Browse the eggs in PLUMED-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 Modules
25.005 Mechanism of Nanocluster Formation from Machine-Learned Potential-based Simulations chemistry WT-metadynamics, metal nanoclusters, nucleation, neural network potential, deepMD Vikas Tiwari, Tarak Karmakar COMBINE COORDINATIONNUMBER COM PRINT UNITS DISTANCES LOWER_WALLS GROUP UPPER_WALLS FLUSH RESTRAINT COORDINATION METAD DISTANCE ANGLE FIXEDATOM core setup vatom function colvar generic symfunc bias multicolvar
25.009 Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water chemistry metadynamics, nitrate photolysis Kam-Tung Chan DUMPGRID GROUP COORDINATION CUSTOM PRINT UPPER_WALLS REWEIGHT_METAD FLUSH METAD DISTANCE READ HISTOGRAM RESTART bias generic setup colvar core function gridtools
24.028 All-atom simulations of RNA-membrane interactions bio metadynamics, membrane, RNA Giovanni Bussi MOLINFO POSITION PRINT GYRATION LOWER_WALLS COMBINE SORT GHOST UPPER_WALLS CENTER DISTANCES MATHEVAL METAD PUCKERING DISTANCE WHOLEMOLECULES GROUP vatom bias multicolvar generic colvar core function
24.002 Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes chemistry metadynamics, ligand design, solvent extraction Xiaoyu Wang UNITS PRINT METAD RESTART TORSION bias setup generic colvar
23.039 Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation chemistry metadynamics, ligand dissociation Eric Beyerle MOLINFO FIXEDATOM PRINT COMBINE DUMPMASSCHARGE UPPER_WALLS CENTER METAD DISTANCE RESTRAINT vatom bias generic colvar function
23.031 Identifying small molecules binding sites in RNA conformational ensembles with SHAMAN bio RNA, metadynamics, probes, mixed-solvent MD, small molecules, binding sites Max Bonomi SHADOW MOLINFO POSITION PRINT FIT_TO_TEMPLATE UPPER_WALLS WRAPAROUND CENTER DISTANCES METAD WHOLEMOLECULES GROUP vatom isdb bias multicolvar generic colvar core
23.025 Probing ion binding to G-quadruplexes and related events chemistry metadynamics, repulsive potential, nucleic acids, G-quadruplexes Marcelo Poleto UNITS DUMPATOMS POSITION FIT_TO_TEMPLATE LOWER_WALLS PRINT UPPER_WALLS WRAPAROUND DISTANCES MATHEVAL FLUSH METAD DISTANCE WHOLEMOLECULES GROUP COM RESTART vatom colvar bias multicolvar generic setup core function
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 Timothy Clark BIASVALUE LOWER_WALLS PRINT UPPER_WALLS CONSTANT MATHEVAL METAD DISTANCE WHOLEMOLECULES bias function generic colvar
22.034 Rationalising the difference in crystallisability of two Sulflowers using efficient in silico methods materials metadynamics, crystallizability, crystal structure prediction, sulflower, persulforated coronene Matteo Salvalaglio CUSTOM LOWER_WALLS PRINT COMMITTOR UPPER_WALLS MATHEVAL CELL METAD DRMSD bias generic colvar function
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 Weiwei He PRINT METAD DISTANCE WHOLEMOLECULES GROUP COM TORSION vatom bias generic colvar core
22.018 Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations bio ligand binding, docking, EMMI, LAT1 Max Bonomi MOLINFO PRINT EMMIVOX BIASVALUE WHOLEMOLECULES GROUP LOAD isdb bias generic setup core
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 Narjes Ansari FIXEDATOM COORDINATION CUSTOM FIT_TO_TEMPLATE LOWER_WALLS PYTORCH_MODEL PRINT COMMITTOR UPPER_WALLS RMSD CENTER MATHEVAL DISTANCE WHOLEMOLECULES GROUP OPES_METAD pytorch vatom opes bias generic colvar core function
22.002 GAMBES_SAMPL5_RATES other GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding Jayashrita Debnath ENDPLUMED FIXEDATOM COORDINATION FIT_TO_TEMPLATE PRINT PYTORCH_MODEL COMMITTOR UPPER_WALLS CENTER MATHEVAL FLUSH ENERGY ANGLE DISTANCE WHOLEMOLECULES GROUP LOAD pytorch vatom bias generic setup colvar core function
22.000 Amyloid precursor protein processing by human γ-secretase bio Bias Exchange Metadynamics, Helix unfolding, coupled binding Xiaoli Lu UNITS MOLINFO DISTANCE COORDINATION PRINT INCLUDE RANDOM_EXCHANGES CENTER METAD ALPHARMSD ANTIBETARMSD CONTACTMAP vatom secondarystructure colvar bias generic setup
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 Elaine Tao UNITS CUSTOM LOWER_WALLS PRINT UPPER_WALLS METAD DISTANCE COM TORSION vatom colvar bias generic setup function
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 Faidon Brotzakis BIASVALUE MOLINFO PRINT EMMI UPPER_WALLS DISTANCE WHOLEMOLECULES GROUP COM RESTART vatom isdb bias generic setup colvar core
21.037 Molecular Dynamics simulations of RBD/hACE2 complexes bio SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain Max Bonomi PRINT RMSD DISTANCE colvar generic
21.031 Photo-switchable sulfonulureas in KATP channel bio metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels Katarzyna Walczewska-Szewc UNITS LOWER_WALLS PRINT UPPER_WALLS METAD DISTANCE WHOLEMOLECULES COM vatom colvar bias generic setup
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 Théo Magrino PRINT generic
21.009 Nucleation rates from small scale atomistic simulations and transition state theory materials kinetics, free energy barriers, nucleation, droplets, metadynamics Kristof Bal UNITS DUMPGRID CONVERT_TO_FES PRINT COMMITTOR COORDINATIONNUMBER UPPER_WALLS MOVINGRESTRAINT FLUSH REWEIGHT_METAD METAD HISTOGRAM LOAD symfunc bias generic setup gridtools
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 Khaled Abdel-Maksoud PRINT METAD DISTANCE TORSION bias colvar generic
20.022 Unified Approach to Enhanced Sampling methods OPES, expanded ensembles, importance sampling Michele Invernizzi ENDPLUMED MOLINFO ECV_LINEAR ENVIRONMENTSIMILARITY UPPER_WALLS ENERGY Q6 TORSION CUSTOM OPES_EXPANDED UNITS VOLUME POSITION ECV_MULTITHERMAL WHOLEMOLECULES PRINT ECV_MULTITHERMAL_MULTIBARIC RMSD ECV_UMBRELLAS_LINE MATHEVAL LOAD envsim symfunc opes bias generic setup colvar function
20.016 Predicting polymorphism in molecular crystals using orientational entropy materials metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy Pablo Piaggi VOLUME PRINT INCLUDE UPPER_WALLS CENTER METAD GROUP LOAD vatom bias generic setup colvar core
20.013 Improving accuracy of biased Alchemistic simulations methods flying Gaussian method, Alchemistic simulations, thermodynamic integration, reweighting Vojtech Spiwok PRINT METAD TORSION bias colvar generic
20.007 Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics bio metadynamics, loop movement, artificial intelligence Pratyush Tiwary MOLINFO PRINT COMBINE RMSD UPPER_WALLS METAD DISTANCE WHOLEMOLECULES RESTART TORSION colvar bias generic setup function
19.078 Iterative unbiasing of quasi-equilibrium sampling methods metadynamics, reweighting Federico Giberti UNITS DUMPATOMS DISTANCE PRINT COLLECT_FRAMES COORDINATIONNUMBER MATHEVAL METAD BIASVALUE REWEIGHT_BIAS symfunc colvar bias generic setup landmarks function
19.068 Rethinking Metadynamics methods metadynamics, opes, convergence Michele Invernizzi UNITS ENDPLUMED POSITION PRINT EXTERNAL METAD OPES_METAD TORSION opes colvar bias generic setup
19.063 Protein-ligand binding through metadynamics with path CVs bio metadynamics, path CVs, ligand binding Mattia Bernetti LOWER_WALLS PRINT UPPER_WALLS METAD WHOLEMOLECULES PATHMSD bias colvar generic
19.059 cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide bio bias-exchange metadynamics, cis-trans isomerization Fabrizio Marinelli PRINT INCLUDE RANDOM_EXCHANGES METAD TORSION bias colvar generic
19.048 Understanding Ligand Binding Selectivity in a Prototypical GPCR Family bio metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding Francesco Gervasio BIASVALUE LOWER_WALLS PRINT UPPER_WALLS CONSTANT MATHEVAL METAD DISTANCE WHOLEMOLECULES COM vatom bias generic colvar function
19.028 pRAVE methods RAVE, reaction coordinate, deep learning, metadynamics, kinetics Pratyush Tiwary EXTERNAL PRINT COMMITTOR COMBINE ALPHABETA DISTANCE WHOLEMOLECULES COM RESTART TORSION vatom bias multicolvar generic setup colvar function
19.012 Martini-Beads multi-scale SAXS methods metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex Carlo Camilloni BIASVALUE MOLINFO ENDPLUMED PRINT INCLUDE SAXS STATS UPPER_WALLS RMSD CENTER DISTANCE WHOLEMOLECULES GROUP RESTRAINT vatom isdb bias generic colvar core function
19.003 EMMI ClpP bio metainference, cryo-EM Max Bonomi MOLINFO PRINT EMMI BIASVALUE GROUP isdb bias core generic
24.032 DeepLNE++ methods PATHCV, OPES Thorben Fröhlking ENERGY COORDINATION LOAD COMBINE CUSTOM TORSION DISTANCE GROUP PRINT OPES_METAD colvar opes setup core function generic
24.029 Combination of OPES and OPES-Explore methods OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin Dhiman Ray COORDINATION MATHEVAL PYTORCH_MODEL OPES_METAD_EXPLORE DISTANCE PRINT ENERGY UNITS WHOLEMOLECULES COMBINE CONTACTMAP FIT_TO_TEMPLATE UPPER_WALLS RMSD MOLINFO FLUSH LOWER_WALLS CUSTOM POSITION GROUP FIXEDATOM CENTER OPES_METAD METAD ENDPLUMED BIASVALUE INCLUDE colvar vatom opes setup core bias function generic pytorch
24.025 Correlating Enzymatic Reactivity for Different Substrates using Transferable Data-Driven Collective Variables bio enzymatic reactivity, k_cat, transfer learning, data-driven CVs, catalysis, ligand-binding modes, water, alpha-amylase, sugar, classical MD, OPES, machine learning, Deep TDA CV, path CV Sudip Das COORDINATION WHOLEMOLECULES PYTORCH_MODEL PATH LOWER_WALLS CUSTOM TORSION FIT_TO_TEMPLATE GROUP DISTANCE FIXEDATOM RESTART CENTER PRINT UPPER_WALLS OPES_METAD colvar vatom opes setup core mapping bias function generic pytorch
24.022 Integrating Path Sampling with Enhanced Sampling for Rare-event Kinetics methods OPES Flooding, Weighted Ensemble, Metadynamics, Kinetics, Infrequent Metadynamics, Integrated Sampling Dhiman Ray MATHEVAL COORDINATION DISTANCE PRINT ANGLE WHOLEMOLECULES COMBINE CONTACTMAP FIT_TO_TEMPLATE UPPER_WALLS RMSD MOLINFO COMMITTOR CUSTOM FIXEDATOM GROUP CENTER OPES_METAD METAD ENDPLUMED TORSION colvar vatom opes core bias function generic
23.037 Estimating binding free energy of solid binding peptides without extensive sampling bio metadynamics, solid binding peptides Xin Qi MOLINFO PBMETAD LOWER_WALLS DISTANCE PRINT UPPER_WALLS COM GYRATION colvar bias vatom generic
23.036 Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? bio NaCl, nucleation, metadynamics Ruiyu Wang ENERGY COORDINATIONNUMBER MATHEVAL VOLUME METAD Q6 COMBINE PRINT Q4 symfunc colvar bias function generic
23.019 Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors bio binding pathway, binding energy, sketch-map, drug development Raitis Bobrovs DISSIMILARITIES COLLECT_FRAMES METAD WHOLEMOLECULES SKETCHMAP_PROJECTION SKETCHMAP LANDMARK_SELECT_FPS PATHMSD VORONOI CUSTOM PRINT DISTANCE VSTACK UPPER_WALLS COM TRANSPOSE landmarks colvar vatom bias dimred function generic matrixtools valtools
23.005 A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs bio metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A Timothy Clark MATHEVAL READ METAD HISTOGRAM WHOLEMOLECULES MOLINFO REWEIGHT_METAD CONVERT_TO_FES DISTANCE PRINT DUMPGRID RMSD colvar bias function generic gridtools
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 Pablo Piaggi OPES_EXPANDED HISTOGRAM ENVIRONMENTSIMILARITY ECV_UMBRELLAS_LINE LOWER_WALLS PRINT RESTART UPPER_WALLS DUMPGRID opes envsim setup bias generic gridtools
23.000 Atomistic simulations of RNA tetraloop folding via PTWTE-WTM bio parallel tempering, well-tempered metadynamics, well-tempered ensemble, RNA, Tetraloop, Folding Gül Zerze ENERGY METAD WHOLEMOLECULES CONTACTMAP LOWER_WALLS PRINT UPPER_WALLS bias generic colvar
22.045 Binding mode and mechanism of enzymatic polyethylene terephthalate degradation bio metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation Francesco Colizzi ANGLE METAD WHOLEMOLECULES LOWER_WALLS MOVINGRESTRAINT DISTANCE PRINT UPPER_WALLS COM vatom bias generic colvar
22.039 Driving and characterizing nucleation of urea and glycine polymorphs in water bio metadynamics, nucleation, amino acids, polymorphism Eric Beyerle COORDINATIONNUMBER MATHEVAL METAD LOAD Q6 COMBINE PRINT GROUP PAIRENTROPY CENTER Q4 INCLUDE symfunc vatom setup core bias function generic gridtools
22.033 Reciprocal barrier restraint. Application to PROTAC passive permeability prediction methods PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR Istvan Kolossvary UNITS METAD FLUSH CUSTOM DRR DISTANCE PRINT BIASVALUE COM colvar vatom drr setup bias function generic
22.025 Bubble nucleation rate predictions in a Lennard-Jones fluid materials free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation Kristof Bal COORDINATIONNUMBER UNITS VOLUME LOAD HISTOGRAM CONVERT_TO_FES ANN FLUSH COMMITTOR RESTRAINT CUSTOM REWEIGHT_BIAS MOVINGRESTRAINT PRINT BIASVALUE UPPER_WALLS DUMPGRID symfunc colvar annfunc setup bias function generic gridtools
21.047 Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations materials pair entropy, metadynamics, ves, solids, crystallization Pablo Piaggi ENERGY VES_LINEAR_EXPANSION VOLUME LOAD METAD OPT_AVERAGED_SGD COMBINE PAIRENTROPY BF_LEGENDRE TD_WELLTEMPERED PRINT RESTART colvar ves setup bias function generic gridtools
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 Denis Maag COORDINATION COORDINATIONNUMBER METAD COMBINE LOWER_WALLS DISTANCE PRINT UPPER_WALLS symfunc colvar bias function generic
21.038 Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics materials metadynamics, SGOOP, nucleation, urea Ziyue Zou ENERGY COORDINATIONNUMBER METAD LOAD VOLUME COMBINE PRINT GROUP CENTER INCLUDE symfunc colvar vatom setup core bias function generic
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 Matteo Salvalaglio ENERGY COORDINATION RANDOM_EXCHANGES METAD WHOLEMOLECULES MOLINFO LOWER_WALLS PARABETARMSD ALPHARMSD PRINT GROUP ANTIBETARMSD UPPER_WALLS GYRATION DIHCOR colvar core secondarystructure multicolvar bias generic
21.034 Efficient sampling of high-dimensional free energy landscapes using adaptive reinforced dynamics bio reinforced dynamics, bias-exchange metadynamics, parallel-bias metadynamics Dongdong Wang METAD RANDOM_EXCHANGES PBMETAD ENDPLUMED TORSION PRINT INCLUDE colvar bias generic
21.016 MD SAXS GTPase associated center bio metadynamics, RNA, folding, SAXS Giovanni Bussi METAD WHOLEMOLECULES MOLINFO SAXS LOWER_WALLS CUSTOM PRINT GROUP ERMSD UPPER_WALLS GYRATION INCLUDE colvar isdb core bias function generic
21.005 Crystallization Collective Variable methods Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA Tarak Karmakar MATHEVAL LOAD FLUSH PYTORCH_MODEL LOWER_WALLS PRINT GROUP UPPER_WALLS OPES_METAD opes setup core bias function generic pytorch
20.029 High Conformational Flexibility of the E2F1/DP1/DNA complex bio SAXS, protein-DNA complex, hySAXS, ensemble determination Cristina Paissoni WHOLEMOLECULES MOLINFO SAXS BIASVALUE ENSEMBLE RESTRAINT DISTANCE GROUP PRINT STATS CENTER INCLUDE colvar isdb vatom core bias function generic
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 Francesco Gervasio MATHEVAL METAD LOAD WHOLEMOLECULES CONSTANT MOLINFO CONTACTMAP LOWER_WALLS PROJECTION_ON_AXIS DISTANCE GROUP PRINT BIASVALUE FUNCPATHGENERAL UPPER_WALLS COM INCLUDE colvar vatom setup core bias function generic
20.011 Uremic toxin analysis bio metadynamics, uremic toxin, serum albumin Jim Pfaendtner COORDINATION WHOLEMOLECULES DISTANCES DISTANCE GROUP PRINT RESTART CENTER colvar vatom setup core multicolvar generic
20.006 Class B GPCR activation mechanism bio metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding Francesco Gervasio ENERGY MATHEVAL METAD WHOLEMOLECULES MOLINFO COMBINE LOWER_WALLS PRINT DISTANCE CENTER UPPER_WALLS RMSD colvar vatom bias function generic
19.077 Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations materials metadynamics, peptide-surface binding Jim Pfaendtner ENERGY METAD MOLINFO DISTANCE PRINT UPPER_WALLS COM GYRATION vatom bias generic colvar
19.075 PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python other Python, automatic differentiation Toni Giorgino ANGLE COMBINE ENDPLUMED RESTRAINT CUSTOM TORSION DISTANCE DUMPDERIVATIVES PRINT GROUP CENTER colvar vatom core bias function generic
19.069 Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen materials ibuprofen, crystal, solvent, surface Matteo Salvalaglio ENDPLUMED PRINT DISTANCE GROUP CENTER INCLUDE core colvar vatom generic
19.042 Harmonic Linear Discriminant Analysis (HLDA) methods metadynamics, chemistry, HLDA GiovanniMaria Piccini ENERGY UNITS METAD COMBINE FLUSH DISTANCE PRINT UPPER_WALLS colvar setup bias function generic
19.038 native state dynamics of human and mouse b2m bio metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation Carlo Camilloni WHOLEMOLECULES MOLINFO PBMETAD ALPHABETA FLUSH CS2BACKBONE ENDPLUMED LOWER_WALLS PRINT GROUP RESTART BIASVALUE UPPER_WALLS ANTIBETARMSD isdb setup core multicolvar secondarystructure bias generic
19.036 Thermodynamics and kinetics of G protein-coupled receptor activation bio metadynamics, allostery, receptor conformation, GPCR, pharmacology Davide Provasi METAD WHOLEMOLECULES CONTACTMAP ENDPLUMED DISTANCE PRINT FUNCPATHMSD COM RMSD colvar vatom bias function generic
19.031 Ice nucleation using PIV-based path coordinates materials phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics Silvio Pipolo PIV METAD LOWER_WALLS CELL PRINT FUNCPATHMSD UPPER_WALLS piv colvar bias function generic
19.018 Excited state FEP/Metadynamics simulations chemistry metadynamics, FEP, excited states, conjugated polymers, torsional potential Adriana Pietropaolo MATHEVAL METAD CONSTANT WHOLEMOLECULES TORSION PRINT BIASVALUE colvar bias function generic
19.016 Succinnic acid gamma polymorph materials Succinnic acid, conformers, polymorphs, metadynamics Matteo Salvalaglio ENERGY MATHEVAL METAD VOLUME COMBINE ENDPLUMED LOWER_WALLS CELL TORSION PRINT UPPER_WALLS bias generic function colvar
19.009 RNA tetraloops folding bio metadynamics, RNA, folding Giovanni Bussi METAD WHOLEMOLECULES MOLINFO ENDPLUMED PRINT ERMSD RMSD colvar bias generic
24.035 Data efficient machine learning potentials for modeling catalytic reactivity via active learning and enhanced sampling chemistry opes, catalysis, ammonia, machine learning potentials Luigi Bonati RESTART LOWER_WALLS GROUP PRINT COORDINATION CUSTOM UNITS UPPER_WALLS DISTANCE OPES_METAD COMMITTOR function colvar core bias setup generic opes
24.033 Transient interactions between the fuzzy coat and the cross-b core of brain-derived Ab42 filaments bio CryoEM, MEMMI, Metadynamics, Metainference, Ab42 Fibrils, structural ensemble Maria Milanesi ALPHARMSD EMMI PBMETAD DUMPMASSCHARGE MOLINFO PARABETARMSD GROUP PRINT COORDINATION DISTANCE CENTER WHOLEMOLECULES DUMPATOMS RMSD UPPER_WALLS BIASVALUE COM colvar isdb secondarystructure core vatom bias generic
24.026 Constant pH metadynamics of RNA oligomers bio metadynamics, pH, RNA Giovanni Bussi TORSION PUCKERING RESTART MOLINFO PRINT METAD bias colvar generic setup
24.018 A new route to the prebiotic synthesis of glycine via ab initio-based machine learning calculations chemistry prebiotic chemistry, glycine, Strecker synthesis, ab initio calculations, machine learning Léon HUET PRINT DISTANCE colvar generic
24.013 Estimating Free Energy Surfaces and their Convergence from multiple, independent static and history-dependent biased molecular-dynamics simulations with Mean Force Integration methods Mean Force Integration, Convergence, FES, Umbrella Sampling Matteo Salvalaglio TORSION FLUSH RESTART MOLINFO PRINT METAD MATHEVAL RESTRAINT DISTANCE COORDINATIONNUMBER BIASVALUE COMMITTOR ENERGY function colvar bias setup generic symfunc
24.011 Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble methods committor, machine learning Peilin Kang COORDINATION ENDPLUMED CUSTOM MATHEVAL UNITS UPPER_WALLS MOLINFO LOAD WHOLEMOLECULES ENERGY PRINT RMSD BIASVALUE TORSION LOWER_WALLS GROUP POSITION DISTANCE CELL INCLUDE function colvar core bias setup generic
24.010 Oxytocin metadynamics simulation bio metadynamics, oxytocin, peptide Jan Beránek TORSION FLUSH RESTART PRINT METAD WHOLEMOLECULES bias colvar generic setup
24.006 Water vapor condensation chemistry metadynamics, homogeneous condensation, chemical potential Shenghui Zhong PRINT METAD CLUSTER_PROPERTIES DFSCLUSTERING CLUSTER_NATOMS UNITS CONTACT_MATRIX UPPER_WALLS COORDINATIONNUMBER clusters bias setup generic symfunc adjmat
24.005 Learning Markovian Dynamics with Spectral Maps methods spectral map, collective variables, machine learning Jakub Rydzewski PRINT CUSTOM UNITS DISTANCE BIASVALUE function colvar bias setup generic
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 Federico Ballabio SAXS WRAPAROUND MOLINFO GROUP PRINT CENTER DISTANCE UPPER_WALLS STATS RMSD BIASVALUE ENSEMBLE function colvar isdb core vatom bias generic
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 Istvan Kolossvary FLUSH LOWER_WALLS PRINT METAD CUSTOM DRR UNITS UPPER_WALLS BIASVALUE TIME PATHMSD function colvar drr bias setup generic
23.012 JAK2 2D meta-eABF PMF with statistical analysis bio 2D meta-eABF, path CV, PMF Istvan Kolossvary FLUSH LOWER_WALLS PRINT METAD CUSTOM DRR UPPER_WALLS BIASVALUE PATHMSD function colvar drr bias generic
22.030 Mixing physics across temperatures with generative artificial intelligence methods REMD, Generative AI, DDPM Yihang Wang WHOLEMOLECULES PRINT TORSION colvar generic
22.029 Angiotensin-1-7_Metadynamics bio Metadynamics, Angiotensin-(1-7), peptide L.-América Chi FLUSH LOWER_WALLS GROUP PRINT COORDINATION METAD WHOLEMOLECULES GYRATION UPPER_WALLS bias colvar generic core
22.024 Conformational Entropy as a Potential Liability of Computationally Designed Antibodies bio metadynamics, conformational entropy, antibody, nanobody Thomas Löhr ALPHARMSD TORSION PBMETAD RESTART MOLINFO PRINT COM WHOLEMOLECULES ANTIBETARMSD ALPHABETA colvar secondarystructure vatom bias setup generic multicolvar
22.021 Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations chemistry Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella Sigbjørn Løland Bore LOWER_WALLS PRINT OPES_EXPANDED ECV_UMBRELLAS_LINE UPPER_WALLS ENVIRONMENTSIMILARITY INCLUDE bias generic envsim opes
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 Pablo Piaggi RESTART PRINT AROUND HISTOGRAM CUSTOM ENVIRONMENTSIMILARITY UPPER_WALLS VOLUME DUMPGRID OPES_METAD ENERGY function colvar volumes bias setup generic envsim opes gridtools
22.008 Ab initio metadynamics determination of temperature-dependent free-energy landscape in ultrasmall silver clusters materials Well tempered metadynamics, ab-initio, ase Daniel Sucerquia FLUSH COMBINE LOWER_WALLS COORDINATION METAD GYRATION UNITS UPPER_WALLS DISTANCE COORDINATIONNUMBER COM function colvar vatom bias setup generic symfunc
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 Huixia Lu TORSION PRINT METAD FIT_TO_TEMPLATE FIXEDATOM bias colvar generic vatom
21.032 Metal-coupled folding mechanism to metallothionein bio parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination Manuel-Peris Diaz PBMETAD GROUP COORDINATION WHOLEMOLECULES UNITS colvar core bias setup generic
21.025 Computational and biochemical analysis of type IV pilus dynamics and stability bio molecular dynamics, calcium binding, Type IV pilus Yasaman Karami PRINT LOWER_WALLS UPPER_WALLS DISTANCE bias colvar generic
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 Gaston Courtade RESTART PRINT COORDINATION CENTER POSITION METAD MATHEVAL REWEIGHT_BIAS WHOLEMOLECULES RESTRAINT function colvar vatom bias setup generic
21.011 CmuMD simulations of NaCl(aq) at graphite chemistry CmuMD, DFS clustering Aaron Finney CLUSTER_DISTRIBUTION MFILTER_MORE GROUP PRINT AROUND LOAD FIXEDATOM DENSITY DFSCLUSTERING RESTRAINT CLUSTER_NATOMS MULTICOLVARDENS CONTACT_MATRIX COORDINATIONNUMBER DUMPGRID volumes core vatom clusters bias setup generic symfunc adjmat multicolvar gridtools
20.033 COVID-19 Spike protein opening transition mechanism bio EMMI, CryoEM, COVID-19, Spike, Metainference Faidon Brotzakis EMMI BIASVALUE MOLINFO READ PRINT GROUP HISTOGRAM WHOLEMOLECULES DISTANCES CONVERT_TO_FES RMSD DUMPGRID colvar isdb core bias generic multicolvar gridtools
20.031 Soft fluorescent nanoshuttles targeting receptors chemistry polymers, receptors, nanoparticles, fluorescent probes Adriana Pietropaolo PBMETAD PRINT COORDINATION CENTER WHOLEMOLECULES bias colvar generic vatom
20.024 Gaussian Mixture Based Enhanced Sampling (GAMBES) methods enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias Jayashrita Debnath TORSION COMBINE GROUP PRINT LOWER_WALLS LOAD DISTANCES UNITS UPPER_WALLS DISTANCE ENERGY function colvar core bias setup generic multicolvar
20.018 Free energy barriers from biased molecular dynamics simulations methods kinetics, free energy barriers, chemical reactions, nucleation, metadynamics Kristof Bal REWEIGHT_METAD COORDINATION PAIRENTROPY HISTOGRAM LOCAL_AVERAGE UNITS UPPER_WALLS FLUSH REWEIGHT_BIAS LOAD CONTACT_MATRIX VOLUME ENERGY PRINT METAD CENTER DENSITY CONVERT_TO_FES SPRINT COMBINE LOWER_WALLS Q6 DISTANCE COORDINATIONNUMBER DUMPGRID function colvar volumes vatom sprint bias symfunc setup generic adjmat gridtools
20.003 Enhanced sampling of transition states methods Variationally Enhanced Sampling, Target distribution, Transition state, Enhanced Sampling, Nucleation, chemical reaction Jayashrita Debnath VES_LINEAR_EXPANSION BF_LEGENDRE PRINT POSITION LOAD UNITS OPT_AVERAGED_SGD ENERGY colvar ves generic setup
20.002 Exploring conformational dynamics of the extracellular Venus flytrap domain of the GABAB receptor, a path-metadynamics study bio Metadynamics, path CVs Riccardo Ocello RESTART MOLINFO GROUP PRINT METAD WHOLEMOLECULES UPPER_WALLS PATHMSD colvar core bias setup generic
19.072 SINE hairpin MD+NMR bio metadynamics, RNA, NMR Giovanni Bussi TORSION FLUSH MOLINFO PRINT COORDINATION METAD SORT MATHEVAL WHOLEMOLECULES DISTANCE MAXENT COM INCLUDE function colvar vatom bias generic
19.050 Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes chemistry metadynamics, membranes, Willard Chandler surface Gareth Tribello RESTART COMBINE READ PRINT METAD REWEIGHT_BIAS HISTOGRAM DISTANCE_FROM_CONTOUR CONVERT_TO_FES UPPER_WALLS DUMPGRID function bias setup generic contour gridtools
19.044 Multithermal-multibaric simulations using VES methods ves, Wang Landau, multicanonical, water, density anomaly Pablo Piaggi VES_LINEAR_EXPANSION RESTART BF_LEGENDRE COMBINE READ PRINT TD_MULTITHERMAL_MULTIBARIC REWEIGHT_BIAS HISTOGRAM OPT_DUMMY REWEIGHT_TEMP_PRESS CONVERT_TO_FES VOLUME DUMPGRID AVERAGE OPT_AVERAGED_SGD ENERGY function colvar bias setup generic ves gridtools
19.043 Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) methods metadynamics, chemistry, HLDA GiovanniMaria Piccini FLUSH RESTART COMBINE PRINT METAD DISTANCES UNITS UPPER_WALLS DISTANCE function colvar bias setup generic multicolvar
19.015 Ibuprofen conformational dynamics and thermodynamics surface materials Ibuprofen, crystal, surface, solvents, conformers, metadynamics Matteo Salvalaglio TORSION LOWER_WALLS PRINT METAD CENTER UPPER_WALLS DISTANCE COMMITTOR bias colvar generic vatom
19.011 Automatic Gradient Computation for Collective Variables other gradient, differentiation, curvature Toni Giorgino ENDPLUMED generic
19.007 EMMI Microtubules bio metainference, cryo-EM Max Bonomi EMMI MOLINFO GROUP PRINT WHOLEMOLECULES BIASVALUE isdb generic core bias
25.011 Chiral perovskite nucleation chemistry metadynamics, chiral perovskites, nucleation Adriana Pietropaolo LOWER_WALLS PBMETAD PRINT MATHEVAL UNITS RESTART UPPER_WALLS MULTI_RMSD DISTANCE bias colvar generic function setup
25.010 Kinetic rates calculation with Ratchet&Pawl MD methods kinetics, ligand binding, ABMD, ratchet&pawl MD Riccardo Capelli ABMD COMMITTOR COM PRINT GROUP WHOLEMOLECULES FLUSH DISTANCE bias colvar core vatom generic
25.007 Shaping the glycan landscape. Hidden relationships between linkage and ring distortion induced by carbohydrate-active enzmyes bio REST-RECT, REST2, glycan, enzyme, CAZyme, steered Isabell Grothaus MOLINFO MOVINGRESTRAINT RESTRAINT DISTANCE METAD TORSION RESTART PUCKERING PRINT bias generic colvar setup
25.006 Characterizing the conformational ensemble of PROTAC degraders in solutions via atomistic simulations methods Enhanced sampling, Atomistic simulations, Conformational ensemble, PROTACs, Targeted Protein Degradation, Chamelonic molecules Shikshya Bhusal, Omar Valsson CENTER GYRATION PBMETAD DISTANCE ENERGY TORSION RESTART INCLUDE VOLUME READ PRINT colvar bias vatom generic setup
25.001 RNA G-quadruplex folding with ST-metaD protocol bio RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD Pavlína Pokorná MOLINFO ERMSD COMBINE WHOLEMOLECULES METAD colvar generic function bias
24.031 DeepLNE methods PATHCV, OPES, OneOPES Thorben Fröhlking MOLINFO COORDINATION OPES_METAD_EXPLORE OPES_EXPANDED ERMSD ECV_MULTITHERMAL PYTORCH_MODEL ENERGY RESTART COMBINE VOLUME PRINT colvar opes pytorch generic function setup
24.030 NMR guided simulation of dsRBD bio Metainference, NMR, protein dynamics Debadutta Patra MOLINFO RDC ALPHABETA METAINFERENCE STATS DISTANCE ENSEMBLE GROUP WHOLEMOLECULES FLUSH PRINT colvar core isdb multicolvar generic function
24.021 Ab initio machine learning simulation of calcium carbonate from aqueous solutions to the solid state chemistry ion pairing, caco3, opes, proton transfer, crystallization Pablo Piaggi COORDINATION DISTANCE ENERGY UPPER_WALLS OPES_METAD PRINT opes colvar generic bias
24.009 Weighted Shape Gaussian Mixture Models bio metadynamics, clustering Glen Hocky PRINT UNITS TORSION GROUP METAD colvar bias core generic setup
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 Samuel Hoff MOLINFO WRAPAROUND EMMIVOX DISTANCE BIASVALUE GROUP INCLUDE UPPER_WALLS WHOLEMOLECULES PRINT colvar bias core isdb generic
23.040 Supramolecular capsules assembly dynamics chemistry Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics Riccardo Capelli POSITION CENTER COM PRINT DISTANCES UNITS METAD GROUP CUSTOM WHOLEMOLECULES FLUSH DISTANCE colvar bias core vatom multicolvar generic function setup
23.021 Into the Dynamics of Rotaxanes at Atomistic Resolution materials metadynamics, rotaxanes, molecular shuttles, molecular machines Luigi Leanza CENTER PRINT MATHEVAL FIXEDATOM METAD TORSION CUSTOM UPPER_WALLS DISTANCE bias colvar vatom generic function
22.044 Colloid Crystallisation Analyses materials Q4, Q6, Pair Entropy, DFS Aaron Finney LOCAL_AVERAGE CONTACT_MATRIX COORDINATIONNUMBER LOCAL_Q6 Q6 CLUSTER_NATOMS DFSCLUSTERING GROUP COMBINE Q4 MFILTER_LESS MFILTER_MORE PRINT LOCAL_Q4 core adjmat multicolvar function generic symfunc clusters
22.043 Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES bio OPES, RNA, Tetraloop, Folding Gül Zerze CONTACTMAP OPES_EXPANDED ECV_MULTITHERMAL ENERGY ECV_UMBRELLAS_LINE WHOLEMOLECULES PRINT opes colvar generic
22.041 Skipping the Replica Exchange Ladder with Normalizing Flows methods OPES, alanine, normalizing flows, replica exchange Michele Invernizzi POSITION OPES_EXPANDED ENDPLUMED ECV_MULTITHERMAL ENERGY TORSION UNITS OPES_METAD PRINT opes colvar generic setup
22.022 Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir bio RMSD, protein-ligand interactions Isabell Grothaus PRINT RMSD colvar generic
22.012 Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT bio contact maps, protein-protein interactions Isabell-Louise Grothaus CONTACTMAP DISTANCE CENTER PRINT colvar generic vatom
22.006 Peptide framework for screening the effects of amino acids on assembly bio metadynamics, peptides Andrew White COM GYRATION PRINT CONVERT_TO_FES HISTOGRAM METAD REWEIGHT_BIAS COMBINE INCLUDE DUMPGRID GROUP DISTANCES colvar bias core vatom multicolvar generic gridtools function
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 Vojtech Spiwok WHOLEMOLECULES LOAD PRINT METAD setup generic bias
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 Benjamin Pampel POSITION BF_WAVELETS BF_CHEBYSHEV TD_UNIFORM BF_LEGENDRE PRINT BF_CUBIC_B_SPLINES UNITS UPPER_WALLS OPT_ADAM VES_OUTPUT_BASISFUNCTIONS ENERGY INCLUDE FLUSH DISTANCE OPT_AVERAGED_SGD VES_LINEAR_EXPANSION COORDINATION TD_WELLTEMPERED BF_GAUSSIANS METAD bias colvar generic setup ves
21.044 NaCl nucleation chemistry metadynamics, DFS clustering Aaron Finney CONTACT_MATRIX COORDINATIONNUMBER INSPHERE PRINT LOCAL_Q6 Q6 FIXEDATOM HISTOGRAM CLUSTER_NATOMS DFSCLUSTERING GROUP COMBINE MFILTER_MORE DUMPGRID CLUSTER_DISTRIBUTION METAD bias volumes core adjmat vatom multicolvar generic gridtools function symfunc clusters
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 Jim Pfaendtner ALPHABETA COORDINATION COM GYRATION PBMETAD PRINT ENERGY TORSION METAD INCLUDE DISTANCE bias colvar vatom multicolvar generic
21.020 Reweighted Jarzynski sampling methods free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions Kristof Bal MOVINGRESTRAINT BF_CHEBYSHEV RESTRAINT CONSTANT PRINT COORDINATIONNUMBER UNITS BIASVALUE CUSTOM UPPER_WALLS OPES_METAD ANN HISTOGRAM COMBINE FLUSH DISTANCE OPT_AVERAGED_SGD LOAD REWEIGHT_METAD TD_WELLTEMPERED VES_LINEAR_EXPANSION CONVERT_TO_FES REWEIGHT_BIAS DUMPGRID METAD bias colvar opes generic function annfunc gridtools setup ves symfunc
21.014 how to determine statistically accurate conformational ensembles bio metadynamics, metainference, errors, cv, SAXS, ensemble determination Cristina Paissoni MOLINFO ALPHABETA CENTER CONTACTMAP GYRATION PBMETAD PRINT ANTIBETARMSD STATS TORSION SAXS BIASVALUE ENSEMBLE WHOLEMOLECULES METAD bias colvar secondarystructure vatom isdb multicolvar generic function
20.015 Rational design of ASCT2 inhibitors using an integrated experimental-computational approach bio ASCT2 transporter, small-molecules, cryo-EM, metainference Max Bonomi MOLINFO LOAD EMMIVOX BIASVALUE DUMPATOMS GROUP WHOLEMOLECULES PRINT bias core isdb generic setup
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 Riccardo Capelli CONTACTMAP PRINT COM FUNCPATHMSD UPPER_WALLS LOWER_WALLS HISTOGRAM COMBINE WHOLEMOLECULES FLUSH DISTANCE MOLINFO ABMD REWEIGHT_METAD ENDPLUMED CONVERT_TO_FES DUMPGRID READ METAD colvar bias vatom generic function gridtools
19.076 Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones bio molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics Salvatore Assenza MOVINGRESTRAINT GYRATION ENDPLUMED UNITS PRINT bias generic colvar setup
19.070 Unexpected Dynamics in the UUCG RNA Tetraloop bio well-tempered metadynamics, RNA, UUCG, maximum entropy Sandro Bottaro MOLINFO PRINT ERMSD DISTANCE METAD TORSION WHOLEMOLECULES RMSD colvar generic bias
19.067 Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways bio metadynamics, ligand unbinding Jakub Rydzewski LOWER_WALLS PRINT UNITS RESTART PATHMSD UPPER_WALLS METAD bias generic colvar setup
19.057 SAXS ensembles using Martini-Beads multi-scale SAXS methods metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics Cristina Paissoni MOLINFO CENTER ALPHABETA COORDINATION PBMETAD MATHEVAL STATS ENDPLUMED BIASVALUE SAXS GROUP INCLUDE ANGLE COMBINE ENSEMBLE WHOLEMOLECULES PRINT bias colvar core vatom isdb multicolvar generic function
19.051 Solid liquid interfacial free energy out of equilibrium materials metadynamics, nucleation, surface excess free energy Gareth Tribello LOWER_WALLS PRINT FCCUBIC CELL ENDPLUMED UNITS UPPER_WALLS AROUND METAD bias colvar volumes generic setup symfunc
19.029 WTE-metaD of FF domain of URNF1 C57D variant bio metadynamics, mutations, post-translational modification, ff domain Elena Papaleo MOLINFO ALPHABETA LOWER_WALLS GYRATION PRINT GROUP UPPER_WALLS WHOLEMOLECULES METAD colvar bias core multicolvar generic
19.010 Multi-domain protein dynamics bio metainference, NMR, protein dynamics Carlo Camilloni MOLINFO DHENERGY RDC ALPHABETA CENTER PBMETAD PRINT METAINFERENCE STATS ENDPLUMED RESTRAINT TORSION ENSEMBLE GROUP UPPER_WALLS WHOLEMOLECULES DIHCOR DISTANCE colvar bias core vatom isdb multicolvar generic function
19.008 anncolvar methods neural network, dimensionality reduction Vojtech Spiwok MOLINFO POSITION ALPHARMSD PRINT MATHEVAL COMBINE FIT_TO_TEMPLATE WHOLEMOLECULES METAD colvar bias secondarystructure generic function
19.004 MI Ubiquitin bio metainference, NMR Max Bonomi MOLINFO RDC METAINFERENCE GROUP CS2BACKBONE WHOLEMOLECULES PRINT core generic isdb
25.000 Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer bio metadynamics, pathCV Sahithya Sridharan Iyer GROUP FUNCPATHGENERAL UPPER_WALLS RESTART COM METAD DISTANCE MOLINFO PRINT WHOLEMOLECULES function vatom colvar setup core generic bias
24.027 Proline cis and trans subensembles of a disordered peptide bio intrinsically disordered proteins, proline cis trans isomerisation, metadynamics, collective variables Alice Pettitt ENDPLUMED GROUP INCLUDE COORDINATION GYRATION PARABETARMSD COMBINE ANTIBETARMSD DISTANCE TORSION FLUSH MOLINFO ALPHARMSD PBMETAD PRINT DIHCOR WHOLEMOLECULES function colvar multicolvar core generic secondarystructure bias
24.023 Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21. A Machine-Learning-Aided Enhanced Sampling Study bio RNA, miRNA, OneOPES, ligand binding, conformational changes Valerio Rizzi CUSTOM GROUP ECV_MULTITHERMAL COORDINATION RESTART COMBINE DISTANCE TORSION ENERGY PRINT OPES_EXPANDED OPES_METAD_EXPLORE function colvar setup core opes generic
24.016 Cryo-EM guided simulations of ribozyme bio metainference, cryo-EM Giovanni Bussi GROUP EMMIVOX INCLUDE ERMSD RESTRAINT MOLINFO PRINT BIASVALUE WHOLEMOLECULES colvar isdb core generic bias
24.008 yCD Metadynamics bio volume-based MetaD, path CVs, infrequent MetaD, product release James McCarty INCLUDE HISTOGRAM DUMPGRID PATH METAD WHOLEMOLECULES GROUP FIXEDATOM RMSD UPPER_WALLS COORDINATION COM MOLINFO FIT_TO_TEMPLATE ENDPLUMED PRINT CONTACTMAP REWEIGHT_METAD MATHEVAL CONVERT_TO_FES READ DISTANCE WRAPAROUND FLUSH COMMITTOR vatom function colvar mapping core generic gridtools bias
23.044 Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition materials metadynamics, interlocked molecules Luigi Leanza ENDPLUMED GROUP COORDINATION HISTOGRAM CONVERT_TO_FES DUMPGRID READ METAD PRINT COMMITTOR colvar core generic gridtools bias
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 Timothy Clark UPPER_WALLS MATHEVAL CENTER METAD CONSTANT DISTANCE LOWER_WALLS PRINT BIASVALUE WHOLEMOLECULES function vatom colvar generic bias
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 Sudip Das CUSTOM GROUP FIXEDATOM OPES_METAD COORDINATION UPPER_WALLS UNITS CENTER PATH TORSION DISTANCE LOWER_WALLS PRINT PYTORCH_MODEL FIT_TO_TEMPLATE OPES_METAD_EXPLORE WHOLEMOLECULES function vatom colvar setup mapping core opes generic pytorch bias
23.011 OneOPES, a combined enhanced sampling method to rule them all bio OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding Valerio Rizzi ENDPLUMED ECV_MULTITHERMAL TORSION ENERGY DISTANCE METAD MOLINFO PRINT OPES_EXPANDED OPES_METAD_EXPLORE opes colvar bias generic
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 Dhiman Ray ANGLE INCLUDE CENTER WHOLEMOLECULES GROUP CUSTOM FIXEDATOM COORDINATION UPPER_WALLS RMSD ENERGY MOLINFO FIT_TO_TEMPLATE ENDPLUMED PRINT PYTORCH_MODEL CONTACTMAP OPES_METAD MATHEVAL COMBINE DISTANCE LOWER_WALLS COMMITTOR vatom function colvar core opes generic pytorch bias
22.038 Enhanced Sampling Aided Design of Molecular Photoswitches chemistry reaction discovery, OPES explore, graph CV Umberto Raucci CUSTOM COORDINATION UNITS PRINT PYTORCH_MODEL OPES_METAD_EXPLORE function colvar setup opes generic pytorch
22.031 Rare Event Kinetics from Adaptive Bias Enhanced Sampling methods OPES Flooding, Kinetics, Rate, OPES, Machine Learning Dhiman Ray INCLUDE TORSION WHOLEMOLECULES CUSTOM GROUP RMSD UNITS CONSTANT ENERGY MOLINFO BIASVALUE ENDPLUMED PRINT PYTORCH_MODEL CONTACTMAP POSITION OPES_METAD COMBINE DISTANCE COMMITTOR function colvar setup core opes generic pytorch bias
22.026 Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification materials Peptoid, silica Jim Pfaendtner UPPER_WALLS COM GYRATION DISTANCE MOLINFO PBMETAD PRINT vatom colvar bias generic
22.015 Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome bio photodynamics, bacteriophytochrome, variationally enhanced sampling Jakub Rydzewski BF_FOURIER VES_LINEAR_EXPANSION OPT_AVERAGED_SGD TORSION PRINT TD_UNIFORM ves colvar generic
22.011 Accelerating all-atom simulations and gaining mechanistic understanding of biophysical systems through State Predictive Information Bottleneck methods metadynamics, membrane permeation, protein folding Shams Mehdi CUSTOM YANGLES UPPER_WALLS XANGLES MATHEVAL COM COMBINE DISTANCE LOWER_WALLS METAD MOLINFO ZANGLES PRINT TORSION ALPHABETA WHOLEMOLECULES function vatom colvar multicolvar generic bias
22.009 Glycosylation in calixarenes capsule chemistry Metadynamics, glycosylation, supramolecular catalysis GiovanniMaria Piccini GROUP WHOLEMOLECULES ANGLE RMSD COORDINATION MATHEVAL UPPER_WALLS UNITS COMBINE DISTANCE LOWER_WALLS METAD PRINT DISTANCES FLUSH FIT_TO_TEMPLATE BRIDGE function colvar multicolvar setup core adjmat generic bias
21.052 On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets materials Ibuprofen, unbinding, WTmetaD Matteo Salvalaglio ENDPLUMED CENTER METAD TORSION DISTANCE COORDINATIONNUMBER PRINT COMMITTOR vatom colvar symfunc generic bias
21.042 Peptoid-mediated Au nanocrystal growth materials parallel-bias metadynamics, peptoid, Au Xin Qi UPPER_WALLS COM GYRATION DISTANCE MOLINFO PBMETAD PRINT vatom colvar bias generic
21.029 Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs bio metadynamics, small peptide, machine learning Pratyush Tiwary RESTART EXTERNAL TORSION ENERGY FLUSH PRINT MOLINFO setup colvar bias generic
21.024 Property map collective variable as a useful tool for force field correction chemistry molecular mechanics Vojtech Spiwok TORSION METAD PRINT PROPERTYMAP BIASVALUE WHOLEMOLECULES colvar bias generic
21.019 Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations materials Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen Matteo Salvalaglio KDE MATHEVAL COM DISTANCE TORSIONS PRINT function vatom colvar multicolvar generic gridtools
21.017 All-atom simulations of the Vav1 AD construct bio metadynamics, parallel-bias, well-tempered Simone Orioli GROUP REWEIGHT_BIAS RESTART METAD ALPHABETA MOLINFO ALPHARMSD PBMETAD CONTACTMAP PRINT WHOLEMOLECULES colvar multicolvar setup core generic secondarystructure bias
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 Dorothea Gobbo UPPER_WALLS RESTART METAD PATHMSD LOWER_WALLS PRINT WHOLEMOLECULES setup colvar bias generic
20.030 Converging experimental and computational views of the knotting mechanism of the smallest knotted protein bio phi-values, transition state, knotted proteins Cristina Paissoni COORDINATION RESTRAINT COMBINE STATS MOLINFO PRINT WHOLEMOLECULES function colvar bias generic
20.020 Parallel Bias Metadynamics methods pbmetad, trp-cage, folding Max Bonomi INCLUDE COORDINATION GYRATION ALPHABETA MOLINFO PRINT PBMETAD DIHCOR WHOLEMOLECULES bias colvar multicolvar generic
20.017 FISST methods FISST, force, peptide, sampling, tempering Glen Hocky GROUP FISST MATHEVAL RESTRAINT UNITS GYRATION DISTANCE ENERGY PRINT BIASVALUE function colvar setup core generic bias fisst
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 Gabriella Heller CS2BACKBONE METAINFERENCE INCLUDE TORSION PBMETAD WHOLEMOLECULES GROUP COORDINATION GYRATION ANTIBETARMSD STATS MOLINFO ALPHARMSD ENDPLUMED PARABETARMSD PRINT ENSEMBLE DIHCOR COMBINE FLUSH function colvar multicolvar isdb core generic secondarystructure bias
20.009 The dynamics of linear polyubiquitin bio saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics Carlo Camilloni METAINFERENCE CENTER GYRATION SAXS TORSION DISTANCE ALPHABETA STATS MOLINFO PBMETAD ENSEMBLE FLUSH PRINT WHOLEMOLECULES vatom function colvar multicolvar isdb generic bias
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 Kevin Rossi CUSTOM COORDINATION UNITS METAD PRINT DISTANCES function colvar multicolvar setup generic bias
20.004 Data-driven collective variables for enhanced sampling methods collective variables, machine learning, deep-lda Luigi Bonati ENDPLUMED GROUP OPES_METAD LOAD UPPER_WALLS MATHEVAL COM UNITS TORSION DISTANCE LOWER_WALLS PRINT PYTORCH_MODEL FLUSH function vatom colvar setup core opes generic pytorch bias
20.000 Muscarinic M2 receptor-ligand funnel metadynamics bio multiple walker metadynamics, well-tempered metadynamics, funnel metadynamics, MC-HLDA, GPCR, receptor, Adiabatic Bias MD Riccardo Capelli ENDPLUMED ABMD REWEIGHT_METAD UPPER_WALLS MATHEVAL HISTOGRAM COM CONVERT_TO_FES DUMPGRID READ COMBINE DISTANCE LOWER_WALLS METAD PRINT function vatom colvar generic gridtools bias
19.083 Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis chemistry metadynamics, chemical reactions, reaction discovery Valerio Rizzi ENDPLUMED GROUP UPPER_WALLS RESTART UNITS COMBINE METAD COORDINATIONNUMBER PRINT DISTANCES FLUSH function symfunc multicolvar setup core generic bias
19.062 Elucidating molecular design principles for charge-alternating peptides bio peptide folding, metadynamics, well-tempered ensemble, parallel tempering Jim Pfaendtner GYRATION METAD ENERGY PRINT WHOLEMOLECULES colvar bias generic
19.061 Diffusion in porous materials materials metadynamics, porous materials, diffusion Kim E. Jelfs GROUP UPPER_WALLS RESTART COM CENTER METAD DISTANCE LOWER_WALLS PRINT vatom colvar setup core generic bias
19.060 Neural networks-based variationally enhanced sampling methods ves, neural networks Luigi Bonati ENDPLUMED LOAD UNITS TORSION ENERGY Q6 PRINT ENVIRONMENTSIMILARITY POSITION colvar setup envsim symfunc generic
19.058 Constrained MD for maintaining a cavity in a calculation chemistry constrained MD, porous molecules, porosity, cavity Kim Jelfs MOVINGRESTRAINT RESTART COM INPLANEDISTANCES FLUSH PRINT DISTANCES vatom multicolvar setup generic bias
19.052 Gibbs free energy of homogeneous nucleation materials nucleation, surface excess free energy Gareth Tribello ENDPLUMED CELL UPPER_WALLS FCCUBIC UNITS METAD PRINT colvar setup symfunc generic bias
19.049 Determining the sizes of solid/liquid clusters in MD trajectories of nucleation methods nucleation, metadynamics, clustering, Steinhardt order parameters Gareth Tribello OUTER_PRODUCT CUSTOM CLUSTER_NATOMS SMAC MATRIX_VECTOR_PRODUCT LOCAL_Q6 ONES OUTPUT_CLUSTER METAD DFSCLUSTERING Q6 CONTACT_MATRIX PRINT CLUSTER_DISTRIBUTION COORDINATIONNUMBER CLUSTER_PROPERTIES DISTANCES MORE_THAN function multicolvar matrixtools adjmat clusters symfunc generic bias
19.047 Close Structure methods metadynamics, RMSD, path collective variables, property map Vojtech Spiwok METAD PRINT WHOLEMOLECULES PROPERTYMAP colvar bias generic
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 Jim Pfaendtner UPPER_WALLS COM METAD ENERGY DISTANCE PRINT vatom colvar bias generic
19.040 Optimal Metric for Path Collective Variables bio metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path Francesco Luigi Gervasio ENDPLUMED MATHEVAL TORSION METAD PRINT function colvar bias generic
19.024 PT-MetaD-WTE methods metadynamics, WTE, trp cage, PT Jim Pfaendtner GROUP COORDINATION EXTERNAL METAD ENERGY bias colvar core
19.020 PTMetaD-WTE simulation of the Ntail IDP bio metadynamics, IDPs, protein folding Mattia Bernetti ENDPLUMED GYRATION METAD ENERGY MOLINFO ALPHARMSD PRINT WHOLEMOLECULES secondarystructure colvar bias generic
19.019 FA-MetaD-JCP-Wang-et-al bio Frequency adaptive metadynamics; peptide Kresten Lindorff-Larsen COMBINE METAD ALPHABETA FLUSH MOLINFO PRINT COMMITTOR function multicolvar bias generic
25.012 A Machine Learning-Driven, Probability-Based Approach to Enzyme Catalysis bio enzyme catalysis, transition state, structure-activity relationship, free energy surface, reaction mechanism, water, alpha-amylase, sugar, QM/MM MD, OPES, committor function, machine learning Sudip Das FLUSH POSITION COMBINE CUSTOM ENERGY PRINT CELL MATHEVAL OPES_METAD INCLUDE BIASVALUE TORSION UNITS DISTANCE LOAD COORDINATION opes function generic colvar setup bias
24.004 Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables materials metadynamics, nucleation, machine learning Ziyue Zou PRINT INCLUDE RESTART METAD GROUP LOAD generic setup core bias
24.003 Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations chemistry steered molecular dynamics, foldamers, peptoids, bio-inspired Kaylyn Torkelson WHOLEMOLECULES ALPHABETA PRINT GYRATION MOVINGRESTRAINT INCLUDE TORSION DISTANCE COM COORDINATION generic colvar vatom bias multicolvar
24.001 A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations bio OPES, OPES-Flooding, QM/MM, Kinetics, Enzyme Catalysis Dhiman Ray FLUSH CUSTOM PRINT COMBINE COMMITTOR UPPER_WALLS OPES_METAD TORSION UNITS DISTANCE LOWER_WALLS opes function generic colvar setup bias
24.000 Ammonia Decomposition on Non-stoichiometric Lithium Imide chemistry ammonia decomposition, non-stoichiometric lithium imide, machine learning interatomic potentials, enhanced sampling, heterogeneous catalysis Francesco Mambretti FLUSH COORDINATIONNUMBER PRINT UPPER_WALLS ZDISTANCES OPES_METAD FIXEDATOM UNITS DISTANCE GROUP core opes generic colvar vatom setup bias symfunc multicolvar
23.032 Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics bio metadynamics, tSNE, neural network, machine learning, trp-cage, folding Vojtech Spiwok WHOLEMOLECULES MOLINFO COMBINE PRINT ALPHARMSD ANN METAD FIT_TO_TEMPLATE POSITION function generic colvar secondarystructure annfunc bias
23.030 Data Driven Classification of Ligand Unbinding Pathways bio OPES Explore, OPES Flooding, Benzene T4 Lysozyme, Ligand unbinding, Pathway classification, Kinetics, Residence time Dhiman Ray MOLINFO WRAPAROUND COMMITTOR BIASVALUE POSITION CENTER COORDINATION ENERGY UPPER_WALLS ENDPLUMED TORSION UNITS DISTANCE WHOLEMOLECULES FLUSH PRINT CUSTOM LOWER_WALLS FIT_TO_TEMPLATE COM OPES_METAD_EXPLORE MATHEVAL OPES_METAD GROUP core opes function generic colvar vatom setup bias
23.028 Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process chemistry Ammonia decomposition; Dynamics;OPES; Neural Network potential Manyi Yang FLUSH COORDINATIONNUMBER PRINT CUSTOM ENERGY COMMITTOR UPPER_WALLS MATHEVAL OPES_METAD ZDISTANCES DISTANCES FIXEDATOM UNITS DISTANCE GROUP LOWER_WALLS COM core opes function generic colvar vatom setup bias symfunc multicolvar
23.020 FEP simulations of ATOX1 homodimer chemistry parallel bias metadynamics, FEP, free-energy of metal ion dissociation Adriana Pietropaolo WHOLEMOLECULES PRINT PBMETAD MATHEVAL BIASVALUE CONSTANT DISTANCE ANGLE generic colvar function bias
23.007 Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains bio metadynamics, peptoids, parallel-bias metadynamics Jim Pfaendtner WHOLEMOLECULES PRINT GYRATION PBMETAD INCLUDE TORSION RESTRAINT COM COORDINATION generic colvar vatom bias
23.006 Transcription factor unbinding bio metadynamics, DNA, conformational changes Malin Lüking MOLINFO PRINT ALPHARMSD CONTACTMAP DUMPFORCES METAD DISTANCE ANGLE COM generic colvar vatom secondarystructure bias
22.037 Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site chemistry metadynamics, DNA, abasic Mike Jones DISTANCE DISTANCES PRINT METAD generic colvar bias multicolvar
22.019 Exploring aspartic protease inhibitor binding to design selective antimalarials bio ligand binding, loop opening, path CV, funnel metadynamics, drug development Raitis Bobrovs WHOLEMOLECULES FUNNEL_PS PRINT PATHMSD UPPER_WALLS FUNNEL METAD DISTANCE LOWER_WALLS COM generic funnel colvar vatom bias
21.039 Deep learning the slow modes for rare events sampling methods collective variables, machine learning, slow modes, deep-tica, opes Luigi Bonati MOLINFO PYTORCH_MODEL LOAD ENERGY ENDPLUMED TORSION ECV_MULTITHERMAL UNITS DISTANCE WHOLEMOLECULES FLUSH PRINT VOLUME COMBINE OPES_EXPANDED Q6 CONTACTMAP ENVIRONMENTSIMILARITY OPES_METAD INCLUDE RMSD GROUP core opes function generic colvar setup envsim symfunc pytorch
21.035 CmuMD simulations of NaCl(aq) at NaCl chemistry CmuMD, interface Aaron Finney PRINT FIXEDATOM RESTRAINT DISTANCE GROUP LOAD core generic colvar vatom setup bias
21.033 Multiple-path-metadynamics applied to DNA base-pairing transitions bio path-CV, metadynamics, multiple-walker, dna Alberto Pérez-de-Alba-Ortíz COMBINE PRINT MOVINGRESTRAINT UPPER_WALLS RESTRAINT INCLUDE METAD CONSTANT generic bias function
21.028 From Enhanced Sampling to Reaction Profiles methods collective variables, multi-state, machine learning, Deep-TDA Enrico Trizio PYTORCH_MODEL LOAD COORDINATION CENTER UPPER_WALLS ENDPLUMED TORSION FIXEDATOM UNITS DISTANCE WHOLEMOLECULES PRINT DISTANCES LOWER_WALLS FIT_TO_TEMPLATE GROUP MATHEVAL OPES_METAD ANGLE core opes function generic colvar vatom setup bias pytorch multicolvar
21.023 Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling methods enhanced sampling, collective variables, machine learning Jakub Rydzewski CUSTOM PRINT ENERGY INCLUDE BIASVALUE TORSION METAD CONSTANT DISTANCE UNITS REWEIGHT_METAD function generic colvar setup bias
21.007 Sampling enhancement by metadynamics driven by machine learning and de novo protein modelling bio metadynamics, machine learning, protein folding Vojtech Spiwok MOLINFO WHOLEMOLECULES COMBINE ALPHARMSD MATHEVAL FIT_TO_TEMPLATE POSITION generic secondarystructure function colvar
21.001 Substrate recognition and catalysis by glycosaminoglycan sulfotransferases bio metadynamics, well-tempered metadynamics, puckering, coordination Tarsis Ferreira MOLINFO WHOLEMOLECULES RANDOM_EXCHANGES PUCKERING PRINT ENERGY REWEIGHT_METAD DUMPGRID UPPER_WALLS HISTOGRAM INCLUDE METAD LOWER_WALLS DISTANCE GROUP COORDINATION core generic colvar bias gridtools
20.025 The role of water in host-guest interaction bio ligand binding, water, opes, SAMPL5 Valerio Rizzi WHOLEMOLECULES DISTANCE PRINT PYTORCH_MODEL ENERGY UPPER_WALLS MATHEVAL OPES_METAD ANGLE ENDPLUMED COORDINATION FIXEDATOM FIT_TO_TEMPLATE GROUP CENTER core opes function generic colvar vatom bias pytorch
20.023 metadynminer and metadynminer3d methods metadynamics, visualization, R Vojtech Spiwok PRINT TORSION METAD generic colvar bias
20.019 Systematic finite-temperature reduction of crystal energy landscapes materials crystals, organics, structure prediction Matteo Salvalaglio PRINT ENERGY CELL UPPER_WALLS MATHEVAL VOLUME METAD LOWER_WALLS generic colvar function bias
19.071 Time-independent free energies from metadynamics via Mean Force Integration methods metadynamics, mean force integration, MFI, thermodynamic integration Matteo Salvalaglio PRINT READ REWEIGHT_BIAS DUMPGRID COMMITTOR EXTERNAL MATHEVAL HISTOGRAM TORSION BIASVALUE METAD DISTANCE CONVERT_TO_FES REWEIGHT_METAD function generic colvar bias gridtools
19.066 Finding ligand unbinding reaction pathways methods maze, ligand unbinding Jakub Rydzewski MAZE_LOSS PRINT MAZE_OPTIMIZER_BIAS UNITS MAZE_SIMULATED_ANNEALING POSITION generic setup colvar maze
19.056 maze methods maze, ligand unbinding Jakub Rydzewski MAZE_LOSS PRINT MAZE_OPTIMIZER_BIAS UNITS MAZE_SIMULATED_ANNEALING POSITION generic setup colvar maze
19.053 Capillary fluctuations with PLUMED methods nucleation, surface tension, capillary fluctuations Gareth Tribello MORE_THAN DUMPGRID FOURIER_TRANSFORM MULTICOLVARDENS FIND_CONTOUR_SURFACE FCCUBIC UNITS GROUP CENTER fourier core function vatom setup gridtools symfunc contour
19.039 Funnel Metadynamics bio funnel-metadynamics, absolute binding free energy, ligand-receptor complexes Vittorio Limongelli WHOLEMOLECULES FUNNEL_PS PRINT UPPER_WALLS RMSD FUNNEL METAD DISTANCE LOWER_WALLS COM generic funnel colvar vatom bias
19.032 Chemical reaction in solution using path collective variables based on coordination patterns chemistry chemical reactions, solutions, metadynamics, coordination patterns Fabio Pietrucci FLUSH PRINT UPPER_WALLS DISTANCES RESTART METAD PATH generic setup mapping bias multicolvar
19.025 Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide bio metainference, NMR, protein dynamics, force-fields Carlo Camilloni MOLINFO WHOLEMOLECULES FLUSH PRINT GYRATION METAINFERENCE STATS PBMETAD ENSEMBLE ENDPLUMED TORSION BIASVALUE RDC JCOUPLING CS2BACKBONE function generic colvar isdb bias
19.022 eABF simulation of NANMA (alanine dipeptide) methods eABF, DRR, alanine dipeptide Haochuan Chen DRR TORSION PRINT generic colvar drr
19.013 RNA FF FITTING methods force field, RNA Giovanni Bussi MOLINFO PUCKERING MATHEVAL INCLUDE TORSION BIASVALUE CONSTANT generic colvar bias function
19.000 VesDeltaF methods VES, convergence, suboptimal CVs Michele Invernizzi PRINT ENERGY ENDPLUMED TORSION RESTART METAD VES_DELTA_F LOAD UNITS POSITION generic colvar ves setup bias
25.002 M3_PCV-ABMD chemistry Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor Gian Marco Elisi UPPER_WALLS PATHMSD ENDPLUMED PRINT UNITS ABMD setup colvar generic bias
24.034 Umbrella sampling of ion in transporter SLC26A7 bio umbrella sampling, transporter, ions Xiaoli Lu PRINT UNITS RESTRAINT POSITION colvar setup generic bias
24.019 Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning bio OPES, machine learning, protein folding, adaptive sampling Mingyuan Zhang COMBINE ALPHARMSD OPES_METAD COORDINATION GYRATION DISTANCE TORSION CUSTOM WHOLEMOLECULES PRINT MOLINFO function opes colvar secondarystructure generic
24.012 Molecular simulations to investigate the impact of N6-methylation in RNA recognition bio metadynamics, alchemistry, RNA modification, RNA:protein interactions Giovanni Bussi COMBINE PRINT BIASVALUE CENTER COORDINATION COM LOWER_WALLS GROUP DISTANCE DEBUG GHBFIX METAD UPPER_WALLS MOLINFO core function colvar generic bias vatom
23.033 DNA G-quadruplex and G-hairpin folding with ST-metaD protocol bio DNA, G4, GQ, quadruplex, hairpin, folding, metadynamics, REST2, ST-metaD Pavlína Pokorná COMBINE BIASVALUE COORDINATION GHBFIX ERMSD WHOLEMOLECULES METAD PRINT MOLINFO colvar generic bias function
23.024 Permutationally Invariant Networks for Enhanced Sampling (PINES) methods collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent Nicholas Herringer LOAD PBMETAD PRINT setup generic bias
23.023 Rational design of novel biomimetic sequence-defined polymers for mineralization applications methods metadynamics, surface binding, biomimetic mineralization Kaylyn Torkelson PRINT COORDINATION COM GYRATION PBMETAD DISTANCE UPPER_WALLS colvar generic bias vatom
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 Timothy Clark REWEIGHT_METAD MATHEVAL DISTANCE DUMPGRID METAD WHOLEMOLECULES CONVERT_TO_FES RMSD PRINT READ HISTOGRAM MOLINFO gridtools function colvar generic bias
23.015 MPCs aggregation bio opes_explore, dimerization, MPCs, self-assembly Vikas Tiwari PRINT CENTER OPES_METAD_EXPLORE COORDINATION COM LOWER_WALLS GROUP DISTANCE CUSTOM METAD WHOLEMOLECULES UPPER_WALLS core function opes colvar generic bias vatom
23.003 Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations methods metadynamics, alchemical variable, alchemical free energy calculations Wei-Tse Hsu TORSION METAD PRINT READ EXTRACV colvar generic bias
23.002 Critical comparison of general-purpose collective variables for crystal nucleation methods metadynamics, umbrella sampling, commitor, entropy, PIV Julien Lam ENERGY FUNCPATHMSD PRINT Q4 RESTRAINT VOLUME PAIRENTROPY CUSTOM Q6 METAD PIV UPPER_WALLS UNITS LOCAL_AVERAGE setup gridtools piv function colvar symfunc generic bias
22.036 Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction bio Well-tempered MetaDynamics with Hamiltonian Replica Exchange Miroslav Krepl COMBINE PRINT BIASVALUE COORDINATION GROUP LOAD CUSTOM GHBFIX METAD UPPER_WALLS MOLINFO FLUSH core setup function colvar generic bias
22.028 N-glycan conformer distributions in atomistic simulation bio REST2, RECT, N-glycan, pucker Isabell Grothaus MOLINFO TORSION METAD CONVERT_TO_FES DUMPGRID PRINT READ HISTOGRAM PUCKERING gridtools colvar generic bias
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 Faidon Brotzakis PRINT BIASVALUE COORDINATION COM GROUP PBMETAD RESTART TORSION EMMI WHOLEMOLECULES RMSD UPPER_WALLS MOLINFO core setup colvar isdb generic bias vatom
22.013 Ligand dissociation from PreQ1 riboswitch bio ligand, RNA, metadynamics, pRAVE Yihang Wang COMMITTOR COMBINE COORDINATIONNUMBER COM DISTANCE METAD WHOLEMOLECULES RMSD PRINT MOLINFO function colvar symfunc generic bias vatom
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 Elena Papaleo PRINT ALPHARMSD COORDINATION DISTANCE TORSION ANGLE WHOLEMOLECULES METAD ALPHABETA UPPER_WALLS MOLINFO FLUSH colvar secondarystructure generic bias multicolvar
21.051 Automatic learning of hydrogen-bond fixes in an AMBER RNA force field methods force field, RNA Giovanni Bussi COMBINE BIASVALUE COORDINATION ERMSD METAD WHOLEMOLECULES PRINT MOLINFO colvar generic bias function
21.049 Multiple-path-metadynamics and PathMaps methods path-CV, metadynamics, multiple-walker, multiple paths, pathmap Alberto Pérez-de-Alba-Ortíz COMBINE PRINT RESTRAINT ENSEMBLE LOWER_WALLS CONSTANT TORSION LOAD CUSTOM METAD UPPER_WALLS UNITS MOVINGRESTRAINT setup function colvar generic bias
21.013 Role of vibrational excitation in heterogeneous catalysis chemistry catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption Kristof Bal REWEIGHT_METAD COMBINE LOWER_WALLS DISTANCES ANGLES UWALLS COORDINATIONNUMBER COORDINATION TD_GRID DISTANCE LOAD CONVERT_TO_FES UNITS OPT_AVERAGED_SGD EXTERNAL VES_LINEAR_EXPANSION REWEIGHT_BIAS BF_CHEBYSHEV PRINT HISTOGRAM FLUSH RESTRAINT METAD DUMPGRID UPPER_WALLS setup ves gridtools function colvar symfunc generic bias multicolvar
21.003 aSYN SAXS metainference bio metainference, SAXS Kresten Lindorff-Larsen ALPHARMSD BIASVALUE EEFSOLV CENTER GYRATION GROUP PBMETAD METAINFERENCE WHOLEMOLECULES PRINT SAXS MOLINFO FLUSH core colvar isdb secondarystructure generic bias vatom
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 Pablo Piaggi ENERGY ECV_MULTITHERMAL_MULTIBARIC MATHEVAL OPT_AVERAGED_SGD VOLUME VES_LINEAR_EXPANSION UPPER_WALLS RESTART ECV_UMBRELLAS_LINE Q6 BF_LEGENDRE PRINT ENVIRONMENTSIMILARITY OPES_EXPANDED TD_UNIFORM setup ves function opes colvar envsim symfunc generic bias
21.000 Uremic toxin time scale dynamics bio uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs) Jim Pfaendtner COM GROUP DISTANCE WHOLEMOLECULES PRINT core colvar generic vatom
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 Sandro Bottaro CENTER DISTANCE RESTART TORSION ERMSD PRINT MOLINFO ABMD setup colvar generic bias vatom
20.028 Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane bio metadynamics, KRas-4B, anionic membrane Huixia Lu FIT_TO_TEMPLATE CENTER DISTANCE RESTART METAD PRINT setup colvar generic bias vatom
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 Carlo Camilloni PRINT BIASVALUE LOWER_WALLS ANTIBETARMSD GROUP PBMETAD CS2BACKBONE WHOLEMOLECULES ENDPLUMED ALPHABETA UPPER_WALLS MOLINFO FLUSH core isdb secondarystructure generic bias multicolvar
19.082 Ammonia Borane Dehydrogenation chemistry metadynamics, reaction discovery, hydrogen production, chemistry Valerio Rizzi COMBINE COORDINATIONNUMBER EXTERNAL GROUP RESTART METAD ENDPLUMED PRINT UNITS FLUSH core setup function symfunc generic bias
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 Sarah Alamdari ENERGY PRINT COM GYRATION GROUP DISTANCE METAD UPPER_WALLS MOLINFO core colvar generic bias vatom
19.074 Asymmetric base pair opening in nucleic acids bio double helix, DNA, RNA, unwindability Giovanni Bussi RESTRAINT COORDINATION LOWER_WALLS DISTANCE WHOLEMOLECULES ENDPLUMED colvar generic bias
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 Matteo Salvalaglio ENERGY PRINT COORDINATIONNUMBER LOWER_WALLS GYRATION METAD ENDPLUMED DISTANCES UPPER_WALLS colvar symfunc generic bias multicolvar
19.055 Flying Gaussian method methods flying Gaussians, alanine dipeptide, peptide bond, Met-enkephalin Vojtech Spiwok COMBINE MATHEVAL DISTANCE TORSION METAD PRINT colvar generic bias function
19.054 MetaFEP methods metadynamics, chemistry, free energy perturbation GiovanniMaria Piccini ENERGY COMBINE PRINT LOWER_WALLS DISTANCE METAD UPPER_WALLS UNITS FLUSH setup function colvar generic bias
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 Faidon Brotzakis REWEIGHT_METAD COMBINE PRINT COM LOWER_WALLS GROUP DISTANCE TORSION ALPHABETA FUNNEL METAD WHOLEMOLECULES DISTANCES BRIDGE RMSD UPPER_WALLS MOLINFO core funnel function colvar generic bias multicolvar vatom adjmat
19.035 Dimerization of GPCRs from coarse-grained umbrella sampling bio Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization Davide Provasi RESTRAINT COM GROUP DISTANCE TORSION PRINT core colvar generic bias vatom
19.017 Ligand binding pathways exploration bio metadynamics, ligand binding Riccardo Capelli REWEIGHT_METAD PRINT FIT_TO_TEMPLATE MATHEVAL COORDINATION COM GROUP WRAPAROUND METAD WHOLEMOLECULES CONVERT_TO_FES ENDPLUMED DUMPGRID UPPER_WALLS READ HISTOGRAM FLUSH POSITION core gridtools function colvar generic bias vatom
19.002 EMMI STRA6 bio metainference, cryo-EM Max Bonomi BIASVALUE GROUP EMMI PRINT MOLINFO core generic bias isdb
25.004 Machine Learning-Driven Molecular Dynamics Unveil a Bulk Phase Transformation Driving Ammonia Synthesis on Barium Hydride chemistry OPES, OPES flooding, Catalysis, Ammonia Synthesis Axel Tosello Gardini COMMITTOR FLUSH UNITS ZDISTANCES DISTANCE CUSTOM COORDINATIONNUMBER OPES_METAD UPPER_WALLS FIXEDATOM GROUP DISTANCES PRINT symfunc opes multicolvar setup colvar vatom core generic function bias
25.003 Surrogate Model CV methods Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding Sompriya Chatterjee GROUP COMMITTOR PYTORCH_MODEL MOLINFO ENERGY DISTANCE MATHEVAL COMBINE OPES_METAD CUSTOM ENDPLUMED WHOLEMOLECULES TORSION PRINT pytorch opes colvar generic function core
24.024 Host-Guest binding free energies à la carte, an automated OneOPES protocol bio OneOPES, ligand binding, binding free energy,SAMPL challenge, host-guest Valerio Rizzi LOWER_WALLS COORDINATION OPES_METAD_EXPLORE ENERGY DISTANCE MATHEVAL UPPER_WALLS FIT_TO_TEMPLATE ANGLE FIXEDATOM ENDPLUMED ECV_MULTITHERMAL OPES_EXPANDED CENTER GROUP TORSION PRINT WHOLEMOLECULES opes colvar vatom core generic function bias
24.007 SWISH-X bio swish-x, SWISH-X, swish, expanded SWISH Alberto Borsatto MOLINFO ENERGY ECV_MULTITHERMAL OPES_EXPANDED WHOLEMOLECULES UPPER_WALLS PRINT CONTACTMAP INCLUDE colvar opes generic bias
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 Lorenzo Gigli SELECT_COMPONENTS TRANSPOSE SUM FLUSH MATHEVAL METAD PRINT INCLUDE valtools generic matrixtools function bias
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 Timothy Clark MOLINFO RMSD DISTANCE MATHEVAL METAD WHOLEMOLECULES PRINT function colvar generic bias
23.034 Urea nucleation in water: do long-range forces matter? materials LMF theory, Metadynamics, Nucleation Ziyue Zou LOAD COORDINATIONNUMBER METAD CENTER GROUP PRINT INCLUDE symfunc setup vatom core generic bias
23.027 CmuMD simulations of NaCl(aq) at NaCl chemistry CmuMD, DFS, Q3, Pair Entropy Aaron Finney DUMPGRID DENSITY AROUND DFSCLUSTERING Q3 HISTOGRAM LOAD CONTACT_MATRIX UNITS RESTRAINT CLUSTER_DISTRIBUTION COORDINATIONNUMBER FIXEDATOM LOCAL_Q3 CLUSTER_NATOMS GROUP PRINT LOCAL_AVERAGE symfunc setup clusters vatom bias core volumes generic gridtools adjmat
23.026 Machine Learning Nucleation Collective Variables with Graph Neural Networks chemistry Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks Florian Dietrich LOCAL_Q6 LOWER_WALLS COMBINE COORDINATIONNUMBER Q6 METAD MOVINGRESTRAINT GROUP PRINT MFILTER_MORE symfunc multicolvar core generic function bias
23.022 A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar methods collective variables, machine learning, toy model Enrico Trizio PYTORCH_MODEL BIASVALUE LOWER_WALLS UNITS CUSTOM OPES_METAD ENDPLUMED POSITION UPPER_WALLS PRINT pytorch opes setup colvar generic function bias
23.014 Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 bio metadynamics, oligomerization, chemokine receptors, GPCR, membrane Vittorio Limongelli FLUSH COMBINE DISTANCE COM UPPER_WALLS METAD WHOLEMOLECULES TORSION PRINT colvar vatom generic function bias
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 Istvan Kolossvary BIASVALUE DRR FLUSH PATHMSD CUSTOM METAD PRINT drr colvar generic function bias
22.004 Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques chemistry reaction discovery, OPES, collective variables Umberto Raucci PYTORCH_MODEL LOAD OPES_METAD_EXPLORE UNITS COORDINATION LOWER_WALLS COM CUSTOM DISTANCE MATHEVAL OPES_METAD GROUP UPPER_WALLS PRINT pytorch opes setup colvar vatom core generic function bias
21.050 N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity methods bio Isabell Louise Grothaus CENTER PRINT DISTANCE colvar vatom generic
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 Elena Papaleo GYRATION LOWER_WALLS ALPHABETA ENDPLUMED METAD GROUP UPPER_WALLS PRINT WHOLEMOLECULES multicolvar colvar core generic bias
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 Matej Badin COORDINATION COMBINE CUSTOM VOLUME ENDPLUMED METAD PRINT function colvar generic bias
21.027 EGFR activating mutations mechanism bio metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA Francesco Gervasio MOLINFO LOWER_WALLS ENERGY DISTANCE MATHEVAL METAD ALPHARMSD WHOLEMOLECULES UPPER_WALLS PRINT CONTACTMAP INCLUDE secondarystructure colvar generic function bias
21.008 Multi-replica biased sampling for photoisomerization processes in conjugated polymers methods metadynamics, FEP, replica-exchange Adriana Pietropaolo BIASVALUE PBMETAD PRINT MATHEVAL RESTART WHOLEMOLECULES TORSION CONSTANT setup colvar generic function bias
20.032 Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil materials clustering, conformational isomers Matteo Salvalaglio TORSION ENDPLUMED PRINT colvar generic
20.026 Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor bio Metadynamics, Umbrella sampling Brandon Peters DUMPGRID MULTI_RMSD REWEIGHT_METAD CONVERT_TO_FES HISTOGRAM RESTRAINT METAD PRINT generic colvar gridtools bias
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 Pablo Piaggi ENVIRONMENTSIMILARITY VES_LINEAR_EXPANSION TD_WELLTEMPERED OPT_DUMMY MATHEVAL OPT_AVERAGED_SGD VOLUME Q6 RESTART UPPER_WALLS PRINT BF_LEGENDRE symfunc ves setup colvar envsim generic function bias
19.065 Molecular Enhanced Sampling with Autoencoders methods enhanced sampling, collective variables, deep learning Wei Chen RESTRAINT ANN COMBINE COM POSITION annfunc colvar vatom function bias
19.064 Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations materials metadynamics, peptide-surface binding Jim Pfaendtner GYRATION MOLINFO DISTANCE COM METAD UPPER_WALLS ENERGY PRINT colvar vatom generic bias
19.037 Scission free energy of organic dyes chemistry metadynamics, multiple walkers, matheval/lepton Paolo Raiteri FLUSH UNITS DISTANCE MATHEVAL METAD RESTART UPPER_WALLS PRINT setup colvar generic function bias
19.030 Coarse-Grained MetaDynamics (CG-MetaD) bio Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy Vittorio Limongelli LOWER_WALLS DISTANCE COM METAD WHOLEMOLECULES UPPER_WALLS PRINT generic colvar vatom bias
19.023 RECT methods metadynamics, replica exchange Giovanni Bussi GYRATION METAD WHOLEMOLECULES TORSION PRINT generic colvar bias
19.021 Coarse-Grained Directed Simulation methods experiment directed simulation, coarse-grain, bias Glen Hocky RESTRAINT COMBINE DISTANCE EDS TORSION PRINT colvar eds generic function bias
19.014 MIL101(Cr) SBUs assembly materials MOFs, nucleation, self-assembly, metadynamics Matteo Salvalaglio GYRATION COORDINATIONNUMBER ENDPLUMED METAD RESTART DISTANCES PRINT symfunc multicolvar setup colvar generic bias
19.006 Flying Gaussian proof methods flying Gaussians, alanine dipeptide Vojtech Spiwok TORSION PRINT METAD colvar generic bias
19.005 Cmyc small molecule interaction bio metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP Gabriella Heller PBMETAD GYRATION MOLINFO COORDINATION DISTANCE CS2BACKBONE ALPHABETA WHOLEMOLECULES CENTER GROUP METAINFERENCE PRINT INCLUDE multicolvar colvar vatom core generic bias isdb
19.001 RNA SHAPE bio metadynamics, RNA, ligand binding Giovanni Bussi RANDOM_EXCHANGES DISTANCES FLUSH MOLINFO LOWER_WALLS COMBINE DISTANCE ANGLE ERMSD METAD UPPER_WALLS PRINT INCLUDE multicolvar colvar generic function bias
25.008 Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting methods metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting Dhiman Ray MOLINFO ENDPLUMED GROUP PRINT WHOLEMOLECULES RMSD BIASVALUE PYTORCH_MODEL ENERGY OPES_METAD UPPER_WALLS DISTANCE LOWER_WALLS POSITION CUSTOM METAD UNITS TORSION bias setup core opes function colvar generic pytorch
24.036 Leveraging cryptic ligand envelopes through enhanced molecular simulations bio HREX, conformational heterogeneity, drug discovery, ligand binding, plitidepsin, aplidin, ligand-target complexes, cryptic ligand envelope Francesco Colizzi HISTOGRAM GROUP PRINT WHOLEMOLECULES COORDINATION ANGLE DISTANCE DUMPGRID CONVERT_TO_FES TORSION gridtools generic core colvar
24.020 Graph Neural Network-State Predictive Information Bottleneck (GNN-SPIB) approach for learning molecular thermodynamics and kinetics bio LJ7, alanine, well-tempered metadynamics, infrequent metadynamics, machine learning Ziyue Zou, Dedi Wang, Pratyush Tiwary GROUP PRINT METAD LOAD COMMITTOR TORSION setup bias core colvar generic
24.017 Absolute Binding Free Energies with OneOPES methods protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy Francesco Gervasio RMSD OPES_EXPANDED COM COORDINATION PROJECTION_ON_AXIS CUSTOM MOLINFO WRAPAROUND WHOLEMOLECULES CONSTANT BIASVALUE MATHEVAL CONTACTMAP PRINT ECV_MULTITHERMAL ENERGY RESTART METAD OPES_METAD_EXPLORE TORSION GROUP LOWER_WALLS UPPER_WALLS INCLUDE bias setup core opes function generic colvar vatom
24.014 Learning Collective Variables with Synthetic Data Augmentation through Physics-inspired Geodesic Interpolation methods data augmentation, geodesic interpolation, collective variables, protein folding Juno Nam MOLINFO RMSD PRINT DRR WHOLEMOLECULES COORDINATION PYTORCH_MODEL FLUSH LOWER_WALLS METAD UPPER_WALLS bias drr colvar generic pytorch
23.046 Lasso Peptides - HLDA CV bio metadynamics, protein folding, HLDA, harmonic Gabriel da Hora COMBINE WHOLEMOLECULES PRINT DISTANCE METAD UNITS setup bias function colvar generic
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 Vittorio Limongelli MOLINFO CONTACTMAP PRINT UPPER_WALLS DISTANCE LOWER_WALLS ALPHARMSD PATHMSD METAD INCLUDE FUNCPATHMSD bias secondarystructure function colvar generic
23.018 Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention materials metadynamics, surface binding, peptide adsorption Kaylyn Torkelson PRINT COM DISTANCE GYRATION UPPER_WALLS PBMETAD generic bias vatom colvar
23.008 PBMetaD simulations of Histatin5 bio metadynamics, IDP, Rg, PPII Francesco Pesce MOLINFO GROUP WHOLEMOLECULES PRINT GYRATION PBMETAD TORSION generic bias core colvar
23.001 Quantum phase diagram of water chemistry Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella Sigbjørn-Løland Bore OPES_EXPANDED PRINT ENVIRONMENTSIMILARITY UPPER_WALLS LOWER_WALLS ECV_UMBRELLAS_LINE RESTART INCLUDE bias setup opes generic envsim
22.042 Metadynamics of NSP10 and variants bio metadynamics, NSP10, crystal structure, variants Shozeb Haider PRINT TORSION METAD generic bias colvar
22.040 From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure bio SARS-CoV-2, Spike, Omicron Miłosz Wieczór WHOLEMOLECULES PRINT LOWER_WALLS PCAVARS METAD UPPER_WALLS generic mapping bias
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 Kresten Lindorff-Larsen MOLINFO WHOLEMOLECULES GYRATION PBMETAD TORSION generic bias colvar
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 Max Bonomi RMSD PRINT generic colvar
22.003 Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling methods opes, metadynamics, reweighting, alanine, muller Michele Invernizzi ENDPLUMED OPES_EXPANDED PRINT ECV_UMBRELLAS_FILE ECV_MULTITHERMAL BIASVALUE OPES_METAD ENERGY UPPER_WALLS LOWER_WALLS POSITION CUSTOM METAD UNITS PBMETAD OPES_METAD_EXPLORE TORSION bias setup opes function colvar generic
21.026 Probing allosteric regulations with coevolution-driven molecular simulations bio metadynamics, coevolution, allostery, adenylate cyclase Francesco Colizzi WHOLEMOLECULES PRINT COM UPPER_WALLS DISTANCE PATHMSD METAD UNITS bias setup colvar generic vatom
21.022 Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly materials parallel bias metadynamics, adsorption, peptide Xin Qi MOLINFO PRINT COM ENERGY LOWER_WALLS DISTANCE GYRATION UPPER_WALLS PBMETAD generic bias vatom colvar
21.021 ATLAS methods Machine Learning, Metadynamics Federico Giberti GROUP PRINT DUMPATOMS WHOLEMOLECULES COORDINATION BIASVALUE MATHEVAL DISTANCE GYRATION METAD UNITS COORDINATIONNUMBER TORSION bias setup core symfunc function colvar generic
21.018 Localized Volume-based Metadynamics bio LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification Riccardo Capelli RMSD HISTOGRAM FIXEDATOM COM COORDINATION DISTANCE FLUSH WHOLEMOLECULES READ MATHEVAL ENDPLUMED PRINT DUMPGRID METAD CONVERT_TO_FES GROUP POSITION UPPER_WALLS REWEIGHT_METAD gridtools bias core function colvar generic vatom
21.012 NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition bio funnel metadynamics Jim Pfaendtner PRINT COM FUNNEL DISTANCE FUNNEL_PS LOWER_WALLS METAD UPPER_WALLS bias funnel colvar generic vatom
21.006 OPES, On-the-fly Probability Enhanced Sampling Method methods opes, alanine dipeptide, well-tempered, multithermal, multiumbrella Michele Invernizzi ENDPLUMED OPES_EXPANDED PRINT ECV_MULTITHERMAL OPES_METAD ENERGY ECV_UMBRELLAS_LINE TORSION generic opes colvar
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 Cristina Paissoni MOLINFO WHOLEMOLECULES PRINT STATS COORDINATION RESTRAINT generic bias colvar function
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 Pablo Piaggi HISTOGRAM TD_WELLTEMPERED OPT_DUMMY BF_LEGENDRE VOLUME REWEIGHT_TEMP_PRESS READ MATHEVAL REWEIGHT_BIAS COMBINE PRINT ENERGY Q6 CELL DUMPGRID RESTART LOAD CONVERT_TO_FES TD_MULTITHERMAL_MULTIBARIC OPT_AVERAGED_SGD VES_LINEAR_EXPANSION LOWER_WALLS UPPER_WALLS gridtools bias setup symfunc function ves colvar generic
19.080 Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium methods ves, variationally enhanced sampling, vibrational excitation, chemical reactions Kristof Bal HISTOGRAM TD_WELLTEMPERED COMBINE PRINT OPT_AVERAGED_SGD COORDINATION TD_GRID UPPER_WALLS ANGLE BF_CHEBYSHEV FLUSH DISTANCE VES_LINEAR_EXPANSION DUMPGRID EXTERNAL LOWER_WALLS UNITS CONVERT_TO_FES gridtools bias setup function ves colvar generic
19.045 Adsorption free energy of Ca/CO3 ions on calcite steps in contact with water materials metadynamics, well-tempered, multiple walkers, LAMMPS Marco De La Pierre GROUP PRINT COORDINATION UPPER_WALLS FLUSH LOWER_WALLS POSITION RESTART METAD UNITS setup bias core colvar generic
19.027 Multithermal-multibaric simulations using VES methods ves, Wang Landau, multicanonical, liquid sodium, density anomaly Pablo Piaggi AVERAGE COMBINE HISTOGRAM PRINT TD_MULTICANONICAL OPT_AVERAGED_SGD REWEIGHT_TEMP_PRESS OPT_DUMMY READ ENERGY BF_LEGENDRE DUMPGRID VES_LINEAR_EXPANSION REWEIGHT_BIAS RESTART UNITS CONVERT_TO_FES gridtools bias setup function ves colvar generic
19.026 Ice Nucleation on Cholesterol Crystals materials forward flux sampling, crystal nucleation, water, ice, organic crystals Gabriele Cesare Sosso MFILTER_MORE ENDPLUMED LOCAL_Q6 OUTPUT_CLUSTER Q6 CONTACT_MATRIX DFSCLUSTERING CLUSTER_WITHSURFACE FLUSH CLUSTER_NATOMS COMMITTOR symfunc adjmat multicolvar generic clusters