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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
24.000 Ammonia Decomposition on Non-stoichiometric Lithium Imide chemistry ammonia decomposition, non-stoichiometric lithium imide, machine learning interatomic potentials, enhanced sampling, heterogeneous catalysis Mambretti F. COORDINATIONNUMBER GROUP FLUSH ZDISTANCES PRINT UNITS OPES_METAD DISTANCE FIXEDATOM UPPER_WALLS
23.036 Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? bio NaCl, nucleation, metadynamics Wang R. COORDINATIONNUMBER METAD ENERGY PRINT Q6 COMBINE VOLUME MATHEVAL Q4
23.026 Machine Learning Nucleation Collective Variables with Graph Neural Networks chemistry Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks Dietrich F. MFILTER_MORE COORDINATIONNUMBER GROUP METAD MOVINGRESTRAINT LOCAL_Q6 PYTHONCV PRINT Q6 COMBINE LOWER_WALLS
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 Clark T. READ METAD RMSD WHOLEMOLECULES MOLINFO DUMPGRID PRINT HISTOGRAM CONVERT_TO_FES DISTANCE MATHEVAL REWEIGHT_METAD
23.006 Transcription factor unbinding bio metadynamics, DNA, conformational changes Lüking M. METAD MOLINFO DUMPFORCES COM PRINT ALPHARMSD DISTANCE CONTACTMAP ANGLE
22.042 Metadynamics of NSP10 and variants bio metadynamics, NSP10, crystal structure, variants Haider S. TORSION PRINT METAD
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 Kolossvary I. PATHMSD METAD CUSTOM FLUSH DRR PRINT BIASVALUE
22.022 Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir bio RMSD, protein-ligand interactions Grothaus I. RMSD PRINT
22.012 Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT bio contact maps, protein-protein interactions Grothaus I. DISTANCE CENTER CONTACTMAP PRINT
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 Pampel B. OPT_AVERAGED_SGD BF_CHEBYSHEV OPT_ADAM TD_WELLTEMPERED PRINT DISTANCE POSITION FLUSH VES_LINEAR_EXPANSION BF_WAVELETS TD_UNIFORM BF_GAUSSIANS BF_CUBIC_B_SPLINES METAD COORDINATION INCLUDE ENERGY BF_LEGENDRE UNITS VES_OUTPUT_BASISFUNCTIONS UPPER_WALLS
21.044 NaCl nucleation chemistry metadynamics, DFS clustering Finney A. MFILTER_MORE COORDINATIONNUMBER GROUP METAD LOCAL_Q6 CLUSTER_DISTRIBUTION CONTACT_MATRIX DFSCLUSTERING CLUSTER_NATOMS DUMPGRID PRINT INSPHERE HISTOGRAM Q6 FIXEDATOM COMBINE
21.034 Efficient sampling of high-dimensional free energy landscapes using adaptive reinforced dynamics bio reinforced dynamics, bias-exchange metadynamics, parallel-bias metadynamics Wang D. METAD ENDPLUMED DEEPFE PBMETAD INCLUDE TORSION PRINT RANDOM_EXCHANGES
21.024 Property map collective variable as a useful tool for force field correction chemistry molecular mechanics Spiwok V. METAD WHOLEMOLECULES TORSION PROPERTYMAP PRINT BIASVALUE
21.014 how to determine statistically accurate conformational ensembles bio metadynamics, metainference, errors, cv, SAXS, ensemble determination Paissoni C. METAD PBMETAD ENSEMBLE WHOLEMOLECULES MOLINFO TORSION CENTER PRINT BIASVALUE ANTIBETARMSD ALPHABETA SAXS STATS CONTACTMAP GYRATION
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 Gobbo D. PATHMSD METAD RESTART LOWER_WALLS WHOLEMOLECULES PRINT UPPER_WALLS
20.029 High Conformational Flexibility of the E2F1/DP1/DNA complex bio SAXS, protein-DNA complex, hySAXS, ensemble determination Paissoni C. GROUP ENSEMBLE INCLUDE WHOLEMOLECULES MOLINFO CENTER RESTRAINT PRINT SAXS BIASVALUE DISTANCE STATS
20.019 Systematic finite-temperature reduction of crystal energy landscapes materials crystals, organics, structure prediction Salvalaglio M. METAD ENERGY UPPER_WALLS PRINT CELL MATHEVAL VOLUME LOWER_WALLS
20.009 The dynamics of linear polyubiquitin bio saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics Camilloni C. FLUSH PBMETAD ENSEMBLE WHOLEMOLECULES MOLINFO METAINFERENCE TORSION CENTER PRINT SAXS ALPHABETA DISTANCE STATS GYRATION
19.083 Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis chemistry metadynamics, chemical reactions, reaction discovery Rizzi V. COORDINATIONNUMBER GROUP DISTANCES METAD ENDPLUMED FLUSH RESTART PRINT UNITS COMBINE UPPER_WALLS
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 Salvalaglio M. COORDINATIONNUMBER DISTANCES METAD ENDPLUMED ENERGY UPPER_WALLS PRINT GYRATION LOWER_WALLS
19.063 Protein-ligand binding through metadynamics with path CVs bio metadynamics, path CVs, ligand binding Bernetti M. PATHMSD METAD WHOLEMOLECULES UPPER_WALLS PRINT LOWER_WALLS
19.053 Capillary fluctuations with PLUMED methods nucleation, surface tension, capillary fluctuations Tribello G. CENTER_OF_MULTICOLVAR FIND_CONTOUR_SURFACE DUMPGRID MULTICOLVARDENS UNITS FCCUBIC MTRANSFORM_MORE FOURIER_TRANSFORM
19.043 Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) methods metadynamics, chemistry, HLDA Piccini G. DISTANCES METAD FLUSH RESTART PRINT UNITS DISTANCE COMBINE UPPER_WALLS
19.023 RECT methods metadynamics, replica exchange Bussi G. METAD WHOLEMOLECULES TORSION PRINT GYRATION
19.013 RNA FF FITTING methods force field, RNA Bussi G. INCLUDE CONSTANT MOLINFO TORSION PUCKERING BIASVALUE MATHEVAL
19.003 EMMI ClpP bio metainference, cryo-EM Bonomi M. GROUP MOLINFO PRINT BIASVALUE EMMI
23.046 Lasso Peptides - HLDA CV bio metadynamics, protein folding, HLDA, harmonic Hora G. COMBINE UNITS PRINT WHOLEMOLECULES DISTANCE METAD
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 Clark T. CENTER METAD CONSTANT MATHEVAL UPPER_WALLS PRINT WHOLEMOLECULES DISTANCE LOWER_WALLS BIASVALUE
23.025 Probing ion binding to G-quadruplexes and related events chemistry metadynamics, repulsive potential, nucleic acids, G-quadruplexes Poleto M. DUMPATOMS POSITION METAD DISTANCES UNITS GROUP COM MATHEVAL RESTART UPPER_WALLS PRINT FLUSH WHOLEMOLECULES FIT_TO_TEMPLATE DISTANCE LOWER_WALLS WRAPAROUND
23.015 MPCs aggregation bio opes_explore, dimerization, MPCs, self-assembly Tiwari V. CENTER LOWER_WALLS OPES_METAD_EXPLORE GROUP COM CUSTOM UPPER_WALLS PRINT WHOLEMOLECULES DISTANCE COORDINATION METAD
23.005 A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs bio metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A Clark T. READ MOLINFO CONVERT_TO_FES MATHEVAL HISTOGRAM PRINT WHOLEMOLECULES REWEIGHT_METAD DISTANCE RMSD METAD DUMPGRID
22.041 Skipping the Replica Exchange Ladder with Normalizing Flows methods OPES, alanine, normalizing flows, replica exchange Invernizzi M. POSITION ECV_MULTITHERMAL UNITS PRINT TORSION OPES_METAD ENERGY OPES_EXPANDED ENDPLUMED
22.031 Rare Event Kinetics from Adaptive Bias Enhanced Sampling methods OPES Flooding, Kinetics, Rate, OPES, Machine Learning Ray D. COMBINE CONSTANT COMMITTOR MOLINFO OPES_METAD WHOLEMOLECULES RMSD ENDPLUMED PRINT INCLUDE PYTORCH_MODEL ENERGY CONTACTMAP UNITS CUSTOM TORSION BIASVALUE POSITION GROUP DISTANCE
22.021 Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations chemistry Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella Bore S. PRINT INCLUDE UPPER_WALLS ENVIRONMENTSIMILARITY LOWER_WALLS OPES_EXPANDED ECV_UMBRELLAS_LINE
22.011 Accelerating all-atom simulations and gaining mechanistic understanding of biophysical systems through State Predictive Information Bottleneck methods metadynamics, membrane permeation, protein folding Mehdi S. COMBINE XANGLES METAD MOLINFO ZANGLES COM YANGLES MATHEVAL CUSTOM UPPER_WALLS PRINT TORSION WHOLEMOLECULES DISTANCE LOWER_WALLS ALPHABETA
22.000 Amyloid precursor protein processing by human γ-secretase bio Bias Exchange Metadynamics, Helix unfolding, coupled binding Lu X. CENTER UNITS MOLINFO RANDOM_EXCHANGES ANTIBETARMSD ALPHARMSD INCLUDE PRINT DISTANCE COORDINATION METAD CONTACTMAP
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 Lu H. PRINT TORSION FIT_TO_TEMPLATE METAD FIXEDATOM
21.033 Multiple-path-metadynamics applied to DNA base-pairing transitions bio path-CV, metadynamics, multiple-walker, dna Pérez-de-Alba-Ortíz A. CENTER COMBINE CONSTANT RESTRAINT UNITS LOAD CUSTOM INCLUDE TORSION PATHCV WHOLEMOLECULES UPPER_WALLS DISTANCE PRINT METAD MOVINGRESTRAINT
21.023 Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling methods enhanced sampling, collective variables, machine learning Rydzewski J. CONSTANT UNITS CUSTOM INCLUDE PRINT TORSION REWEIGHT_METAD ENERGY DISTANCE METAD BIASVALUE
21.013 Role of vibrational excitation in heterogeneous catalysis chemistry catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption Bal K. COMBINE DISTANCES TD_GRID RESTRAINT ANGLES BF_CHEBYSHEV DUMPGRID CONVERT_TO_FES UWALLS PRINT EXTERNAL REWEIGHT_GEOMFES OPT_AVERAGED_SGD LOWER_WALLS UNITS VES_LINEAR_EXPANSION COORDINATION REWEIGHT_BIAS METAD LOAD HISTOGRAM UPPER_WALLS FLUSH REWEIGHT_METAD DISTANCE COORDINATIONNUMBER
21.003 aSYN SAXS metainference bio metainference, SAXS Lindorff-Larsen K. EEFSOLV CENTER MOLINFO GYRATION GROUP ALPHARMSD PRINT PBMETAD FLUSH WHOLEMOLECULES METAINFERENCE SAXS BIASVALUE
20.028 Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane bio metadynamics, KRas-4B, anionic membrane Lu H. CENTER RESTART PRINT FIT_TO_TEMPLATE DISTANCE METAD
20.018 Free energy barriers from biased molecular dynamics simulations methods kinetics, free energy barriers, chemical reactions, nucleation, metadynamics Bal K. COMBINE CONTACT_MATRIX SPRINT LOCAL_AVERAGE DUMPGRID CONVERT_TO_FES PRINT DENSITY ENERGY REWEIGHT_GEOMFES LOWER_WALLS CENTER UNITS PAIRENTROPY VOLUME COORDINATION REWEIGHT_BIAS METAD Q6 LOAD HISTOGRAM UPPER_WALLS FLUSH REWEIGHT_METAD DISTANCE COORDINATIONNUMBER
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 Rossi K. DISTANCES UNITS CUSTOM PRINT COORDINATION METAD
19.082 Ammonia Borane Dehydrogenation chemistry metadynamics, reaction discovery, hydrogen production, chemistry Rizzi V. COMBINE UNITS GROUP RESTART PRINT FLUSH EXTERNAL COORDINATIONNUMBER METAD ENDPLUMED
19.072 SINE hairpin MD+NMR bio metadynamics, RNA, NMR Bussi G. SORT MOLINFO COM MATHEVAL INCLUDE TORSION PRINT WHOLEMOLECULES FLUSH DISTANCE COORDINATION METAD MAXENT
19.062 Elucidating molecular design principles for charge-alternating peptides bio peptide folding, metadynamics, well-tempered ensemble, parallel tempering Pfaendtner J. GYRATION PRINT WHOLEMOLECULES ENERGY METAD
19.052 Gibbs free energy of homogeneous nucleation materials nucleation, surface excess free energy Tribello G. FCCUBIC UNITS UPPER_WALLS PRINT CELL METAD ENDPLUMED
19.042 Harmonic Linear Discriminant Analysis (HLDA) methods metadynamics, chemistry, HLDA Piccini G. COMBINE UNITS UPPER_WALLS PRINT FLUSH ENERGY DISTANCE METAD
19.032 Chemical reaction in solution using path collective variables based on coordination patterns chemistry chemical reactions, solutions, metadynamics, coordination patterns Pietrucci F. PATH DISTANCES RESTART UPPER_WALLS PRINT FLUSH METAD
19.022 eABF simulation of NANMA (alanine dipeptide) methods eABF, DRR, alanine dipeptide Chen H. PRINT TORSION DRR
19.012 Martini-Beads multi-scale SAXS methods metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex Camilloni C. CENTER RESTRAINT MOLINFO GROUP INCLUDE UPPER_WALLS PRINT WHOLEMOLECULES STATS DISTANCE RMSD ENDPLUMED SAXS BIASVALUE
19.002 EMMI STRA6 bio metainference, cryo-EM Bonomi M. MOLINFO GROUP PRINT EMMI BIASVALUE
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 Limongelli V. DISTANCE PATHMSD ALPHARMSD INCLUDE PRINT LOWER_WALLS CONTACTMAP METAD MOLINFO FUNCPATHMSD UPPER_WALLS
23.034 Urea nucleation in water: do long-range forces matter? materials LMF theory, Metadynamics, Nucleation Zou Z. MANY_ANGLE_PLUS INCLUDE PRINT LOAD PAIR_ORIENTATIONAL_ENTROPY GROUP METAD COORDINATIONNUMBER CENTER
23.024 Permutationally Invariant Networks for Enhanced Sampling (PINES) methods collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent Herringer N. PBMETAD PINES PRINT LOAD ANNB
23.014 Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 bio metadynamics, oligomerization, chemokine receptors, GPCR, membrane Limongelli V. DISTANCE COMBINE PRINT WHOLEMOLECULES COM METAD FLUSH TORSION UPPER_WALLS
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 Piaggi P. ENVIRONMENTSIMILARITY DUMPGRID UPPER_WALLS HISTOGRAM PRINT LOWER_WALLS OPES_EXPANDED ECV_UMBRELLAS_LINE RESTART
22.040 From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure bio SARS-CoV-2, Spike, Omicron Wieczór M. PCAVARS PRINT LOWER_WALLS WHOLEMOLECULES METAD UPPER_WALLS
22.030 Mixing physics across temperatures with generative artificial intelligence methods REMD, Generative AI, DDPM Wang Y. WHOLEMOLECULES TORSION PRINT
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 He W. DISTANCE PRINT WHOLEMOLECULES GROUP COM METAD TORSION
22.009 Glycosylation in calixarenes capsule chemistry Metadynamics, glycosylation, supramolecular catalysis Piccini G. DISTANCE UPPER_WALLS COMBINE RMSD PRINT FIT_TO_TEMPLATE MATHEVAL LOWER_WALLS WHOLEMOLECULES DISTANCES GROUP METAD FLUSH UNITS BRIDGE COORDINATION ANGLE
21.052 On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets materials Ibuprofen, unbinding, WTmetaD Salvalaglio M. DISTANCE COMMITTOR PRINT ENDPLUMED METAD COORDINATIONNUMBER TORSION CENTER
21.042 Peptoid-mediated Au nanocrystal growth materials parallel-bias metadynamics, peptoid, Au Qi X. DISTANCE PBMETAD PRINT COM MOLINFO GYRATION UPPER_WALLS
21.032 Metal-coupled folding mechanism to metallothionein bio parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination Diaz M. PBMETAD MFILTER_MORE DRMSD DUMPGRID REWEIGHT_METAD COMBINE HISTOGRAM COORDINATIONNUMBER PRINT WHOLEMOLECULES GROUP REWEIGHT_BIAS CONVERT_TO_FES UNITS READ COORDINATION
21.022 Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly materials parallel bias metadynamics, adsorption, peptide Qi X. DISTANCE PBMETAD ENERGY PRINT LOWER_WALLS COM MOLINFO GYRATION UPPER_WALLS
21.012 NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition bio funnel metadynamics Pfaendtner J. DISTANCE PRINT LOWER_WALLS FUNNEL METAD COM FUNNEL_PS UPPER_WALLS
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 Piaggi P. ENVIRONMENTSIMILARITY UPPER_WALLS VES_LINEAR_EXPANSION BF_LEGENDRE ENERGY PRINT MATHEVAL VOLUME TD_UNIFORM ECV_MULTITHERMAL_MULTIBARIC OPES_EXPANDED Q6 OPT_AVERAGED_SGD ECV_UMBRELLAS_LINE RESTART
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 Abdel-Maksoud K. DISTANCE TORSION METAD PRINT
20.017 FISST methods FISST, force, peptide, sampling, tempering Hocky G. DISTANCE FISST RESTRAINT ENERGY BIASVALUE PRINT MATHEVAL GROUP UNITS GYRATION
20.007 Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics bio metadynamics, loop movement, artificial intelligence Tiwary P. DISTANCE UPPER_WALLS COMBINE RMSD PRINT WHOLEMOLECULES METAD MOLINFO TORSION RESTART
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 Piaggi P. CELL BF_LEGENDRE PRINT REFCV TD_WELLTEMPERED TD_MULTITHERMAL_MULTIBARIC VOLUME Q6 UPPER_WALLS VES_LINEAR_EXPANSION ENERGY HISTOGRAM REWEIGHT_BIAS OPT_AVERAGED_SGD REWEIGHT_TEMP_PRESS OPT_DUMMY DUMPGRID COMBINE LOWER_WALLS MATHEVAL LOAD CONVERT_TO_FES READ RESTART
19.071 Time-independent free energies from metadynamics via Mean Force Integration methods metadynamics, mean force integration, MFI, thermodynamic integration Salvalaglio M. DISTANCE EXTERNAL DUMPGRID REWEIGHT_METAD HISTOGRAM BIASVALUE PRINT COMMITTOR MATHEVAL METAD REWEIGHT_BIAS CONVERT_TO_FES READ TORSION
19.061 Diffusion in porous materials materials metadynamics, porous materials, diffusion Jelfs K. DISTANCE RESTART UPPER_WALLS PRINT LOWER_WALLS COM GROUP METAD CENTER
19.051 Solid liquid interfacial free energy out of equilibrium materials metadynamics, nucleation, surface excess free energy Tribello G. CELL AROUND LOWER_WALLS PRINT ENDPLUMED METAD UNITS UPPER_WALLS FCCUBIC
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 Pfaendtner J. DISTANCE ENERGY PRINT METAD COM UPPER_WALLS
19.031 Ice nucleation using PIV-based path coordinates materials phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics Pipolo S. PIV CELL PRINT LOWER_WALLS METAD FUNCPATHMSD UPPER_WALLS
19.021 Coarse-Grained Directed Simulation methods experiment directed simulation, coarse-grain, bias Hocky G. DISTANCE COMBINE RESTRAINT PRINT TORSION EDS
19.011 Automatic Gradient Computation for Collective Variables other gradient, differentiation, curvature Giorgino T. ENDPLUMED
19.001 RNA SHAPE bio metadynamics, RNA, ligand binding Bussi G. DISTANCE UPPER_WALLS COMBINE MOLINFO INCLUDE PRINT LOWER_WALLS DISTANCES ERMSD METAD FLUSH RANDOM_EXCHANGES ANGLE
23.044 Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition materials metadynamics, interlocked molecules Leanza L. ENDPLUMED METAD READ COMMITTOR PRINT HISTOGRAM GROUP CONVERT_TO_FES DUMPGRID COORDINATION
23.033 DNA G-quadruplex and G-hairpin folding with ST-metaD protocol bio DNA, G4, GQ, quadruplex, hairpin, folding, metadynamics, REST2, ST-metaD Pokorná P. WHOLEMOLECULES METAD ERMSD PRINT COMBINE MOLINFO COORDINATION GHBFIX BIASVALUE
23.023 Rational design of novel biomimetic sequence-defined polymers for mineralization applications methods metadynamics, surface binding, biomimetic mineralization Torkelson K. PRINT DISTANCE UPPER_WALLS GYRATION COORDINATION PBMETAD COM
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 Kolossvary I. METAD LOWER_WALLS CUSTOM TIME FLUSH PRINT PATHMSD UPPER_WALLS BIASVALUE UNITS DRR
23.003 Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations methods metadynamics, alchemical variable, alchemical free energy calculations Hsu W. METAD READ PRINT TORSION EXTRACV
22.039 Driving and characterizing nucleation of urea and glycine polymorphs in water bio metadynamics, nucleation, amino acids, polymorphism Beyerle E. METAD Q6 PAIR_ORIENTATIONAL_ENTROPY Q4 COORDINATIONNUMBER PRINT COMBINE GROUP INTERFACE INCLUDE MANY_ANGLE CENTER LOAD MATHEVAL PAIRENTROPY
22.029 Angiotensin-1-7_Metadynamics bio Metadynamics, Angiotensin-(1-7), peptide Chi L. WHOLEMOLECULES METAD LOWER_WALLS PRINT UPPER_WALLS GYRATION GROUP COORDINATION FLUSH
22.019 Exploring aspartic protease inhibitor binding to design selective antimalarials bio ligand binding, loop opening, path CV, funnel metadynamics, drug development Bobrovs R. WHOLEMOLECULES METAD LOWER_WALLS FUNNEL PRINT DISTANCE PATHMSD UPPER_WALLS COM FUNNEL_PS
22.008 Ab initio metadynamics determination of temperature-dependent free-energy landscape in ultrasmall silver clusters materials Well tempered metadynamics, ab-initio, ase Sucerquia D. METAD LOWER_WALLS COORDINATIONNUMBER UPPER_WALLS GYRATION COMBINE DISTANCE COORDINATION COM UNITS FLUSH
21.051 Automatic learning of hydrogen-bond fixes in an AMBER RNA force field methods force field, RNA Bussi G. WHOLEMOLECULES METAD ERMSD PRINT COMBINE COORDINATION MOLINFO BIASVALUE
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 Badin M. ENDPLUMED METAD CUSTOM PRINT COMBINE VOLUME COORDINATION
21.031 Photo-switchable sulfonulureas in KATP channel bio metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels Walczewska-Szewc K. WHOLEMOLECULES METAD LOWER_WALLS PRINT DISTANCE UPPER_WALLS COM UNITS
21.021 ATLAS methods Machine Learning, Metadynamics Giberti F. METAD WHOLEMOLECULES PRINT COORDINATIONNUMBER DISTANCE GYRATION ATLAS GROUP TORSION COORDINATION UNITS MATHEVAL DUMPATOMS BIASVALUE
21.011 CmuMD simulations of NaCl(aq) at graphite chemistry CmuMD, DFS clustering Finney A. COORDINATIONNUMBER PRINT CLUSTER_DISTRIBUTION GROUP CLUSTER_NATOMS AROUND DENSITY FIXEDATOM DFSCLUSTERING RESTRAINT MFILTER_MORE LOAD CONTACT_MATRIX DUMPGRID MULTICOLVARDENS CMUMD
21.001 Substrate recognition and catalysis by glycosaminoglycan sulfotransferases bio metadynamics, well-tempered metadynamics, puckering, coordination Ferreira T. METAD WHOLEMOLECULES LOWER_WALLS REWEIGHT_METAD PUCKERING PRINT HISTOGRAM DISTANCE UPPER_WALLS GROUP DUMPGRID MOLINFO COORDINATION INCLUDE ENERGY RANDOM_EXCHANGES
20.026 Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor bio Metadynamics, Umbrella sampling Peters B. METAD REWEIGHT_METAD PRINT HISTOGRAM MULTI_RMSD CONVERT_TO_FES DUMPGRID RESTRAINT
20.016 Predicting polymorphism in molecular crystals using orientational entropy materials metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy Piaggi P. PAIR_ORIENTATIONAL_ENTROPY METAD PRINT UPPER_WALLS GROUP VOLUME INCLUDE CENTER LOAD PAIR_ORIENTATIONAL_ENTROPY_PERPENDICULAR
20.006 Class B GPCR activation mechanism bio metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding Gervasio F. WHOLEMOLECULES RMSD METAD LOWER_WALLS PRINT UPPER_WALLS COMBINE DISTANCE MOLINFO ENERGY CENTER MATHEVAL
19.080 Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium methods ves, variationally enhanced sampling, vibrational excitation, chemical reactions Bal K. ANGLE BF_CHEBYSHEV LOWER_WALLS PRINT VES_LINEAR_EXPANSION UPPER_WALLS DISTANCE EXTERNAL COMBINE HISTOGRAM COORDINATION CONVERT_TO_FES DUMPGRID TD_WELLTEMPERED OPT_AVERAGED_SGD TD_GRID UNITS FLUSH
19.070 Unexpected Dynamics in the UUCG RNA Tetraloop bio well-tempered metadynamics, RNA, UUCG, maximum entropy Bottaro S. WHOLEMOLECULES RMSD METAD ERMSD PRINT DISTANCE TORSION MOLINFO
19.060 Neural networks-based variationally enhanced sampling methods ves, neural networks Bonati L. ENDPLUMED Q6 ENVIRONMENTSIMILARITY NN_VES POSITION PRINT TORSION ENERGY LOAD UNITS
19.050 Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes chemistry metadynamics, membranes, Willard Chandler surface Tribello G. READ METAD PRINT REWEIGHT_BIAS HISTOGRAM UPPER_WALLS CONVERT_TO_FES COMBINE DUMPGRID DENSITY DISTANCE_FROM_CONTOUR RESTART
19.040 Optimal Metric for Path Collective Variables bio metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path Gervasio F. ENDPLUMED METAD PRINT TORSION MATHEVAL
19.030 Coarse-Grained MetaDynamics (CG-MetaD) bio Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy Limongelli V. METAD WHOLEMOLECULES LOWER_WALLS PRINT DISTANCE UPPER_WALLS COM
19.020 PTMetaD-WTE simulation of the Ntail IDP bio metadynamics, IDPs, protein folding Bernetti M. ENDPLUMED WHOLEMOLECULES METAD PRINT GYRATION MOLINFO ENERGY ALPHARMSD
19.010 Multi-domain protein dynamics bio metainference, NMR, protein dynamics Camilloni C. ENDPLUMED WHOLEMOLECULES ENSEMBLE PRINT ALPHABETA DISTANCE UPPER_WALLS GROUP RDC MOLINFO TORSION DHENERGY PBMETAD RESTRAINT CENTER METAINFERENCE STATS DIHCOR
19.000 VesDeltaF methods VES, convergence, suboptimal CVs Invernizzi M. ENDPLUMED METAD DEBYE_STRUCTURE_FACTOR POSITION PRINT TORSION ENERGY LOAD RESTART UNITS VES_DELTA_F
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 Gigli L. METAD PRINT SELECT_COMPONENTS TRANSPOSE CONSTANT_VALUE SPHERICAL_EXPANSION SUM MATHEVAL FLUSH DOT INCLUDE
23.032 Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics bio metadynamics, tSNE, neural network, machine learning, trp-cage, folding Spiwok V. METAD PRINT ANN FIT_TO_TEMPLATE POSITION PYTORCH_MODEL_CV WHOLEMOLECULES MOLINFO COMBINE ALPHARMSD
23.022 A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar methods collective variables, machine learning, toy model Trizio E. PRINT OPES_METAD UNITS UPPER_WALLS POSITION CUSTOM PYTORCH_MODEL ENDPLUMED LOWER_WALLS BIASVALUE
23.012 JAK2 2D meta-eABF PMF with statistical analysis bio 2D meta-eABF, path CV, PMF Kolossvary I. METAD PRINT UPPER_WALLS CUSTOM BIASVALUE LOWER_WALLS FLUSH DRR PATHMSD
23.002 Critical comparison of general-purpose collective variables for crystal nucleation methods metadynamics, umbrella sampling, commitor, entropy, PIV Lam J. METAD PRINT Q6 UNITS UPPER_WALLS CUSTOM PAIRENTROPY LOCAL_AVERAGE PIV VOLUME FUNCPATHMSD ENERGY Q4 RESTRAINT
22.038 Enhanced Sampling Aided Design of Molecular Photoswitches chemistry reaction discovery, OPES explore, graph CV Raucci U. PRINT UNITS COORDINATION CUSTOM PYTORCH_MODEL OPES_METAD_EXPLORE
22.028 N-glycan conformer distributions in atomistic simulation bio REST2, RECT, N-glycan, pucker Grothaus I. METAD PRINT DUMPGRID MOLINFO HISTOGRAM PUCKERING CONVERT_TO_FES READ TORSION
22.018 Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations bio ligand binding, docking, EMMI, LAT1 Bonomi M. EMMIVOX PRINT GROUP WHOLEMOLECULES LOAD MOLINFO BIASVALUE
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 Papaleo E. METAD PRINT UPPER_WALLS COORDINATION WHOLEMOLECULES MOLINFO ANGLE ALPHARMSD TORSION ALPHABETA FLUSH DISTANCE
21.050 N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity methods bio Grothaus I. PRINT DISTANCE CENTER
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 Brotzakis F. PRINT UPPER_WALLS GROUP COM WHOLEMOLECULES MOLINFO EMMI RESTART DISTANCE BIASVALUE
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 Pfaendtner J. METAD PRINT PBMETAD COM COORDINATION ENERGY GYRATION TORSION ALPHABETA DISTANCE INCLUDE
21.020 Reweighted Jarzynski sampling methods free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions Bal K. ANN UNITS VES_LINEAR_EXPANSION OPES_METAD CUSTOM OPT_AVERAGED_SGD BF_CHEBYSHEV CONSTANT BIASVALUE REWEIGHT_BIAS METAD DUMPGRID LOAD FLUSH COORDINATIONNUMBER RESTRAINT PRINT TD_WELLTEMPERED REWEIGHT_METAD REWEIGHT_GEOMFES CONVERT_TO_FES MOVINGRESTRAINT DISTANCE UPPER_WALLS HISTOGRAM COMBINE
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 Magrino T. PRINT N LOOP ONO71 HILLS ZPATHCOORDTABLE 1 O LWALL 3 ENDMETA 84 UWALL COORD H C SPATHCOORDTABLE
21.000 Uremic toxin time scale dynamics bio uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs) Pfaendtner J. PRINT GROUP COM WHOLEMOLECULES DISTANCE
20.025 The role of water in host-guest interaction bio ligand binding, water, opes, SAMPL5 Rizzi V. PRINT OPES_METAD UPPER_WALLS FIT_TO_TEMPLATE GROUP FIXEDATOM COORDINATION WHOLEMOLECULES ENERGY ENDPLUMED CENTER PYTORCH_MODEL ANGLE MATHEVAL DISTANCE
20.015 Rational design of ASCT2 inhibitors using an integrated experimental-computational approach bio ASCT2 transporter, small-molecules, cryo-EM, metainference Bonomi M. EMMIVOX PRINT GROUP WHOLEMOLECULES DUMPATOMS LOAD MOLINFO BIASVALUE
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 Capelli R. COM CONTACTMAP FUNCPATHMSD LOWER_WALLS METAD DUMPGRID FLUSH PRINT ABMD REWEIGHT_METAD WHOLEMOLECULES CONVERT_TO_FES ENDPLUMED DISTANCE UPPER_WALLS MOLINFO HISTOGRAM COMBINE READ
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 Alamdari S. METAD PRINT UPPER_WALLS GROUP ENERGY COM MOLINFO GYRATION DISTANCE
19.069 Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen materials ibuprofen, crystal, solvent, surface Salvalaglio M. PRINT GROUP DISTANCES CENTER GYRATION ENDPLUMED DISTANCE INCLUDE DUMPMULTICOLVAR
19.059 cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide bio bias-exchange metadynamics, cis-trans isomerization Marinelli F. METAD PRINT TORSION RANDOM_EXCHANGES INCLUDE
19.049 Determining the sizes of solid/liquid clusters in MD trajectories of nucleation methods nucleation, metadynamics, clustering, Steinhardt order parameters Tribello G. Q6 MFILTER_MORE PRINT METAD SMAC LOCAL_Q6 CONTACT_MATRIX DFSCLUSTERING OUTPUT_CLUSTER MOLECULES CLUSTER_PROPERTIES CLUSTER_DISTRIBUTION CLUSTER_NATOMS COORDINATIONNUMBER
19.039 Funnel Metadynamics bio funnel-metadynamics, absolute binding free energy, ligand-receptor complexes Limongelli V. METAD PRINT UPPER_WALLS FUNNEL_PS RMSD WHOLEMOLECULES COM LOWER_WALLS DISTANCE FUNNEL
19.029 WTE-metaD of FF domain of URNF1 C57D variant bio metadynamics, mutations, post-translational modification, ff domain Papaleo E. METAD LOWER_WALLS PRINT UPPER_WALLS GROUP WHOLEMOLECULES MOLINFO GYRATION ALPHABETA
19.019 FA-MetaD-JCP-Wang-et-al bio Frequency adaptive metadynamics; peptide Lindorff-Larsen K. METAD PRINT COMMITTOR MOLINFO COMBINE ALPHABETA FLUSH
19.009 RNA tetraloops folding bio metadynamics, RNA, folding Bussi G. METAD PRINT RMSD WHOLEMOLECULES MOLINFO ENDPLUMED ERMSD
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 Hoff S. WRAPAROUND WHOLEMOLECULES DISTANCE BIASVALUE MOLINFO UPPER_WALLS INCLUDE PRINT EMMIVOX GROUP
23.031 Identifying small molecules binding sites in RNA conformational ensembles with SHAMAN bio RNA, metadynamics, probes, mixed-solvent MD, small molecules, binding sites Bonomi M. WRAPAROUND WHOLEMOLECULES METAD SHADOW FIT_TO_TEMPLATE CENTER MOLINFO POSITION DISTANCES UPPER_WALLS PRINT GROUP
23.021 Into the Dynamics of Rotaxanes at Atomistic Resolution materials metadynamics, rotaxanes, molecular shuttles, molecular machines Leanza L. DISTANCE METAD CENTER MATHEVAL FIXEDATOM TORSION UPPER_WALLS PRINT CUSTOM
23.011 OneOPES, a combined enhanced sampling method to rule them all bio OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding Rizzi V. DISTANCE ENERGY METAD ENDPLUMED ECV_MULTITHERMAL MOLINFO OPES_METAD_EXPLORE TORSION OPES_EXPANDED PRINT
23.001 Quantum phase diagram of water chemistry Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella Bore S. ENVIRONMENTSIMILARITY RESTART OPES_EXPANDED ECV_UMBRELLAS_LINE INCLUDE PRINT UPPER_WALLS LOWER_WALLS
22.037 Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site chemistry metadynamics, DNA, abasic Jones M. METAD PRINT DISTANCE DISTANCES
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 Bonomi M. PRINT RMSD
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 Ansari N. WHOLEMOLECULES RMSD DISTANCE PYTORCH_MODEL FIT_TO_TEMPLATE CENTER OPES_METAD MATHEVAL FIXEDATOM CUSTOM COMMITTOR UPPER_WALLS PRINT COORDINATION GROUP LOWER_WALLS
22.006 Peptide framework for screening the effects of amino acids on assembly bio metadynamics, peptides White A. GYRATION COM METAD REWEIGHT_BIAS HISTOGRAM DUMPGRID DISTANCES CONVERT_TO_FES INCLUDE PRINT COMBINE GROUP
21.049 Multiple-path-metadynamics and PathMaps methods path-CV, metadynamics, multiple-walker, multiple paths, pathmap Pérez-de-Alba-Ortíz A. CONSTANT PATHCV METAD MOVINGRESTRAINT ENSEMBLE TORSION UNITS LOAD RESTRAINT UPPER_WALLS PRINT COMBINE CUSTOM LOWER_WALLS
21.039 Deep learning the slow modes for rare events sampling methods collective variables, machine learning, slow modes, deep-tica, opes Bonati L. WHOLEMOLECULES VOLUME ECV_MULTITHERMAL PYTORCH_MODEL INCLUDE GROUP OPES_METAD STRUCTURE_FACTOR_DESCRIPTOR_TEST MOLINFO LOAD PRINT RMSD CONTACTMAP Q6 ENDPLUMED TORSION ENVIRONMENTSIMILARITY DISTANCE ENERGY UNITS OPES_EXPANDED COMBINE FLUSH
21.029 Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs bio metadynamics, small peptide, machine learning Tiwary P. ENERGY RESTART MOLINFO TORSION EXTERNAL PRINT FLUSH
21.019 Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations materials Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen Salvalaglio M. DOTPRODUCT_MATRIX DISTANCE COM NORMALIZE COMPONENTS TORSIONS MATHEVAL KDE PRINT
21.009 Nucleation rates from small scale atomistic simulations and transition state theory materials kinetics, free energy barriers, nucleation, droplets, metadynamics Bal K. METAD HISTOGRAM DUMPGRID MOVINGRESTRAINT REWEIGHT_GEOMFES REWEIGHT_METAD CONVERT_TO_FES UNITS LOAD COMMITTOR UPPER_WALLS PRINT COORDINATIONNUMBER FLUSH
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 Bottaro S. DISTANCE ABMD CENTER MOLINFO RESTART ERMSD TORSION PRINT
20.024 Gaussian Mixture Based Enhanced Sampling (GAMBES) methods enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias Debnath J. DISTANCE ENERGY GAMBES DISTANCES TORSION LOAD UNITS UPPER_WALLS PRINT COMBINE GROUP LOWER_WALLS
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 Heller G. WHOLEMOLECULES INCLUDE COORDINATION GROUP MOLINFO DIHCOR METAINFERENCE PRINT PARABETARMSD ENDPLUMED ENSEMBLE FLUSH TORSION GYRATION ALPHARMSD ANTIBETARMSD STATS COMBINE PBMETAD CS2BACKBONE
20.004 Data-driven collective variables for enhanced sampling methods collective variables, machine learning, deep-lda Bonati L. DISTANCE COM ENDPLUMED OPES_METAD PYTORCH_MODEL CONTACTS MATHEVAL TORSION UNITS LOAD UPPER_WALLS PRINT FLUSH GROUP LOWER_WALLS
19.078 Iterative unbiasing of quasi-equilibrium sampling methods metadynamics, reweighting Giberti F. ITRE COLLECT_FRAMES DISTANCE BIASVALUE METAD REWEIGHT_BIAS MATHEVAL UNITS DUMPATOMS PRINT COORDINATIONNUMBER
19.068 Rethinking Metadynamics methods metadynamics, opes, convergence Invernizzi M. METAD ENDPLUMED OPES_METAD POSITION TORSION UNITS EXTERNAL PRINT
19.058 Constrained MD for maintaining a cavity in a calculation chemistry constrained MD, porous molecules, porosity, cavity Jelfs K. INPLANEDISTANCES COM MOVINGRESTRAINT RESTART DISTANCES PRINT FLUSH
19.048 Understanding Ligand Binding Selectivity in a Prototypical GPCR Family bio metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding Gervasio F. WHOLEMOLECULES CONSTANT DISTANCE COM METAD BIASVALUE MATHEVAL UPPER_WALLS PRINT LOWER_WALLS
19.038 native state dynamics of human and mouse b2m bio metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation Camilloni C. WHOLEMOLECULES BIASVALUE LOWER_WALLS ENDPLUMED RESTART MOLINFO ANTIBETARMSD FLUSH UPPER_WALLS PRINT PBMETAD GROUP CS2BACKBONE ALPHABETA
19.028 pRAVE methods RAVE, reaction coordinate, deep learning, metadynamics, kinetics Tiwary P. WHOLEMOLECULES DISTANCE COM RESTART EXTERNAL TORSION COMMITTOR PRINT COMBINE ALPHABETA
19.018 Excited state FEP/Metadynamics simulations chemistry metadynamics, FEP, excited states, conjugated polymers, torsional potential Pietropaolo A. WHOLEMOLECULES CONSTANT BIASVALUE METAD MATHEVAL TORSION PRINT
19.008 anncolvar methods neural network, dimensionality reduction Spiwok V. WHOLEMOLECULES METAD ALPHARMSD FIT_TO_TEMPLATE POSITION MOLINFO MATHEVAL PRINT COMBINE
23.040 Supramolecular capsules assembly dynamics chemistry Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics Capelli R. FLUSH METAD DISTANCE DISTANCES POSITION GROUP WHOLEMOLECULES CENTER UNITS CUSTOM COM PRINT
23.030 Data Driven Classification of Ligand Unbinding Pathways bio OPES Explore, OPES Flooding, Benzene T4 Lysozyme, Ligand unbinding, Pathway classification, Kinetics, Residence time Ray D. MOLINFO OPES_METAD_EXPLORE DISTANCE POSITION FIT_TO_TEMPLATE COMMITTOR OPES_METAD CENTER CUSTOM PRINT UPPER_WALLS FLUSH ENDPLUMED GROUP WHOLEMOLECULES ENERGY UNITS WRAPAROUND TORSION MATHEVAL LOWER_WALLS COORDINATION BIASVALUE COM
23.020 FEP simulations of ATOX1 homodimer chemistry parallel bias metadynamics, FEP, free-energy of metal ion dissociation Pietropaolo A. MATHEVAL DISTANCE BIASVALUE PBMETAD WHOLEMOLECULES CONSTANT PRINT ANGLE
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 Clark T. MATHEVAL METAD DISTANCE BIASVALUE LOWER_WALLS WHOLEMOLECULES CONSTANT PRINT UPPER_WALLS
23.000 Atomistic simulations of RNA tetraloop folding via PTWTE-WTM bio parallel tempering, well-tempered metadynamics, well-tempered ensemble, RNA, Tetraloop, Folding Zerze G. METAD WHOLEMOLECULES LOWER_WALLS CONTACTMAP ENERGY PRINT UPPER_WALLS
22.036 Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction bio Well-tempered MetaDynamics with Hamiltonian Replica Exchange Krepl M. FLUSH MOLINFO METAD UPPER_WALLS COMBINE GROUP COORDINATION BIASVALUE CUSTOM LOAD PRINT GHBFIX
22.026 Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification materials Peptoid, silica Pfaendtner J. MOLINFO DISTANCE PBMETAD COM PRINT GYRATION UPPER_WALLS
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 Piaggi P. ENVIRONMENTSIMILARITY AROUND RESTART HISTOGRAM DUMPGRID ENERGY OPES_METAD VOLUME CUSTOM PRINT UPPER_WALLS
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 Spiwok V. METAD AF_DISTPROB WHOLEMOLECULES LOAD PRINT
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 Tao E. TORSION METAD DISTANCE LOWER_WALLS UNITS CUSTOM COM PRINT UPPER_WALLS
21.038 Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics materials metadynamics, SGOOP, nucleation, urea Zou Z. METAD COORDINATIONNUMBER MANY_ANGLE GROUP COMBINE ENERGY PAIR_ORIENTATIONAL_ENTROPY CENTER VOLUME LOAD PRINT INCLUDE
21.028 From Enhanced Sampling to Reaction Profiles methods collective variables, multi-state, machine learning, Deep-TDA Trizio E. DISTANCE LOAD DISTANCES FIT_TO_TEMPLATE OPES_METAD CENTER PRINT UPPER_WALLS PYTORCH_MODEL ENDPLUMED WHOLEMOLECULES GROUP FIXEDATOM UNITS CONTACTS ANGLE TORSION MATHEVAL LOWER_WALLS COORDINATION
21.018 Localized Volume-based Metadynamics bio LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification Capelli R. DISTANCE POSITION DUMPGRID REWEIGHT_METAD CONVERT_TO_FES METAD PRINT UPPER_WALLS FLUSH ENDPLUMED HISTOGRAM GROUP WHOLEMOLECULES FIXEDATOM MATHEVAL RMSD COORDINATION READ COM
21.008 Multi-replica biased sampling for photoisomerization processes in conjugated polymers methods metadynamics, FEP, replica-exchange Pietropaolo A. TORSION MATHEVAL PBMETAD BIASVALUE RESTART WHOLEMOLECULES CONSTANT PRINT
20.033 COVID-19 Spike protein opening transition mechanism bio EMMI, CryoEM, COVID-19, Spike, Metainference Brotzakis F. MOLINFO RMSD DISTANCES HISTOGRAM GROUP WHOLEMOLECULES DUMPGRID EMMI READ BIASVALUE CONVERT_TO_FES PRINT
20.023 metadynminer and metadynminer3d methods metadynamics, visualization, R Spiwok V. TORSION METAD PRINT
20.013 Improving accuracy of biased Alchemistic simulations methods flying Gaussian method, Alchemistic simulations, thermodynamic integration, reweighting Spiwok V. TORSION METAD PRINT
20.003 Enhanced sampling of transition states methods Variationally Enhanced Sampling, Target distribution, Transition state, Enhanced Sampling, Nucleation, chemical reaction Debnath J. BF_LEGENDRE OPT_AVERAGED_SGD POSITION ENERGY VES_LINEAR_EXPANSION TD_TS_TARGET UNITS LOAD PRINT
19.077 Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations materials metadynamics, peptide-surface binding Pfaendtner J. MOLINFO METAD DISTANCE ENERGY COM PRINT GYRATION UPPER_WALLS
19.067 Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways bio metadynamics, ligand unbinding Rydzewski J. PATHMSD METAD RESTART LOWER_WALLS UNITS PRINT UPPER_WALLS
19.057 SAXS ensembles using Martini-Beads multi-scale SAXS methods metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics Paissoni C. MOLINFO ENDPLUMED MATHEVAL PBMETAD SAXS ENSEMBLE STATS GROUP WHOLEMOLECULES COORDINATION ALPHABETA COMBINE ANGLE CENTER BIASVALUE PRINT INCLUDE
19.047 Close Structure methods metadynamics, RMSD, path collective variables, property map Spiwok V. METAD PROPERTYMAP PRINT WHOLEMOLECULES
19.037 Scission free energy of organic dyes chemistry metadynamics, multiple walkers, matheval/lepton Raiteri P. FLUSH MATHEVAL METAD DISTANCE RESTART UNITS PRINT UPPER_WALLS
19.027 Multithermal-multibaric simulations using VES methods ves, Wang Landau, multicanonical, liquid sodium, density anomaly Piaggi P. BF_LEGENDRE OPT_AVERAGED_SGD RESTART AVERAGE COMBINE REWEIGHT_BIAS HISTOGRAM DUMPGRID READ ENERGY TD_MULTICANONICAL VES_LINEAR_EXPANSION UNITS CONVERT_TO_FES OPT_DUMMY REWEIGHT_TEMP_PRESS PRINT
19.017 Ligand binding pathways exploration bio metadynamics, ligand binding Capelli R. FLUSH WRAPAROUND ENDPLUMED MATHEVAL METAD POSITION FIT_TO_TEMPLATE GROUP WHOLEMOLECULES COORDINATION HISTOGRAM READ DUMPGRID REWEIGHT_METAD CONVERT_TO_FES COM PRINT UPPER_WALLS
19.007 EMMI Microtubules bio metainference, cryo-EM Bonomi M. MOLINFO WHOLEMOLECULES GROUP EMMI BIASVALUE PRINT
23.039 Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation chemistry metadynamics, ligand dissociation Beyerle E. MOLINFO PRINT UPPER_WALLS DISTANCE RESTRAINT CENTER METAD COMBINE DUMPMASSCHARGE FIXEDATOM
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 Ballabio F. MOLINFO ENSEMBLE BIASVALUE PRINT SAXS GROUP STATS UPPER_WALLS DISTANCE CENTER WRAPAROUND RMSD
23.019 Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors bio binding pathway, binding energy, sketch-map, drug development Bobrovs R. DOT SKETCHMAP_PROJECTION WHOLEMOLECULES PRINT COLLECT_FRAMES CUSTOM METAD UPPER_WALLS COM DISTANCE VSTACK LANDMARK_SELECT_FPS PATHMSD SKETCHMAP TRANSPOSE DISSIMILARITIES VORONOI
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 Ray D. MOLINFO COMMITTOR INCLUDE COORDINATION ANGLE PYTORCH_MODEL PRINT UPPER_WALLS FIXEDATOM COMBINE MATHEVAL FIT_TO_TEMPLATE ENDPLUMED GROUP CUSTOM LOWER_WALLS CONTACTMAP DISTANCE RMSD OPES_METAD WHOLEMOLECULES CENTER ENERGY
22.045 Binding mode and mechanism of enzymatic polyethylene terephthalate degradation bio metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation Colizzi F. ANGLE WHOLEMOLECULES PRINT LOWER_WALLS UPPER_WALLS METAD DISTANCE COM MOVINGRESTRAINT
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 Lindorff-Larsen K. TORSION MOLINFO GYRATION WHOLEMOLECULES PBMETAD
22.025 Bubble nucleation rate predictions in a Lennard-Jones fluid materials free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation Bal K. UNITS LOAD VOLUME COMMITTOR BIASVALUE REWEIGHT_GEOMFES CONVERT_TO_FES PRINT CUSTOM ANN UPPER_WALLS HISTOGRAM RESTRAINT MOVINGRESTRAINT COORDINATIONNUMBER REWEIGHT_BIAS FLUSH DUMPGRID
22.015 Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome bio photodynamics, bacteriophytochrome, variationally enhanced sampling Rydzewski J. TORSION PRINT BF_FOURIER VES_LINEAR_EXPANSION OPT_AVERAGED_SGD TD_UNIFORM
22.004 Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques chemistry reaction discovery, OPES, collective variables Raucci U. UNITS LOAD CONTACTS PYTORCH_MODEL PRINT GROUP CUSTOM OPES_METAD_EXPLORE LOWER_WALLS UPPER_WALLS DISTANCE COM COORDINATION OPES_METAD MATHEVAL
21.047 Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations materials pair entropy, metadynamics, ves, solids, crystallization Piaggi P. PAIRENTROPY LOAD TD_WELLTEMPERED VOLUME PRINT METAD VES_LINEAR_EXPANSION RESTART COMBINE OPT_AVERAGED_SGD BF_LEGENDRE ENERGY
21.037 Molecular Dynamics simulations of RBD/hACE2 complexes bio SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain Bonomi M. RMSD DISTANCE PRINT
21.027 EGFR activating mutations mechanism bio metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA Gervasio F. MOLINFO ALPHARMSD WHOLEMOLECULES PRINT CONTACTMAP LOWER_WALLS DISTANCE UPPER_WALLS METAD INCLUDE ENERGY MATHEVAL
21.017 All-atom simulations of the Vav1 AD construct bio metadynamics, parallel-bias, well-tempered Orioli S. MOLINFO ALPHARMSD WHOLEMOLECULES ALPHABETA PRINT GROUP CONTACTMAP PBMETAD METAD RESTART REWEIGHT_BIAS
21.007 Sampling enhancement by metadynamics driven by machine learning and de novo protein modelling bio metadynamics, machine learning, protein folding Spiwok V. MOLINFO POSITION ALPHARMSD WHOLEMOLECULES MATHEVAL COMBINE FIT_TO_TEMPLATE
20.032 Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil materials clustering, conformational isomers Salvalaglio M. TORSION PRINT ENDPLUMED
20.022 Unified Approach to Enhanced Sampling methods OPES, expanded ensembles, importance sampling Invernizzi M. TORSION MOLINFO POSITION ECV_UMBRELLAS_LINE LENNARDJONES UNITS OPES_EXPANDED PRINT ECV_MULTITHERMAL_MULTIBARIC UPPER_WALLS Q6 MATHEVAL VOLUME ENDPLUMED CUSTOM ECV_LINEAR RMSD LOAD WHOLEMOLECULES ENVIRONMENTSIMILARITY ENERGY ECV_MULTITHERMAL
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 Gervasio F. MOLINFO LOAD FUNCPATHGENERAL WHOLEMOLECULES BIASVALUE PRINT GROUP LOWER_WALLS UPPER_WALLS DISTANCE COM METAD CONTACTMAP PROJECTION_ON_AXIS INCLUDE CONSTANT MATHEVAL
20.002 Exploring conformational dynamics of the extracellular Venus flytrap domain of the GABAB receptor, a path-metadynamics study bio Metadynamics, path CVs Ocello R. MOLINFO WHOLEMOLECULES PRINT GROUP METAD UPPER_WALLS RESTART PATHMSD
19.076 Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones bio molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics Assenza S. UNITS GYRATION ENDPLUMED PRINT MOVINGRESTRAINT
19.066 Finding ligand unbinding reaction pathways methods maze, ligand unbinding Rydzewski J. MAZE_OPTIMIZER_BIAS POSITION UNITS PRINT MAZE_SIMULATED_ANNEALING MAZE_LOSS
19.056 maze methods maze, ligand unbinding Rydzewski J. MAZE_OPTIMIZER_BIAS POSITION UNITS PRINT MAZE_SIMULATED_ANNEALING MAZE_LOSS
19.036 Thermodynamics and kinetics of G protein-coupled receptor activation bio metadynamics, allostery, receptor conformation, GPCR, pharmacology Provasi D. WHOLEMOLECULES PRINT ENDPLUMED CONTACTMAP METAD DISTANCE COM FUNCPATHMSD RMSD
19.026 Ice Nucleation on Cholesterol Crystals materials forward flux sampling, crystal nucleation, water, ice, organic crystals Sosso G. COMMITTOR CONTACT_MATRIX CLUSTER_WITHSURFACE OUTPUT_CLUSTER ENDPLUMED MFILTER_MORE HBOND_COORD LOCAL_Q6 CLUSTER_NATOMS Q6 MFILTER_BETWEEN DFSCLUSTERING FLUSH
19.016 Succinnic acid gamma polymorph materials Succinnic acid, conformers, polymorphs, metadynamics Salvalaglio M. TORSION VOLUME ENDPLUMED PRINT CELL LOWER_WALLS METAD UPPER_WALLS COMBINE ENERGY MATHEVAL
19.006 Flying Gaussian proof methods flying Gaussians, alanine dipeptide Spiwok V. TORSION METAD PRINT
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 Clark T. WHOLEMOLECULES MATHEVAL RMSD MOLINFO METAD DISTANCE PRINT
23.028 Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process chemistry Ammonia decomposition; Dynamics;OPES; Neural Network potential Yang M. ENERGY GROUP COM MATHEVAL ZDISTANCES FIXEDATOM UPPER_WALLS CUSTOM DISTANCES FLUSH COMMITTOR DISTANCE LOWER_WALLS PRINT COORDINATIONNUMBER UNITS OPES_METAD
23.018 Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention materials metadynamics, surface binding, peptide adsorption Torkelson K. COM UPPER_WALLS PBMETAD DISTANCE PRINT GYRATION
23.008 PBMetaD simulations of Histatin5 bio metadynamics, IDP, Rg, PPII Pesce F. GROUP WHOLEMOLECULES TORSION MOLINFO PBMETAD PRINT GYRATION
22.044 Colloid Crystallisation Analyses materials Q4, Q6, Pair Entropy, DFS Finney A. GROUP LOCAL_AVERAGE MFILTER_LESS DFSCLUSTERING CLUSTER_NATOMS LOCAL_Q4 CONTACT_MATRIX Q4 COMBINE Q6 LOCAL_Q6 PRINT COORDINATIONNUMBER MFILTER_MORE
22.034 Rationalising the difference in crystallisability of two Sulflowers using efficient in silico methods materials metadynamics, crystallizability, crystal structure prediction, sulflower, persulforated coronene Salvalaglio M. MATHEVAL UPPER_WALLS CUSTOM DRMSD COMMITTOR METAD LOWER_WALLS PRINT CELL
22.024 Conformational Entropy as a Potential Liability of Computationally Designed Antibodies bio metadynamics, conformational entropy, antibody, nanobody Löhr T. WHOLEMOLECULES COM TORSION RESTART MOLINFO ALPHABETA PBMETAD PRINT ALPHARMSD ANTIBETARMSD
22.014 Quasi Liquid Layer Order Parameters materials Quasi-Liquid Layer, Steinhardt Order Parameter, Entropy Fingerprint Shi J. LOCAL_AVERAGE DUMPMULTICOLVAR LOCAL_Q3 Q3 HISTOGRAM LOCAL_Q4 DUMPGRID ENDPLUMED Q4 LOAD Q6 LOCAL_Q6 UNITS PAIRENTROPIES
22.003 Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling methods opes, metadynamics, reweighting, alanine, muller Invernizzi M. ENERGY ECV_UMBRELLAS_FILE TORSION POSITION UPPER_WALLS BIASVALUE CUSTOM OPES_METAD_EXPLORE ENDPLUMED ECV_MULTITHERMAL OPES_EXPANDED PBMETAD METAD LOWER_WALLS PRINT OPES_METAD UNITS
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 Papaleo E. GROUP WHOLEMOLECULES UPPER_WALLS ALPHABETA ENDPLUMED METAD LOWER_WALLS PRINT GYRATION
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 Salvalaglio M. ENERGY GROUP WHOLEMOLECULES DIHCOR GYRATION UPPER_WALLS COORDINATION MOLINFO RANDOM_EXCHANGES PARABETARMSD METAD LOWER_WALLS PRINT ALPHARMSD ANTIBETARMSD
21.026 Probing allosteric regulations with coevolution-driven molecular simulations bio metadynamics, coevolution, allostery, adenylate cyclase Colizzi F. COM WHOLEMOLECULES UPPER_WALLS PATHMSD METAD DISTANCE PRINT UNITS
21.016 MD SAXS GTPase associated center bio metadynamics, RNA, folding, SAXS Bussi G. GROUP WHOLEMOLECULES UPPER_WALLS MOLINFO CUSTOM METAD SAXS ERMSD INCLUDE CENTER LOWER_WALLS PRINT GYRATION
21.006 OPES, On-the-fly Probability Enhanced Sampling Method methods opes, alanine dipeptide, well-tempered, multithermal, multiumbrella Invernizzi M. ENERGY TORSION ECV_MULTITHERMAL ENDPLUMED OPES_EXPANDED ECV_UMBRELLAS_LINE PRINT OPES_METAD
20.031 Soft fluorescent nanoshuttles targeting receptors chemistry polymers, receptors, nanoparticles, fluorescent probes Pietropaolo A. WHOLEMOLECULES COORDINATION PBMETAD CENTER PRINT
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 Paissoni C. STATS WHOLEMOLECULES COORDINATION MOLINFO RESTRAINT PRINT
20.011 Uremic toxin analysis bio metadynamics, uremic toxin, serum albumin Pfaendtner J. DISTANCE GROUP WHOLEMOLECULES RESTART COORDINATION DISTANCES CENTER PRINT
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 Camilloni C. GROUP WHOLEMOLECULES UPPER_WALLS BIASVALUE MOLINFO FLUSH ALPHABETA ENDPLUMED PBMETAD LOWER_WALLS PRINT ANTIBETARMSD CS2BACKBONE
19.075 PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python other Python, automatic differentiation Giorgino T. DISTANCE GROUP TORSION ANGLE CUSTOM ENDPLUMED CENTER COMBINE PYTHONCV RESTRAINT DUMPDERIVATIVES PYTHONFUNCTION PRINT
19.065 Molecular Enhanced Sampling with Autoencoders methods enhanced sampling, collective variables, deep learning Chen W. COM POSITION ANN COMBINE RESTRAINT
19.055 Flying Gaussian method methods flying Gaussians, alanine dipeptide, peptide bond, Met-enkephalin Spiwok V. DISTANCE MATHEVAL TORSION COMBINE METAD PRINT
19.045 Adsorption free energy of Ca/CO3 ions on calcite steps in contact with water materials metadynamics, well-tempered, multiple walkers, LAMMPS Pierre M. GROUP POSITION RESTART COORDINATION UPPER_WALLS FLUSH METAD LOWER_WALLS PRINT UNITS
19.035 Dimerization of GPCRs from coarse-grained umbrella sampling bio Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization Provasi D. DISTANCE GROUP COM TORSION RESTRAINT PRINT
19.025 Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide bio metainference, NMR, protein dynamics, force-fields Camilloni C. STATS WHOLEMOLECULES JCOUPLING ENSEMBLE TORSION BIASVALUE MOLINFO FLUSH RDC METAINFERENCE ENDPLUMED PBMETAD PRINT GYRATION CS2BACKBONE
19.015 Ibuprofen conformational dynamics and thermodynamics surface materials Ibuprofen, crystal, surface, solvents, conformers, metadynamics Salvalaglio M. TORSION UPPER_WALLS METAD CENTER COMMITTOR DISTANCE LOWER_WALLS PRINT
19.005 Cmyc small molecule interaction bio metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP Heller G. DISTANCE GROUP WHOLEMOLECULES COORDINATION MOLINFO ALPHABETA METAINFERENCE PBMETAD INCLUDE CENTER PRINT GYRATION CS2BACKBONE
23.037 Estimating binding free energy of solid binding peptides without extensive sampling bio metadynamics, solid binding peptides Qi X. LOWER_WALLS MOLINFO PBMETAD PRINT DISTANCE UPPER_WALLS COM GYRATION
23.027 CmuMD simulations of NaCl(aq) at NaCl chemistry CmuMD, DFS, Q3, Pair Entropy Finney A. CLUSTER_DISTRIBUTION LOAD LOCAL_Q3 DUMPGRID HISTOGRAM FIXEDATOM CONTACT_MATRIX CMUMD UNITS DFSCLUSTERING GROUP RESTRAINT AROUND PRINT LOCAL_AVERAGE CLUSTER_NATOMS DENSITY Q3 COORDINATIONNUMBER
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 Das S. LOWER_WALLS GROUP WHOLEMOLECULES PATH PYTORCH_MODEL PRINT CUSTOM FIT_TO_TEMPLATE FIXEDATOM OPES_METAD DISTANCE UNITS UPPER_WALLS COORDINATION CENTER TORSION OPES_METAD_EXPLORE
23.007 Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains bio metadynamics, peptoids, parallel-bias metadynamics Pfaendtner J. COORDINATION INCLUDE WHOLEMOLECULES RESTRAINT PBMETAD PRINT COM GYRATION TORSION
22.043 Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES bio OPES, RNA, Tetraloop, Folding Zerze G. OPES_EXPANDED WHOLEMOLECULES ENERGY CONTACTMAP PRINT ECV_UMBRELLAS_LINE ECV_MULTITHERMAL
22.033 Reciprocal barrier restraint. Application to PROTAC passive permeability prediction methods PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR Kolossvary I. METAD PRINT CUSTOM DISTANCE FLUSH DRR BIASVALUE COM UNITS
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 Brotzakis F. RMSD GROUP MOLINFO WHOLEMOLECULES PBMETAD PRINT EMMI COM RESTART UPPER_WALLS BIASVALUE COORDINATION TORSION
22.013 Ligand dissociation from PreQ1 riboswitch bio ligand, RNA, metadynamics, pRAVE Wang Y. RMSD COMMITTOR WHOLEMOLECULES MOLINFO METAD PRINT DISTANCE COM COMBINE COORDINATIONNUMBER
22.002 GAMBES_SAMPL5_RATES other GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding Debnath J. MATHEVAL ANGLE GROUP WHOLEMOLECULES ENDPLUMED COMMITTOR ENERGY PYTORCH_MODEL LOAD FIT_TO_TEMPLATE FIXEDATOM PRINT DISTANCE UPPER_WALLS FLUSH GAMBESL COORDINATION CENTER
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 Maag D. LOWER_WALLS METAD PRINT DISTANCE UPPER_WALLS COORDINATION COMBINE COORDINATIONNUMBER
21.035 CmuMD simulations of NaCl(aq) at NaCl chemistry CmuMD, interface Finney A. GROUP RESTRAINT LOAD PRINT FIXEDATOM DISTANCE CMUMD
21.025 Computational and biochemical analysis of type IV pilus dynamics and stability bio molecular dynamics, calcium binding, Type IV pilus Karami Y. DISTANCE LOWER_WALLS UPPER_WALLS PRINT
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 Courtade G. MATHEVAL WHOLEMOLECULES METAD POSITION RESTRAINT PRINT REWEIGHT_BIAS RESTART COORDINATION CENTER
21.005 Crystallization Collective Variable methods Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA Karmakar T. MATHEVAL LOWER_WALLS GROUP PYTORCH_MODEL LOAD PRINT STRUCTURE_FACTOR_DESCRIPTOR_TEST OPES_METAD UPPER_WALLS FLUSH STRUCTURE_FACTOR_SPHERICALLY_AVERAGED
20.030 Converging experimental and computational views of the knotting mechanism of the smallest knotted protein bio phi-values, transition state, knotted proteins Paissoni C. RESTRAINT WHOLEMOLECULES MOLINFO STATS PRINT COORDINATION COMBINE
20.020 Parallel Bias Metadynamics methods pbmetad, trp-cage, folding Bonomi M. INCLUDE MOLINFO WHOLEMOLECULES PBMETAD PRINT ALPHABETA DIHCOR COORDINATION GYRATION
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 Piaggi P. MATHEVAL OPT_DUMMY OPT_AVERAGED_SGD VOLUME PRINT VES_LINEAR_EXPANSION TD_WELLTEMPERED Q6 RESTART UPPER_WALLS ENVIRONMENTSIMILARITY BF_LEGENDRE
20.000 Muscarinic M2 receptor-ligand funnel metadynamics bio multiple walker metadynamics, well-tempered metadynamics, funnel metadynamics, MC-HLDA, GPCR, receptor, Adiabatic Bias MD Capelli R. MATHEVAL LOWER_WALLS ENDPLUMED READ METAD HISTOGRAM ABMD PRINT DISTANCE UPPER_WALLS REWEIGHT_METAD CONVERT_TO_FES COM COMBINE DUMPGRID
19.074 Asymmetric base pair opening in nucleic acids bio double helix, DNA, RNA, unwindability Bussi G. LOWER_WALLS ENDPLUMED RESTRAINT WHOLEMOLECULES DISTANCE COORDINATION
19.064 Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations materials metadynamics, peptide-surface binding Pfaendtner J. MOLINFO METAD ENERGY PRINT DISTANCE UPPER_WALLS COM GYRATION
19.054 MetaFEP methods metadynamics, chemistry, free energy perturbation Piccini G. LOWER_WALLS ENERGY PRINT DISTANCE UPPER_WALLS FLUSH METAD COMBINE UNITS
19.044 Multithermal-multibaric simulations using VES methods ves, Wang Landau, multicanonical, water, density anomaly Piaggi P. AVERAGE READ HISTOGRAM BF_LEGENDRE OPT_AVERAGED_SGD ENERGY VOLUME PRINT VES_LINEAR_EXPANSION REWEIGHT_TEMP_PRESS REWEIGHT_BIAS RESTART TD_MULTITHERMAL_MULTIBARIC CONVERT_TO_FES OPT_DUMMY COMBINE DUMPGRID
19.024 PT-MetaD-WTE methods metadynamics, WTE, trp cage, PT Pfaendtner J. GROUP METAD ENERGY COORDINATION EXTERNAL
19.014 MIL101(Cr) SBUs assembly materials MOFs, nucleation, self-assembly, metadynamics Salvalaglio M. ENDPLUMED PRINT DISTANCES RESTART METAD GYRATION COORDINATIONNUMBER
19.004 MI Ubiquitin bio metainference, NMR Bonomi M. RDC GROUP MOLINFO WHOLEMOLECULES PRINT CS2BACKBONE METAINFERENCE