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