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
21.025 Computational and biochemical analysis of type IV pilus dynamics and stability bio molecular dynamics, calcium binding, Type IV pilus Karami Y.
21.024 Property map collective variable as a useful tool for force field correction chemistry molecular mechanics Spiwok V.
21.023 Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling methods enhanced sampling, collective variables, machine learning Rydzewski J.
21.022 Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly materials parallel bias metadynamics, adsorption, peptide Qi X.
21.021 ATLAS methods Machine Learning, Metadynamics Giberti F.
21.020 Reweighted Jarzynski sampling methods free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions Bal K.
21.019 Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations materials Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen Salvalaglio M.
21.018 Localized Volume-based Metadynamics bio LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification Capelli R.
21.017 All-atom simulations of the Vav1 AD construct bio metadynamics, parallel-bias, well-tempered Orioli S.
21.016 MD SAXS GTPase associated center bio metadynamics, RNA, folding, SAXS Bussi G.
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.
21.014 how to determine statistically accurate conformational ensembles bio metadynamics, metainference, errors, cv, SAXS, ensemble determination Paissoni C.
21.013 Role of vibrational excitation in heterogeneous catalysis chemistry catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption Bal K.
21.012 NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition bio funnel metadynamics Pfaendtner J.
21.011 CmuMD simulations of NaCl(aq) at graphite chemistry CmuMD, DFS clustering Finney A.
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.
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 Rational design of ASCT2 inhibitors using an integrated experimental-computational approach 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.