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