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 |
---|---|---|---|---|
21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Bal K. |
21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Pietropaolo A. |
21.007 | Sampling enhancement by metadynamics driven by machine learning and de novo protein modelling | bio | metadynamics, machine learning, protein folding | Spiwok V. |
21.006 | OPES, On-the-fly Probability Enhanced Sampling Method | methods | opes, alanine dipeptide, well-tempered, multithermal, multiumbrella | Invernizzi M. |
21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Karmakar T. |
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. |
21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Lindorff-Larsen K. |
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. |
21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Ferreira T. |
21.000 | Uremic toxin time scale dynamics | bio | uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs) | Pfaendtner J. |
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. |
20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Brotzakis F. |
20.032 | Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil | materials | clustering, conformational isomers | Salvalaglio M. |
20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Pietropaolo A. |
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. |
20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Paissoni C. |
20.028 | Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane | bio | metadynamics, KRas-4B, anionic membrane | Lu H. |
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. |
20.026 | Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor | bio | Metadynamics, Umbrella sampling | Peters B. |
20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Rizzi V. |
20.024 | Gaussian Mixture Based Enhanced Sampling (GAMBES) | methods | enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias | Debnath J. |
20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Spiwok V. |
20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Invernizzi M. |
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. |
20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Bonomi M. |
20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Salvalaglio M. |
20.018 | Free energy barriers from biased molecular dynamics simulations | methods | kinetics, free energy barriers, chemical reactions, nucleation, metadynamics | Bal K. |
20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Hocky G. |
20.016 | Predicting polymorphism in molecular crystals using orientational entropy | materials | metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy | Piaggi P. |
20.015 | Structural basis for stereospecific inhibition of ASCT2 from rational design | bio | ASCT2 transporter, small-molecules, cryo-EM, metainference | Bonomi M. |
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. |
20.013 | Improving accuracy of biased Alchemistic simulations | methods | flying Gaussian method, Alchemistic simulations, thermodynamic integration, reweighting | Spiwok V. |
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. |
20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Pfaendtner J. |
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. |
20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Camilloni C. |
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. |
20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Tiwary P. |
20.006 | Class B GPCR activation mechanism | bio | metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding | Gervasio F. |
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. |
20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Bonati L. |
20.003 | Enhanced sampling of transition states | methods | Variationally Enhanced Sampling, Target distribution, Transition state, Enhanced Sampling, Nucleation, chemical reaction | Debnath J. |
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. |
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. |
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. |
19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Rizzi V. |
19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Rizzi V. |
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. |
19.080 | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | methods | ves, variationally enhanced sampling, vibrational excitation, chemical reactions | Bal K. |
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. |
19.078 | Iterative unbiasing of quasi-equilibrium sampling | methods | metadynamics, reweighting | Giberti F. |
19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Pfaendtner J. |
19.076 | Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones | bio | molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics | Assenza S. |
19.075 | PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python | other | Python, automatic differentiation | Giorgino T. |
19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Bussi G. |
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. |
19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Bussi G. |
19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Salvalaglio M. |
19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Bottaro S. |
19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Salvalaglio M. |
19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Invernizzi M. |
19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Rydzewski J. |
19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Rydzewski J. |
19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Chen W. |
19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Pfaendtner J. |
19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Bernetti M. |
19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Pfaendtner J. |
19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Jelfs K. |
19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Bonati L. |
19.059 | cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide | bio | bias-exchange metadynamics, cis-trans isomerization | Marinelli F. |
19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Jelfs K. |
19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Paissoni C. |
19.056 | maze | methods | maze, ligand unbinding | Rydzewski J. |
19.055 | Flying Gaussian method | methods | flying Gaussians, alanine dipeptide, peptide bond, Met-enkephalin | Spiwok V. |
19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | Piccini G. |
19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Tribello G. |
19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Tribello G. |
19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Tribello G. |
19.050 | Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes | chemistry | metadynamics, membranes, Willard Chandler surface | Tribello G. |
19.049 | Determining the sizes of solid/liquid clusters in MD trajectories of nucleation | methods | nucleation, metadynamics, clustering, Steinhardt order parameters | Tribello G. |
19.048 | Understanding Ligand Binding Selectivity in a Prototypical GPCR Family | bio | metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding | Gervasio F. |
19.047 | Close Structure | methods | metadynamics, RMSD, path collective variables, property map | Spiwok V. |
19.046 | Optimal Collective from short simulations for Benzamidine-Trypsin ligand binding | bio | VAC-MetaD, optimised collective variables, binding free energy, unbinding rates, benzamidine trypsin, Structure Activity Relation | Brotzakis F. |
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. |
19.044 | Multithermal-multibaric simulations using VES | methods | ves, Wang Landau, multicanonical, water, density anomaly | Piaggi P. |
19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | Piccini G. |
19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | Piccini G. |
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. |
19.040 | Optimal Metric for Path Collective Variables | bio | metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path | Gervasio F. |
19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Limongelli V. |
19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Camilloni C. |
19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Raiteri P. |
19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Provasi D. |
19.035 | Dimerization of GPCRs from coarse-grained umbrella sampling | bio | Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization | Provasi D. |
19.034 | PTCV (proton tracker collective variable) | methods | proton tracker collective variable, path-metadynamics, CP2K, DFT-MD, acetic acid | Ensing B. |
19.033 | PMD (path-metadynamics) | methods | path-CV, metadynamics, multiple-walker, polyproline | Ensing B. |
19.032 | Chemical reaction in solution using path collective variables based on coordination patterns | chemistry | chemical reactions, solutions, metadynamics, coordination patterns | Pietrucci F. |
19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Pipolo S. |
19.030 | Coarse-Grained MetaDynamics (CG-MetaD) | bio | Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy | Limongelli V. |
19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Papaleo E. |
19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Tiwary P. |
19.027 | Multithermal-multibaric simulations using VES | methods | ves, Wang Landau, multicanonical, liquid sodium, density anomaly | Piaggi P. |
19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Sosso G. |
19.025 | Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide | bio | metainference, NMR, protein dynamics, force-fields | Camilloni C. |
19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Pfaendtner J. |
19.023 | RECT | methods | metadynamics, replica exchange | Bussi G. |
19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Chen H. |
19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Hocky G. |
19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Bernetti M. |
19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Lindorff-Larsen K. |
19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Pietropaolo A. |
19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Capelli R. |
19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Salvalaglio M. |
19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Salvalaglio M. |
19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Salvalaglio M. |
19.013 | RNA FF FITTING | methods | force field, RNA | Bussi G. |
19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Camilloni C. |
19.011 | Automatic Gradient Computation for Collective Variables | other | gradient, differentiation, curvature | Giorgino T. |
19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Camilloni C. |
19.009 | RNA tetraloops folding | bio | metadynamics, RNA, folding | Bussi G. |
19.008 | anncolvar | methods | neural network, dimensionality reduction | Spiwok V. |
19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Bonomi M. |
19.006 | Flying Gaussian proof | methods | flying Gaussians, alanine dipeptide | Spiwok V. |
19.005 | Cmyc small molecule interaction | bio | metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP | Heller G. |
19.004 | MI Ubiquitin | bio | metainference, NMR | Bonomi M. |
19.003 | EMMI ClpP | bio | metainference, cryo-EM | Bonomi M. |
19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Bonomi M. |
19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Bussi G. |
19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Invernizzi M. |