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 |
---|---|---|---|---|---|
24.010 | 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 |