Browse the eggs in PLUMED-NEST

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

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

plumID	Name	Category	Keywords	Contributor	Actions	Modules
25.005	Mechanism of Nanocluster Formation from Machine-Learned Potential-based Simulations	chemistry	WT-metadynamics, metal nanoclusters, nucleation, neural network potential, deepMD	Vikas Tiwari, Tarak Karmakar	COM COMBINE LOWER_WALLS DISTANCES COORDINATIONNUMBER GROUP DISTANCE PRINT FIXEDATOM COORDINATION FLUSH ANGLE RESTRAINT METAD UPPER_WALLS UNITS	generic function multicolvar colvar symfunc core bias setup vatom
25.013	Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices	bio	umbrella sampling, temperature ramping	Alexander Berlaga	RESTRAINT PYTORCH_MODEL GYRATION DISTANCE PRINT	colvar pytorch bias generic
25.007	Shaping the glycan landscape. Hidden relationships between linkage and ring distortion induced by carbohydrate-active enzmyes	bio	REST-RECT, REST2, glycan, enzyme, CAZyme, steered	Isabell Grothaus	RESTRAINT PUCKERING DISTANCE PRINT MOLINFO MOVINGRESTRAINT TORSION METAD RESTART	colvar setup bias generic
25.004	Machine Learning-Driven Molecular Dynamics Unveil a Bulk Phase Transformation Driving Ammonia Synthesis on Barium Hydride	chemistry	OPES, OPES flooding, Catalysis, Ammonia Synthesis	Axel Tosello Gardini	UPPER_WALLS DISTANCES OPES_METAD UNITS GROUP ZDISTANCES DISTANCE COMMITTOR PRINT FIXEDATOM FLUSH CUSTOM COORDINATIONNUMBER	symfunc bias multicolvar vatom opes setup core function colvar generic
25.000	Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer	bio	metadynamics, pathCV	Sahithya Sridharan Iyer	FUNCPATHGENERAL UPPER_WALLS GROUP WHOLEMOLECULES DISTANCE COM PRINT MOLINFO METAD RESTART	bias vatom function core setup colvar 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	CENTER UPPER_WALLS RMSD WHOLEMOLECULES DISTANCE GROUP EMMI COORDINATION ALPHARMSD PBMETAD BIASVALUE MOLINFO PRINT DUMPATOMS PARABETARMSD DUMPMASSCHARGE COM	bias vatom isdb core colvar generic secondarystructure
24.026	Constant pH metadynamics of RNA oligomers	bio	metadynamics, pH, RNA	Giovanni Bussi	PUCKERING PRINT MOLINFO TORSION METAD RESTART	colvar setup bias generic
24.009	Weighted Shape Gaussian Mixture Models	bio	metadynamics, clustering	Glen Hocky	UNITS GROUP PRINT TORSION METAD	bias setup core colvar generic
24.006	Water vapor condensation	chemistry	metadynamics, homogeneous condensation, chemical potential	Shenghui Zhong	UPPER_WALLS DFSCLUSTERING UNITS CONTACT_MATRIX CLUSTER_NATOMS PRINT CLUSTER_PROPERTIES METAD COORDINATIONNUMBER	symfunc bias clusters setup adjmat generic
24.003	Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations	chemistry	steered molecular dynamics, foldamers, peptoids, bio-inspired	Kaylyn Torkelson	GYRATION WHOLEMOLECULES DISTANCE ALPHABETA COORDINATION PRINT MOVINGRESTRAINT INCLUDE TORSION COM	bias multicolvar vatom colvar generic
23.015	MPCs aggregation	bio	opes_explore, dimerization, MPCs, self-assembly	Vikas Tiwari	CENTER UPPER_WALLS LOWER_WALLS WHOLEMOLECULES GROUP DISTANCE CUSTOM COORDINATION PRINT OPES_METAD_EXPLORE METAD COM	bias vatom opes function core colvar generic
23.014	Structural basis of dimerization of chemokine receptors CCR5 and CXCR4	bio	metadynamics, oligomerization, chemokine receptors, GPCR, membrane	Vittorio Limongelli	COMBINE UPPER_WALLS WHOLEMOLECULES DISTANCE PRINT TORSION FLUSH METAD COM	bias vatom 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	RESTRAINT GYRATION WHOLEMOLECULES COORDINATION PBMETAD PRINT INCLUDE TORSION COM	colvar vatom bias generic
23.005	A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs	bio	metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A	Timothy Clark	RMSD WHOLEMOLECULES DISTANCE CONVERT_TO_FES READ REWEIGHT_METAD HISTOGRAM PRINT DUMPGRID MATHEVAL MOLINFO METAD	bias gridtools function 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	OPES_EXPANDED UPPER_WALLS LOWER_WALLS ECV_UMBRELLAS_LINE HISTOGRAM ENVIRONMENTSIMILARITY DUMPGRID PRINT RESTART	envsim bias opes gridtools setup generic
22.037	Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site	chemistry	metadynamics, DNA, abasic	Mike Jones	PRINT DISTANCE METAD DISTANCES	multicolvar colvar bias 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	CELL UPPER_WALLS LOWER_WALLS DRMSD CUSTOM COMMITTOR PRINT MATHEVAL METAD	colvar generic bias function
22.026	Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification	materials	Peptoid, silica	Jim Pfaendtner	UPPER_WALLS GYRATION DISTANCE PBMETAD PRINT MOLINFO COM	colvar vatom bias generic
22.017	Water regulates the residence time of Benzamidine in Trypsin	bio	ligand binding, water, opes, benzamidine trypsin, unbinding rates, machine learning, Deep-LDA, Deep-TICA	Narjes Ansari	CENTER PYTORCH_MODEL UPPER_WALLS LOWER_WALLS OPES_METAD RMSD WHOLEMOLECULES GROUP DISTANCE CUSTOM FIT_TO_TEMPLATE COORDINATION PRINT COMMITTOR MATHEVAL FIXEDATOM	bias vatom opes function core colvar pytorch generic
22.002	GAMBES_SAMPL5_RATES	other	GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding	Jayashrita Debnath	ENDPLUMED LOAD CENTER PYTORCH_MODEL UPPER_WALLS WHOLEMOLECULES GROUP DISTANCE FIT_TO_TEMPLATE COORDINATION ANGLE PRINT MATHEVAL COMMITTOR ENERGY FLUSH FIXEDATOM	bias vatom setup core function colvar pytorch generic
21.042	Peptoid-mediated Au nanocrystal growth	materials	parallel-bias metadynamics, peptoid, Au	Xin Qi	UPPER_WALLS GYRATION DISTANCE PBMETAD PRINT MOLINFO COM	colvar vatom bias generic
21.031	Photo-switchable sulfonulureas in KATP channel	bio	metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels	Katarzyna Walczewska-Szewc	UPPER_WALLS LOWER_WALLS UNITS WHOLEMOLECULES DISTANCE PRINT METAD COM	bias vatom setup colvar generic
21.011	CmuMD simulations of NaCl(aq) at graphite	chemistry	CmuMD, DFS clustering	Aaron Finney	CLUSTER_DISTRIBUTION RESTRAINT MULTICOLVARDENS MFILTER_MORE DFSCLUSTERING DENSITY GROUP CONTACT_MATRIX CLUSTER_NATOMS AROUND DUMPGRID PRINT LOAD FIXEDATOM COORDINATIONNUMBER	volumes symfunc bias multicolvar clusters vatom gridtools setup core adjmat 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 GROUP DISTANCE PRINT COM	colvar vatom generic core
20.022	Unified Approach to Enhanced Sampling	methods	OPES, expanded ensembles, importance sampling	Michele Invernizzi	ENDPLUMED OPES_EXPANDED RMSD WHOLEMOLECULES ECV_UMBRELLAS_LINE ENERGY Q6 UPPER_WALLS VOLUME MATHEVAL TORSION ECV_MULTITHERMAL UNITS ENVIRONMENTSIMILARITY ECV_MULTITHERMAL_MULTIBARIC LOAD ECV_LINEAR PRINT MOLINFO POSITION CUSTOM	envsim symfunc bias opes function setup colvar generic
20.003	Enhanced sampling of transition states	methods	Variationally Enhanced Sampling, Target distribution, Transition state, Enhanced Sampling, Nucleation, chemical reaction	Jayashrita Debnath	BF_LEGENDRE UNITS PRINT OPT_AVERAGED_SGD POSITION LOAD ENERGY VES_LINEAR_EXPANSION	ves generic colvar setup
19.062	Elucidating molecular design principles for charge-alternating peptides	bio	peptide folding, metadynamics, well-tempered ensemble, parallel tempering	Jim Pfaendtner	GYRATION WHOLEMOLECULES PRINT ENERGY METAD	colvar bias generic
19.061	Diffusion in porous materials	materials	metadynamics, porous materials, diffusion	Kim E. Jelfs	CENTER UPPER_WALLS LOWER_WALLS GROUP DISTANCE COM PRINT METAD RESTART	bias vatom setup core colvar generic
19.023	RECT	methods	metadynamics, replica exchange	Giovanni Bussi	GYRATION WHOLEMOLECULES PRINT TORSION METAD	colvar bias generic
19.017	Ligand binding pathways exploration	bio	metadynamics, ligand binding	Riccardo Capelli	ENDPLUMED UPPER_WALLS WRAPAROUND WHOLEMOLECULES GROUP CONVERT_TO_FES READ FIT_TO_TEMPLATE COORDINATION PRINT REWEIGHT_METAD MATHEVAL HISTOGRAM POSITION DUMPGRID FLUSH METAD COM	bias vatom gridtools function core colvar generic
19.016	Succinnic acid gamma polymorph	materials	Succinnic acid, conformers, polymorphs, metadynamics	Matteo Salvalaglio	ENDPLUMED CELL COMBINE UPPER_WALLS LOWER_WALLS PRINT VOLUME MATHEVAL TORSION ENERGY METAD	colvar function generic bias
24.034	Umbrella sampling of ion in transporter SLC26A7	bio	umbrella sampling, transporter, ions	Xiaoli Lu	RESTRAINT UNITS POSITION PRINT	colvar bias setup generic
24.031	DeepLNE	methods	PATHCV, OPES, OneOPES	Thorben Fröhlking	ECV_MULTITHERMAL COORDINATION VOLUME MOLINFO PYTORCH_MODEL ENERGY RESTART OPES_METAD_EXPLORE OPES_EXPANDED ERMSD COMBINE PRINT	colvar function setup pytorch generic opes
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	ECV_MULTITHERMAL FIT_TO_TEMPLATE COORDINATION WHOLEMOLECULES DISTANCE CENTER GROUP LOWER_WALLS ENERGY MATHEVAL ENDPLUMED TORSION OPES_METAD_EXPLORE OPES_EXPANDED UPPER_WALLS FIXEDATOM ANGLE PRINT	bias colvar function vatom core generic opes
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 DISTANCE ENERGY UPPER_WALLS PRINT OPES_METAD	bias colvar generic opes
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	MOLINFO DISTANCE FLUSH ENERGY MATHEVAL METAD RESTRAINT BIASVALUE COORDINATIONNUMBER RESTART COMMITTOR TORSION PRINT	bias colvar function symfunc setup generic
24.002	Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes	chemistry	metadynamics, ligand design, solvent extraction	Xiaoyu Wang	METAD RESTART TORSION UNITS PRINT	colvar bias setup generic
23.044	Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition	materials	metadynamics, interlocked molecules	Luigi Leanza	COORDINATION READ GROUP COMMITTOR METAD CONVERT_TO_FES ENDPLUMED DUMPGRID HISTOGRAM PRINT	bias colvar core generic gridtools
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	FIT_TO_TEMPLATE COORDINATION MOLINFO FLUSH CUSTOM TORSION OPES_METAD_EXPLORE PRINT WRAPAROUND DISTANCE CENTER POSITION ENDPLUMED UNITS OPES_METAD WHOLEMOLECULES LOWER_WALLS MATHEVAL BIASVALUE UPPER_WALLS ENERGY GROUP COMMITTOR COM	bias colvar function setup vatom core generic opes
23.024	Permutationally Invariant Networks for Enhanced Sampling (PINES)	methods	collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent	Nicholas Herringer	LOAD PBMETAD PRINT	bias setup generic
22.032	Reciprocal barrier restraint. Application to path-meta-eABF	methods	restraint, upper wall, lower wall, path colvar, meta-eABF, metadynamics, DRR, protein conformational transition, PROTAC	Istvan Kolossvary	DRR FLUSH CUSTOM PATHMSD METAD BIASVALUE PRINT	bias colvar function generic drr
22.030	Mixing physics across temperatures with generative artificial intelligence	methods	REMD, Generative AI, DDPM	Yihang Wang	WHOLEMOLECULES TORSION PRINT	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
22.024	Conformational Entropy as a Potential Liability of Computationally Designed Antibodies	bio	metadynamics, conformational entropy, antibody, nanobody	Thomas Löhr	ALPHARMSD ANTIBETARMSD WHOLEMOLECULES MOLINFO PBMETAD ALPHABETA RESTART TORSION PRINT COM	secondarystructure bias colvar multicolvar setup vatom generic
22.013	Ligand dissociation from PreQ1 riboswitch	bio	ligand, RNA, metadynamics, pRAVE	Yihang Wang	WHOLEMOLECULES MOLINFO DISTANCE COORDINATIONNUMBER RMSD METAD COMMITTOR COMBINE PRINT COM	bias colvar function symfunc vatom generic
22.008	Ab initio metadynamics determination of temperature-dependent free-energy landscape in ultrasmall silver clusters	materials	Well tempered metadynamics, ab-initio, ase	Daniel Sucerquia	COORDINATION DISTANCE FLUSH LOWER_WALLS COORDINATIONNUMBER METAD GYRATION UPPER_WALLS UNITS COMBINE COM	bias colvar function symfunc setup vatom generic
22.001	Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials	methods	enhanced sampling, variationally enhanced sampling, ves, metadynamics, bias representation, wavelets, adam	Benjamin Pampel	COORDINATION FLUSH OPT_AVERAGED_SGD BF_GAUSSIANS INCLUDE PRINT TD_UNIFORM DISTANCE POSITION TD_WELLTEMPERED UNITS BF_LEGENDRE BF_CUBIC_B_SPLINES METAD VES_OUTPUT_BASISFUNCTIONS UPPER_WALLS ENERGY BF_WAVELETS OPT_ADAM BF_CHEBYSHEV VES_LINEAR_EXPANSION	ves bias colvar setup generic
21.046	Ubiquitin Interacting Motifs, Duality Between Structured and Disordered Motifs	bio	wt metadynamics, ubiquitin, ataxin-3, short linear motifs, ubiquitin binding motif, moonlight functions, intrinsic disorder	Elena Papaleo	WHOLEMOLECULES GROUP LOWER_WALLS ALPHABETA METAD ENDPLUMED GYRATION UPPER_WALLS PRINT	bias colvar multicolvar core generic
21.035	CmuMD simulations of NaCl(aq) at NaCl	chemistry	CmuMD, interface	Aaron Finney	DISTANCE LOAD GROUP RESTRAINT FIXEDATOM PRINT	bias colvar setup vatom core generic
21.026	Probing allosteric regulations with coevolution-driven molecular simulations	bio	metadynamics, coevolution, allostery, adenylate cyclase	Francesco Colizzi	WHOLEMOLECULES DISTANCE PATHMSD METAD UPPER_WALLS UNITS PRINT COM	bias colvar setup vatom generic
20.030	Converging experimental and computational views of the knotting mechanism of the smallest knotted protein	bio	phi-values, transition state, knotted proteins	Cristina Paissoni	COORDINATION WHOLEMOLECULES MOLINFO RESTRAINT STATS COMBINE PRINT	function bias colvar generic
20.016	Predicting polymorphism in molecular crystals using orientational entropy	materials	metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy	Pablo Piaggi	VOLUME CENTER LOAD GROUP METAD UPPER_WALLS INCLUDE PRINT	bias colvar setup vatom core 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	MOLINFO FLUSH CONTACTMAP HISTOGRAM PRINT DISTANCE REWEIGHT_METAD ENDPLUMED ABMD COMBINE WHOLEMOLECULES READ FUNCPATHMSD LOWER_WALLS METAD DUMPGRID UPPER_WALLS CONVERT_TO_FES COM	bias colvar function vatom generic gridtools
19.068	Rethinking Metadynamics	methods	metadynamics, opes, convergence	Michele Invernizzi	EXTERNAL POSITION METAD ENDPLUMED TORSION UNITS PRINT OPES_METAD	bias colvar setup generic opes
19.067	Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways	bio	metadynamics, ligand unbinding	Jakub Rydzewski	PATHMSD LOWER_WALLS METAD RESTART UPPER_WALLS UNITS PRINT	bias colvar generic setup
19.064	Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations	materials	metadynamics, peptide-surface binding	Jim Pfaendtner	MOLINFO DISTANCE ENERGY METAD GYRATION UPPER_WALLS PRINT COM	bias colvar generic vatom
19.050	Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes	chemistry	metadynamics, membranes, Willard Chandler surface	Gareth Tribello	READ CONVERT_TO_FES METAD RESTART COMBINE REWEIGHT_BIAS DUMPGRID DISTANCE_FROM_CONTOUR HISTOGRAM PRINT UPPER_WALLS	bias function setup contour generic gridtools
19.019	FA-MetaD-JCP-Wang-et-al	bio	Frequency adaptive metadynamics; peptide	Kresten Lindorff-Larsen	MOLINFO FLUSH ALPHABETA COMMITTOR METAD COMBINE PRINT	function bias generic multicolvar
19.005	Cmyc small molecule interaction	bio	metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP	Gabriella Heller	COORDINATION WHOLEMOLECULES MOLINFO METAINFERENCE DISTANCE CENTER PBMETAD GROUP CS2BACKBONE ALPHABETA GYRATION INCLUDE PRINT	bias colvar multicolvar vatom core generic isdb
19.002	EMMI STRA6	bio	metainference, cryo-EM	Max Bonomi	EMMI MOLINFO GROUP BIASVALUE PRINT	core bias generic isdb
19.001	RNA SHAPE	bio	metadynamics, RNA, ligand binding	Giovanni Bussi	MOLINFO DISTANCE FLUSH LOWER_WALLS METAD DISTANCES RANDOM_EXCHANGES ERMSD ANGLE INCLUDE COMBINE PRINT UPPER_WALLS	bias colvar function multicolvar generic
24.011	Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble	methods	committor, machine learning	Peilin Kang	GROUP TORSION UPPER_WALLS WHOLEMOLECULES MOLINFO RMSD PRINT INCLUDE LOWER_WALLS POSITION UNITS MATHEVAL ENERGY CELL COORDINATION LOAD CUSTOM DISTANCE BIASVALUE ENDPLUMED	setup colvar generic function bias core
23.028	Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process	chemistry	Ammonia decomposition; Dynamics;OPES; Neural Network potential	Manyi Yang	PRINT GROUP DISTANCES LOWER_WALLS COM FLUSH UNITS FIXEDATOM MATHEVAL COMMITTOR CUSTOM DISTANCE COORDINATIONNUMBER ZDISTANCES OPES_METAD ENERGY UPPER_WALLS	opes multicolvar setup colvar generic function vatom symfunc bias core
23.027	CmuMD simulations of NaCl(aq) at NaCl	chemistry	CmuMD, DFS, Q3, Pair Entropy	Aaron Finney	PRINT CLUSTER_DISTRIBUTION AROUND CLUSTER_NATOMS DENSITY DUMPGRID GROUP DFSCLUSTERING Q3 CONTACT_MATRIX LOAD COORDINATIONNUMBER RESTRAINT UNITS FIXEDATOM LOCAL_AVERAGE LOCAL_Q3 HISTOGRAM	setup clusters volumes gridtools generic adjmat vatom symfunc bias core
23.023	Rational design of novel biomimetic sequence-defined polymers for mineralization applications	methods	metadynamics, surface binding, biomimetic mineralization	Kaylyn Torkelson	PRINT PBMETAD COM DISTANCE COORDINATION GYRATION UPPER_WALLS	vatom generic colvar bias
22.044	Colloid Crystallisation Analyses	materials	Q4, Q6, Pair Entropy, DFS	Aaron Finney	Q6 CLUSTER_NATOMS PRINT LOCAL_Q6 DFSCLUSTERING GROUP MFILTER_LESS Q4 MFILTER_MORE LOCAL_Q4 CONTACT_MATRIX COORDINATIONNUMBER LOCAL_AVERAGE COMBINE	multicolvar clusters generic adjmat symfunc function core
22.025	Bubble nucleation rate predictions in a Lennard-Jones fluid	materials	free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation	Kristof Bal	CONVERT_TO_FES REWEIGHT_BIAS VOLUME PRINT LOAD DUMPGRID RESTRAINT COORDINATIONNUMBER FLUSH UNITS CUSTOM COMMITTOR BIASVALUE MOVINGRESTRAINT HISTOGRAM ANN UPPER_WALLS	setup gridtools colvar generic annfunc symfunc bias function
22.022	Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir	bio	RMSD, protein-ligand interactions	Isabell Grothaus	PRINT RMSD	generic colvar
22.018	Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations	bio	ligand binding, docking, EMMI, LAT1	Max Bonomi	PRINT LOAD GROUP EMMIVOX BIASVALUE WHOLEMOLECULES MOLINFO	isdb setup generic bias core
22.015	Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome	bio	photodynamics, bacteriophytochrome, variationally enhanced sampling	Jakub Rydzewski	BF_FOURIER TD_UNIFORM PRINT TORSION OPT_AVERAGED_SGD VES_LINEAR_EXPANSION	colvar generic ves
22.005	Collective Variable for Metadynamics Derived from AlphaFold Output	bio	AlphaFold, protein folding, protein structure prediction, metadynamics, deep learning, free energy simulation, collective variable	Vojtech Spiwok	LOAD WHOLEMOLECULES METAD PRINT	generic setup bias
22.003	Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling	methods	opes, metadynamics, reweighting, alanine, muller	Michele Invernizzi	UPPER_WALLS PRINT PBMETAD BIASVALUE LOWER_WALLS POSITION TORSION ECV_MULTITHERMAL OPES_METAD_EXPLORE METAD UNITS CUSTOM ECV_UMBRELLAS_FILE OPES_EXPANDED OPES_METAD ENERGY ENDPLUMED	opes setup colvar generic bias function
22.000	Amyloid precursor protein processing by human γ-secretase	bio	Bias Exchange Metadynamics, Helix unfolding, coupled binding	Xiaoli Lu	PRINT INCLUDE MOLINFO CENTER CONTACTMAP ANTIBETARMSD UNITS METAD DISTANCE ALPHARMSD COORDINATION RANDOM_EXCHANGES	setup colvar generic secondarystructure vatom bias
21.034	Efficient sampling of high-dimensional free energy landscapes using adaptive reinforced dynamics	bio	reinforced dynamics, bias-exchange metadynamics, parallel-bias metadynamics	Dongdong Wang	PRINT INCLUDE PBMETAD TORSION METAD RANDOM_EXCHANGES ENDPLUMED	colvar generic bias
21.017	All-atom simulations of the Vav1 AD construct	bio	metadynamics, parallel-bias, well-tempered	Simone Orioli	ALPHABETA REWEIGHT_BIAS PRINT PBMETAD RESTART GROUP CONTACTMAP METAD ALPHARMSD WHOLEMOLECULES MOLINFO	multicolvar setup colvar generic secondarystructure bias core
20.019	Systematic finite-temperature reduction of crystal energy landscapes	materials	crystals, organics, structure prediction	Matteo Salvalaglio	PRINT VOLUME CELL LOWER_WALLS MATHEVAL METAD ENERGY UPPER_WALLS	generic bias function colvar
20.011	Uremic toxin analysis	bio	metadynamics, uremic toxin, serum albumin	Jim Pfaendtner	PRINT RESTART GROUP CENTER DISTANCES DISTANCE WHOLEMOLECULES COORDINATION	multicolvar setup colvar generic vatom core
20.009	The dynamics of linear polyubiquitin	bio	saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics	Carlo Camilloni	SAXS ENSEMBLE ALPHABETA PRINT PBMETAD CENTER FLUSH TORSION DISTANCE METAINFERENCE WHOLEMOLECULES MOLINFO GYRATION STATS	bias isdb multicolvar colvar generic vatom function
19.082	Ammonia Borane Dehydrogenation	chemistry	metadynamics, reaction discovery, hydrogen production, chemistry	Valerio Rizzi	PRINT RESTART GROUP FLUSH UNITS EXTERNAL METAD COORDINATIONNUMBER COMBINE ENDPLUMED	setup generic function symfunc bias core
19.072	SINE hairpin MD+NMR	bio	metadynamics, RNA, NMR	Giovanni Bussi	PRINT INCLUDE SORT MOLINFO MAXENT COM FLUSH TORSION MATHEVAL METAD DISTANCE WHOLEMOLECULES COORDINATION	bias colvar generic vatom function
19.069	Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen	materials	ibuprofen, crystal, solvent, surface	Matteo Salvalaglio	PRINT INCLUDE GROUP CENTER DISTANCE ENDPLUMED	vatom generic core colvar
19.065	Molecular Enhanced Sampling with Autoencoders	methods	enhanced sampling, collective variables, deep learning	Wei Chen	RESTRAINT POSITION COM COMBINE ANN	colvar annfunc vatom bias function
19.058	Constrained MD for maintaining a cavity in a calculation	chemistry	constrained MD, porous molecules, porosity, cavity	Kim Jelfs	INPLANEDISTANCES PRINT RESTART DISTANCES COM FLUSH MOVINGRESTRAINT	multicolvar setup generic vatom bias
19.044	Multithermal-multibaric simulations using VES	methods	ves, Wang Landau, multicanonical, water, density anomaly	Pablo Piaggi	CONVERT_TO_FES REWEIGHT_BIAS PRINT VOLUME RESTART DUMPGRID REWEIGHT_TEMP_PRESS READ BF_LEGENDRE TD_MULTITHERMAL_MULTIBARIC ENERGY OPT_AVERAGED_SGD VES_LINEAR_EXPANSION OPT_DUMMY AVERAGE COMBINE HISTOGRAM	setup gridtools colvar generic ves bias function
19.042	Harmonic Linear Discriminant Analysis (HLDA)	methods	metadynamics, chemistry, HLDA	GiovanniMaria Piccini	PRINT FLUSH UNITS METAD DISTANCE COMBINE ENERGY UPPER_WALLS	bias setup colvar generic function
19.020	PTMetaD-WTE simulation of the Ntail IDP	bio	metadynamics, IDPs, protein folding	Mattia Bernetti	PRINT MOLINFO METAD ALPHARMSD WHOLEMOLECULES GYRATION ENERGY ENDPLUMED	colvar generic secondarystructure bias
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	PRINT RESTART LOAD POSITION TORSION UNITS METAD ENERGY VES_DELTA_F ENDPLUMED	setup colvar generic ves bias
25.002	M3_PCV-ABMD	chemistry	Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor	Gian Marco Elisi	PRINT ABMD PATHMSD ENDPLUMED UNITS UPPER_WALLS	bias colvar setup generic
24.032	DeepLNE++	methods	PATHCV, OPES	Thorben Fröhlking	CUSTOM OPES_METAD TORSION COORDINATION ENERGY PRINT LOAD COMBINE DISTANCE GROUP	function opes generic colvar setup core
24.016	Cryo-EM guided simulations of ribozyme	bio	metainference, cryo-EM	Giovanni Bussi	BIASVALUE ERMSD INCLUDE PRINT EMMIVOX RESTRAINT WHOLEMOLECULES MOLINFO GROUP	isdb generic colvar bias core
24.012	Molecular simulations to investigate the impact of N6-methylation in RNA recognition	bio	metadynamics, alchemistry, RNA modification, RNA:protein interactions	Giovanni Bussi	BIASVALUE COORDINATION DEBUG PRINT COMBINE LOWER_WALLS DISTANCE GHBFIX METAD MOLINFO CENTER COM UPPER_WALLS GROUP	function generic colvar bias core vatom
24.007	SWISH-X	bio	swish-x, SWISH-X, swish, expanded SWISH	Alberto Borsatto	INCLUDE ENERGY PRINT CONTACTMAP ECV_MULTITHERMAL WHOLEMOLECULES OPES_EXPANDED UPPER_WALLS MOLINFO	bias colvar opes generic
23.045	Minute-timescale simulations of G Protein Coupled Receptor A2A activation mechanism reveal a receptor pseudo-active state	bio	Path CVs Metadynamics, GPCRs activation transition	Vittorio Limongelli	INCLUDE PRINT FUNCPATHMSD CONTACTMAP LOWER_WALLS DISTANCE METAD PATHMSD MOLINFO UPPER_WALLS ALPHARMSD	function secondarystructure generic colvar bias
23.040	Supramolecular capsules assembly dynamics	chemistry	Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics	Riccardo Capelli	CUSTOM DISTANCES PRINT POSITION DISTANCE METAD WHOLEMOLECULES UNITS CENTER COM GROUP FLUSH	function multicolvar generic colvar setup bias core vatom
23.035	An Extended Metadynamics Protocol for Binding/Unbinding of Peptide Ligands to Class A G-Protein Coupled Receptors	bio	G protein coupled receptor, peptide ligands, metadynamics, multiple-walker	Timothy Clark	BIASVALUE MATHEVAL PRINT LOWER_WALLS DISTANCE METAD WHOLEMOLECULES CENTER UPPER_WALLS CONSTANT	function generic colvar bias vatom
23.012	JAK2 2D meta-eABF PMF with statistical analysis	bio	2D meta-eABF, path CV, PMF	Istvan Kolossvary	BIASVALUE CUSTOM PRINT LOWER_WALLS METAD DRR PATHMSD UPPER_WALLS FLUSH	function generic drr colvar bias
23.011	OneOPES, a combined enhanced sampling method to rule them all	bio	OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding	Valerio Rizzi	OPES_METAD_EXPLORE TORSION ENERGY PRINT OPES_EXPANDED ECV_MULTITHERMAL DISTANCE METAD ENDPLUMED MOLINFO	bias colvar opes generic
22.038	Enhanced Sampling Aided Design of Molecular Photoswitches	chemistry	reaction discovery, OPES explore, graph CV	Umberto Raucci	CUSTOM PYTORCH_MODEL OPES_METAD_EXPLORE COORDINATION PRINT UNITS	pytorch function opes generic colvar setup
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 GYRATION WHOLEMOLECULES PBMETAD MOLINFO	bias colvar generic
22.016	Homogeneous ice nucleation in an ab initio machine learning model of water	chemistry	ice, water, nucleation, seeding, environment similarity, interfacial free energy, interfaces	Pablo Piaggi	CUSTOM AROUND OPES_METAD ENVIRONMENTSIMILARITY VOLUME ENERGY DUMPGRID PRINT HISTOGRAM UPPER_WALLS RESTART	function opes bias generic colvar envsim volumes setup gridtools
22.009	Glycosylation in calixarenes capsule	chemistry	Metadynamics, glycosylation, supramolecular catalysis	GiovanniMaria Piccini	DISTANCES COORDINATION MATHEVAL PRINT FIT_TO_TEMPLATE BRIDGE COMBINE ANGLE LOWER_WALLS DISTANCE METAD WHOLEMOLECULES UNITS UPPER_WALLS RMSD GROUP FLUSH	function multicolvar generic colvar adjmat setup bias core
21.044	NaCl nucleation	chemistry	metadynamics, DFS clustering	Aaron Finney	CLUSTER_NATOMS FIXEDATOM DUMPGRID HISTOGRAM PRINT COORDINATIONNUMBER COMBINE MFILTER_MORE Q6 DFSCLUSTERING LOCAL_Q6 CLUSTER_DISTRIBUTION METAD INSPHERE CONTACT_MATRIX GROUP	function multicolvar bias generic adjmat volumes symfunc clusters gridtools core vatom
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	COORDINATION ENERGY PRINT DIHCOR GYRATION RANDOM_EXCHANGES LOWER_WALLS PARABETARMSD ANTIBETARMSD METAD WHOLEMOLECULES MOLINFO UPPER_WALLS ALPHARMSD GROUP	multicolvar secondarystructure generic colvar bias core
21.033	Multiple-path-metadynamics applied to DNA base-pairing transitions	bio	path-CV, metadynamics, multiple-walker, dna	Alberto Pérez-de-Alba-Ortíz	INCLUDE PRINT COMBINE RESTRAINT METAD MOVINGRESTRAINT UPPER_WALLS CONSTANT	bias function generic
21.032	Metal-coupled folding mechanism to metallothionein	bio	parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination	Manuel-Peris Diaz	COORDINATION WHOLEMOLECULES PBMETAD UNITS GROUP	generic colvar setup bias core
21.027	EGFR activating mutations mechanism	bio	metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA	Francesco Gervasio	INCLUDE MATHEVAL ENERGY PRINT CONTACTMAP LOWER_WALLS DISTANCE METAD WHOLEMOLECULES MOLINFO UPPER_WALLS ALPHARMSD	function secondarystructure generic colvar bias
21.025	Computational and biochemical analysis of type IV pilus dynamics and stability	bio	molecular dynamics, calcium binding, Type IV pilus	Yasaman Karami	LOWER_WALLS UPPER_WALLS DISTANCE PRINT	bias colvar generic
21.021	ATLAS	methods	Machine Learning, Metadynamics	Federico Giberti	BIASVALUE TORSION MATHEVAL COORDINATION DUMPATOMS PRINT COORDINATIONNUMBER GYRATION DISTANCE METAD WHOLEMOLECULES UNITS GROUP	function generic colvar symfunc setup bias core
21.004	Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy	bio	machine learning, well-tempered metadynamics, path collective variable, potential of mean force, standard binding free energy calculations, host-guest, protein-ligand unbinding	Dorothea Gobbo	PRINT LOWER_WALLS METAD WHOLEMOLECULES PATHMSD UPPER_WALLS RESTART	bias colvar setup generic
20.032	Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil	materials	clustering, conformational isomers	Matteo Salvalaglio	PRINT TORSION ENDPLUMED	colvar generic
20.029	High Conformational Flexibility of the E2F1/DP1/DNA complex	bio	SAXS, protein-DNA complex, hySAXS, ensemble determination	Cristina Paissoni	BIASVALUE INCLUDE ENSEMBLE SAXS PRINT STATS RESTRAINT DISTANCE WHOLEMOLECULES MOLINFO CENTER GROUP	isdb function generic colvar bias core vatom
20.025	The role of water in host-guest interaction	bio	ligand binding, water, opes, SAMPL5	Valerio Rizzi	FIXEDATOM PYTORCH_MODEL OPES_METAD COORDINATION MATHEVAL ENERGY PRINT FIT_TO_TEMPLATE ANGLE DISTANCE WHOLEMOLECULES ENDPLUMED CENTER UPPER_WALLS GROUP	pytorch function opes generic colvar bias core vatom
20.024	Gaussian Mixture Based Enhanced Sampling (GAMBES)	methods	enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias	Jayashrita Debnath	DISTANCES TORSION ENERGY PRINT LOAD COMBINE LOWER_WALLS DISTANCE UNITS UPPER_WALLS GROUP	function multicolvar generic colvar setup bias core
20.023	metadynminer and metadynminer3d	methods	metadynamics, visualization, R	Vojtech Spiwok	METAD PRINT TORSION	bias colvar generic
20.020	Parallel Bias Metadynamics	methods	pbmetad, trp-cage, folding	Max Bonomi	INCLUDE COORDINATION PRINT GYRATION DIHCOR ALPHABETA WHOLEMOLECULES PBMETAD MOLINFO	bias colvar multicolvar generic
20.004	Data-driven collective variables for enhanced sampling	methods	collective variables, machine learning, deep-lda	Luigi Bonati	PYTORCH_MODEL OPES_METAD TORSION MATHEVAL PRINT LOAD LOWER_WALLS DISTANCE ENDPLUMED UNITS UPPER_WALLS COM GROUP FLUSH	pytorch function opes generic colvar setup bias core vatom
19.066	Finding ligand unbinding reaction pathways	methods	maze, ligand unbinding	Jakub Rydzewski	MAZE_LOSS PRINT POSITION UNITS MAZE_OPTIMIZER_BIAS MAZE_SIMULATED_ANNEALING	colvar setup generic maze
19.051	Solid liquid interfacial free energy out of equilibrium	materials	metadynamics, nucleation, surface excess free energy	Gareth Tribello	AROUND CELL PRINT LOWER_WALLS METAD ENDPLUMED UNITS UPPER_WALLS FCCUBIC	generic colvar volumes symfunc setup bias
19.043	Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA)	methods	metadynamics, chemistry, HLDA	GiovanniMaria Piccini	DISTANCES PRINT COMBINE DISTANCE METAD UNITS UPPER_WALLS FLUSH RESTART	function multicolvar generic colvar setup bias
19.022	eABF simulation of NANMA (alanine dipeptide)	methods	eABF, DRR, alanine dipeptide	Haochuan Chen	DRR PRINT TORSION	drr colvar generic
19.008	anncolvar	methods	neural network, dimensionality reduction	Vojtech Spiwok	MATHEVAL PRINT POSITION FIT_TO_TEMPLATE COMBINE METAD WHOLEMOLECULES MOLINFO ALPHARMSD	function secondarystructure generic colvar bias
19.007	EMMI Microtubules	bio	metainference, cryo-EM	Max Bonomi	BIASVALUE PRINT EMMI WHOLEMOLECULES MOLINFO GROUP	bias isdb core generic
19.004	MI Ubiquitin	bio	metainference, NMR	Max Bonomi	RDC METAINFERENCE PRINT WHOLEMOLECULES MOLINFO GROUP CS2BACKBONE	isdb core generic
25.009	Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water	chemistry	metadynamics, nitrate photolysis	Kam-Tung Chan	FLUSH METAD READ DUMPGRID REWEIGHT_METAD RESTART DISTANCE CUSTOM PRINT GROUP UPPER_WALLS HISTOGRAM COORDINATION	core function generic colvar setup bias gridtools
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	GYRATION ENERGY READ RESTART CENTER TORSION DISTANCE INCLUDE PRINT VOLUME PBMETAD	vatom generic colvar setup bias
25.003	Surrogate Model CV	methods	Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding	Sompriya Chatterjee	WHOLEMOLECULES PYTORCH_MODEL GROUP ENERGY TORSION COMMITTOR DISTANCE OPES_METAD PRINT COMBINE MOLINFO CUSTOM ENDPLUMED MATHEVAL	core function opes generic colvar pytorch
24.017	Absolute Binding Free Energies with OneOPES	methods	protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy	Francesco Gervasio	RMSD TORSION ECV_MULTITHERMAL GROUP CONTACTMAP WHOLEMOLECULES CONSTANT RESTART OPES_METAD_EXPLORE PROJECTION_ON_AXIS PRINT LOWER_WALLS COM OPES_EXPANDED ENERGY BIASVALUE CUSTOM COORDINATION WRAPAROUND METAD INCLUDE MATHEVAL MOLINFO UPPER_WALLS	core function opes vatom generic colvar setup bias
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	RMSD FLUSH WHOLEMOLECULES PYTORCH_MODEL METAD DRR PRINT COORDINATION MOLINFO UPPER_WALLS LOWER_WALLS	drr generic colvar pytorch 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	FLUSH TRANSPOSE SUM METAD INCLUDE PRINT SELECT_COMPONENTS MATHEVAL	valtools function generic matrixtools bias
23.034	Urea nucleation in water: do long-range forces matter?	materials	LMF theory, Metadynamics, Nucleation	Ziyue Zou	COORDINATIONNUMBER LOAD METAD CENTER INCLUDE PRINT GROUP	core vatom generic setup bias symfunc
23.032	Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics	bio	metadynamics, tSNE, neural network, machine learning, trp-cage, folding	Vojtech Spiwok	POSITION WHOLEMOLECULES ANN METAD ALPHARMSD FIT_TO_TEMPLATE PRINT COMBINE MOLINFO	function generic colvar bias secondarystructure annfunc
23.020	FEP simulations of ATOX1 homodimer	chemistry	parallel bias metadynamics, FEP, free-energy of metal ion dissociation	Adriana Pietropaolo	WHOLEMOLECULES CONSTANT BIASVALUE DISTANCE ANGLE PRINT MATHEVAL PBMETAD	function bias generic colvar
22.036	Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction	bio	Well-tempered MetaDynamics with Hamiltonian Replica Exchange	Miroslav Krepl	FLUSH COMBINE LOAD METAD BIASVALUE GHBFIX CUSTOM PRINT GROUP MOLINFO UPPER_WALLS COORDINATION	core function generic colvar setup bias
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	COM XANGLES ZANGLES WHOLEMOLECULES LOWER_WALLS METAD TORSION ALPHABETA DISTANCE UPPER_WALLS CUSTOM PRINT COMBINE MOLINFO MATHEVAL YANGLES	multicolvar function vatom generic colvar bias
21.051	Automatic learning of hydrogen-bond fixes in an AMBER RNA force field	methods	force field, RNA	Giovanni Bussi	WHOLEMOLECULES METAD BIASVALUE PRINT COMBINE MOLINFO ERMSD COORDINATION	function bias generic colvar
21.050	N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity	methods	bio	Isabell Louise Grothaus	DISTANCE CENTER PRINT	vatom generic 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	COM WHOLEMOLECULES BIASVALUE RESTART DISTANCE EMMI PRINT GROUP MOLINFO UPPER_WALLS	core vatom generic colvar isdb setup bias
21.039	Deep learning the slow modes for rare events sampling	methods	collective variables, machine learning, slow modes, deep-tica, opes	Luigi Bonati	RMSD FLUSH TORSION ECV_MULTITHERMAL COMBINE GROUP VOLUME CONTACTMAP WHOLEMOLECULES PYTORCH_MODEL DISTANCE PRINT ENDPLUMED OPES_EXPANDED LOAD ENERGY OPES_METAD ENVIRONMENTSIMILARITY Q6 INCLUDE MOLINFO UNITS	core envsim function opes generic colvar setup pytorch symfunc
21.038	Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics	materials	metadynamics, SGOOP, nucleation, urea	Ziyue Zou	VOLUME COORDINATIONNUMBER LOAD GROUP METAD CENTER ENERGY INCLUDE PRINT COMBINE	core function vatom generic colvar setup bias symfunc
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	COM GYRATION ENERGY TORSION ALPHABETA METAD DISTANCE INCLUDE PRINT COORDINATION PBMETAD	multicolvar vatom generic colvar bias
21.029	Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs	bio	metadynamics, small peptide, machine learning	Pratyush Tiwary	FLUSH EXTERNAL ENERGY TORSION RESTART PRINT MOLINFO	setup bias generic colvar
21.028	From Enhanced Sampling to Reaction Profiles	methods	collective variables, multi-state, machine learning, Deep-TDA	Enrico Trizio	TORSION FIXEDATOM DISTANCES GROUP WHOLEMOLECULES PYTORCH_MODEL CENTER DISTANCE UPPER_WALLS PRINT ENDPLUMED LOWER_WALLS LOAD FIT_TO_TEMPLATE COORDINATION OPES_METAD ANGLE UNITS MATHEVAL	core multicolvar function vatom opes generic colvar setup pytorch bias
21.022	Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly	materials	parallel bias metadynamics, adsorption, peptide	Xin Qi	COM GYRATION ENERGY DISTANCE PRINT MOLINFO UPPER_WALLS PBMETAD LOWER_WALLS	bias vatom generic colvar
21.015	Coarse-grained metadynamics and umbrella sampling simulations to investigate interactions of carbohydrate-binding modules with chitin	bio	metadynamics, umbrella sampling, coarse-grained, MARTINI, chitin, carbohydrate-binding module	Gaston Courtade	POSITION WHOLEMOLECULES METAD CENTER RESTART RESTRAINT PRINT COORDINATION MATHEVAL REWEIGHT_BIAS	function vatom generic colvar setup bias
21.009	Nucleation rates from small scale atomistic simulations and transition state theory	materials	kinetics, free energy barriers, nucleation, droplets, metadynamics	Kristof Bal	FLUSH COORDINATIONNUMBER CONVERT_TO_FES LOAD METAD DUMPGRID REWEIGHT_METAD COMMITTOR MOVINGRESTRAINT PRINT UNITS UPPER_WALLS HISTOGRAM	symfunc generic setup bias gridtools
21.007	Sampling enhancement by metadynamics driven by machine learning and de novo protein modelling	bio	metadynamics, machine learning, protein folding	Vojtech Spiwok	POSITION WHOLEMOLECULES COMBINE FIT_TO_TEMPLATE ALPHARMSD MOLINFO MATHEVAL	function secondarystructure generic colvar
20.031	Soft fluorescent nanoshuttles targeting receptors	chemistry	polymers, receptors, nanoparticles, fluorescent probes	Adriana Pietropaolo	WHOLEMOLECULES CENTER PRINT COORDINATION PBMETAD	bias vatom generic colvar
20.014	amyloid beta small molecule interaction	bio	intrinsically disordered proteins, disordered proteins, IDPs, fuzzy binding, small molecule, drugs, entropy, binding, Alzheimer’s disease, amyloid beta	Gabriella Heller	FLUSH TORSION DIHCOR GROUP COMBINE PBMETAD WHOLEMOLECULES CS2BACKBONE ANTIBETARMSD STATS PARABETARMSD ENSEMBLE PRINT ENDPLUMED METAINFERENCE GYRATION ALPHARMSD COORDINATION INCLUDE MOLINFO	core multicolvar function generic colvar isdb bias secondarystructure
19.083	Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis	chemistry	metadynamics, chemical reactions, reaction discovery	Valerio Rizzi	FLUSH COORDINATIONNUMBER GROUP METAD RESTART DISTANCES UNITS PRINT COMBINE ENDPLUMED UPPER_WALLS	core multicolvar function generic setup bias symfunc
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	GYRATION COORDINATIONNUMBER ENERGY METAD DISTANCES PRINT ENDPLUMED UPPER_WALLS LOWER_WALLS	multicolvar generic colvar bias symfunc
19.059	cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide	bio	bias-exchange metadynamics, cis-trans isomerization	Fabrizio Marinelli	METAD TORSION RANDOM_EXCHANGES INCLUDE PRINT	bias generic colvar
19.057	SAXS ensembles using Martini-Beads multi-scale SAXS	methods	metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics	Cristina Paissoni	WHOLEMOLECULES SAXS GROUP CENTER ALPHABETA BIASVALUE STATS ANGLE INCLUDE ENSEMBLE PRINT COMBINE MOLINFO ENDPLUMED MATHEVAL PBMETAD COORDINATION	core multicolvar function vatom generic colvar isdb bias
19.056	maze	methods	maze, ligand unbinding	Jakub Rydzewski	MAZE_OPTIMIZER_BIAS POSITION MAZE_LOSS MAZE_SIMULATED_ANNEALING PRINT UNITS	maze setup generic colvar
19.048	Understanding Ligand Binding Selectivity in a Prototypical GPCR Family	bio	metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding	Francesco Gervasio	COM WHOLEMOLECULES CONSTANT BIASVALUE METAD DISTANCE PRINT MATHEVAL UPPER_WALLS LOWER_WALLS	function vatom generic colvar bias
19.047	Close Structure	methods	metadynamics, RMSD, path collective variables, property map	Vojtech Spiwok	METAD WHOLEMOLECULES PROPERTYMAP PRINT	bias generic colvar
19.041	Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces	bio	metadynamics, collective variables, conformational changes, multiple walkers, Well-Tempered MetaD, peptide, binding, phosphorylation, post-transitional motif, sio2, adsorption	Jim Pfaendtner	COM ENERGY METAD DISTANCE PRINT UPPER_WALLS	generic vatom bias colvar
19.035	Dimerization of GPCRs from coarse-grained umbrella sampling	bio	Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization	Davide Provasi	COM RESTRAINT TORSION DISTANCE PRINT GROUP	core vatom generic colvar bias
19.026	Ice Nucleation on Cholesterol Crystals	materials	forward flux sampling, crystal nucleation, water, ice, organic crystals	Gabriele Cesare Sosso	FLUSH LOCAL_Q6 CLUSTER_NATOMS OUTPUT_CLUSTER Q6 CLUSTER_WITHSURFACE COMMITTOR MFILTER_MORE CONTACT_MATRIX DFSCLUSTERING ENDPLUMED	adjmat multicolvar clusters generic symfunc
19.013	RNA FF FITTING	methods	force field, RNA	Giovanni Bussi	PUCKERING CONSTANT TORSION BIASVALUE INCLUDE MOLINFO MATHEVAL	function bias generic colvar
19.003	EMMI ClpP	bio	metainference, cryo-EM	Max Bonomi	BIASVALUE EMMI PRINT GROUP MOLINFO	isdb bias generic core
24.029	Combination of OPES and OPES-Explore	methods	OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin	Dhiman Ray	COMBINE FIT_TO_TEMPLATE LOWER_WALLS WHOLEMOLECULES COORDINATION PYTORCH_MODEL ENDPLUMED CONTACTMAP INCLUDE DISTANCE MOLINFO POSITION ENERGY METAD GROUP OPES_METAD_EXPLORE UPPER_WALLS CUSTOM FIXEDATOM UNITS BIASVALUE MATHEVAL PRINT RMSD FLUSH OPES_METAD CENTER	core vatom generic colvar function bias setup pytorch opes
24.028	All-atom simulations of RNA-membrane interactions	bio	metadynamics, membrane, RNA	Giovanni Bussi	POSITION PUCKERING WHOLEMOLECULES MATHEVAL PRINT GROUP GYRATION MOLINFO GHOST DISTANCES COMBINE UPPER_WALLS CENTER LOWER_WALLS SORT DISTANCE METAD	core vatom generic colvar function bias multicolvar
24.008	yCD Metadynamics	bio	volume-based MetaD, path CVs, infrequent MetaD, product release	James McCarty	HISTOGRAM FIT_TO_TEMPLATE COM WHOLEMOLECULES PATH CONVERT_TO_FES COORDINATION COMMITTOR WRAPAROUND ENDPLUMED CONTACTMAP INCLUDE DISTANCE MOLINFO METAD GROUP DUMPGRID UPPER_WALLS FIXEDATOM MATHEVAL PRINT RMSD REWEIGHT_METAD FLUSH READ	mapping core vatom generic colvar function bias gridtools
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	PRINT GROUP COORDINATIONNUMBER FIXEDATOM FLUSH UPPER_WALLS OPES_METAD DISTANCE ZDISTANCES UNITS	core vatom generic colvar bias opes setup multicolvar symfunc
23.046	Lasso Peptides - HLDA CV	bio	metadynamics, protein folding, HLDA, harmonic	Gabriel da Hora	WHOLEMOLECULES PRINT COMBINE DISTANCE UNITS METAD	generic colvar function bias setup
23.039	Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation	chemistry	metadynamics, ligand dissociation	Eric Beyerle	RESTRAINT DUMPMASSCHARGE PRINT MOLINFO COMBINE UPPER_WALLS CENTER DISTANCE FIXEDATOM METAD	vatom generic colvar function bias
23.036	Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water?	bio	NaCl, nucleation, metadynamics	Ruiyu Wang	ENERGY MATHEVAL PRINT COORDINATIONNUMBER Q4 Q6 COMBINE VOLUME METAD	generic colvar function bias symfunc
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 GROUP COORDINATIONNUMBER Q6 COMBINE LOCAL_Q6 LOWER_WALLS MOVINGRESTRAINT MFILTER_MORE METAD	core generic function bias multicolvar symfunc
23.025	Probing ion binding to G-quadruplexes and related events	chemistry	metadynamics, repulsive potential, nucleic acids, G-quadruplexes	Marcelo Poleto	WHOLEMOLECULES POSITION DUMPATOMS MATHEVAL PRINT GROUP DISTANCES FLUSH UPPER_WALLS FIT_TO_TEMPLATE WRAPAROUND LOWER_WALLS RESTART DISTANCE COM UNITS METAD	core vatom generic colvar function bias setup multicolvar
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 PRINT ENDPLUMED PYTORCH_MODEL UPPER_WALLS OPES_METAD LOWER_WALLS CUSTOM UNITS BIASVALUE	generic colvar function bias setup pytorch opes
23.021	Into the Dynamics of Rotaxanes at Atomistic Resolution	materials	metadynamics, rotaxanes, molecular shuttles, molecular machines	Luigi Leanza	TORSION MATHEVAL PRINT UPPER_WALLS CENTER CUSTOM DISTANCE FIXEDATOM METAD	vatom generic colvar function bias
23.013	Path meta-eABF simulation of large scale conformational change in STING protein	methods	meta-eABF, path CV, large scale conformational change, STING protein, reciprocal barrier restraint	Istvan Kolossvary	TIME PRINT DRR PATHMSD FLUSH UPPER_WALLS LOWER_WALLS CUSTOM UNITS BIASVALUE METAD	drr generic colvar function bias setup
23.006	Transcription factor unbinding	bio	metadynamics, DNA, conformational changes	Malin Lüking	ALPHARMSD DUMPFORCES ANGLE PRINT DISTANCE METAD CONTACTMAP COM MOLINFO	vatom generic secondarystructure colvar bias
23.001	Quantum phase diagram of water	chemistry	Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella	Sigbjørn-Løland Bore	PRINT ECV_UMBRELLAS_LINE UPPER_WALLS ENVIRONMENTSIMILARITY RESTART LOWER_WALLS OPES_EXPANDED INCLUDE	envsim generic bias setup opes
22.043	Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES	bio	OPES, RNA, Tetraloop, Folding	Gül Zerze	WHOLEMOLECULES ENERGY PRINT ECV_UMBRELLAS_LINE ECV_MULTITHERMAL OPES_EXPANDED CONTACTMAP	colvar opes generic
22.040	From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure	bio	SARS-CoV-2, Spike, Omicron	Miłosz Wieczór	WHOLEMOLECULES PRINT PCAVARS UPPER_WALLS LOWER_WALLS METAD	mapping bias generic
22.020	Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix–Junction–Helix RNA	bio	RNA force field, Helix-Junction-Helix RNA, SAXS, Well tempered metadynamics	Weiwei He	WHOLEMOLECULES TORSION PRINT GROUP DISTANCE COM METAD	core vatom generic colvar bias
22.019	Exploring aspartic protease inhibitor binding to design selective antimalarials	bio	ligand binding, loop opening, path CV, funnel metadynamics, drug development	Raitis Bobrovs	WHOLEMOLECULES PRINT PATHMSD UPPER_WALLS LOWER_WALLS FUNNEL DISTANCE FUNNEL_PS COM METAD	vatom generic colvar bias funnel
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	WHOLEMOLECULES ALPHARMSD TORSION ANGLE PRINT COORDINATION MOLINFO FLUSH UPPER_WALLS ALPHABETA DISTANCE METAD	generic secondarystructure colvar bias multicolvar
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 PRINT FIT_TO_TEMPLATE FIXEDATOM METAD	colvar bias vatom 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	PRINT COORDINATION COMBINE CUSTOM ENDPLUMED VOLUME METAD	colvar function bias generic
21.019	Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations	materials	Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen	Matteo Salvalaglio	MATHEVAL KDE PRINT TORSIONS DISTANCE COM	vatom generic colvar function gridtools multicolvar
21.018	Localized Volume-based Metadynamics	bio	LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification	Riccardo Capelli	HISTOGRAM COM WHOLEMOLECULES CONVERT_TO_FES COORDINATION ENDPLUMED DISTANCE METAD POSITION GROUP DUMPGRID UPPER_WALLS FIXEDATOM MATHEVAL PRINT RMSD REWEIGHT_METAD FLUSH READ	core vatom generic colvar function bias gridtools
21.014	how to determine statistically accurate conformational ensembles	bio	metadynamics, metainference, errors, cv, SAXS, ensemble determination	Cristina Paissoni	WHOLEMOLECULES TORSION ENSEMBLE PRINT GYRATION SAXS MOLINFO STATS CENTER ALPHABETA ANTIBETARMSD PBMETAD CONTACTMAP BIASVALUE METAD	vatom generic secondarystructure colvar function bias isdb multicolvar
21.013	Role of vibrational excitation in heterogeneous catalysis	chemistry	catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption	Kristof Bal	RESTRAINT HISTOGRAM TD_GRID COMBINE LOWER_WALLS REWEIGHT_BIAS CONVERT_TO_FES COORDINATION COORDINATIONNUMBER EXTERNAL BF_CHEBYSHEV DISTANCE METAD OPT_AVERAGED_SGD LOAD DUMPGRID DISTANCES UPPER_WALLS UNITS UWALLS PRINT ANGLES REWEIGHT_METAD FLUSH VES_LINEAR_EXPANSION	generic colvar function bias ves gridtools setup multicolvar symfunc
21.001	Substrate recognition and catalysis by glycosaminoglycan sulfotransferases	bio	metadynamics, well-tempered metadynamics, puckering, coordination	Tarsis Ferreira	WHOLEMOLECULES PUCKERING ENERGY HISTOGRAM RANDOM_EXCHANGES PRINT GROUP COORDINATION DUMPGRID MOLINFO INCLUDE REWEIGHT_METAD UPPER_WALLS LOWER_WALLS DISTANCE METAD	core generic colvar bias gridtools
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	TORSION ERMSD PRINT ABMD CENTER RESTART DISTANCE MOLINFO	vatom generic colvar bias setup
20.013	Improving accuracy of biased Alchemistic simulations	methods	flying Gaussian method, Alchemistic simulations, thermodynamic integration, reweighting	Vojtech Spiwok	TORSION PRINT METAD	colvar bias generic
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 COORDINATION DISTANCES CUSTOM UNITS METAD	generic colvar function bias setup multicolvar
20.006	Class B GPCR activation mechanism	bio	metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding	Francesco Gervasio	WHOLEMOLECULES ENERGY MATHEVAL PRINT RMSD MOLINFO COMBINE UPPER_WALLS CENTER LOWER_WALLS DISTANCE METAD	vatom generic colvar function bias
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	HISTOGRAM COMBINE LOWER_WALLS REWEIGHT_BIAS CONVERT_TO_FES TD_WELLTEMPERED ENERGY OPT_AVERAGED_SGD LOAD DUMPGRID CELL UPPER_WALLS VOLUME BF_LEGENDRE MATHEVAL PRINT Q6 VES_LINEAR_EXPANSION RESTART READ REWEIGHT_TEMP_PRESS TD_MULTITHERMAL_MULTIBARIC OPT_DUMMY	generic colvar function bias ves gridtools setup symfunc
19.079	Impact of Glutamate Carboxylation in the Adsorption of the alpha-1 Domain of Osteocalcin to Hydroxyapatite and Titania	bio	metadynamics, peptide adsorption, parallel tempering, well-tempered ensemble	Sarah Alamdari	ENERGY PRINT GYRATION GROUP MOLINFO UPPER_WALLS DISTANCE COM METAD	core vatom generic colvar bias
19.075	PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python	other	Python, automatic differentiation	Toni Giorgino	RESTRAINT TORSION ANGLE PRINT GROUP COMBINE CENTER CUSTOM ENDPLUMED DISTANCE DUMPDERIVATIVES	core vatom generic colvar function bias
19.053	Capillary fluctuations with PLUMED	methods	nucleation, surface tension, capillary fluctuations	Gareth Tribello	GROUP DUMPGRID MORE_THAN FCCUBIC FIND_CONTOUR_SURFACE FOURIER_TRANSFORM CENTER MULTICOLVARDENS UNITS	contour fourier core vatom function gridtools setup symfunc
19.039	Funnel Metadynamics	bio	funnel-metadynamics, absolute binding free energy, ligand-receptor complexes	Vittorio Limongelli	WHOLEMOLECULES PRINT RMSD UPPER_WALLS LOWER_WALLS FUNNEL DISTANCE FUNNEL_PS COM METAD	vatom generic colvar bias funnel
19.038	native state dynamics of human and mouse b2m	bio	metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation	Carlo Camilloni	WHOLEMOLECULES PRINT CS2BACKBONE GROUP FLUSH UPPER_WALLS ANTIBETARMSD RESTART ALPHABETA PBMETAD ENDPLUMED LOWER_WALLS BIASVALUE MOLINFO	core generic secondarystructure bias setup isdb multicolvar
19.030	Coarse-Grained MetaDynamics (CG-MetaD)	bio	Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy	Vittorio Limongelli	WHOLEMOLECULES PRINT UPPER_WALLS LOWER_WALLS DISTANCE COM METAD	colvar vatom bias generic
19.028	pRAVE	methods	RAVE, reaction coordinate, deep learning, metadynamics, kinetics	Pratyush Tiwary	WHOLEMOLECULES TORSION PRINT COMMITTOR EXTERNAL COMBINE RESTART ALPHABETA DISTANCE COM	vatom generic colvar function bias setup multicolvar
19.027	Multithermal-multibaric simulations using VES	methods	ves, Wang Landau, multicanonical, liquid sodium, density anomaly	Pablo Piaggi	REWEIGHT_BIAS ENERGY HISTOGRAM BF_LEGENDRE CONVERT_TO_FES PRINT OPT_AVERAGED_SGD DUMPGRID COMBINE VES_LINEAR_EXPANSION TD_MULTICANONICAL RESTART READ AVERAGE REWEIGHT_TEMP_PRESS UNITS OPT_DUMMY	generic colvar function bias ves gridtools setup
19.018	Excited state FEP/Metadynamics simulations	chemistry	metadynamics, FEP, excited states, conjugated polymers, torsional potential	Adriana Pietropaolo	WHOLEMOLECULES TORSION MATHEVAL PRINT CONSTANT BIASVALUE METAD	colvar function bias generic
19.009	RNA tetraloops folding	bio	metadynamics, RNA, folding	Giovanni Bussi	WHOLEMOLECULES ERMSD PRINT RMSD ENDPLUMED METAD MOLINFO	colvar bias 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	UNITS COMBINE LOAD FLUSH CUSTOM INCLUDE CELL BIASVALUE COORDINATION MATHEVAL TORSION POSITION ENERGY DISTANCE OPES_METAD PRINT	generic opes bias function colvar setup
25.008	Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting	methods	metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting	Dhiman Ray	METAD ENDPLUMED UPPER_WALLS UNITS POSITION PYTORCH_MODEL WHOLEMOLECULES CUSTOM MOLINFO BIASVALUE RMSD LOWER_WALLS TORSION GROUP ENERGY DISTANCE OPES_METAD PRINT	generic core opes bias function pytorch colvar setup
24.027	Proline cis and trans subensembles of a disordered peptide	bio	intrinsically disordered proteins, proline cis trans isomerisation, metadynamics, collective variables	Alice Pettitt	ENDPLUMED ALPHARMSD COMBINE GYRATION FLUSH ANTIBETARMSD INCLUDE PBMETAD DIHCOR COORDINATION PARABETARMSD TORSION GROUP WHOLEMOLECULES DISTANCE MOLINFO PRINT	generic secondarystructure core bias function colvar multicolvar
24.022	Integrating Path Sampling with Enhanced Sampling for Rare-event Kinetics	methods	OPES Flooding, Weighted Ensemble, Metadynamics, Kinetics, Infrequent Metadynamics, Integrated Sampling	Dhiman Ray	UPPER_WALLS RMSD WHOLEMOLECULES DISTANCE OPES_METAD COORDINATION ANGLE FIT_TO_TEMPLATE ENDPLUMED CUSTOM CONTACTMAP TORSION GROUP MOLINFO METAD COMBINE CENTER COMMITTOR MATHEVAL FIXEDATOM PRINT	generic opes core bias function colvar vatom
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 LOAD COMMITTOR TORSION GROUP PRINT	generic core bias colvar setup
24.010	Oxytocin metadynamics simulation	bio	metadynamics, oxytocin, peptide	Jan Beránek	METAD FLUSH RESTART TORSION WHOLEMOLECULES PRINT	colvar generic setup bias
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 METAD COMBINE ERMSD BIASVALUE COORDINATION WHOLEMOLECULES MOLINFO PRINT	colvar generic function bias
23.031	Identifying small molecules binding sites in RNA conformational ensembles with SHAMAN	bio	RNA, metadynamics, probes, mixed-solvent MD, small molecules, binding sites	Max Bonomi	METAD UPPER_WALLS POSITION CENTER DISTANCES FIT_TO_TEMPLATE SHADOW GROUP WHOLEMOLECULES WRAPAROUND MOLINFO PRINT	generic core bias isdb colvar vatom multicolvar
23.018	Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention	materials	metadynamics, surface binding, peptide adsorption	Kaylyn Torkelson	UPPER_WALLS GYRATION PBMETAD COM DISTANCE PRINT	colvar generic vatom bias
23.000	Atomistic simulations of RNA tetraloop folding via PTWTE-WTM	bio	parallel tempering, well-tempered metadynamics, well-tempered ensemble, RNA, Tetraloop, Folding	Gül Zerze	METAD UPPER_WALLS CONTACTMAP LOWER_WALLS ENERGY WHOLEMOLECULES PRINT	colvar generic bias
22.042	Metadynamics of NSP10 and variants	bio	metadynamics, NSP10, crystal structure, variants	Shozeb Haider	METAD TORSION PRINT	colvar generic bias
22.039	Driving and characterizing nucleation of urea and glycine polymorphs in water	bio	metadynamics, nucleation, amino acids, polymorphism	Eric Beyerle	METAD COORDINATIONNUMBER GROUP COMBINE LOAD CENTER INCLUDE Q6 MATHEVAL PAIRENTROPY Q4 PRINT	core generic gridtools symfunc bias function vatom setup
22.033	Reciprocal barrier restraint. Application to PROTAC passive permeability prediction	methods	PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR	Istvan Kolossvary	METAD UNITS FLUSH CUSTOM COM BIASVALUE DISTANCE DRR PRINT	generic drr bias function colvar vatom setup
22.031	Rare Event Kinetics from Adaptive Bias Enhanced Sampling	methods	OPES Flooding, Kinetics, Rate, OPES, Machine Learning	Dhiman Ray	UNITS RMSD ENERGY DISTANCE OPES_METAD WHOLEMOLECULES CONSTANT INCLUDE POSITION ENDPLUMED CUSTOM BIASVALUE CONTACTMAP TORSION GROUP MOLINFO COMBINE PYTORCH_MODEL COMMITTOR PRINT	generic opes core bias function pytorch colvar setup
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	UPPER_WALLS EMMI PBMETAD COM BIASVALUE RMSD COORDINATION RESTART TORSION GROUP WHOLEMOLECULES MOLINFO PRINT	core generic bias isdb colvar vatom setup
22.021	Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations	chemistry	Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella	Sigbjørn Løland Bore	UPPER_WALLS ENVIRONMENTSIMILARITY INCLUDE LOWER_WALLS ECV_UMBRELLAS_LINE OPES_EXPANDED PRINT	envsim generic opes bias
22.012	Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT	bio	contact maps, protein-protein interactions	Isabell-Louise Grothaus	CONTACTMAP CENTER DISTANCE PRINT	colvar generic vatom
22.006	Peptide framework for screening the effects of amino acids on assembly	bio	metadynamics, peptides	Andrew White	METAD GROUP COMBINE HISTOGRAM GYRATION INCLUDE COM DUMPGRID CONVERT_TO_FES REWEIGHT_BIAS DISTANCES PRINT	core generic gridtools bias function colvar vatom multicolvar
21.048	Enhancing ligand exploration within a channel pore and fenestrations using metadynamics	bio	well-tempered metadynamics, protein-ligand enhanced sampling, sodium channel, Nav, small molecule drug	Elaine Tao	METAD UPPER_WALLS UNITS CUSTOM COM LOWER_WALLS TORSION DISTANCE PRINT	generic bias function 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	METAD VES_LINEAR_EXPANSION COMBINE VOLUME LOAD BF_LEGENDRE TD_WELLTEMPERED RESTART OPT_AVERAGED_SGD PAIRENTROPY ENERGY PRINT	generic gridtools bias function ves colvar setup
21.024	Property map collective variable as a useful tool for force field correction	chemistry	molecular mechanics	Vojtech Spiwok	METAD PROPERTYMAP BIASVALUE TORSION WHOLEMOLECULES PRINT	colvar generic bias
21.008	Multi-replica biased sampling for photoisomerization processes in conjugated polymers	methods	metadynamics, FEP, replica-exchange	Adriana Pietropaolo	CONSTANT PBMETAD BIASVALUE MATHEVAL RESTART TORSION WHOLEMOLECULES PRINT	generic bias function colvar setup
21.006	OPES, On-the-fly Probability Enhanced Sampling Method	methods	opes, alanine dipeptide, well-tempered, multithermal, multiumbrella	Michele Invernizzi	ENDPLUMED OPES_EXPANDED ECV_UMBRELLAS_LINE ENERGY TORSION ECV_MULTITHERMAL OPES_METAD PRINT	colvar generic opes
20.033	COVID-19 Spike protein opening transition mechanism	bio	EMMI, CryoEM, COVID-19, Spike, Metainference	Faidon Brotzakis	HISTOGRAM EMMI BIASVALUE RMSD READ DUMPGRID DISTANCES CONVERT_TO_FES GROUP WHOLEMOLECULES MOLINFO PRINT	generic core gridtools bias isdb colvar multicolvar
20.007	Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics	bio	metadynamics, loop movement, artificial intelligence	Pratyush Tiwary	METAD UPPER_WALLS COMBINE RMSD RESTART TORSION WHOLEMOLECULES DISTANCE MOLINFO PRINT	generic bias function colvar setup
19.080	Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium	methods	ves, variationally enhanced sampling, vibrational excitation, chemical reactions	Kristof Bal	UPPER_WALLS VES_LINEAR_EXPANSION UNITS EXTERNAL COMBINE HISTOGRAM FLUSH TD_GRID DUMPGRID COORDINATION ANGLE CONVERT_TO_FES TD_WELLTEMPERED LOWER_WALLS OPT_AVERAGED_SGD BF_CHEBYSHEV DISTANCE PRINT	generic gridtools bias function ves colvar setup
19.036	Thermodynamics and kinetics of G protein-coupled receptor activation	bio	metadynamics, allostery, receptor conformation, GPCR, pharmacology	Davide Provasi	METAD ENDPLUMED COM RMSD CONTACTMAP FUNCPATHMSD DISTANCE WHOLEMOLECULES PRINT	generic bias function colvar vatom
19.032	Chemical reaction in solution using path collective variables based on coordination patterns	chemistry	chemical reactions, solutions, metadynamics, coordination patterns	Fabio Pietrucci	METAD UPPER_WALLS FLUSH PATH RESTART DISTANCES PRINT	generic setup bias mapping multicolvar
19.031	Ice nucleation using PIV-based path coordinates	materials	phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics	Silvio Pipolo	METAD UPPER_WALLS PIV CELL FUNCPATHMSD LOWER_WALLS PRINT	generic piv bias function colvar
19.029	WTE-metaD of FF domain of URNF1 C57D variant	bio	metadynamics, mutations, post-translational modification, ff domain	Elena Papaleo	METAD UPPER_WALLS GYRATION ALPHABETA LOWER_WALLS GROUP WHOLEMOLECULES MOLINFO PRINT	core generic bias colvar multicolvar
19.024	PT-MetaD-WTE	methods	metadynamics, WTE, trp cage, PT	Jim Pfaendtner	METAD EXTERNAL COORDINATION GROUP ENERGY	colvar core bias
19.021	Coarse-Grained Directed Simulation	methods	experiment directed simulation, coarse-grain, bias	Glen Hocky	EDS COMBINE RESTRAINT TORSION DISTANCE PRINT	generic bias function eds colvar
25.011	Chiral perovskite nucleation	chemistry	metadynamics, chiral perovskites, nucleation	Adriana Pietropaolo	UNITS PBMETAD MULTI_RMSD PRINT MATHEVAL RESTART LOWER_WALLS UPPER_WALLS DISTANCE	generic setup bias function colvar
25.010	Kinetic rates calculation with Ratchet&Pawl MD	methods	kinetics, ligand binding, ABMD, ratchet&pawl MD	Riccardo Capelli	COMMITTOR COM WHOLEMOLECULES ABMD PRINT GROUP FLUSH DISTANCE	generic core bias vatom colvar
25.001	RNA G-quadruplex folding with ST-metaD protocol	bio	RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD	Pavlína Pokorná	WHOLEMOLECULES METAD ERMSD COMBINE MOLINFO	generic function bias colvar
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	HISTOGRAM WHOLEMOLECULES DUMPGRID CONVERT_TO_FES COORDINATION PRINT ANGLE GROUP TORSION DISTANCE	generic core gridtools colvar
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	FIT_TO_TEMPLATE CUSTOM CENTER WHOLEMOLECULES COORDINATION PYTORCH_MODEL PRINT FIXEDATOM RESTART GROUP LOWER_WALLS OPES_METAD UPPER_WALLS TORSION PATH DISTANCE	mapping generic setup core bias opes pytorch function vatom colvar
24.019	Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning	bio	OPES, machine learning, protein folding, adaptive sampling	Mingyuan Zhang	CUSTOM COORDINATION WHOLEMOLECULES PRINT ALPHARMSD GYRATION COMBINE OPES_METAD MOLINFO TORSION DISTANCE	secondarystructure generic opes function colvar
24.018	A new route to the prebiotic synthesis of glycine via ab initio-based machine learning calculations	chemistry	prebiotic chemistry, glycine, Strecker synthesis, ab initio calculations, machine learning	Léon HUET	PRINT DISTANCE	generic colvar
24.004	Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables	materials	metadynamics, nucleation, machine learning	Ziyue Zou	METAD INCLUDE PRINT GROUP RESTART LOAD	generic setup core 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	RMSD WHOLEMOLECULES METAD PRINT MATHEVAL MOLINFO DISTANCE	generic function 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	COM CUSTOM SKETCHMAP WHOLEMOLECULES METAD COLLECT_FRAMES PATHMSD VSTACK DISSIMILARITIES PRINT LANDMARK_SELECT_FPS SKETCHMAP_PROJECTION TRANSPOSE UPPER_WALLS VORONOI DISTANCE	valtools matrixtools generic dimred bias landmarks function vatom colvar
23.017	How and When Does an Enzyme React? Unraveling α-Amylase Catalytic Activity with Enhanced Sampling Techniques	bio	enzymatic reaction discovery, reaction mechanism, catalysis, ligand-binding modes, water, alpha-amylase, sugar, QM/MM MD, OPES, OPES explore, graph CV, machine learning, Deep TDA CV, path CV	Sudip Das	OPES_METAD_EXPLORE FIT_TO_TEMPLATE CUSTOM CENTER COORDINATION PYTORCH_MODEL WHOLEMOLECULES PRINT FIXEDATOM GROUP DISTANCE LOWER_WALLS OPES_METAD UNITS TORSION PATH UPPER_WALLS	mapping generic setup core bias opes pytorch function vatom colvar
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	HISTOGRAM RMSD WHOLEMOLECULES METAD READ DUMPGRID CONVERT_TO_FES PRINT MATHEVAL MOLINFO REWEIGHT_METAD DISTANCE	generic bias function gridtools colvar
23.010	An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G‑Protein-Coupled Receptor Ligands	bio	GPCR, binding free energy, free energy surface	Timothy Clark	WHOLEMOLECULES METAD PRINT MATHEVAL CONSTANT LOWER_WALLS UPPER_WALLS BIASVALUE DISTANCE	generic function bias colvar
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 RMSD CENTER WHOLEMOLECULES FIXEDATOM CONTACTMAP FIT_TO_TEMPLATE COORDINATION ENERGY PRINT MATHEVAL GROUP COMBINE MOLINFO UPPER_WALLS DISTANCE PYTORCH_MODEL CUSTOM ENDPLUMED INCLUDE ANGLE LOWER_WALLS OPES_METAD	generic core bias opes pytorch function vatom colvar
23.008	PBMetaD simulations of Histatin5	bio	metadynamics, IDP, Rg, PPII	Francesco Pesce	WHOLEMOLECULES PBMETAD PRINT GROUP GYRATION MOLINFO TORSION	generic core bias colvar
22.045	Binding mode and mechanism of enzymatic polyethylene terephthalate degradation	bio	metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation	Francesco Colizzi	MOVINGRESTRAINT COM WHOLEMOLECULES METAD PRINT ANGLE LOWER_WALLS UPPER_WALLS DISTANCE	generic vatom bias colvar
22.041	Skipping the Replica Exchange Ladder with Normalizing Flows	methods	OPES, alanine, normalizing flows, replica exchange	Michele Invernizzi	POSITION OPES_EXPANDED ENDPLUMED ENERGY PRINT ECV_MULTITHERMAL OPES_METAD UNITS TORSION	opes generic setup colvar
22.029	Angiotensin-1-7_Metadynamics	bio	Metadynamics, Angiotensin-(1-7), peptide	L.-América Chi	COORDINATION METAD WHOLEMOLECULES PRINT GROUP GYRATION LOWER_WALLS FLUSH UPPER_WALLS	generic core bias colvar
21.052	On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets	materials	Ibuprofen, unbinding, WTmetaD	Matteo Salvalaglio	COORDINATIONNUMBER COMMITTOR CENTER METAD ENDPLUMED PRINT TORSION DISTANCE	generic symfunc bias vatom colvar
21.045	QM/MM metadynamics of thiol-disulfide exchange between methylthiolate and dimethyldisulfide in water with an imposed external electrostatic potential (ESP)	chemistry	metadynamics, QM/MM, electrostatic potential, thiol-disulfide exchange	Denis Maag	COORDINATIONNUMBER COORDINATION METAD PRINT LOWER_WALLS COMBINE UPPER_WALLS DISTANCE	generic symfunc bias function colvar
21.037	Molecular Dynamics simulations of RBD/hACE2 complexes	bio	SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain	Max Bonomi	RMSD PRINT DISTANCE	generic colvar
21.023	Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling	methods	enhanced sampling, collective variables, machine learning	Jakub Rydzewski	CUSTOM METAD INCLUDE ENERGY PRINT CONSTANT BIASVALUE UNITS REWEIGHT_METAD TORSION DISTANCE	generic setup bias function colvar
21.020	Reweighted Jarzynski sampling	methods	free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions	Kristof Bal	FLUSH UNITS TD_WELLTEMPERED REWEIGHT_METAD METAD CONVERT_TO_FES BF_CHEBYSHEV PRINT VES_LINEAR_EXPANSION REWEIGHT_BIAS COMBINE MOVINGRESTRAINT UPPER_WALLS LOAD RESTRAINT DISTANCE COORDINATIONNUMBER CONSTANT ANN BIASVALUE HISTOGRAM CUSTOM DUMPGRID OPT_AVERAGED_SGD OPES_METAD	generic setup annfunc symfunc bias opes ves function gridtools colvar
21.016	MD SAXS GTPase associated center	bio	metadynamics, RNA, folding, SAXS	Giovanni Bussi	CUSTOM WHOLEMOLECULES ERMSD SAXS METAD INCLUDE PRINT GROUP GYRATION LOWER_WALLS MOLINFO UPPER_WALLS	isdb generic core bias function colvar
21.005	Crystallization Collective Variable	methods	Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA	Tarak Karmakar	OPES_METAD PYTORCH_MODEL PRINT MATHEVAL GROUP LOWER_WALLS FLUSH UPPER_WALLS LOAD	generic setup core bias opes pytorch function
20.028	Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane	bio	metadynamics, KRas-4B, anionic membrane	Huixia Lu	FIT_TO_TEMPLATE CENTER METAD PRINT RESTART DISTANCE	generic setup bias vatom colvar
20.027	Allosteric Regulation of SARS-CoV-2 Protease. Towards Informed Structure-Based Drug Discovery	bio	SARS-CoV2, MPro, Covid-19, Molecular Dynamics, Metadynamics, Computer-Aided Drug Discovery	Khaled Abdel-Maksoud	METAD DISTANCE TORSION PRINT	generic bias 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	HISTOGRAM METAD CONVERT_TO_FES DUMPGRID MULTI_RMSD PRINT REWEIGHT_METAD RESTRAINT	generic bias gridtools colvar
20.018	Free energy barriers from biased molecular dynamics simulations	methods	kinetics, free energy barriers, chemical reactions, nucleation, metadynamics	Kristof Bal	CENTER DENSITY FLUSH UNITS REWEIGHT_METAD COORDINATION METAD CONVERT_TO_FES ENERGY PRINT CONTACT_MATRIX REWEIGHT_BIAS COMBINE UPPER_WALLS SPRINT LOAD DISTANCE COORDINATIONNUMBER LOCAL_AVERAGE Q6 HISTOGRAM VOLUME DUMPGRID LOWER_WALLS PAIRENTROPY	generic setup sprint symfunc bias volumes adjmat function vatom gridtools colvar
20.017	FISST	methods	FISST, force, peptide, sampling, tempering	Glen Hocky	FISST ENERGY PRINT MATHEVAL GROUP GYRATION UNITS BIASVALUE RESTRAINT DISTANCE	generic setup core bias fisst function colvar
20.015	Rational design of ASCT2 inhibitors using an integrated experimental-computational approach	bio	ASCT2 transporter, small-molecules, cryo-EM, metainference	Max Bonomi	WHOLEMOLECULES PRINT EMMIVOX GROUP MOLINFO BIASVALUE DUMPATOMS LOAD	isdb generic setup core bias
19.078	Iterative unbiasing of quasi-equilibrium sampling	methods	metadynamics, reweighting	Federico Giberti	COORDINATIONNUMBER METAD COLLECT_FRAMES PRINT MATHEVAL REWEIGHT_BIAS UNITS BIASVALUE DUMPATOMS DISTANCE	generic setup symfunc landmarks bias function colvar
19.077	Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations	materials	metadynamics, peptide-surface binding	Jim Pfaendtner	COM METAD ENERGY PRINT GYRATION MOLINFO UPPER_WALLS DISTANCE	generic vatom bias colvar
19.074	Asymmetric base pair opening in nucleic acids	bio	double helix, DNA, RNA, unwindability	Giovanni Bussi	WHOLEMOLECULES COORDINATION ENDPLUMED LOWER_WALLS RESTRAINT DISTANCE	generic bias colvar
19.071	Time-independent free energies from metadynamics via Mean Force Integration	methods	metadynamics, mean force integration, MFI, thermodynamic integration	Matteo Salvalaglio	REWEIGHT_METAD COMMITTOR HISTOGRAM READ METAD DUMPGRID CONVERT_TO_FES EXTERNAL PRINT MATHEVAL REWEIGHT_BIAS BIASVALUE TORSION DISTANCE	generic bias function gridtools colvar
19.055	Flying Gaussian method	methods	flying Gaussians, alanine dipeptide, peptide bond, Met-enkephalin	Vojtech Spiwok	METAD PRINT MATHEVAL COMBINE TORSION DISTANCE	generic function bias colvar
19.054	MetaFEP	methods	metadynamics, chemistry, free energy perturbation	GiovanniMaria Piccini	METAD ENERGY PRINT DISTANCE LOWER_WALLS COMBINE FLUSH UNITS UPPER_WALLS	generic setup bias function colvar
19.052	Gibbs free energy of homogeneous nucleation	materials	nucleation, surface excess free energy	Gareth Tribello	METAD FCCUBIC ENDPLUMED PRINT CELL UNITS UPPER_WALLS	generic setup symfunc bias colvar
19.049	Determining the sizes of solid/liquid clusters in MD trajectories of nucleation	methods	nucleation, metadynamics, clustering, Steinhardt order parameters	Gareth Tribello	MORE_THAN COORDINATIONNUMBER Q6 DFSCLUSTERING CUSTOM LOCAL_Q6 METAD ONES CLUSTER_NATOMS PRINT CLUSTER_PROPERTIES DISTANCES CONTACT_MATRIX MATRIX_VECTOR_PRODUCT CLUSTER_DISTRIBUTION SMAC OUTPUT_CLUSTER OUTER_PRODUCT	matrixtools generic multicolvar clusters symfunc bias adjmat function
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	COM RMSD WHOLEMOLECULES METAD DISTANCES PRINT GROUP DISTANCE LOWER_WALLS COMBINE ALPHABETA UPPER_WALLS MOLINFO REWEIGHT_METAD TORSION BRIDGE FUNNEL	funnel generic multicolvar core bias adjmat function vatom colvar
19.040	Optimal Metric for Path Collective Variables	bio	metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path	Francesco Luigi Gervasio	METAD ENDPLUMED PRINT MATHEVAL TORSION	generic function bias colvar
19.037	Scission free energy of organic dyes	chemistry	metadynamics, multiple walkers, matheval/lepton	Paolo Raiteri	METAD PRINT MATHEVAL UPPER_WALLS RESTART FLUSH UNITS DISTANCE	generic setup bias function colvar
19.015	Ibuprofen conformational dynamics and thermodynamics surface	materials	Ibuprofen, crystal, surface, solvents, conformers, metadynamics	Matteo Salvalaglio	COMMITTOR CENTER METAD PRINT LOWER_WALLS UPPER_WALLS TORSION DISTANCE	generic vatom bias colvar
19.010	Multi-domain protein dynamics	bio	metainference, NMR, protein dynamics	Carlo Camilloni	DIHCOR ENSEMBLE STATS CENTER WHOLEMOLECULES DHENERGY METAINFERENCE PBMETAD RDC PRINT ENDPLUMED GROUP ALPHABETA UPPER_WALLS MOLINFO TORSION RESTRAINT DISTANCE	isdb generic multicolvar core bias function vatom colvar
19.006	Flying Gaussian proof	methods	flying Gaussians, alanine dipeptide	Vojtech Spiwok	METAD TORSION PRINT	generic bias colvar
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	UNITS COORDINATION DISTANCE GROUP COMMITTOR LOWER_WALLS OPES_METAD CUSTOM PRINT RESTART UPPER_WALLS	generic function core opes colvar setup bias
24.030	NMR guided simulation of dsRBD	bio	Metainference, NMR, protein dynamics	Debadutta Patra	WHOLEMOLECULES DISTANCE FLUSH RDC GROUP MOLINFO ENSEMBLE STATS METAINFERENCE PRINT ALPHABETA	generic function core colvar multicolvar isdb
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	ECV_MULTITHERMAL COORDINATION DISTANCE COMBINE ENERGY GROUP OPES_EXPANDED TORSION OPES_METAD_EXPLORE CUSTOM PRINT RESTART	generic function core opes colvar setup
24.005	Learning Markovian Dynamics with Spectral Maps	methods	spectral map, collective variables, machine learning	Jakub Rydzewski	UNITS DISTANCE BIASVALUE CUSTOM PRINT	generic function colvar setup 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	UNITS DISTANCE FLUSH COMMITTOR LOWER_WALLS OPES_METAD TORSION CUSTOM PRINT COMBINE UPPER_WALLS	generic function opes colvar setup bias
23.041	Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference	methods	EMMIVox, cryo-EM, single-structure refinement, ensemble refinement, Bayesian inference, B-factors, structural ensembles	Samuel Hoff	WHOLEMOLECULES DISTANCE EMMIVOX GROUP BIASVALUE MOLINFO INCLUDE PRINT UPPER_WALLS WRAPAROUND	generic core colvar bias isdb
23.037	Estimating binding free energy of solid binding peptides without extensive sampling	bio	metadynamics, solid binding peptides	Xin Qi	DISTANCE PBMETAD COM MOLINFO LOWER_WALLS GYRATION PRINT UPPER_WALLS	vatom generic bias colvar
23.029	An accurate and efficient SAXS/SANS implementation including solvation layer effects suitable for restrained Molecular Dynamics simulations	bio	SAXS, SANS, SAS, metainference, proteins, nucleic-acid	Federico Ballabio	DISTANCE GROUP BIASVALUE MOLINFO CENTER ENSEMBLE STATS RMSD PRINT SAXS UPPER_WALLS WRAPAROUND	generic vatom function core colvar bias isdb
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	EXTRACV READ TORSION METAD PRINT	generic bias colvar
23.002	Critical comparison of general-purpose collective variables for crystal nucleation	methods	metadynamics, umbrella sampling, commitor, entropy, PIV	Julien Lam	LOCAL_AVERAGE UNITS ENERGY RESTRAINT PAIRENTROPY Q6 METAD Q4 CUSTOM PIV PRINT FUNCPATHMSD UPPER_WALLS VOLUME	colvar generic symfunc function piv setup bias gridtools
22.028	N-glycan conformer distributions in atomistic simulation	bio	REST2, RECT, N-glycan, pucker	Isabell Grothaus	READ MOLINFO DUMPGRID TORSION CONVERT_TO_FES METAD HISTOGRAM PRINT PUCKERING	colvar generic bias gridtools
22.004	Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques	chemistry	reaction discovery, OPES, collective variables	Umberto Raucci	UNITS COORDINATION DISTANCE PYTORCH_MODEL COM GROUP LOAD LOWER_WALLS MATHEVAL OPES_METAD OPES_METAD_EXPLORE CUSTOM PRINT UPPER_WALLS	generic vatom function core opes pytorch colvar setup bias
21.049	Multiple-path-metadynamics and PathMaps	methods	path-CV, metadynamics, multiple-walker, multiple paths, pathmap	Alberto Pérez-de-Alba-Ortíz	UNITS MOVINGRESTRAINT LOAD RESTRAINT LOWER_WALLS TORSION ENSEMBLE METAD CUSTOM PRINT COMBINE CONSTANT UPPER_WALLS	generic function colvar setup bias
21.012	NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition	bio	funnel metadynamics	Jim Pfaendtner	FUNNEL DISTANCE COM LOWER_WALLS FUNNEL_PS METAD PRINT UPPER_WALLS	generic vatom funnel colvar bias
21.003	aSYN SAXS metainference	bio	metainference, SAXS	Kresten Lindorff-Larsen	WHOLEMOLECULES PBMETAD FLUSH GROUP EEFSOLV BIASVALUE MOLINFO GYRATION CENTER ALPHARMSD METAINFERENCE PRINT SAXS	secondarystructure generic vatom core colvar bias isdb
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	ECV_UMBRELLAS_LINE UPPER_WALLS ENERGY ECV_MULTITHERMAL_MULTIBARIC OPT_AVERAGED_SGD OPES_EXPANDED VES_LINEAR_EXPANSION MATHEVAL Q6 BF_LEGENDRE VOLUME PRINT RESTART ENVIRONMENTSIMILARITY TD_UNIFORM	envsim generic symfunc ves function opes colvar setup bias
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 COORDINATION RESTRAINT MOLINFO STATS PRINT	generic function bias colvar
20.012	Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies	bio	metadynamics, well-tempered ensemble, ligand binding, binding affinity calculations, novel COLVAR, funnel restraints, Hamiltonian replica-exchange, PathCV, COMetPath, SWISH	Francesco Gervasio	PROJECTION_ON_AXIS WHOLEMOLECULES DISTANCE COM GROUP LOAD BIASVALUE MOLINFO LOWER_WALLS INCLUDE MATHEVAL CONTACTMAP FUNCPATHGENERAL METAD PRINT CONSTANT UPPER_WALLS	colvar generic vatom function core setup bias
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	ENVIRONMENTSIMILARITY OPT_AVERAGED_SGD TD_WELLTEMPERED VES_LINEAR_EXPANSION MATHEVAL Q6 BF_LEGENDRE VOLUME PRINT RESTART UPPER_WALLS OPT_DUMMY	envsim generic symfunc ves function colvar setup 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	WHOLEMOLECULES GROUP MOLINFO METAD PRINT RESTART UPPER_WALLS PATHMSD	colvar generic core setup bias
20.001	Conformational stability and dynamics in solution and in crystals report similarly on unfolding and aggregation propensity of amyloidogenic proteins	bio	metainference, metadynamics, NMR, protein dynamics, b2m, protein crystals	Carlo Camilloni	WHOLEMOLECULES PBMETAD FLUSH GROUP BIASVALUE MOLINFO LOWER_WALLS ENDPLUMED ANTIBETARMSD CS2BACKBONE PRINT UPPER_WALLS ALPHABETA	secondarystructure generic core multicolvar bias isdb
20.000	Muscarinic M2 receptor-ligand funnel metadynamics	bio	multiple walker metadynamics, well-tempered metadynamics, funnel metadynamics, MC-HLDA, GPCR, receptor, Adiabatic Bias MD	Riccardo Capelli	REWEIGHT_METAD DISTANCE COM READ LOWER_WALLS DUMPGRID ENDPLUMED MATHEVAL CONVERT_TO_FES METAD HISTOGRAM PRINT COMBINE UPPER_WALLS ABMD	generic vatom function colvar bias gridtools
19.076	Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones	bio	molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics	Salvatore Assenza	UNITS MOVINGRESTRAINT ENDPLUMED GYRATION PRINT	colvar generic bias setup
19.070	Unexpected Dynamics in the UUCG RNA Tetraloop	bio	well-tempered metadynamics, RNA, UUCG, maximum entropy	Sandro Bottaro	WHOLEMOLECULES DISTANCE MOLINFO ERMSD TORSION RMSD METAD PRINT	generic bias colvar
19.063	Protein-ligand binding through metadynamics with path CVs	bio	metadynamics, path CVs, ligand binding	Mattia Bernetti	WHOLEMOLECULES LOWER_WALLS METAD PRINT PATHMSD UPPER_WALLS	generic bias colvar
19.060	Neural networks-based variationally enhanced sampling	methods	ves, neural networks	Luigi Bonati	UNITS POSITION ENERGY LOAD ENDPLUMED TORSION Q6 PRINT ENVIRONMENTSIMILARITY	envsim generic symfunc colvar setup
19.045	Adsorption free energy of Ca/CO3 ions on calcite steps in contact with water	materials	metadynamics, well-tempered, multiple walkers, LAMMPS	Marco De La Pierre	UNITS COORDINATION POSITION FLUSH GROUP LOWER_WALLS METAD PRINT RESTART UPPER_WALLS	generic core colvar setup bias
19.025	Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide	bio	metainference, NMR, protein dynamics, force-fields	Carlo Camilloni	WHOLEMOLECULES PBMETAD FLUSH RDC JCOUPLING BIASVALUE MOLINFO ENDPLUMED TORSION GYRATION CS2BACKBONE ENSEMBLE STATS METAINFERENCE PRINT	generic function colvar bias isdb
19.014	MIL101(Cr) SBUs assembly	materials	MOFs, nucleation, self-assembly, metadynamics	Matteo Salvalaglio	DISTANCES COORDINATIONNUMBER ENDPLUMED GYRATION METAD PRINT RESTART	generic symfunc colvar setup multicolvar bias
19.012	Martini-Beads multi-scale SAXS	methods	metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex	Carlo Camilloni	WHOLEMOLECULES DISTANCE GROUP RESTRAINT BIASVALUE MOLINFO INCLUDE ENDPLUMED CENTER RMSD STATS PRINT SAXS UPPER_WALLS	generic vatom function core colvar bias isdb

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