Browse the nest
PLUMED-NEST provides all the data needed to reproduce the results of a PLUMED-enhanced molecular dynamics simulation or analysis contained in a published paper. Furthermore, PLUMED-NEST monitors the compatibility of the provided PLUMED input files with the current and development versions of the code and integrates links from these files to the PLUMED manual.
Here is the list of projects already deposited in PLUMED-NEST, while a complete bibliography can be found here.
plumID | Name | Category | Keywords | Contributor | Actions |
---|---|---|---|---|---|
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 |