamics and stability	bio	molecular dynamics, calcium binding, Type IV pilus	Yasaman Karami	LOWER_WALLS DISTANCE PRINT UPPER_WALLS	generic bias colvar
21.004	Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy	bio	machine learning, well-tempered metadynamics, path collective variable, potential of mean force, standard binding free energy calculations, host-guest, protein-ligand unbinding	Dorothea Gobbo	METAD PATHMSD RESTART LOWER_WALLS UPPER_WALLS PRINT WHOLEMOLECULES	setup generic bias colvar
20.028	Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane	bio	metadynamics, KRas-4B, anionic membrane	Huixia Lu	METAD RESTART DISTANCE FIT_TO_TEMPLATE PRINT CENTER	colvar vatom setup generic bias
20.018	Free energy barriers from biased molecular dynamics simulations	methods	kinetics, free energy barriers, chemical reactions, nucleation, metadynamics	Kristof Bal	METAD REWEIGHT_BIAS COORDINATIONNUMBER CONVERT_TO_FES PAIRENTROPY CENTER HISTOGRAM Q6 LOWER_WALLS UPPER_WALLS PRINT DENSITY REWEIGHT_METAD FLUSH VOLUME ENERGY DUMPGRID SPRINT UNITS COORDINATION COMBINE DISTANCE LOCAL_AVERAGE CONTACT_MATRIX LOAD	gridtools volumes colvar vatom function sprint setup adjmat symfunc generic bias
20.016	Predicting polymorphism in molecular crystals using orientational entropy	materials	metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy	Pablo Piaggi	VOLUME METAD INCLUDE UPPER_WALLS GROUP PRINT CENTER LOAD	core colvar vatom setup generic bias
20.002	Exploring conformational dynamics of the extracellular Venus flytrap domain of the GABAB receptor, a path-metadynamics study	bio	Metadynamics, path CVs	Riccardo Ocello	METAD PATHMSD RESTART MOLINFO UPPER_WALLS GROUP PRINT WHOLEMOLECULES	core colvar setup generic bias
20.000	Muscarinic M2 receptor-ligand funnel metadynamics	bio	multiple walker metadynamics, well-tempered metadynamics, funnel metadynamics, MC-HLDA, GPCR, receptor, Adiabatic Bias MD	Riccardo Capelli	METAD ABMD LOWER_WALLS HISTOGRAM DISTANCE READ MATHEVAL UPPER_WALLS DUMPGRID CONVERT_TO_FES PRINT REWEIGHT_METAD ENDPLUMED COMBINE COM	gridtools colvar function vatom generic bias
19.080	Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium	methods	ves, variationally enhanced sampling, vibrational excitation, chemical reactions	Kristof Bal	BF_CHEBYSHEV EXTERNAL VES_LINEAR_EXPANSION LOWER_WALLS COMBINE DISTANCE TD_WELLTEMPERED UPPER_WALLS DUMPGRID CONVERT_TO_FES TD_GRID OPT_AVERAGED_SGD PRINT HISTOGRAM ANGLE UNITS COORDINATION FLUSH	gridtools colvar function setup ves generic bias
19.077	Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations	materials	metadynamics, peptide-surface binding	Jim Pfaendtner	METAD GYRATION MOLINFO DISTANCE ENERGY UPPER_WALLS PRINT COM	vatom generic bias colvar
19.075	PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python	other	Python, automatic differentiation	Toni Giorgino	RESTRAINT DUMPDERIVATIVES DISTANCE GROUP CUSTOM PRINT ANGLE ENDPLUMED CENTER TORSION COMBINE	core colvar function vatom generic bias
19.063	Protein-ligand binding through metadynamics with path CVs	bio	metadynamics, path CVs, ligand binding	Mattia Bernetti	METAD PATHMSD LOWER_WALLS UPPER_WALLS PRINT WHOLEMOLECULES	generic bias colvar
19.053	Capillary fluctuations with PLUMED	methods	nucleation, surface tension, capillary fluctuations	Gareth Tribello	MULTICOLVARDENS FIND_CONTOUR_SURFACE FOURIER_TRANSFORM MORE_THAN DUMPGRID GROUP FCCUBIC UNITS CENTER	core gridtools function vatom setup symfunc fourier contour
19.051	Solid liquid interfacial free energy out of equilibrium	materials	metadynamics, nucleation, surface excess free energy	Gareth Tribello	METAD LOWER_WALLS UPPER_WALLS PRINT ENDPLUMED UNITS FCCUBIC AROUND CELL	volumes colvar setup symfunc generic bias
19.041	Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces	bio	metadynamics, collective variables, conformational changes, multiple walkers, Well-Tempered MetaD, peptide, binding, phosphorylation, post-transitional motif, sio2, adsorption	Jim Pfaendtner	METAD DISTANCE ENERGY UPPER_WALLS PRINT COM	vatom generic bias colvar
19.030	Coarse-Grained MetaDynamics (CG-MetaD)	bio	Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy	Vittorio Limongelli	METAD LOWER_WALLS DISTANCE UPPER_WALLS PRINT COM WHOLEMOLECULES	vatom generic bias colvar
19.004	MI Ubiquitin	bio	metainference, NMR	Max Bonomi	RDC MOLINFO METAINFERENCE GROUP CS2BACKBONE PRINT WHOLEMOLECULES	core generic isdb
19.001	RNA SHAPE	bio	metadynamics, RNA, ligand binding	Giovanni Bussi	RANDOM_EXCHANGES METAD MOLINFO LOWER_WALLS DISTANCE INCLUDE UPPER_WALLS DISTANCES ERMSD PRINT ANGLE COMBINE FLUSH	colvar multicolvar function generic bias
25.008	Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting	methods	metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting	Dhiman Ray	METAD CUSTOM LOWER_WALLS OPES_METAD RMSD WHOLEMOLECULES UPPER_WALLS PYTORCH_MODEL GROUP PRINT ENDPLUMED UNITS TORSION BIASVALUE POSITION MOLINFO DISTANCE ENERGY	colvar opes function setup pytorch core bias generic
24.031	DeepLNE	methods	PATHCV, OPES, OneOPES	Thorben Fröhlking	RESTART COMBINE OPES_METAD_EXPLORE ECV_MULTITHERMAL ERMSD VOLUME PYTORCH_MODEL PRINT COORDINATION OPES_EXPANDED MOLINFO ENERGY	colvar function setup pytorch opes generic
24.014	Learning Collective Variables with Synthetic Data Augmentation through Physics-inspired Geodesic Interpolation	methods	data augmentation, geodesic interpolation, collective variables, protein folding	Juno Nam	METAD RMSD WHOLEMOLECULES DRR UPPER_WALLS PYTORCH_MODEL PRINT COORDINATION FLUSH MOLINFO LOWER_WALLS	drr colvar pytorch bias generic
24.012	Molecular simulations to investigate the impact of N6-methylation in RNA recognition	bio	metadynamics, alchemistry, RNA modification, RNA:protein interactions	Giovanni Bussi	METAD COMBINE DEBUG COM UPPER_WALLS GROUP PRINT BIASVALUE CENTER COORDINATION GHBFIX MOLINFO DISTANCE LOWER_WALLS	vatom colvar function core bias generic
24.007	SWISH-X	bio	swish-x, SWISH-X, swish, expanded SWISH	Alberto Borsatto	ECV_MULTITHERMAL WHOLEMOLECULES INCLUDE UPPER_WALLS PRINT OPES_EXPANDED CONTACTMAP MOLINFO ENERGY	opes colvar generic bias
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 COMMITTOR LOWER_WALLS OPES_METAD UPPER_WALLS UNITS PRINT TORSION FLUSH DISTANCE COMBINE	colvar opes function setup bias generic
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	OPES_METAD COORDINATIONNUMBER ZDISTANCES UPPER_WALLS GROUP UNITS FIXEDATOM PRINT FLUSH DISTANCE	vatom colvar bias setup multicolvar symfunc core opes generic
23.032	Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics	bio	metadynamics, tSNE, neural network, machine learning, trp-cage, folding	Vojtech Spiwok	METAD WHOLEMOLECULES ANN PRINT FIT_TO_TEMPLATE POSITION ALPHARMSD MOLINFO COMBINE	secondarystructure colvar function annfunc bias generic
23.020	FEP simulations of ATOX1 homodimer	chemistry	parallel bias metadynamics, FEP, free-energy of metal ion dissociation	Adriana Pietropaolo	WHOLEMOLECULES ANGLE PBMETAD CONSTANT PRINT BIASVALUE MATHEVAL DISTANCE	bias function colvar generic
23.018	Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention	materials	metadynamics, surface binding, peptide adsorption	Kaylyn Torkelson	GYRATION COM UPPER_WALLS PBMETAD PRINT DISTANCE	vatom colvar generic bias
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	COMMITTOR INCLUDE FIXEDATOM PRINT MATHEVAL MOLINFO COMBINE ENERGY OPES_METAD RMSD WHOLEMOLECULES UPPER_WALLS ANGLE CENTER FIT_TO_TEMPLATE COORDINATION DISTANCE LOWER_WALLS CONTACTMAP CUSTOM PYTORCH_MODEL GROUP ENDPLUMED	vatom colvar function bias pytorch core opes generic
23.003	Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations	methods	metadynamics, alchemical variable, alchemical free energy calculations	Wei-Tse Hsu	METAD READ EXTRACV PRINT TORSION	bias colvar generic
22.045	Binding mode and mechanism of enzymatic polyethylene terephthalate degradation	bio	metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation	Francesco Colizzi	METAD WHOLEMOLECULES ANGLE COM UPPER_WALLS MOVINGRESTRAINT PRINT DISTANCE LOWER_WALLS	bias vatom colvar generic
22.044	Colloid Crystallisation Analyses	materials	Q4, Q6, Pair Entropy, DFS	Aaron Finney	MFILTER_LESS COORDINATIONNUMBER CLUSTER_NATOMS LOCAL_Q4 Q4 LOCAL_AVERAGE CONTACT_MATRIX DFSCLUSTERING LOCAL_Q6 GROUP PRINT MFILTER_MORE Q6 COMBINE	function adjmat multicolvar symfunc core clusters generic
22.036	Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction	bio	Well-tempered MetaDynamics with Hamiltonian Replica Exchange	Miroslav Krepl	METAD CUSTOM UPPER_WALLS GROUP PRINT LOAD BIASVALUE COORDINATION GHBFIX FLUSH MOLINFO COMBINE	colvar function setup core bias generic
22.028	N-glycan conformer distributions in atomistic simulation	bio	REST2, RECT, N-glycan, pucker	Isabell Grothaus	METAD CONVERT_TO_FES READ DUMPGRID PUCKERING PRINT TORSION MOLINFO HISTOGRAM	bias gridtools colvar generic
22.026	Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification	materials	Peptoid, silica	Jim Pfaendtner	GYRATION COM PBMETAD UPPER_WALLS PRINT MOLINFO DISTANCE	vatom colvar generic bias
22.022	Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir	bio	RMSD, protein-ligand interactions	Isabell Grothaus	RMSD PRINT	colvar generic
22.021	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	ECV_UMBRELLAS_LINE INCLUDE UPPER_WALLS PRINT OPES_EXPANDED ENVIRONMENTSIMILARITY LOWER_WALLS	opes envsim generic bias
22.013	Ligand dissociation from PreQ1 riboswitch	bio	ligand, RNA, metadynamics, pRAVE	Yihang Wang	METAD COMMITTOR COORDINATIONNUMBER RMSD WHOLEMOLECULES COM PRINT MOLINFO DISTANCE COMBINE	vatom colvar function symfunc bias generic
22.006	Peptide framework for screening the effects of amino acids on assembly	bio	metadynamics, peptides	Andrew White	GYRATION METAD CONVERT_TO_FES COMBINE DISTANCES INCLUDE COM DUMPGRID GROUP PRINT REWEIGHT_BIAS HISTOGRAM	vatom colvar function gridtools multicolvar core bias generic
22.005	Collective Variable for Metadynamics Derived from AlphaFold Output	bio	AlphaFold, protein folding, protein structure prediction, metadynamics, deep learning, free energy simulation, collective variable	Vojtech Spiwok	METAD WHOLEMOLECULES LOAD PRINT	bias setup generic
21.049	Multiple-path-metadynamics and PathMaps	methods	path-CV, metadynamics, multiple-walker, multiple paths, pathmap	Alberto Pérez-de-Alba-Ortíz	METAD CUSTOM LOWER_WALLS UPPER_WALLS CONSTANT MOVINGRESTRAINT UNITS LOAD ENSEMBLE TORSION PRINT RESTRAINT COMBINE	colvar function setup bias generic
21.045	QM/MM metadynamics of thiol-disulfide exchange between methylthiolate and dimethyldisulfide in water with an imposed external electrostatic potential (ESP)	chemistry	metadynamics, QM/MM, electrostatic potential, thiol-disulfide exchange	Denis Maag	METAD COMBINE COORDINATIONNUMBER UPPER_WALLS PRINT COORDINATION DISTANCE LOWER_WALLS	colvar function symfunc bias generic
21.035	CmuMD simulations of NaCl(aq) at NaCl	chemistry	CmuMD, interface	Aaron Finney	GROUP PRINT LOAD RESTRAINT FIXEDATOM DISTANCE	vatom colvar setup core bias generic
21.018	Localized Volume-based Metadynamics	bio	LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification	Riccardo Capelli	READ FIXEDATOM PRINT POSITION MATHEVAL CONVERT_TO_FES RMSD WHOLEMOLECULES COM UPPER_WALLS METAD DUMPGRID COORDINATION FLUSH DISTANCE HISTOGRAM GROUP REWEIGHT_METAD ENDPLUMED	vatom colvar function gridtools core bias generic
21.013	Role of vibrational excitation in heterogeneous catalysis	chemistry	catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption	Kristof Bal	VES_LINEAR_EXPANSION UNITS PRINT COMBINE CONVERT_TO_FES DISTANCES OPT_AVERAGED_SGD UPPER_WALLS UWALLS EXTERNAL METAD COORDINATIONNUMBER DUMPGRID COORDINATION FLUSH DISTANCE ANGLES HISTOGRAM LOWER_WALLS RESTRAINT REWEIGHT_METAD LOAD REWEIGHT_BIAS BF_CHEBYSHEV TD_GRID	ves colvar function setup gridtools multicolvar symfunc bias generic
21.006	OPES, On-the-fly Probability Enhanced Sampling Method	methods	opes, alanine dipeptide, well-tempered, multithermal, multiumbrella	Michele Invernizzi	ECV_UMBRELLAS_LINE ECV_MULTITHERMAL OPES_METAD PRINT ENDPLUMED TORSION OPES_EXPANDED ENERGY	opes colvar generic
20.006	Class B GPCR activation mechanism	bio	metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding	Francesco Gervasio	METAD COMBINE LOWER_WALLS RMSD WHOLEMOLECULES UPPER_WALLS PRINT CENTER MATHEVAL MOLINFO DISTANCE ENERGY	vatom colvar function bias generic
20.005	Muscarinic M2 receptor/ligand Frequency-Adaptive Metadynamics and QM/MM calculations	bio	Frequency-adaptive metadynamics, multiple-walkers metadynamics, well-tempered metadynamics, GPCR, receptor, Adiabatic Bias MD	Riccardo Capelli	READ PRINT MOLINFO COMBINE CONVERT_TO_FES WHOLEMOLECULES COM UPPER_WALLS ABMD METAD DUMPGRID FLUSH DISTANCE HISTOGRAM CONTACTMAP LOWER_WALLS REWEIGHT_METAD ENDPLUMED FUNCPATHMSD	vatom colvar function gridtools bias generic
20.004	Data-driven collective variables for enhanced sampling	methods	collective variables, machine learning, deep-lda	Luigi Bonati	OPES_METAD COM UPPER_WALLS PYTORCH_MODEL GROUP PRINT ENDPLUMED UNITS TORSION LOAD MATHEVAL FLUSH DISTANCE LOWER_WALLS	vatom colvar function bias setup pytorch core opes generic
19.062	Elucidating molecular design principles for charge-alternating peptides	bio	peptide folding, metadynamics, well-tempered ensemble, parallel tempering	Jim Pfaendtner	GYRATION METAD WHOLEMOLECULES PRINT ENERGY	bias colvar generic
19.042	Harmonic Linear Discriminant Analysis (HLDA)	methods	metadynamics, chemistry, HLDA	GiovanniMaria Piccini	METAD COMBINE UPPER_WALLS UNITS PRINT FLUSH DISTANCE ENERGY	colvar function setup bias generic
19.037	Scission free energy of organic dyes	chemistry	metadynamics, multiple walkers, matheval/lepton	Paolo Raiteri	METAD UPPER_WALLS UNITS PRINT MATHEVAL FLUSH DISTANCE RESTART	colvar function setup bias generic
19.036	Thermodynamics and kinetics of G protein-coupled receptor activation	bio	metadynamics, allostery, receptor conformation, GPCR, pharmacology	Davide Provasi	METAD RMSD WHOLEMOLECULES COM PRINT ENDPLUMED FUNCPATHMSD DISTANCE CONTACTMAP	vatom colvar function bias generic
19.020	PTMetaD-WTE simulation of the Ntail IDP	bio	metadynamics, IDPs, protein folding	Mattia Bernetti	GYRATION METAD WHOLEMOLECULES PRINT ENDPLUMED ALPHARMSD MOLINFO ENERGY	bias colvar secondarystructure generic
19.017	Ligand binding pathways exploration	bio	metadynamics, ligand binding	Riccardo Capelli	METAD CONVERT_TO_FES READ WHOLEMOLECULES COM DUMPGRID UPPER_WALLS GROUP PRINT REWEIGHT_METAD ENDPLUMED WRAPAROUND FIT_TO_TEMPLATE MATHEVAL POSITION COORDINATION FLUSH HISTOGRAM	vatom colvar function gridtools core bias generic
19.014	MIL101(Cr) SBUs assembly	materials	MOFs, nucleation, self-assembly, metadynamics	Matteo Salvalaglio	METAD GYRATION COORDINATIONNUMBER DISTANCES PRINT ENDPLUMED RESTART	colvar setup multicolvar symfunc bias generic
19.010	Multi-domain protein dynamics	bio	metainference, NMR, protein dynamics	Carlo Camilloni	RDC METAINFERENCE DIHCOR DHENERGY WHOLEMOLECULES UPPER_WALLS PBMETAD GROUP PRINT ENSEMBLE ALPHABETA CENTER TORSION ENDPLUMED RESTRAINT STATS MOLINFO DISTANCE	vatom colvar function isdb multicolvar core bias generic
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	LOWER_WALLS FUNNEL_PS UPPER_WALLS PRINT COM FUNNEL METAD	bias vatom generic funnel
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	FIT_TO_TEMPLATE WHOLEMOLECULES DISTANCE OPES_METAD_EXPLORE ANGLE MATHEVAL COORDINATION CENTER GROUP UPPER_WALLS PRINT FIXEDATOM ENERGY	core opes function vatom bias colvar generic
25.019	The Arch from the Stones. Understanding Protein Folding Energy Landscapes via Bio-inspired Collective Variables	bio	protein folding, OPES, OneOPES, binding free energy	Valerio Rizzi	OPES_EXPANDED CUSTOM DISTANCE OPES_METAD_EXPLORE COMBINE RMSD ECV_MULTITHERMAL MOLINFO COORDINATION CENTER GROUP PRINT GHOST ENERGY	core opes function vatom colvar generic
25.018	Metainference simulation for dimerization of RNA binding protein	bio	Metainference, Metadynamics, SAXS, protein dimer	Debadutta Patra	PBMETAD WHOLEMOLECULES DISTANCE STATS GYRATION MOLINFO SAXS METAINFERENCE CENTER UPPER_WALLS PRINT TORSION ENSEMBLE FLUSH	isdb function vatom bias colvar generic
25.002	M3_PCV-ABMD	chemistry	Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor	Gian Marco Elisi	PATHMSD ABMD ENDPLUMED UNITS UPPER_WALLS PRINT	bias colvar generic setup
25.000	Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer	bio	metadynamics, pathCV	Sahithya Sridharan Iyer	WHOLEMOLECULES DISTANCE FUNCPATHGENERAL MOLINFO UPPER_WALLS GROUP COM PRINT RESTART METAD	core setup function vatom bias colvar generic
24.035	Data efficient machine learning potentials for modeling catalytic reactivity via active learning and enhanced sampling	chemistry	opes, catalysis, ammonia, machine learning potentials	Luigi Bonati	LOWER_WALLS DISTANCE CUSTOM UNITS COMMITTOR COORDINATION UPPER_WALLS GROUP PRINT RESTART OPES_METAD	core setup opes function bias colvar generic
24.029	Combination of OPES and OPES-Explore	methods	OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin	Dhiman Ray	FIT_TO_TEMPLATE OPES_METAD_EXPLORE COMBINE ENDPLUMED RMSD CONTACTMAP UPPER_WALLS OPES_METAD METAD FLUSH WHOLEMOLECULES PYTORCH_MODEL POSITION MOLINFO COORDINATION GROUP INCLUDE ENERGY BIASVALUE FIXEDATOM LOWER_WALLS DISTANCE CUSTOM UNITS MATHEVAL CENTER PRINT	core setup opes function vatom bias pytorch colvar generic
24.027	Proline cis and trans subensembles of a disordered peptide	bio	intrinsically disordered proteins, proline cis trans isomerisation, metadynamics, collective variables	Alice Pettitt	PBMETAD WHOLEMOLECULES DISTANCE ALPHARMSD COMBINE ENDPLUMED ANTIBETARMSD MOLINFO COORDINATION INCLUDE GROUP PRINT PARABETARMSD TORSION DIHCOR GYRATION FLUSH	multicolvar core secondarystructure function bias colvar generic
24.011	Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble	methods	committor, machine learning	Peilin Kang	ENDPLUMED RMSD UPPER_WALLS TORSION LOAD WHOLEMOLECULES POSITION MOLINFO CELL COORDINATION GROUP INCLUDE ENERGY BIASVALUE LOWER_WALLS DISTANCE CUSTOM UNITS MATHEVAL PRINT	core setup function bias colvar generic
24.010	Oxytocin metadynamics simulation	bio	metadynamics, oxytocin, peptide	Jan Beránek	WHOLEMOLECULES PRINT RESTART TORSION METAD FLUSH	colvar bias setup generic
23.046	Lasso Peptides - HLDA CV	bio	metadynamics, protein folding, HLDA, harmonic	Gabriel da Hora	WHOLEMOLECULES DISTANCE UNITS COMBINE PRINT METAD	setup function bias colvar generic
23.033	DNA G-quadruplex and G-hairpin folding with ST-metaD protocol	bio	DNA, G4, GQ, quadruplex, hairpin, folding, metadynamics, REST2, ST-metaD	Pavlína Pokorná	GHBFIX BIASVALUE WHOLEMOLECULES COMBINE MOLINFO ERMSD COORDINATION PRINT METAD	bias colvar generic function
23.028	Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process	chemistry	Ammonia decomposition; Dynamics;OPES; Neural Network potential	Manyi Yang	LOWER_WALLS DISTANCE CUSTOM UNITS COMMITTOR ZDISTANCES MATHEVAL UPPER_WALLS COORDINATIONNUMBER GROUP COM FIXEDATOM PRINT OPES_METAD ENERGY DISTANCES FLUSH	multicolvar core setup opes function symfunc vatom bias colvar generic
23.025	Probing ion binding to G-quadruplexes and related events	chemistry	metadynamics, repulsive potential, nucleic acids, G-quadruplexes	Marcelo Poleto	FIT_TO_TEMPLATE LOWER_WALLS WHOLEMOLECULES DISTANCE UNITS POSITION DUMPATOMS MATHEVAL UPPER_WALLS GROUP COM PRINT RESTART WRAPAROUND DISTANCES METAD FLUSH	multicolvar core setup function vatom bias colvar generic
23.021	Into the Dynamics of Rotaxanes at Atomistic Resolution	materials	metadynamics, rotaxanes, molecular shuttles, molecular machines	Luigi Leanza	DISTANCE CUSTOM MATHEVAL CENTER UPPER_WALLS PRINT FIXEDATOM TORSION METAD	function vatom bias colvar generic
23.001	Quantum phase diagram of water	chemistry	Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella	Sigbjørn-Løland Bore	OPES_EXPANDED LOWER_WALLS UPPER_WALLS PRINT ENVIRONMENTSIMILARITY RESTART INCLUDE ECV_UMBRELLAS_LINE	setup envsim opes bias generic
22.042	Metadynamics of NSP10 and variants	bio	metadynamics, NSP10, crystal structure, variants	Shozeb Haider	PRINT TORSION METAD	bias colvar generic
22.034	Rationalising the difference in crystallisability of two Sulflowers using efficient in silico methods	materials	metadynamics, crystallizability, crystal structure prediction, sulflower, persulforated coronene	Matteo Salvalaglio	LOWER_WALLS DRMSD CUSTOM COMMITTOR MATHEVAL CELL UPPER_WALLS PRINT METAD	bias colvar generic function
22.030	Mixing physics across temperatures with generative artificial intelligence	methods	REMD, Generative AI, DDPM	Yihang Wang	PRINT WHOLEMOLECULES TORSION	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 CUSTOM ENDPLUMED COMBINE COORDINATION PRINT METAD	bias colvar generic function
21.039	Deep learning the slow modes for rare events sampling	methods	collective variables, machine learning, slow modes, deep-tica, opes	Luigi Bonati	OPES_EXPANDED ENDPLUMED COMBINE RMSD ECV_MULTITHERMAL CONTACTMAP TORSION OPES_METAD FLUSH LOAD WHOLEMOLECULES VOLUME PYTORCH_MODEL Q6 MOLINFO GROUP INCLUDE ENERGY DISTANCE UNITS PRINT ENVIRONMENTSIMILARITY	core setup opes function symfunc envsim pytorch colvar generic
21.036	Modelling the structure and interactions of intrinsically disordered peptides with multiple-replica, metadynamics-based sampling methods and force-field combinations	bio	Bias Exchange Metadynamics, PTWTE-metaD	Matteo Salvalaglio	RANDOM_EXCHANGES LOWER_WALLS WHOLEMOLECULES ALPHARMSD ANTIBETARMSD MOLINFO COORDINATION UPPER_WALLS GROUP PRINT PARABETARMSD DIHCOR ENERGY GYRATION METAD	multicolvar core secondarystructure bias colvar generic
21.031	Photo-switchable sulfonulureas in KATP channel	bio	metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels	Katarzyna Walczewska-Szewc	LOWER_WALLS WHOLEMOLECULES DISTANCE UNITS UPPER_WALLS COM PRINT METAD	setup vatom bias colvar generic
21.029	Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs	bio	metadynamics, small peptide, machine learning	Pratyush Tiwary	MOLINFO EXTERNAL PRINT RESTART TORSION ENERGY FLUSH	colvar bias setup generic
21.026	Probing allosteric regulations with coevolution-driven molecular simulations	bio	metadynamics, coevolution, allostery, adenylate cyclase	Francesco Colizzi	PATHMSD WHOLEMOLECULES DISTANCE UNITS UPPER_WALLS COM PRINT METAD	setup vatom bias colvar generic
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
21.000	Uremic toxin time scale dynamics	bio	uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs)	Jim Pfaendtner	WHOLEMOLECULES DISTANCE GROUP COM PRINT	core vatom colvar generic
20.015	Rational design of ASCT2 inhibitors using an integrated experimental-computational approach	bio	ASCT2 transporter, small-molecules, cryo-EM, metainference	Max Bonomi	BIASVALUE LOAD WHOLEMOLECULES DUMPATOMS EMMIVOX MOLINFO GROUP PRINT	core isdb setup bias generic
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	COMBINE TD_MULTITHERMAL_MULTIBARIC UPPER_WALLS CONVERT_TO_FES REWEIGHT_TEMP_PRESS RESTART LOAD VOLUME Q6 CELL ENERGY BF_LEGENDRE READ REWEIGHT_BIAS HISTOGRAM DUMPGRID OPT_AVERAGED_SGD TD_WELLTEMPERED LOWER_WALLS MATHEVAL OPT_DUMMY PRINT VES_LINEAR_EXPANSION	setup ves function symfunc bias colvar generic gridtools
19.071	Time-independent free energies from metadynamics via Mean Force Integration	methods	metadynamics, mean force integration, MFI, thermodynamic integration	Matteo Salvalaglio	BIASVALUE DISTANCE COMMITTOR READ MATHEVAL CONVERT_TO_FES REWEIGHT_BIAS EXTERNAL PRINT HISTOGRAM DUMPGRID TORSION REWEIGHT_METAD METAD	function bias colvar generic gridtools
19.070	Unexpected Dynamics in the UUCG RNA Tetraloop	bio	well-tempered metadynamics, RNA, UUCG, maximum entropy	Sandro Bottaro	WHOLEMOLECULES DISTANCE RMSD MOLINFO ERMSD PRINT TORSION METAD	bias colvar generic
19.065	Molecular Enhanced Sampling with Autoencoders	methods	enhanced sampling, collective variables, deep learning	Wei Chen	COMBINE POSITION COM RESTRAINT ANN	annfunc function vatom bias colvar
19.048	Understanding Ligand Binding Selectivity in a Prototypical GPCR Family	bio	metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding	Francesco Gervasio	BIASVALUE LOWER_WALLS WHOLEMOLECULES DISTANCE MATHEVAL UPPER_WALLS COM PRINT CONSTANT METAD	function vatom bias colvar generic
19.043	Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA)	methods	metadynamics, chemistry, HLDA	GiovanniMaria Piccini	DISTANCE COMBINE UNITS UPPER_WALLS PRINT RESTART DISTANCES METAD FLUSH	multicolvar setup function bias colvar generic
19.039	Funnel Metadynamics	bio	funnel-metadynamics, absolute binding free energy, ligand-receptor complexes	Vittorio Limongelli	LOWER_WALLS WHOLEMOLECULES DISTANCE FUNNEL_PS RMSD UPPER_WALLS COM PRINT FUNNEL METAD	funnel vatom bias colvar generic
19.026	Ice Nucleation on Cholesterol Crystals	materials	forward flux sampling, crystal nucleation, water, ice, organic crystals	Gabriele Cesare Sosso	CLUSTER_NATOMS CLUSTER_WITHSURFACE OUTPUT_CLUSTER ENDPLUMED Q6 COMMITTOR CONTACT_MATRIX MFILTER_MORE LOCAL_Q6 DFSCLUSTERING FLUSH	multicolvar adjmat symfunc clusters generic
19.013	RNA FF FITTING	methods	force field, RNA	Giovanni Bussi	BIASVALUE PUCKERING MOLINFO MATHEVAL TORSION INCLUDE CONSTANT	bias colvar generic function
19.011	Automatic Gradient Computation for Collective Variables	other	gradient, differentiation, curvature	Toni Giorgino	ENDPLUMED	generic
19.000	VesDeltaF	methods	VES, convergence, suboptimal CVs	Michele Invernizzi	LOAD ENDPLUMED UNITS POSITION PRINT RESTART TORSION VES_DELTA_F ENERGY METAD	setup ves bias colvar generic
25.013	Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices	bio	umbrella sampling, temperature ramping	Alexander Berlaga	PRINT GYRATION PYTORCH_MODEL RESTRAINT DISTANCE	pytorch generic bias colvar
24.034	Umbrella sampling of ion in transporter SLC26A7	bio	umbrella sampling, transporter, ions	Xiaoli Lu	POSITION UNITS PRINT RESTRAINT	setup generic bias colvar
24.030	NMR guided simulation of dsRBD	bio	Metainference, NMR, protein dynamics	Debadutta Patra	PRINT FLUSH WHOLEMOLECULES MOLINFO RDC ENSEMBLE DISTANCE STATS METAINFERENCE GROUP ALPHABETA	core generic isdb function multicolvar colvar
24.028	All-atom simulations of RNA-membrane interactions	bio	metadynamics, membrane, RNA	Giovanni Bussi	CENTER PRINT SORT GYRATION PUCKERING MATHEVAL DISTANCES WHOLEMOLECULES LOWER_WALLS MOLINFO METAD COMBINE UPPER_WALLS POSITION DISTANCE GHOST GROUP	core generic vatom function multicolvar bias colvar
24.024	Host-Guest binding free energies à la carte, an automated OneOPES protocol	bio	OneOPES, ligand binding, binding free energy,SAMPL challenge, host-guest	Valerio Rizzi	CENTER FIXEDATOM PRINT ENERGY ENDPLUMED OPES_METAD_EXPLORE ANGLE OPES_EXPANDED FIT_TO_TEMPLATE WHOLEMOLECULES MATHEVAL GROUP COORDINATION ECV_MULTITHERMAL UPPER_WALLS TORSION DISTANCE LOWER_WALLS	core generic vatom function bias colvar opes
24.008	yCD Metadynamics	bio	volume-based MetaD, path CVs, infrequent MetaD, product release	James McCarty	FIT_TO_TEMPLATE WHOLEMOLECULES COM UPPER_WALLS RMSD GROUP CONTACTMAP ENDPLUMED MATHEVAL COORDINATION READ REWEIGHT_METAD HISTOGRAM INCLUDE FIXEDATOM COMMITTOR METAD CONVERT_TO_FES DUMPGRID PRINT FLUSH PATH MOLINFO DISTANCE WRAPAROUND	core generic gridtools mapping vatom function bias colvar
23.040	Supramolecular capsules assembly dynamics	chemistry	Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics	Riccardo Capelli	CENTER PRINT FLUSH WHOLEMOLECULES DISTANCES UNITS COM CUSTOM METAD POSITION DISTANCE GROUP	core generic vatom function multicolvar setup bias colvar
23.019	Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors	bio	binding pathway, binding energy, sketch-map, drug development	Raitis Bobrovs	PRINT DISSIMILARITIES WHOLEMOLECULES TRANSPOSE SKETCHMAP COM VSTACK SKETCHMAP_PROJECTION CUSTOM METAD LANDMARK_SELECT_FPS COLLECT_FRAMES UPPER_WALLS VORONOI PATHMSD DISTANCE	dimred generic landmarks vatom valtools function bias colvar matrixtools
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 MATHEVAL WHOLEMOLECULES READ MOLINFO REWEIGHT_METAD DUMPGRID METAD HISTOGRAM CONVERT_TO_FES DISTANCE RMSD	generic gridtools function bias colvar
23.013	Path meta-eABF simulation of large scale conformational change in STING protein	methods	meta-eABF, path CV, large scale conformational change, STING protein, reciprocal barrier restraint	Istvan Kolossvary	PRINT FLUSH DRR UNITS TIME CUSTOM METAD BIASVALUE UPPER_WALLS PATHMSD LOWER_WALLS	generic function setup bias colvar drr
22.024	Conformational Entropy as a Potential Liability of Computationally Designed Antibodies	bio	metadynamics, conformational entropy, antibody, nanobody	Thomas Löhr	PRINT RESTART ALPHARMSD WHOLEMOLECULES COM PBMETAD MOLINFO TORSION ANTIBETARMSD ALPHABETA	generic secondarystructure vatom multicolvar setup 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	PRINT WHOLEMOLECULES COM METAD TORSION DISTANCE GROUP	core generic vatom bias colvar
21.046	Ubiquitin Interacting Motifs, Duality Between Structured and Disordered Motifs	bio	wt metadynamics, ubiquitin, ataxin-3, short linear motifs, ubiquitin binding motif, moonlight functions, intrinsic disorder	Elena Papaleo	PRINT GYRATION ENDPLUMED WHOLEMOLECULES LOWER_WALLS METAD UPPER_WALLS GROUP ALPHABETA	core generic multicolvar bias colvar
21.040	A structural ensemble of a tau-microtubule complex reveals regulatory tau phosphorylation and acetylation mechanisms	bio	EMMI, CryoEM, tau-microtubules, post-translational modifications, chemical mutagenesis, structural ensemble, Metainference	Faidon Brotzakis	PRINT RESTART WHOLEMOLECULES COM EMMI MOLINFO BIASVALUE UPPER_WALLS DISTANCE GROUP	core generic isdb vatom setup bias colvar
21.032	Metal-coupled folding mechanism to metallothionein	bio	parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination	Manuel-Peris Diaz	WHOLEMOLECULES UNITS COORDINATION PBMETAD GROUP	core generic setup bias colvar
21.020	Reweighted Jarzynski sampling	methods	free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions	Kristof Bal	OPT_AVERAGED_SGD BF_CHEBYSHEV MOVINGRESTRAINT OPES_METAD COMBINE UPPER_WALLS REWEIGHT_METAD LOAD CUSTOM REWEIGHT_BIAS ANN HISTOGRAM COORDINATIONNUMBER VES_LINEAR_EXPANSION UNITS TD_WELLTEMPERED RESTRAINT METAD CONSTANT CONVERT_TO_FES DUMPGRID FLUSH PRINT BIASVALUE DISTANCE	symfunc generic gridtools function ves bias setup annfunc colvar opes
21.017	All-atom simulations of the Vav1 AD construct	bio	metadynamics, parallel-bias, well-tempered	Simone Orioli	PRINT RESTART CONTACTMAP ALPHARMSD WHOLEMOLECULES PBMETAD MOLINFO METAD REWEIGHT_BIAS GROUP ALPHABETA	core generic secondarystructure multicolvar setup bias colvar
21.011	CmuMD simulations of NaCl(aq) at graphite	chemistry	CmuMD, DFS clustering	Aaron Finney	FIXEDATOM CLUSTER_NATOMS PRINT DENSITY MULTICOLVARDENS DFSCLUSTERING RESTRAINT LOAD CLUSTER_DISTRIBUTION CONTACT_MATRIX MFILTER_MORE AROUND DUMPGRID COORDINATIONNUMBER GROUP	symfunc core generic gridtools vatom multicolvar setup bias volumes clusters adjmat
21.008	Multi-replica biased sampling for photoisomerization processes in conjugated polymers	methods	metadynamics, FEP, replica-exchange	Adriana Pietropaolo	PRINT RESTART MATHEVAL WHOLEMOLECULES PBMETAD CONSTANT BIASVALUE TORSION	generic function setup bias colvar
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	PRINT VOLUME ENERGY OPT_AVERAGED_SGD ENVIRONMENTSIMILARITY RESTART OPES_EXPANDED ECV_UMBRELLAS_LINE MATHEVAL VES_LINEAR_EXPANSION ECV_MULTITHERMAL_MULTIBARIC Q6 TD_UNIFORM BF_LEGENDRE UPPER_WALLS	symfunc generic envsim function ves setup bias colvar opes
21.001	Substrate recognition and catalysis by glycosaminoglycan sulfotransferases	bio	metadynamics, well-tempered metadynamics, puckering, coordination	Tarsis Ferreira	PRINT ENERGY PUCKERING GROUP WHOLEMOLECULES COORDINATION DUMPGRID MOLINFO REWEIGHT_METAD RANDOM_EXCHANGES METAD HISTOGRAM UPPER_WALLS DISTANCE INCLUDE LOWER_WALLS	core generic gridtools bias colvar
20.032	Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil	materials	clustering, conformational isomers	Matteo Salvalaglio	TORSION PRINT ENDPLUMED	generic colvar
20.026	Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor	bio	Metadynamics, Umbrella sampling	Brandon Peters	PRINT DUMPGRID RESTRAINT REWEIGHT_METAD METAD HISTOGRAM CONVERT_TO_FES MULTI_RMSD	generic bias gridtools colvar
20.020	Parallel Bias Metadynamics	methods	pbmetad, trp-cage, folding	Max Bonomi	PRINT GYRATION WHOLEMOLECULES PBMETAD COORDINATION MOLINFO DIHCOR INCLUDE ALPHABETA	multicolvar generic bias colvar
19.083	Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis	chemistry	metadynamics, chemical reactions, reaction discovery	Valerio Rizzi	PRINT RESTART FLUSH ENDPLUMED DISTANCES UNITS METAD COMBINE UPPER_WALLS COORDINATIONNUMBER GROUP	symfunc core generic function multicolvar setup bias
19.076	Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones	bio	molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics	Salvatore Assenza	PRINT GYRATION ENDPLUMED UNITS MOVINGRESTRAINT	setup generic bias colvar
19.068	Rethinking Metadynamics	methods	metadynamics, opes, convergence	Michele Invernizzi	PRINT POSITION ENDPLUMED UNITS EXTERNAL METAD OPES_METAD TORSION	generic setup bias colvar opes
19.066	Finding ligand unbinding reaction pathways	methods	maze, ligand unbinding	Jakub Rydzewski	PRINT MAZE_SIMULATED_ANNEALING MAZE_OPTIMIZER_BIAS UNITS MAZE_LOSS POSITION	setup generic maze colvar
19.061	Diffusion in porous materials	materials	metadynamics, porous materials, diffusion	Kim E. Jelfs	CENTER RESTART PRINT GROUP COM METAD UPPER_WALLS DISTANCE LOWER_WALLS	core generic vatom setup bias colvar
19.058	Constrained MD for maintaining a cavity in a calculation	chemistry	constrained MD, porous molecules, porosity, cavity	Kim Jelfs	PRINT FLUSH RESTART DISTANCES COM INPLANEDISTANCES MOVINGRESTRAINT	generic vatom multicolvar setup bias
19.049	Determining the sizes of solid/liquid clusters in MD trajectories of nucleation	methods	nucleation, metadynamics, clustering, Steinhardt order parameters	Gareth Tribello	PRINT CLUSTER_NATOMS CLUSTER_PROPERTIES OUTPUT_CLUSTER DISTANCES DFSCLUSTERING MORE_THAN Q6 COORDINATIONNUMBER CUSTOM CLUSTER_DISTRIBUTION LOCAL_Q6 METAD CONTACT_MATRIX SMAC ONES OUTER_PRODUCT MATRIX_VECTOR_PRODUCT	symfunc generic function multicolvar bias clusters adjmat matrixtools
19.032	Chemical reaction in solution using path collective variables based on coordination patterns	chemistry	chemical reactions, solutions, metadynamics, coordination patterns	Fabio Pietrucci	FLUSH RESTART PRINT DISTANCES PATH METAD UPPER_WALLS	generic mapping multicolvar setup bias
19.023	RECT	methods	metadynamics, replica exchange	Giovanni Bussi	PRINT GYRATION WHOLEMOLECULES METAD TORSION	generic bias colvar
19.018	Excited state FEP/Metadynamics simulations	chemistry	metadynamics, FEP, excited states, conjugated polymers, torsional potential	Adriana Pietropaolo	PRINT MATHEVAL WHOLEMOLECULES METAD CONSTANT BIASVALUE TORSION	function generic bias colvar
19.009	RNA tetraloops folding	bio	metadynamics, RNA, folding	Giovanni Bussi	PRINT ENDPLUMED WHOLEMOLECULES ERMSD MOLINFO METAD RMSD	generic bias colvar
19.007	EMMI Microtubules	bio	metainference, cryo-EM	Max Bonomi	PRINT WHOLEMOLECULES EMMI MOLINFO BIASVALUE GROUP	core generic isdb bias
19.003	EMMI ClpP	bio	metainference, cryo-EM	Max Bonomi	PRINT EMMI MOLINFO BIASVALUE GROUP	core generic isdb bias
25.009	Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water	chemistry	metadynamics, nitrate photolysis	Kam-Tung Chan	DUMPGRID HISTOGRAM DISTANCE UPPER_WALLS REWEIGHT_METAD GROUP FLUSH CUSTOM COORDINATION RESTART PRINT METAD READ	core setup gridtools colvar bias function generic
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	COMBINE ECV_MULTITHERMAL DISTANCE GROUP TORSION OPES_EXPANDED OPES_METAD_EXPLORE CUSTOM COORDINATION ENERGY RESTART PRINT	core generic opes colvar function setup
24.006	Water vapor condensation	chemistry	metadynamics, homogeneous condensation, chemical potential	Shenghui Zhong	CLUSTER_NATOMS UNITS UPPER_WALLS CLUSTER_PROPERTIES CONTACT_MATRIX DFSCLUSTERING PRINT METAD COORDINATIONNUMBER	adjmat symfunc generic bias clusters setup
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	WRAPAROUND WHOLEMOLECULES UPPER_WALLS GROUP SHADOW DISTANCES FIT_TO_TEMPLATE POSITION CENTER PRINT METAD MOLINFO	core isdb bias colvar multicolvar vatom generic
23.027	CmuMD simulations of NaCl(aq) at NaCl	chemistry	CmuMD, DFS, Q3, Pair Entropy	Aaron Finney	DUMPGRID CLUSTER_NATOMS DENSITY RESTRAINT UNITS LOCAL_AVERAGE HISTOGRAM FIXEDATOM GROUP LOAD PRINT CLUSTER_DISTRIBUTION CONTACT_MATRIX AROUND DFSCLUSTERING LOCAL_Q3 Q3 COORDINATIONNUMBER	core adjmat symfunc generic volumes gridtools bias clusters vatom setup
23.011	OneOPES, a combined enhanced sampling method to rule them all	bio	OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding	Valerio Rizzi	DISTANCE TORSION OPES_EXPANDED ENDPLUMED OPES_METAD_EXPLORE ENERGY ECV_MULTITHERMAL PRINT METAD MOLINFO	bias colvar generic opes
23.005	A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs	bio	metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A	Timothy Clark	MATHEVAL DUMPGRID WHOLEMOLECULES HISTOGRAM DISTANCE READ REWEIGHT_METAD CONVERT_TO_FES RMSD PRINT METAD MOLINFO	gridtools bias colvar function generic
23.002	Critical comparison of general-purpose collective variables for crystal nucleation	methods	metadynamics, umbrella sampling, commitor, entropy, PIV	Julien Lam	RESTRAINT UNITS FUNCPATHMSD LOCAL_AVERAGE VOLUME PIV PAIRENTROPY UPPER_WALLS CUSTOM ENERGY Q4 PRINT METAD Q6	symfunc generic gridtools bias colvar function piv setup
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	CONTACTMAP WHOLEMOLECULES UPPER_WALLS LOWER_WALLS ENERGY PRINT METAD	bias colvar generic
22.027	Molecular Dynamics simulations of BANAL-236 RBD-hACE2 complexes	bio	SARS-CoV-2, COVID-19, MD, human-ACE2, spike, BANAL-236, receptor-binding domain	Max Bonomi	RMSD PRINT	colvar generic
22.023	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	WHOLEMOLECULES EMMI PBMETAD UPPER_WALLS GROUP TORSION RMSD BIASVALUE COORDINATION RESTART COM PRINT MOLINFO	core isdb setup bias colvar vatom 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	PATHMSD WHOLEMOLECULES DISTANCE UPPER_WALLS FUNNEL_PS LOWER_WALLS FUNNEL COM PRINT METAD	funnel bias colvar vatom generic
22.018	Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations	bio	ligand binding, docking, EMMI, LAT1	Max Bonomi	WHOLEMOLECULES EMMIVOX LOAD GROUP BIASVALUE PRINT MOLINFO	core isdb setup bias generic
22.012	Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT	bio	contact maps, protein-protein interactions	Isabell-Louise Grothaus	CONTACTMAP PRINT DISTANCE CENTER	colvar vatom generic
22.011	Accelerating all-atom simulations and gaining mechanistic understanding of biophysical systems through State Predictive Information Bottleneck	methods	metadynamics, membrane permeation, protein folding	Shams Mehdi	MATHEVAL XANGLES WHOLEMOLECULES COMBINE DISTANCE UPPER_WALLS YANGLES ALPHABETA LOWER_WALLS ZANGLES TORSION CUSTOM COM PRINT METAD MOLINFO	bias colvar function multicolvar vatom generic
22.009	Glycosylation in calixarenes capsule	chemistry	Metadynamics, glycosylation, supramolecular catalysis	GiovanniMaria Piccini	MATHEVAL WHOLEMOLECULES ANGLE COMBINE UNITS DISTANCE UPPER_WALLS GROUP LOWER_WALLS FLUSH DISTANCES FIT_TO_TEMPLATE COORDINATION BRIDGE RMSD PRINT METAD	core adjmat generic bias colvar function multicolvar 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	BF_WAVELETS COORDINATION METAD DISTANCE UPPER_WALLS BF_GAUSSIANS BF_LEGENDRE ENERGY PRINT BF_CUBIC_B_SPLINES VES_LINEAR_EXPANSION VES_OUTPUT_BASISFUNCTIONS TD_UNIFORM BF_CHEBYSHEV OPT_ADAM POSITION OPT_AVERAGED_SGD UNITS TD_WELLTEMPERED FLUSH INCLUDE	generic colvar bias ves setup
21.022	Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly	materials	parallel bias metadynamics, adsorption, peptide	Xin Qi	DISTANCE UPPER_WALLS GYRATION PBMETAD LOWER_WALLS ENERGY COM PRINT MOLINFO	colvar vatom bias generic
20.029	High Conformational Flexibility of the E2F1/DP1/DNA complex	bio	SAXS, protein-DNA complex, hySAXS, ensemble determination	Cristina Paissoni	WHOLEMOLECULES RESTRAINT DISTANCE GROUP SAXS BIASVALUE CENTER PRINT INCLUDE ENSEMBLE MOLINFO STATS	core isdb bias colvar function vatom generic
20.021	Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins.	bio	phi-values, restrained MD, transition-state, protein folding, disordered proteins, protein evolution	Cristina Paissoni	WHOLEMOLECULES RESTRAINT COORDINATION PRINT MOLINFO STATS	bias generic colvar function
19.074	Asymmetric base pair opening in nucleic acids	bio	double helix, DNA, RNA, unwindability	Giovanni Bussi	WHOLEMOLECULES RESTRAINT DISTANCE LOWER_WALLS ENDPLUMED COORDINATION	bias generic colvar
19.069	Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen	materials	ibuprofen, crystal, solvent, surface	Matteo Salvalaglio	DISTANCE GROUP ENDPLUMED CENTER PRINT INCLUDE	colvar core generic vatom
19.052	Gibbs free energy of homogeneous nucleation	materials	nucleation, surface excess free energy	Gareth Tribello	UNITS UPPER_WALLS CELL ENDPLUMED PRINT METAD FCCUBIC	symfunc generic bias colvar setup
19.050	Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes	chemistry	metadynamics, membranes, Willard Chandler surface	Gareth Tribello	DISTANCE_FROM_CONTOUR DUMPGRID COMBINE HISTOGRAM UPPER_WALLS REWEIGHT_BIAS CONVERT_TO_FES RESTART PRINT METAD READ	contour generic gridtools bias function setup
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	WHOLEMOLECULES COMBINE DISTANCE UPPER_WALLS REWEIGHT_METAD GROUP TORSION LOWER_WALLS ALPHABETA DISTANCES COM FUNNEL BRIDGE RMSD PRINT METAD MOLINFO	funnel core adjmat bias colvar function multicolvar vatom 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	DISTANCE UPPER_WALLS TORSION LOWER_WALLS CENTER COMMITTOR PRINT METAD	colvar vatom bias generic
19.002	EMMI STRA6	bio	metainference, cryo-EM	Max Bonomi	EMMI GROUP BIASVALUE PRINT MOLINFO	isdb bias core generic

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