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 |
|---|---|---|---|---|---|---|
| 26.015 | Ensemble Dynamics | methods | State Exploration, Protein Folding, Drug Binding, Phase Transition | Florian M. Dietrich | POSITION LOAD TORSION PRINT GROUP CUSTOM BIASVALUE CELL UNITS OPES_METAD_EXPLORE DISTANCE | colvar generic function setup bias opes core |
| 25.026 | Deciphering the Molecular Mechanisms of Startle Disease - the Role of the Asn46Lys Mutation in the Glycine Receptor | bio | metadynamics, glycine receptors, funnel metadynamics | Jacob Adam Clark | COM UPPER_WALLS FUNNEL_PS LOWER_WALLS PRINT METAD FUNNEL | bias generic vatom funnel |
| 25.010 | Kinetic rates calculation with Ratchet&Pawl MD | methods | kinetics, ligand binding, ABMD, ratchet&pawl MD | Riccardo Capelli | COM ABMD PRINT FLUSH COMMITTOR GROUP WHOLEMOLECULES DISTANCE | colvar generic core bias vatom |
| 25.008 | Deep TICA CV from Nonequilibrium Metadynamics using Koopman Reweighting | methods | metadynamics, OPES, Machine Learning CV, PyTorch, Koopman Reweighting | Dhiman Ray | POSITION UPPER_WALLS MOLINFO TORSION PRINT LOWER_WALLS GROUP METAD PYTORCH_MODEL OPES_METAD BIASVALUE CUSTOM UNITS WHOLEMOLECULES ENDPLUMED RMSD DISTANCE ENERGY | colvar generic function pytorch bias setup opes core |
| 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 | MOLINFO INCLUDE PRINT TORSION GYRATION PBMETAD UPDATE_IF ENERGY VOLUME DUMPATOMS READ WHOLEMOLECULES CENTER DISTANCE RESTART | colvar generic setup bias vatom |
| 24.017 | Absolute Binding Free Energies with OneOPES | methods | protein ligand binding free energy, oneopes, metadynamics, brd4, hsp90, absolute binding free energy | Francesco Gervasio | WRAPAROUND UPPER_WALLS MOLINFO METAD COORDINATION WHOLEMOLECULES ECV_MULTITHERMAL OPES_METAD_EXPLORE RESTART LOWER_WALLS CONTACTMAP OPES_EXPANDED ENERGY COM TORSION PRINT GROUP CUSTOM PROJECTION_ON_AXIS INCLUDE MATHEVAL BIASVALUE RMSD CONSTANT | colvar generic core function setup bias vatom opes |
| 24.011 | Computing the Committor with the Committor, an Anatomy of the Transition State Ensemble | methods | committor, machine learning | Peilin Kang | UPPER_WALLS MOLINFO COORDINATION CELL WHOLEMOLECULES ENDPLUMED POSITION LOWER_WALLS UNITS DISTANCE ENERGY TORSION PRINT GROUP CUSTOM LOAD INCLUDE MATHEVAL BIASVALUE RMSD | colvar generic function setup bias core |
| 24.007 | SWISH-X | bio | swish-x, SWISH-X, swish, expanded SWISH | Alberto Borsatto | UPPER_WALLS INCLUDE MOLINFO PRINT CONTACTMAP OPES_EXPANDED ECV_MULTITHERMAL WHOLEMOLECULES ENERGY | bias colvar generic opes |
| 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 | UPPER_WALLS TORSION LOWER_WALLS PRINT FLUSH COMMITTOR CUSTOM OPES_METAD COMBINE UNITS DISTANCE | colvar generic function setup bias opes |
| 23.036 | Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? | bio | NaCl, nucleation, metadynamics | Ruiyu Wang | PRINT METAD Q4 MATHEVAL VOLUME COMBINE COORDINATIONNUMBER Q6 ENERGY | colvar generic function bias symfunc |
| 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 | WRAPAROUND UPPER_WALLS MOLINFO COORDINATION WHOLEMOLECULES OPES_METAD_EXPLORE ENDPLUMED CENTER POSITION FIT_TO_TEMPLATE LOWER_WALLS COMMITTOR UNITS DISTANCE ENERGY COM TORSION PRINT FLUSH GROUP CUSTOM MATHEVAL OPES_METAD BIASVALUE | colvar generic core function vatom bias setup opes |
| 23.002 | Critical comparison of general-purpose collective variables for crystal nucleation | methods | metadynamics, umbrella sampling, commitor, entropy, PIV | Julien Lam | UPPER_WALLS PRINT FUNCPATHMSD PIV METAD Q4 CUSTOM LOCAL_AVERAGE RESTRAINT VOLUME PAIRENTROPY UNITS Q6 ENERGY | colvar generic function piv setup bias symfunc gridtools |
| 22.029 | Angiotensin-1-7_Metadynamics | bio | Metadynamics, Angiotensin-(1-7), peptide | L.-América Chi | UPPER_WALLS LOWER_WALLS PRINT FLUSH GROUP GYRATION METAD COORDINATION WHOLEMOLECULES | bias colvar generic 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 | UPPER_WALLS FIT_TO_TEMPLATE LOWER_WALLS PRINT COMMITTOR GROUP MATHEVAL FIXEDATOM PYTORCH_MODEL COORDINATION OPES_METAD CUSTOM RMSD DISTANCE CENTER WHOLEMOLECULES | colvar generic function vatom bias pytorch opes core |
| 22.003 | Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling | methods | opes, metadynamics, reweighting, alanine, muller | Michele Invernizzi | POSITION UPPER_WALLS TORSION LOWER_WALLS PRINT ECV_UMBRELLAS_FILE METAD PBMETAD OPES_METAD BIASVALUE CUSTOM OPES_EXPANDED UNITS ECV_MULTITHERMAL OPES_METAD_EXPLORE ENDPLUMED ENERGY | colvar generic function setup bias opes |
| 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 | UPPER_WALLS TD_UNIFORM OPT_ADAM METAD BF_LEGENDRE BF_CUBIC_B_SPLINES COORDINATION BF_GAUSSIANS POSITION BF_WAVELETS TD_WELLTEMPERED OPT_AVERAGED_SGD UNITS VES_OUTPUT_BASISFUNCTIONS DISTANCE ENERGY PRINT FLUSH VES_LINEAR_EXPANSION BF_CHEBYSHEV INCLUDE | colvar generic setup bias ves |
| 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 | UPPER_WALLS LOWER_WALLS PRINT GROUP GYRATION METAD ALPHABETA WHOLEMOLECULES ENDPLUMED | colvar generic multicolvar bias core |
| 21.044 | NaCl nucleation | chemistry | metadynamics, DFS clustering | Aaron Finney | COORDINATIONNUMBER DUMPGRID PRINT GROUP MFILTER_MORE CLUSTER_NATOMS Q6 METAD FIXEDATOM CONTACT_MATRIX INSPHERE DFSCLUSTERING CLUSTER_DISTRIBUTION COMBINE HISTOGRAM LOCAL_Q6 | generic function multicolvar vatom bias adjmat symfunc gridtools clusters core volumes |
| 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 | FIT_TO_TEMPLATE TORSION PRINT METAD FIXEDATOM | bias 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 | COM UPPER_WALLS LOWER_WALLS MOLINFO PRINT GYRATION PBMETAD DISTANCE ENERGY | bias colvar generic vatom |
| 21.016 | MD SAXS GTPase associated center | bio | metadynamics, RNA, folding, SAXS | Giovanni Bussi | UPPER_WALLS INCLUDE LOWER_WALLS MOLINFO PRINT GROUP GYRATION SAXS METAD ERMSD CUSTOM WHOLEMOLECULES | colvar generic isdb function bias core |
| 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 | POSITION PRINT METAD MATHEVAL COORDINATION RESTRAINT WHOLEMOLECULES CENTER REWEIGHT_BIAS RESTART | colvar generic function setup bias vatom |
| 21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Kresten Lindorff-Larsen | MOLINFO PRINT FLUSH GROUP METAINFERENCE GYRATION PBMETAD SAXS BIASVALUE ALPHARMSD EEFSOLV WHOLEMOLECULES CENTER | colvar generic isdb vatom bias core secondarystructure |
| 20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Adriana Pietropaolo | PRINT PBMETAD COORDINATION WHOLEMOLECULES CENTER | bias colvar generic vatom |
| 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 | MOLINFO PRINT STATS COORDINATION COMBINE WHOLEMOLECULES RESTRAINT | bias function generic colvar |
| 20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Valerio Rizzi | UPPER_WALLS FIT_TO_TEMPLATE PRINT GROUP ANGLE MATHEVAL FIXEDATOM PYTORCH_MODEL COORDINATION OPES_METAD WHOLEMOLECULES ENDPLUMED CENTER DISTANCE ENERGY | colvar generic function vatom bias pytorch opes core |
| 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 | PRINT METAD CUSTOM COORDINATION DISTANCES UNITS | colvar generic function multicolvar setup bias |
| 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 | UPPER_WALLS MOLINFO PRINT PATHMSD GROUP METAD WHOLEMOLECULES RESTART | colvar generic setup bias core |
| 19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Sandro Bottaro | MOLINFO TORSION PRINT METAD ERMSD WHOLEMOLECULES RMSD DISTANCE | bias colvar generic |
| 19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Luigi Bonati | POSITION LOAD TORSION PRINT ENVIRONMENTSIMILARITY UNITS ENDPLUMED Q6 ENERGY | colvar envsim generic setup symfunc |
| 19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Cristina Paissoni | MOLINFO INCLUDE PRINT GROUP SAXS PBMETAD ANGLE STATS MATHEVAL ALPHABETA BIASVALUE COORDINATION ENSEMBLE COMBINE ENDPLUMED CENTER WHOLEMOLECULES | colvar generic isdb function multicolvar vatom bias core |
| 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 TORSION PRINT FLUSH METAINFERENCE GYRATION PBMETAD CS2BACKBONE STATS BIASVALUE ENSEMBLE WHOLEMOLECULES RDC ENDPLUMED JCOUPLING | colvar generic isdb function bias |
| 19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Adriana Pietropaolo | TORSION PRINT METAD MATHEVAL BIASVALUE WHOLEMOLECULES CONSTANT | bias colvar generic function |
| 19.013 | RNA FF FITTING | methods | force field, RNA | Giovanni Bussi | INCLUDE MOLINFO TORSION MATHEVAL BIASVALUE PUCKERING CONSTANT | bias colvar generic function |
| 19.009 | RNA tetraloops folding | bio | metadynamics, RNA, folding | Giovanni Bussi | MOLINFO PRINT METAD ERMSD WHOLEMOLECULES ENDPLUMED RMSD | bias colvar generic |
| 19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Max Bonomi | MOLINFO PRINT GROUP BIASVALUE EMMI | bias isdb generic core |
| 26.002 | A Transferable and Robust Computational Framework for Class A GPCR Activation Free Energies | bio | OneOPES, GPCR, ADRB1, activation, euclidean path, microswitches, conformational changes, allostery | Valerio Rizzi | UPPER_WALLS ECV_MULTITHERMAL DISTANCE COORDINATION CENTER LOWER_WALLS RMSD PATH OPES_EXPANDED ENERGY PATHMSD VOLUME GROUP CUSTOM OPES_METAD_EXPLORE PRINT | mapping vatom bias function core generic opes colvar |
| 25.018 | Metainference simulation for dimerization of RNA binding protein | bio | Metainference, Metadynamics, SAXS, protein dimer | Debadutta Patra | UPPER_WALLS DISTANCE FLUSH CENTER TORSION GYRATION METAINFERENCE ENSEMBLE SAXS STATS PBMETAD WHOLEMOLECULES MOLINFO PRINT | vatom bias isdb function generic colvar |
| 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 | UPPER_WALLS DISTANCE COMBINE COORDINATION FLUSH LOWER_WALLS METAD COM FIXEDATOM UNITS GROUP COORDINATIONNUMBER ANGLE RESTRAINT DISTANCES PRINT | vatom bias setup function core generic symfunc multicolvar colvar |
| 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 | UPPER_WALLS COORDINATION FLUSH PYTORCH_MODEL LOWER_WALLS RMSD DRR METAD WHOLEMOLECULES MOLINFO PRINT | drr bias generic colvar pytorch |
| 24.006 | Water vapor condensation | chemistry | metadynamics, homogeneous condensation, chemical potential | Shenghui Zhong | UPPER_WALLS CLUSTER_NATOMS CONTACT_MATRIX UNITS CLUSTER_PROPERTIES COORDINATIONNUMBER METAD DFSCLUSTERING PRINT | setup clusters adjmat bias generic symfunc |
| 23.018 | Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention | materials | metadynamics, surface binding, peptide adsorption | Kaylyn Torkelson | UPPER_WALLS DISTANCE COM GYRATION PBMETAD PRINT | generic vatom colvar bias |
| 22.042 | Metadynamics of NSP10 and variants | bio | metadynamics, NSP10, crystal structure, variants | Shozeb Haider | METAD TORSION PRINT | generic colvar 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 | UPPER_WALLS COORDINATION RMSD COM TORSION BIASVALUE RESTART GROUP EMMI PBMETAD WHOLEMOLECULES MOLINFO PRINT | setup vatom bias isdb core generic colvar |
| 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 | DISTANCE COM TORSION GROUP METAD WHOLEMOLECULES PRINT | vatom bias core generic colvar |
| 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 | UPPER_WALLS DISTANCE COMBINE COORDINATION FLUSH LOWER_WALLS COM GYRATION UNITS COORDINATIONNUMBER METAD | vatom bias setup function generic symfunc colvar |
| 21.050 | N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity | methods | bio | Isabell Louise Grothaus | DISTANCE CENTER PRINT | generic vatom colvar |
| 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 | RANDOM_EXCHANGES TORSION INCLUDE METAD PBMETAD ENDPLUMED PRINT | generic colvar bias |
| 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 | DISTANCE COORDINATION COM TORSION GYRATION ENERGY PRINT INCLUDE METAD PBMETAD ALPHABETA | vatom bias generic multicolvar colvar |
| 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 | generic | |
| 20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Cristina Paissoni | DISTANCE CENTER BIASVALUE ENSEMBLE INCLUDE GROUP SAXS RESTRAINT STATS WHOLEMOLECULES MOLINFO PRINT | vatom bias isdb function core generic colvar |
| 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 | TORSION GYRATION CS2BACKBONE COORDINATION ENSEMBLE INCLUDE ENDPLUMED MOLINFO FLUSH METAINFERENCE ALPHARMSD PARABETARMSD STATS PBMETAD PRINT ANTIBETARMSD COMBINE DIHCOR GROUP WHOLEMOLECULES | bias isdb secondarystructure function core generic multicolvar colvar |
| 20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Jim Pfaendtner | DISTANCE COORDINATION CENTER RESTART GROUP WHOLEMOLECULES DISTANCES PRINT | setup vatom core generic multicolvar colvar |
| 20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Luigi Bonati | UPPER_WALLS DISTANCE LOWER_WALLS PYTORCH_MODEL FLUSH COM OPES_METAD TORSION MATHEVAL LOAD UNITS GROUP ENDPLUMED PRINT | vatom bias setup function core generic opes colvar pytorch |
| 19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Valerio Rizzi | COMBINE FLUSH RESTART UNITS EXTERNAL GROUP COORDINATIONNUMBER METAD ENDPLUMED PRINT | setup bias function core generic symfunc |
| 19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Michele Invernizzi | TORSION OPES_METAD UNITS POSITION EXTERNAL METAD ENDPLUMED PRINT | setup bias generic opes colvar |
| 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 DISTANCE COM ENERGY METAD PRINT | generic vatom colvar bias |
| 19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Elena Papaleo | UPPER_WALLS LOWER_WALLS GYRATION GROUP ALPHABETA METAD WHOLEMOLECULES MOLINFO PRINT | bias core generic multicolvar colvar |
| 19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Kresten Lindorff-Larsen | METAD COMBINE FLUSH ALPHABETA COMMITTOR MOLINFO PRINT | generic multicolvar function bias |
| 26.014 | Dissociation free energy (DFE) calculationsfor GPR15L–polySia | bio | metadynamics, protein-carbohydrate interaction | Davide Luciano and Gaston Courtade | UPPER_WALLS DISTANCE COM PRINT GROUP METAD | colvar vatom bias generic core |
| 26.004 | Resolving the ambiguous binding site of quercetin at the calcineurin subunit junction using funnel metadynamics with deep learning collective variables | bio | metadynamics, funnel metadynamics, DeepTICA | Jason Loo | GROUP COM DISTANCE WHOLEMOLECULES WRAPAROUND UPPER_WALLS COORDINATION PYTORCH_MODEL MATHEVAL LOWER_WALLS FUNNEL RMSD PRINT FUNNEL_PS METAD ENERGY | funnel function colvar vatom core pytorch generic bias |
| 26.001 | Molecular simulations Alx riboswitch | bio | RNA, riboswitch | Giovanni Bussi | MOLINFO ERMSD DISTANCE MATHEVAL PRINT MOVINGRESTRAINT RESTRAINT | generic colvar function bias |
| 25.016 | Advancing in silico drug design with Bayesian refinement of AlphaFold models | bio | bAIes, AlphaFold, Bayesian refinement, virtual screening, docking, small-molecule, enrichment | Samiran Sen | BAIES BIASVALUE PRINT GROUP | generic core isdb bias |
| 25.003 | Surrogate Model CV | methods | Metadynamics, OPES, Machine Learning, Collective Variable, Protein Folding | Sompriya Chatterjee | MOLINFO CUSTOM COMMITTOR DISTANCE WHOLEMOLECULES COMBINE TORSION PYTORCH_MODEL ENDPLUMED PRINT GROUP MATHEVAL ENERGY OPES_METAD | function colvar pytorch generic opes core |
| 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 | CUSTOM RESTART UPPER_WALLS CENTER WHOLEMOLECULES DISTANCE COORDINATION TORSION PYTORCH_MODEL LOWER_WALLS FIT_TO_TEMPLATE FIXEDATOM PRINT GROUP PATH OPES_METAD | function vatom colvar pytorch core generic setup opes mapping bias |
| 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 | FIT_TO_TEMPLATE ENDPLUMED METAD MOLINFO COMMITTOR UPPER_WALLS CENTER CONTACTMAP COMBINE COORDINATION CUSTOM WHOLEMOLECULES DISTANCE ANGLE RMSD FIXEDATOM MATHEVAL OPES_METAD TORSION PRINT GROUP | function vatom colvar core generic opes bias |
| 23.034 | Urea nucleation in water: do long-range forces matter? | materials | LMF theory, Metadynamics, Nucleation | Ziyue Zou | CENTER COORDINATIONNUMBER LOAD PRINT GROUP METAD INCLUDE | vatom bias generic setup symfunc core |
| 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 CUSTOM LANDMARK_SELECT_FPS SKETCHMAP UPPER_WALLS WHOLEMOLECULES COM DISTANCE COLLECT_FRAMES VORONOI TRANSPOSE PATHMSD PRINT SKETCHMAP_PROJECTION METAD VSTACK | function vatom matrixtools colvar valtools generic dimred landmarks bias |
| 23.014 | Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 | bio | metadynamics, oligomerization, chemokine receptors, GPCR, membrane | Vittorio Limongelli | UPPER_WALLS WHOLEMOLECULES COM DISTANCE COMBINE TORSION FLUSH PRINT METAD | function vatom colvar generic bias |
| 23.005 | A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs | bio | metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A | Timothy Clark | MOLINFO WHOLEMOLECULES DISTANCE READ HISTOGRAM REWEIGHT_METAD MATHEVAL RMSD DUMPGRID PRINT CONVERT_TO_FES METAD | function colvar gridtools generic bias |
| 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 | UPPER_WALLS CONTACTMAP WHOLEMOLECULES LOWER_WALLS PRINT METAD ENERGY | generic colvar bias |
| 22.041 | Skipping the Replica Exchange Ladder with Normalizing Flows | methods | OPES, alanine, normalizing flows, replica exchange | Michele Invernizzi | OPES_EXPANDED POSITION TORSION ENDPLUMED UNITS PRINT ECV_MULTITHERMAL ENERGY OPES_METAD | generic colvar opes setup |
| 22.036 | Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction | bio | Well-tempered MetaDynamics with Hamiltonian Replica Exchange | Miroslav Krepl | MOLINFO BIASVALUE CUSTOM UPPER_WALLS COMBINE LOAD GHBFIX FLUSH COORDINATION PRINT GROUP METAD | function colvar bias core generic setup |
| 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 | CUSTOM BIASVALUE DRR FLUSH PATHMSD PRINT METAD | function colvar generic drr bias |
| 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 | ECV_UMBRELLAS_LINE UPPER_WALLS OPES_EXPANDED ENVIRONMENTSIMILARITY LOWER_WALLS PRINT INCLUDE | generic opes envsim bias |
| 22.000 | Amyloid precursor protein processing by human γ-secretase | bio | Bias Exchange Metadynamics, Helix unfolding, coupled binding | Xiaoli Lu | MOLINFO ANTIBETARMSD CONTACTMAP DISTANCE CENTER COORDINATION RANDOM_EXCHANGES ALPHARMSD UNITS PRINT METAD INCLUDE | colvar vatom bias generic secondarystructure setup |
| 21.051 | Automatic learning of hydrogen-bond fixes in an AMBER RNA force field | methods | force field, RNA | Giovanni Bussi | MOLINFO BIASVALUE ERMSD WHOLEMOLECULES COMBINE COORDINATION PRINT METAD | generic colvar function bias |
| 21.037 | Molecular Dynamics simulations of RBD/hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain | Max Bonomi | RMSD DISTANCE PRINT | generic colvar |
| 21.032 | Metal-coupled folding mechanism to metallothionein | bio | parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination | Manuel-Peris Diaz | WHOLEMOLECULES COORDINATION PBMETAD UNITS GROUP | colvar core bias generic setup |
| 21.031 | Photo-switchable sulfonulureas in KATP channel | bio | metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels | Katarzyna Walczewska-Szewc | UPPER_WALLS DISTANCE WHOLEMOLECULES COM LOWER_WALLS UNITS PRINT METAD | colvar vatom bias generic setup |
| 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 | MOLINFO ERMSD CENTER DISTANCE TORSION ABMD PRINT RESTART | colvar vatom bias generic setup |
| 20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Faidon Brotzakis | MOLINFO BIASVALUE GROUP DISTANCES WHOLEMOLECULES READ HISTOGRAM RMSD DUMPGRID PRINT CONVERT_TO_FES EMMI | bias colvar gridtools generic multicolvar isdb core |
| 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 | TORSION METAD DISTANCE PRINT | generic colvar bias |
| 20.024 | Gaussian Mixture Based Enhanced Sampling (GAMBES) | methods | enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias | Jayashrita Debnath | UPPER_WALLS DISTANCE DISTANCES COMBINE LOAD TORSION LOWER_WALLS UNITS PRINT GROUP ENERGY | function colvar bias core generic multicolvar setup |
| 20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Max Bonomi | MOLINFO WHOLEMOLECULES ALPHABETA COORDINATION DIHCOR PBMETAD PRINT GYRATION INCLUDE | generic colvar multicolvar bias |
| 20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Carlo Camilloni | MOLINFO CENTER WHOLEMOLECULES DISTANCE ALPHABETA SAXS TORSION FLUSH PBMETAD METAINFERENCE ENSEMBLE GYRATION PRINT STATS | function vatom colvar generic multicolvar isdb 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 | UPPER_WALLS DISTANCES COORDINATIONNUMBER LOWER_WALLS ENDPLUMED PRINT GYRATION METAD ENERGY | colvar generic multicolvar symfunc bias |
| 19.056 | maze | methods | maze, ligand unbinding | Jakub Rydzewski | MAZE_LOSS MAZE_OPTIMIZER_BIAS MAZE_SIMULATED_ANNEALING POSITION UNITS PRINT | generic colvar maze setup |
| 19.048 | Understanding Ligand Binding Selectivity in a Prototypical GPCR Family | bio | metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | BIASVALUE UPPER_WALLS WHOLEMOLECULES COM DISTANCE MATHEVAL CONSTANT LOWER_WALLS PRINT METAD | function vatom colvar generic bias |
| 19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | UPPER_WALLS DISTANCE COMBINE FLUSH UNITS PRINT METAD ENERGY | function colvar bias generic setup |
| 19.040 | Optimal Metric for Path Collective Variables | bio | metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path | Francesco Luigi Gervasio | TORSION METAD ENDPLUMED PRINT MATHEVAL | generic colvar function bias |
| 19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Riccardo Capelli | UPPER_WALLS COM WHOLEMOLECULES WRAPAROUND READ CONVERT_TO_FES HISTOGRAM POSITION REWEIGHT_METAD COORDINATION MATHEVAL FLUSH FIT_TO_TEMPLATE ENDPLUMED PRINT GROUP DUMPGRID METAD | function vatom colvar core gridtools generic bias |
| 19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Matteo Salvalaglio | UPPER_WALLS VOLUME COMBINE MATHEVAL TORSION LOWER_WALLS ENDPLUMED CELL PRINT METAD ENERGY | generic colvar function bias |
| 19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Matteo Salvalaglio | COMMITTOR UPPER_WALLS CENTER DISTANCE TORSION LOWER_WALLS PRINT METAD | generic vatom colvar bias |
| 26.010 | Solvation-Mediated Ammonia Synthesis in a Nanoheterogeneous Liquid Alloy | materials | OPES, Catalysis, Ammonia Synthesis | Axel Tosello Gardini | COORDINATIONNUMBER FLUSH INCLUDE UNITS DISTANCES COORDINATION DISTANCE PRINT OPES_METAD_EXPLORE OPES_METAD UPPER_WALLS GROUP CUSTOM | function multicolvar setup symfunc colvar bias core opes generic |
| 25.023 | Molecular simulations of Tau-protein oligomers | bio | metadynamics, proteins, aggregation | Giovanni Bussi | DUMPGRID METAD RESTRAINT FLUSH CONTACTMAP RMSD PRINT REWEIGHT_BIAS RESTART CONVERT_TO_FES CUSTOM HISTOGRAM | function gridtools setup bias colvar generic |
| 25.022 | Imidazole Diffusion in SALEM-2 MOF | materials | OPES, Diffusion, Ring opening, MOFs, Machine Learning Potentials | Sudheesh Kumar Ethirajan | UNITS PROJECTION_ON_AXIS MOLINFO DISTANCES DISTANCE PRINT CENTER OPES_METAD GROUP WHOLEMOLECULES ENDPLUMED | multicolvar vatom setup colvar core opes generic |
| 25.011 | Chiral perovskite nucleation | chemistry | metadynamics, chiral perovskites, nucleation | Adriana Pietropaolo | MATHEVAL LOWER_WALLS UNITS DISTANCE PRINT MULTI_RMSD UPPER_WALLS RESTART PBMETAD | function setup bias colvar 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 | LOWER_WALLS UNITS COORDINATION COMMITTOR DISTANCE PRINT OPES_METAD UPPER_WALLS GROUP RESTART CUSTOM | function setup bias colvar core opes generic |
| 24.026 | Constant pH metadynamics of RNA oligomers | bio | metadynamics, pH, RNA | Giovanni Bussi | TORSION METAD MOLINFO PUCKERING PRINT RESTART | colvar bias setup generic |
| 24.016 | Cryo-EM guided simulations of ribozyme | bio | metainference, cryo-EM | Giovanni Bussi | RESTRAINT INCLUDE MOLINFO PRINT EMMIVOX GROUP WHOLEMOLECULES ERMSD BIASVALUE | isdb bias colvar core generic |
| 24.009 | Weighted Shape Gaussian Mixture Models | bio | metadynamics, clustering | Glen Hocky | TORSION METAD UNITS PRINT GROUP | setup colvar bias core generic |
| 24.002 | Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes | chemistry | metadynamics, ligand design, solvent extraction | Xiaoyu Wang | TORSION METAD UNITS PRINT RESTART | colvar bias setup 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 | METAD PATHMSD ALPHARMSD INCLUDE FUNCPATHMSD LOWER_WALLS MOLINFO DISTANCE CONTACTMAP PRINT UPPER_WALLS | function secondarystructure bias colvar generic |
| 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 | MATHEVAL SUM METAD FLUSH INCLUDE SELECT_COMPONENTS PRINT TRANSPOSE | valtools function bias matrixtools generic |
| 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 | MATHEVAL METAD MOLINFO DISTANCE PRINT RMSD WHOLEMOLECULES | bias function colvar generic |
| 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 | METAD MOLINFO COORDINATION GHBFIX PRINT COMBINE WHOLEMOLECULES ERMSD BIASVALUE | bias function colvar generic |
| 23.027 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, DFS, Q3, Pair Entropy | Aaron Finney | DUMPGRID RESTRAINT COORDINATIONNUMBER CLUSTER_DISTRIBUTION DENSITY UNITS FIXEDATOM LOCAL_AVERAGE LOCAL_Q3 LOAD AROUND PRINT Q3 CONTACT_MATRIX GROUP DFSCLUSTERING HISTOGRAM CLUSTER_NATOMS | vatom gridtools adjmat symfunc setup bias volumes core clusters generic |
| 23.021 | Into the Dynamics of Rotaxanes at Atomistic Resolution | materials | metadynamics, rotaxanes, molecular shuttles, molecular machines | Luigi Leanza | MATHEVAL TORSION METAD FIXEDATOM DISTANCE PRINT CENTER UPPER_WALLS CUSTOM | function vatom colvar bias generic |
| 23.020 | FEP simulations of ATOX1 homodimer | chemistry | parallel bias metadynamics, FEP, free-energy of metal ion dissociation | Adriana Pietropaolo | MATHEVAL DISTANCE PRINT WHOLEMOLECULES ANGLE BIASVALUE PBMETAD CONSTANT | colvar function bias generic |
| 23.015 | MPCs aggregation | bio | opes_explore, dimerization, MPCs, self-assembly | Vikas Tiwari | COM METAD LOWER_WALLS COORDINATION DISTANCE PRINT OPES_METAD_EXPLORE CENTER UPPER_WALLS GROUP WHOLEMOLECULES CUSTOM | function vatom bias colvar core opes 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 | LOWER_WALLS COMMITTOR ENERGY MATHEVAL INCLUDE CONTACTMAP CENTER OPES_METAD WHOLEMOLECULES ANGLE ENDPLUMED FIXEDATOM MOLINFO COORDINATION DISTANCE PRINT COMBINE UPPER_WALLS PYTORCH_MODEL RMSD GROUP CUSTOM FIT_TO_TEMPLATE | pytorch function vatom bias colvar core opes generic |
| 23.008 | PBMetaD simulations of Histatin5 | bio | metadynamics, IDP, Rg, PPII | Francesco Pesce | TORSION GYRATION MOLINFO GROUP PRINT WHOLEMOLECULES PBMETAD | colvar bias core generic |
| 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 | PRINT RMSD | colvar generic |
| 22.025 | Bubble nucleation rate predictions in a Lennard-Jones fluid | materials | free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation | Kristof Bal | DUMPGRID RESTRAINT COORDINATIONNUMBER FLUSH UNITS ANN LOAD BIASVALUE COMMITTOR PRINT REWEIGHT_BIAS UPPER_WALLS MOVINGRESTRAINT CONVERT_TO_FES CUSTOM HISTOGRAM VOLUME | function annfunc gridtools setup symfunc bias colvar generic |
| 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 | DUMPGRID VOLUME AROUND PRINT OPES_METAD ENERGY UPPER_WALLS RESTART CUSTOM HISTOGRAM ENVIRONMENTSIMILARITY | function gridtools setup colvar bias volumes envsim opes generic |
| 21.047 | Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations | materials | pair entropy, metadynamics, ves, solids, crystallization | Pablo Piaggi | METAD VOLUME OPT_AVERAGED_SGD LOAD BF_LEGENDRE PRINT COMBINE ENERGY RESTART VES_LINEAR_EXPANSION TD_WELLTEMPERED PAIRENTROPY | ves function gridtools setup bias colvar generic |
| 21.042 | Peptoid-mediated Au nanocrystal growth | materials | parallel-bias metadynamics, peptoid, Au | Xin Qi | COM GYRATION MOLINFO DISTANCE PRINT UPPER_WALLS PBMETAD | colvar generic bias vatom |
| 21.039 | Deep learning the slow modes for rare events sampling | methods | collective variables, machine learning, slow modes, deep-tica, opes | Luigi Bonati | ENERGY ECV_MULTITHERMAL VOLUME INCLUDE CONTACTMAP OPES_METAD WHOLEMOLECULES ENDPLUMED ENVIRONMENTSIMILARITY TORSION FLUSH UNITS MOLINFO LOAD DISTANCE PRINT COMBINE PYTORCH_MODEL Q6 OPES_EXPANDED RMSD GROUP | pytorch function setup symfunc colvar envsim core opes generic |
| 21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Kristof Bal | DUMPGRID METAD COORDINATIONNUMBER FLUSH UNITS REWEIGHT_METAD LOAD COMMITTOR PRINT UPPER_WALLS CONVERT_TO_FES MOVINGRESTRAINT HISTOGRAM | gridtools setup symfunc bias generic |
| 21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Tarak Karmakar | MATHEVAL FLUSH LOWER_WALLS LOAD PRINT OPES_METAD UPPER_WALLS GROUP PYTORCH_MODEL | pytorch function setup bias core opes generic |
| 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 PRINT WHOLEMOLECULES | colvar generic core vatom |
| 20.016 | Predicting polymorphism in molecular crystals using orientational entropy | materials | metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy | Pablo Piaggi | METAD INCLUDE LOAD PRINT CENTER UPPER_WALLS GROUP VOLUME | vatom setup bias colvar core generic |
| 19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | COM METAD GYRATION MOLINFO DISTANCE PRINT ENERGY UPPER_WALLS | bias generic colvar vatom |
| 19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Mattia Bernetti | METAD PATHMSD LOWER_WALLS PRINT UPPER_WALLS WHOLEMOLECULES | bias generic colvar |
| 19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Kim Jelfs | COM FLUSH DISTANCES PRINT INPLANEDISTANCES RESTART MOVINGRESTRAINT | multicolvar vatom setup bias generic |
| 19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Gareth Tribello | DUMPGRID MULTICOLVARDENS UNITS FIND_CONTOUR_SURFACE MORE_THAN FCCUBIC CENTER FOURIER_TRANSFORM GROUP | function vatom gridtools symfunc setup contour fourier core |
| 19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Gareth Tribello | METAD LOWER_WALLS UNITS CELL FCCUBIC AROUND PRINT UPPER_WALLS ENDPLUMED | symfunc setup bias colvar volumes generic |
| 19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Vittorio Limongelli | COM METAD LOWER_WALLS DISTANCE FUNNEL FUNNEL_PS RMSD PRINT UPPER_WALLS WHOLEMOLECULES | vatom funnel bias colvar generic |
| 19.035 | Dimerization of GPCRs from coarse-grained umbrella sampling | bio | Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization | Davide Provasi | TORSION COM RESTRAINT DISTANCE PRINT GROUP | vatom colvar bias core generic |
| 19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Gabriele Cesare Sosso | CLUSTER_WITHSURFACE FLUSH Q6 CLUSTER_NATOMS LOCAL_Q6 COMMITTOR OUTPUT_CLUSTER CONTACT_MATRIX DFSCLUSTERING ENDPLUMED MFILTER_MORE | multicolvar adjmat symfunc clusters generic |
| 19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Glen Hocky | TORSION RESTRAINT DISTANCE PRINT COMBINE EDS | function colvar bias eds generic |
| 25.024 | Sampling glycan-glycan interactions for B22 calculations | bio | B22, glycan, carbohydrates, distance, REST2, metadynamics, RECT, replica exchange | Isabell Louise Grothaus | COMBINE RESTRAINT COM PRINT METAD DISTANCE POSITION | colvar generic vatom bias function |
| 25.020 | Revealing Water-Mediated Activation Mechanisms in the Beta 1-Adrenergic Receptor via OneOPES-Enhanced Free Energy Landscapes | bio | OneOPES, GPCR, ADRB1, activation, microswitches, conformational changes, allostery | Valerio Rizzi | ECV_MULTITHERMAL ENERGY PATHMSD COORDINATION CENTER OPES_EXPANDED DISTANCES GROUP RMSD PRINT UPPER_WALLS DISTANCE GHOST CUSTOM LOWER_WALLS OPES_METAD_EXPLORE | opes function colvar generic vatom core bias multicolvar |
| 25.009 | Ab Initio Multiple Walkers Metadynamics Simulations of Nitrate Photolysis in Water | chemistry | metadynamics, nitrate photolysis | Kam-Tung Chan | COORDINATION FLUSH RESTART REWEIGHT_METAD GROUP PRINT UPPER_WALLS METAD HISTOGRAM DISTANCE DUMPGRID READ CUSTOM | colvar setup generic gridtools core bias function |
| 24.034 | Umbrella sampling of ion in transporter SLC26A7 | bio | umbrella sampling, transporter, ions | Xiaoli Lu | RESTRAINT UNITS PRINT POSITION | generic colvar bias setup |
| 24.028 | All-atom simulations of RNA-membrane interactions | bio | metadynamics, membrane, RNA | Giovanni Bussi | CENTER DISTANCES COMBINE GROUP WHOLEMOLECULES PRINT SORT PUCKERING UPPER_WALLS METAD DISTANCE MOLINFO POSITION GHOST MATHEVAL LOWER_WALLS GYRATION | colvar generic multicolvar vatom core bias 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 | ENERGY COORDINATION OPES_METAD PRINT UPPER_WALLS DISTANCE | bias colvar opes generic |
| 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 | colvar setup generic core bias |
| 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 | PATHMSD BIASVALUE UNITS FLUSH PRINT UPPER_WALLS METAD DRR CUSTOM LOWER_WALLS TIME | drr colvar generic setup bias function |
| 23.011 | OneOPES, a combined enhanced sampling method to rule them all | bio | OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding | Valerio Rizzi | ECV_MULTITHERMAL ENERGY OPES_EXPANDED ENDPLUMED PRINT METAD DISTANCE MOLINFO OPES_METAD_EXPLORE TORSION | bias colvar opes generic |
| 22.044 | Colloid Crystallisation Analyses | materials | Q4, Q6, Pair Entropy, DFS | Aaron Finney | LOCAL_AVERAGE COMBINE COORDINATIONNUMBER GROUP Q4 Q6 DFSCLUSTERING PRINT LOCAL_Q4 MFILTER_LESS MFILTER_MORE CLUSTER_NATOMS CONTACT_MATRIX LOCAL_Q6 | symfunc clusters generic multicolvar core adjmat function |
| 22.038 | Enhanced Sampling Aided Design of Molecular Photoswitches | chemistry | reaction discovery, OPES explore, graph CV | Umberto Raucci | COORDINATION UNITS PYTORCH_MODEL PRINT CUSTOM OPES_METAD_EXPLORE | pytorch opes colvar generic setup function |
| 22.022 | Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir | bio | RMSD, protein-ligand interactions | Isabell Grothaus | RMSD PRINT | 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 | DISTANCE CONTACTMAP CENTER PRINT | vatom colvar generic |
| 22.006 | Peptide framework for screening the effects of amino acids on assembly | bio | metadynamics, peptides | Andrew White | DISTANCES COMBINE COM GROUP PRINT METAD HISTOGRAM INCLUDE DUMPGRID REWEIGHT_BIAS CONVERT_TO_FES GYRATION | colvar generic multicolvar vatom gridtools core bias 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 | METAD WHOLEMOLECULES PRINT LOAD | bias setup generic |
| 22.004 | Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques | chemistry | reaction discovery, OPES, collective variables | Umberto Raucci | COORDINATION UNITS PYTORCH_MODEL MATHEVAL COM GROUP OPES_METAD PRINT UPPER_WALLS DISTANCE LOAD CUSTOM LOWER_WALLS OPES_METAD_EXPLORE | pytorch opes colvar setup generic vatom core bias function |
| 22.002 | GAMBES_SAMPL5_RATES | other | GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding | Jayashrita Debnath | ENERGY COORDINATION CENTER FLUSH PYTORCH_MODEL ENDPLUMED FIT_TO_TEMPLATE GROUP WHOLEMOLECULES ANGLE PRINT UPPER_WALLS DISTANCE LOAD FIXEDATOM MATHEVAL COMMITTOR | pytorch colvar generic setup vatom core bias function |
| 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 ANTIBETARMSD COORDINATION PARABETARMSD DIHCOR ALPHARMSD RANDOM_EXCHANGES GROUP WHOLEMOLECULES PRINT UPPER_WALLS METAD MOLINFO LOWER_WALLS GYRATION | secondarystructure colvar generic core bias multicolvar |
| 21.035 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, interface | Aaron Finney | GROUP RESTRAINT PRINT DISTANCE LOAD FIXEDATOM | colvar setup generic vatom core bias |
| 21.018 | Localized Volume-based Metadynamics | bio | LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification | Riccardo Capelli | COORDINATION FLUSH COM REWEIGHT_METAD UPPER_WALLS DUMPGRID HISTOGRAM DISTANCE POSITION READ MATHEVAL CONVERT_TO_FES GROUP WHOLEMOLECULES PRINT METAD FIXEDATOM ENDPLUMED RMSD | colvar generic vatom gridtools core bias function |
| 21.011 | CmuMD simulations of NaCl(aq) at graphite | chemistry | CmuMD, DFS clustering | Aaron Finney | DENSITY COORDINATIONNUMBER GROUP RESTRAINT PRINT DFSCLUSTERING MFILTER_MORE AROUND CLUSTER_NATOMS LOAD FIXEDATOM DUMPGRID CLUSTER_DISTRIBUTION MULTICOLVARDENS CONTACT_MATRIX | symfunc core clusters generic setup vatom gridtools volumes adjmat bias multicolvar |
| 21.006 | OPES, On-the-fly Probability Enhanced Sampling Method | methods | opes, alanine dipeptide, well-tempered, multithermal, multiumbrella | Michele Invernizzi | ECV_MULTITHERMAL ENERGY OPES_EXPANDED ENDPLUMED OPES_METAD PRINT ECV_UMBRELLAS_LINE TORSION | colvar opes generic |
| 21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Tarsis Ferreira | ENERGY COORDINATION GROUP RANDOM_EXCHANGES WHOLEMOLECULES PRINT PUCKERING REWEIGHT_METAD UPPER_WALLS METAD HISTOGRAM DISTANCE MOLINFO INCLUDE DUMPGRID LOWER_WALLS | colvar generic bias core gridtools |
| 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 | BIASVALUE GROUP COM WHOLEMOLECULES PRINT UPPER_WALLS METAD CONTACTMAP PROJECTION_ON_AXIS DISTANCE LOAD INCLUDE MOLINFO MATHEVAL LOWER_WALLS FUNCPATHGENERAL CONSTANT | colvar generic setup vatom core bias function |
| 20.006 | Class B GPCR activation mechanism | bio | metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding | Francesco Gervasio | ENERGY CENTER COMBINE WHOLEMOLECULES RMSD PRINT UPPER_WALLS METAD DISTANCE MOLINFO MATHEVAL LOWER_WALLS | colvar generic vatom bias function |
| 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 | FLUSH COM REWEIGHT_METAD UPPER_WALLS DUMPGRID LOWER_WALLS FUNCPATHMSD ABMD HISTOGRAM DISTANCE READ CONVERT_TO_FES COMBINE WHOLEMOLECULES PRINT METAD CONTACTMAP ENDPLUMED MOLINFO | colvar generic vatom gridtools bias function |
| 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 COM COMBINE REWEIGHT_METAD PRINT ABMD UPPER_WALLS METAD HISTOGRAM DISTANCE DUMPGRID READ MATHEVAL LOWER_WALLS CONVERT_TO_FES | colvar generic vatom gridtools bias function |
| 19.080 | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | methods | ves, variationally enhanced sampling, vibrational excitation, chemical reactions | Kristof Bal | TD_WELLTEMPERED COORDINATION UNITS FLUSH TD_GRID COMBINE ANGLE EXTERNAL PRINT UPPER_WALLS BF_CHEBYSHEV HISTOGRAM DISTANCE DUMPGRID LOWER_WALLS OPT_AVERAGED_SGD CONVERT_TO_FES VES_LINEAR_EXPANSION | colvar generic setup gridtools bias function ves |
| 19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Jim Pfaendtner | ENERGY COM PRINT UPPER_WALLS METAD DISTANCE MOLINFO GYRATION | vatom colvar bias generic |
| 19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Jim Pfaendtner | ENERGY WHOLEMOLECULES PRINT METAD GYRATION | colvar bias generic |
| 19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Kim E. Jelfs | CENTER RESTART GROUP COM PRINT UPPER_WALLS METAD DISTANCE LOWER_WALLS | colvar generic setup vatom core bias |
| 19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Carlo Camilloni | ANTIBETARMSD BIASVALUE FLUSH CS2BACKBONE PBMETAD RESTART GROUP ENDPLUMED WHOLEMOLECULES PRINT UPPER_WALLS ALPHABETA MOLINFO LOWER_WALLS | isdb secondarystructure generic setup core bias multicolvar |
| 19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Paolo Raiteri | UNITS FLUSH RESTART PRINT UPPER_WALLS METAD DISTANCE MATHEVAL | colvar generic setup bias function |
| 19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Davide Provasi | FUNCPATHMSD ENDPLUMED COM WHOLEMOLECULES RMSD PRINT METAD CONTACTMAP DISTANCE | colvar generic vatom bias function |
| 19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Pratyush Tiwary | RESTART COMBINE COM EXTERNAL WHOLEMOLECULES PRINT ALPHABETA DISTANCE COMMITTOR TORSION | colvar generic setup multicolvar vatom bias function |
| 19.005 | Cmyc small molecule interaction | bio | metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP | Gabriella Heller | METAINFERENCE COORDINATION CENTER CS2BACKBONE PBMETAD GROUP WHOLEMOLECULES PRINT ALPHABETA DISTANCE MOLINFO INCLUDE GYRATION | isdb colvar generic vatom core bias multicolvar |
| 19.003 | EMMI ClpP | bio | metainference, cryo-EM | Max Bonomi | BIASVALUE GROUP PRINT EMMI MOLINFO | core isdb bias generic |
| 26.009 | Exploring the Conformational Landscape of HIV-1 TAR RNA by PT-WTE | bio | RNA, PT-WTE, HIV-1 TAR | Stefano Bosio | METAD WHOLEMOLECULES GROUP ENERGY MOLINFO PRINT | generic core colvar bias |
| 26.008 | Ensemble Dynamics | methods | State Exploration, Protein Folding, Drug Binding, Phase Transition | Florian M. Dietrich | DISTANCE POSITION LOAD UNITS CUSTOM BIASVALUE GROUP OPES_METAD_EXPLORE CELL TORSION PRINT | setup opes generic core colvar bias function |
| 26.000 | OPES simulations of disordered proteins | bio | OPES, IDPs | Julian Streit | ECV_MULTITHERMAL OPES_EXPANDED ENERGY RESTART PRINT | generic setup opes colvar |
| 25.015 | Assessment of Force Fields for Describing Conformational Polymorphic Crystals of ROY | materials | Molecular crystal, Force Field, Collective Variable | Pradip Si and Omar Valsson | TORSIONS DISTANCES DUMPMULTICOLVAR SMAC PRINT | generic symfunc multicolvar |
| 25.013 | Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices | bio | umbrella sampling, temperature ramping | Alexander Berlaga | PYTORCH_MODEL GYRATION DISTANCE RESTRAINT PRINT | generic bias pytorch colvar |
| 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 | MATHEVAL DISTANCE OPES_METAD POSITION LOAD UNITS COORDINATION INCLUDE CUSTOM BIASVALUE ENERGY CELL FLUSH COMBINE TORSION PRINT | bias setup opes colvar generic function |
| 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 | PUCKERING DISTANCE RESTRAINT METAD PRINT RESTART MOLINFO TORSION MOVINGRESTRAINT | generic bias setup colvar |
| 25.000 | Molecular mechanism of Arp2/3 activation by nucleation promoting factors and actin monomer | bio | metadynamics, pathCV | Sahithya Sridharan Iyer | DISTANCE METAD WHOLEMOLECULES FUNCPATHGENERAL UPPER_WALLS COM GROUP RESTART MOLINFO PRINT | bias setup vatom core colvar generic function |
| 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 | DISTANCE RMSD PBMETAD WHOLEMOLECULES PARABETARMSD CENTER UPPER_WALLS COORDINATION DUMPMASSCHARGE BIASVALUE GROUP COM DUMPATOMS MOLINFO ALPHARMSD PRINT EMMI | bias secondarystructure isdb vatom core colvar generic |
| 24.032 | DeepLNE++ | methods | PATHCV, OPES | Thorben Fröhlking | DISTANCE OPES_METAD LOAD COORDINATION CUSTOM GROUP ENERGY COMBINE TORSION PRINT | setup opes generic core colvar function |
| 24.029 | Combination of OPES and OPES-Explore | methods | OPES, OPES-Explore, Metadynamics, Protein Folding, Ligand Binding, Chignolin, Trypsin | Dhiman Ray | WHOLEMOLECULES CONTACTMAP LOWER_WALLS ENDPLUMED PYTORCH_MODEL MATHEVAL DISTANCE POSITION UNITS CUSTOM OPES_METAD_EXPLORE FLUSH RMSD METAD FIXEDATOM COORDINATION FIT_TO_TEMPLATE UPPER_WALLS COMBINE MOLINFO OPES_METAD CENTER INCLUDE BIASVALUE GROUP ENERGY PRINT | setup opes vatom generic core pytorch colvar bias function |
| 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 GYRATION DISTANCE WHOLEMOLECULES PARABETARMSD INCLUDE COORDINATION PRINT GROUP ANTIBETARMSD FLUSH COMBINE TORSION MOLINFO ALPHARMSD PBMETAD DIHCOR | bias secondarystructure generic core multicolvar colvar function |
| 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 | ECV_MULTITHERMAL DISTANCE OPES_EXPANDED COORDINATION CUSTOM GROUP ENERGY OPES_METAD_EXPLORE COMBINE RESTART TORSION PRINT | setup opes generic core colvar function |
| 24.003 | Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations | chemistry | steered molecular dynamics, foldamers, peptoids, bio-inspired | Kaylyn Torkelson | ALPHABETA GYRATION DISTANCE WHOLEMOLECULES COORDINATION INCLUDE COM TORSION PRINT MOVINGRESTRAINT | bias multicolvar vatom colvar generic |
| 23.037 | Estimating binding free energy of solid binding peptides without extensive sampling | bio | metadynamics, solid binding peptides | Xin Qi | GYRATION DISTANCE PBMETAD UPPER_WALLS COM MOLINFO LOWER_WALLS PRINT | generic bias vatom colvar |
| 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 | DISTANCES POSITION WHOLEMOLECULES METAD CENTER UPPER_WALLS FIT_TO_TEMPLATE SHADOW GROUP MOLINFO WRAPAROUND PRINT | bias multicolvar isdb vatom core colvar generic |
| 23.023 | Rational design of novel biomimetic sequence-defined polymers for mineralization applications | methods | metadynamics, surface binding, biomimetic mineralization | Kaylyn Torkelson | GYRATION DISTANCE PBMETAD COORDINATION UPPER_WALLS COM PRINT | generic bias vatom colvar |
| 23.022 | A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar | methods | collective variables, machine learning, toy model | Enrico Trizio | ENDPLUMED PYTORCH_MODEL OPES_METAD POSITION UNITS UPPER_WALLS CUSTOM BIASVALUE LOWER_WALLS PRINT | bias setup opes generic pytorch colvar function |
| 23.012 | JAK2 2D meta-eABF PMF with statistical analysis | bio | 2D meta-eABF, path CV, PMF | Istvan Kolossvary | METAD DRR UPPER_WALLS CUSTOM BIASVALUE FLUSH PATHMSD LOWER_WALLS PRINT | bias drr colvar generic function |
| 22.043 | Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES | bio | OPES, RNA, Tetraloop, Folding | Gül Zerze | ECV_MULTITHERMAL WHOLEMOLECULES OPES_EXPANDED ENERGY CONTACTMAP ECV_UMBRELLAS_LINE PRINT | opes colvar generic |
| 22.040 | From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure | bio | SARS-CoV-2, Spike, Omicron | Miłosz Wieczór | METAD WHOLEMOLECULES UPPER_WALLS LOWER_WALLS PRINT PCAVARS | generic mapping bias |
| 22.033 | Reciprocal barrier restraint. Application to PROTAC passive permeability prediction | methods | PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR | Istvan Kolossvary | DISTANCE METAD UNITS DRR CUSTOM BIASVALUE COM FLUSH PRINT | setup drr vatom generic colvar bias function |
| 22.018 | Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations | bio | ligand binding, docking, EMMI, LAT1 | Max Bonomi | LOAD WHOLEMOLECULES BIASVALUE GROUP MOLINFO EMMIVOX PRINT | setup isdb generic core 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 | ENDPLUMED METAD COORDINATION CUSTOM VOLUME COMBINE PRINT | bias colvar generic function |
| 21.038 | Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics | materials | metadynamics, SGOOP, nucleation, urea | Ziyue Zou | COORDINATIONNUMBER METAD LOAD CENTER INCLUDE VOLUME GROUP ENERGY COMBINE PRINT | colvar bias setup vatom core symfunc generic function |
| 21.026 | Probing allosteric regulations with coevolution-driven molecular simulations | bio | metadynamics, coevolution, allostery, adenylate cyclase | Francesco Colizzi | DISTANCE METAD WHOLEMOLECULES UNITS UPPER_WALLS COM PATHMSD PRINT | bias setup vatom colvar generic |
| 21.025 | Computational and biochemical analysis of type IV pilus dynamics and stability | bio | molecular dynamics, calcium binding, Type IV pilus | Yasaman Karami | DISTANCE LOWER_WALLS PRINT UPPER_WALLS | generic bias colvar |
| 21.019 | Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations | materials | Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen | Matteo Salvalaglio | MATHEVAL KDE TORSIONS DISTANCE COM PRINT | gridtools vatom generic multicolvar colvar function |
| 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 | TD_UNIFORM OPT_AVERAGED_SGD MATHEVAL BF_LEGENDRE OPES_EXPANDED UPPER_WALLS ECV_MULTITHERMAL_MULTIBARIC VOLUME ENERGY ENVIRONMENTSIMILARITY RESTART VES_LINEAR_EXPANSION ECV_UMBRELLAS_LINE PRINT Q6 | bias setup opes generic envsim ves symfunc colvar function |
| 20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Pratyush Tiwary | RMSD DISTANCE METAD WHOLEMOLECULES UPPER_WALLS COMBINE RESTART TORSION MOLINFO PRINT | bias setup colvar generic function |
| 19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Valerio Rizzi | COORDINATIONNUMBER ENDPLUMED DISTANCES METAD UNITS UPPER_WALLS GROUP FLUSH COMBINE RESTART PRINT | setup symfunc generic core multicolvar bias function |
| 19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Jakub Rydzewski | METAD UNITS UPPER_WALLS RESTART PATHMSD LOWER_WALLS PRINT | generic setup colvar bias |
| 19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Jim Pfaendtner | EXTERNAL METAD COORDINATION ENERGY GROUP | core colvar bias |
| 19.023 | RECT | methods | metadynamics, replica exchange | Giovanni Bussi | GYRATION METAD WHOLEMOLECULES TORSION PRINT | generic bias colvar |
| 19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Haochuan Chen | TORSION DRR PRINT | generic drr colvar |
| 19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Max Bonomi | WHOLEMOLECULES BIASVALUE GROUP MOLINFO PRINT EMMI | bias isdb core generic |
| 26.013 | Characterizing Partially Unfolded States of the C-Terminal Domain in WT and 3PA Mouse Prion Protein | bio | parallel-bias metadynamics, PBMetaD, metadynamics, mouse prion protein, prion protein, protein folding, partially unfolded states, molecular dynamics | Sonali M. Jadhav | DUMPMASSCHARGE COORDINATION PBMETAD CONTACTMAP PRINT GYRATION DISTANCE MOLINFO COM WHOLEMOLECULES GROUP INCLUDE ALPHARMSD | secondarystructure colvar vatom generic bias core |
| 26.011 | Lets Stalk About Membranes. Committor-Based Enhanced Sampling of Stalk Formation. | bio | committor, machine learning, enhanced sampling, OPES, membrane fusion, stalk formation, nanoparticles | Giorgia Rossi | LOAD COORDINATION CENTER CUSTOM PRINT LOWER_WALLS GROUP BIASVALUE OPES_METAD_EXPLORE | function colvar vatom generic bias core setup opes |
| 25.030 | Committor Regularization | methods | metadynamics, enhanced sampling, mlcvs, committor, machine learning | Florian Dietrich | PRINT METAD MOVINGRESTRAINT UNITS | setup generic bias |
| 25.029 | Energetic Constraints in the Enzymatic Depolymerization of Crystalline PET from enhanced molecular simulations | bio | HREX-Metadynamics, PETase, crystalline PET, amorphous PET, conformational ensembles, substrate binding, chain detachment | Ania Di Pede-Mattatelli and Francesco Colizzi | REWEIGHT_BIAS METAD CONVERT_TO_FES PRINT DUMPGRID DISTANCE LOWER_WALLS UPPER_WALLS COM WHOLEMOLECULES HISTOGRAM MOLINFO FIXEDATOM | colvar vatom generic gridtools bias |
| 25.028 | Designing transferable transition state guided collective variable via interpretable machine learning model for enhanced sampling. A case study on polymer collapse transition | bio | metadynamics, polymer collapse transition, transferable CV,interpretable ML-model | Saikat Dhibar and Biman Jana | CENTER COORDINATION METAD PRINT MATHEVAL GYRATION DISTANCE UPPER_WALLS COMBINE WHOLEMOLECULES LOWER_WALLS GROUP | function colvar vatom generic bias core |
| 25.019 | The Arch from the Stones. Understanding Protein Folding Energy Landscapes via Bio-inspired Collective Variables | bio | protein folding, OPES, OneOPES, binding free energy | Valerio Rizzi | CENTER COORDINATION OPES_EXPANDED CUSTOM RMSD ENERGY PRINT DISTANCE MOLINFO COMBINE GROUP ECV_MULTITHERMAL GHOST OPES_METAD_EXPLORE | function colvar vatom generic core opes |
| 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 | COORDINATION TORSION PRINT DUMPGRID ANGLE DISTANCE HISTOGRAM WHOLEMOLECULES GROUP CONVERT_TO_FES | generic core gridtools colvar |
| 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 | FLUSH METAD ENERGY TORSION PRINT COMMITTOR MATHEVAL DISTANCE COORDINATIONNUMBER MOLINFO BIASVALUE RESTART RESTRAINT | function symfunc colvar generic bias setup |
| 24.010 | Oxytocin metadynamics simulation | bio | metadynamics, oxytocin, peptide | Jan Beránek | FLUSH METAD TORSION PRINT WHOLEMOLECULES RESTART | setup generic bias colvar |
| 24.008 | yCD Metadynamics | bio | volume-based MetaD, path CVs, infrequent MetaD, product release | James McCarty | RMSD COMMITTOR ENDPLUMED DISTANCE MOLINFO PRINT DUMPGRID GROUP FIT_TO_TEMPLATE CONVERT_TO_FES READ MATHEVAL HISTOGRAM COM WHOLEMOLECULES FIXEDATOM CONTACTMAP COORDINATION FLUSH METAD PATH WRAPAROUND UPPER_WALLS REWEIGHT_METAD INCLUDE | function mapping colvar vatom generic gridtools bias core |
| 23.046 | Lasso Peptides - HLDA CV | bio | metadynamics, protein folding, HLDA, harmonic | Gabriel da Hora | METAD UNITS PRINT DISTANCE COMBINE WHOLEMOLECULES | function colvar generic bias setup |
| 23.044 | Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition | materials | metadynamics, interlocked molecules | Luigi Leanza | COORDINATION METAD PRINT DUMPGRID READ COMMITTOR ENDPLUMED HISTOGRAM CONVERT_TO_FES GROUP | colvar generic gridtools bias core |
| 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 | CENTER CONSTANT METAD PRINT MATHEVAL LOWER_WALLS DISTANCE UPPER_WALLS WHOLEMOLECULES BIASVALUE | function colvar vatom generic 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 DISTANCES ENERGY CUSTOM UNITS OPES_METAD PRINT COMMITTOR COORDINATIONNUMBER DISTANCE MATHEVAL UPPER_WALLS COM LOWER_WALLS GROUP ZDISTANCES FIXEDATOM | function symfunc colvar vatom generic multicolvar bias core setup opes |
| 23.026 | Machine Learning Nucleation Collective Variables with Graph Neural Networks | chemistry | Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks | Florian Dietrich | Q6 MFILTER_MORE METAD PRINT COORDINATIONNUMBER LOWER_WALLS MOVINGRESTRAINT COMBINE GROUP LOCAL_Q6 | function symfunc generic multicolvar bias core |
| 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 PINES | setup generic pines bias |
| 23.006 | Transcription factor unbinding | bio | metadynamics, DNA, conformational changes | Malin Lüking | CONTACTMAP METAD ANGLE PRINT DUMPFORCES DISTANCE MOLINFO COM ALPHARMSD | secondarystructure colvar vatom generic bias |
| 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 | METAD TORSION PRINT READ EXTRACV | generic bias colvar |
| 22.024 | Conformational Entropy as a Potential Liability of Computationally Designed Antibodies | bio | metadynamics, conformational entropy, antibody, nanobody | Thomas Löhr | PBMETAD TORSION RESTART PRINT ALPHABETA MOLINFO COM WHOLEMOLECULES ANTIBETARMSD ALPHARMSD | secondarystructure colvar vatom generic multicolvar bias setup |
| 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 METAD TORSION PRINT XANGLES ALPHABETA MATHEVAL DISTANCE LOWER_WALLS UPPER_WALLS MOLINFO WHOLEMOLECULES COM COMBINE ZANGLES YANGLES | function colvar vatom generic multicolvar bias |
| 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 | COORDINATION FLUSH METAD TORSION ANGLE PRINT ALPHABETA DISTANCE MOLINFO UPPER_WALLS WHOLEMOLECULES ALPHARMSD | secondarystructure colvar generic multicolvar bias |
| 21.049 | Multiple-path-metadynamics and PathMaps | methods | path-CV, metadynamics, multiple-walker, multiple paths, pathmap | Alberto Pérez-de-Alba-Ortíz | LOAD CONSTANT METAD CUSTOM UNITS TORSION PRINT ENSEMBLE LOWER_WALLS MOVINGRESTRAINT UPPER_WALLS COMBINE RESTRAINT | function colvar generic bias setup |
| 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 | EMMI PRINT DISTANCE MOLINFO COM WHOLEMOLECULES UPPER_WALLS GROUP BIASVALUE RESTART | isdb colvar vatom generic bias core setup |
| 21.033 | Multiple-path-metadynamics applied to DNA base-pairing transitions | bio | path-CV, metadynamics, multiple-walker, dna | Alberto Pérez-de-Alba-Ortíz | CONSTANT METAD PRINT MOVINGRESTRAINT UPPER_WALLS COMBINE INCLUDE RESTRAINT | function generic bias |
| 21.029 | Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs | bio | metadynamics, small peptide, machine learning | Pratyush Tiwary | FLUSH ENERGY TORSION PRINT MOLINFO EXTERNAL RESTART | setup generic bias colvar |
| 21.017 | All-atom simulations of the Vav1 AD construct | bio | metadynamics, parallel-bias, well-tempered | Simone Orioli | CONTACTMAP PBMETAD REWEIGHT_BIAS METAD PRINT ALPHABETA MOLINFO WHOLEMOLECULES GROUP RESTART ALPHARMSD | secondarystructure colvar generic multicolvar bias core setup |
| 21.013 | Role of vibrational excitation in heterogeneous catalysis | chemistry | catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption | Kristof Bal | OPT_AVERAGED_SGD DISTANCE EXTERNAL UWALLS DISTANCES PRINT DUMPGRID CONVERT_TO_FES REWEIGHT_BIAS TD_GRID VES_LINEAR_EXPANSION COORDINATIONNUMBER HISTOGRAM LOWER_WALLS RESTRAINT LOAD COORDINATION FLUSH METAD UNITS UPPER_WALLS COMBINE REWEIGHT_METAD ANGLES BF_CHEBYSHEV | function ves symfunc colvar generic gridtools multicolvar bias setup |
| 21.012 | NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition | bio | funnel metadynamics | Jim Pfaendtner | METAD FUNNEL_PS PRINT DISTANCE LOWER_WALLS UPPER_WALLS COM FUNNEL | colvar funnel vatom generic bias |
| 20.026 | Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor | bio | Metadynamics, Umbrella sampling | Brandon Peters | MULTI_RMSD METAD CONVERT_TO_FES PRINT DUMPGRID HISTOGRAM REWEIGHT_METAD RESTRAINT | generic gridtools bias colvar |
| 19.076 | Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones | bio | molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics | Salvatore Assenza | UNITS PRINT ENDPLUMED GYRATION MOVINGRESTRAINT | setup generic bias colvar |
| 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 | COORDINATION FLUSH METAD UNITS PRINT LOWER_WALLS POSITION UPPER_WALLS GROUP RESTART | colvar generic bias core setup |
| 19.004 | MI Ubiquitin | bio | metainference, NMR | Max Bonomi | CS2BACKBONE PRINT METAINFERENCE RDC MOLINFO WHOLEMOLECULES GROUP | generic isdb core |
| 26.006 | Metadynamics simulations of buried phosphorylation sites and proline isomerisation | bio | metadynamics | Julian Streit | WHOLEMOLECULES TORSION COORDINATION PRINT MOLINFO METAD | colvar generic bias |
| 25.027 | Enhanced-sampling MD simulations of a protein-peptide complex integrating SAXS and XL-MS experimental information | bio | steered MD, metadynamics, SAXS, XL-MS, ensemble reconstruction | Mattia Bernetti | WHOLEMOLECULES PRINT CENTER MOLINFO INCLUDE GROUP METAD SAXS UPPER_WALLS MOVINGRESTRAINT DISTANCE GYRATION | generic bias core colvar vatom isdb |
| 25.021 | All You Need Is Water. Converging Ligand Binding Simulations with Hydration Collective Variables | bio | OPES Explore, ligand binding, binding free energy, water, hydration CVs, SAMPL challenge, host-guest | Valerio Rizzi | WHOLEMOLECULES COORDINATION ENERGY PRINT FIT_TO_TEMPLATE CENTER MATHEVAL GROUP FIXEDATOM OPES_METAD_EXPLORE UPPER_WALLS DISTANCE ANGLE | generic bias core opes colvar vatom function |
| 25.017 | Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity | bio | EMMIVox, cryo-EM, allostery, decamer, filament, ensemble refinement, glutamine synthetase | Samuel Hoff | WHOLEMOLECULES PRINT MOLINFO EMMIVOX GROUP BIASVALUE | generic core bias isdb |
| 25.014 | Atomic resolution ensembles of intrinsically disordered proteins with Alphafold | bio | bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement | Vincent Schnapka | BAIES GROUP PRINT BIASVALUE | generic core bias isdb |
| 24.031 | DeepLNE | methods | PATHCV, OPES, OneOPES | Thorben Fröhlking | COORDINATION RESTART PYTORCH_MODEL ENERGY PRINT VOLUME MOLINFO OPES_EXPANDED ECV_MULTITHERMAL OPES_METAD_EXPLORE ERMSD COMBINE | pytorch generic opes colvar setup function |
| 24.012 | Molecular simulations to investigate the impact of N6-methylation in RNA recognition | bio | metadynamics, alchemistry, RNA modification, RNA:protein interactions | Giovanni Bussi | COORDINATION LOWER_WALLS PRINT GHBFIX CENTER COM MOLINFO GROUP METAD UPPER_WALLS DEBUG DISTANCE COMBINE BIASVALUE | generic bias core colvar vatom function |
| 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 | WHOLEMOLECULES PRINT WRAPAROUND MOLINFO EMMIVOX INCLUDE GROUP UPPER_WALLS DISTANCE BIASVALUE | generic bias core colvar isdb |
| 23.040 | Supramolecular capsules assembly dynamics | chemistry | Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics | Riccardo Capelli | WHOLEMOLECULES UNITS DISTANCES PRINT CENTER FLUSH COM GROUP METAD CUSTOM POSITION DISTANCE | generic multicolvar bias core colvar vatom setup function |
| 23.039 | Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation | chemistry | metadynamics, ligand dissociation | Eric Beyerle | RESTRAINT PRINT CENTER MOLINFO METAD FIXEDATOM DUMPMASSCHARGE UPPER_WALLS DISTANCE COMBINE | generic bias colvar vatom function |
| 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 | PRINT ENSEMBLE WRAPAROUND CENTER MOLINFO GROUP STATS RMSD SAXS UPPER_WALLS DISTANCE BIASVALUE | generic bias core colvar vatom function isdb |
| 22.037 | Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site | chemistry | metadynamics, DNA, abasic | Mike Jones | DISTANCES DISTANCE METAD PRINT | colvar multicolvar bias generic |
| 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 | WHOLEMOLECULES TORSION MOLINFO PBMETAD GYRATION | colvar generic bias |
| 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 | DRMSD LOWER_WALLS PRINT COMMITTOR MATHEVAL METAD CUSTOM CELL UPPER_WALLS | colvar bias function generic |
| 22.031 | Rare Event Kinetics from Adaptive Bias Enhanced Sampling | methods | OPES Flooding, Kinetics, Rate, OPES, Machine Learning | Dhiman Ray | ENERGY INCLUDE GROUP CONTACTMAP POSITION DISTANCE BIASVALUE ENDPLUMED COMMITTOR MOLINFO OPES_METAD CONSTANT TORSION RMSD WHOLEMOLECULES UNITS PYTORCH_MODEL PRINT CUSTOM COMBINE | pytorch generic bias core opes colvar setup function |
| 22.030 | Mixing physics across temperatures with generative artificial intelligence | methods | REMD, Generative AI, DDPM | Yihang Wang | WHOLEMOLECULES TORSION PRINT | colvar generic |
| 22.028 | N-glycan conformer distributions in atomistic simulation | bio | REST2, RECT, N-glycan, pucker | Isabell Grothaus | TORSION DUMPGRID PRINT MOLINFO CONVERT_TO_FES READ METAD PUCKERING HISTOGRAM | colvar generic bias gridtools |
| 22.026 | Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification | materials | Peptoid, silica | Jim Pfaendtner | PRINT COM MOLINFO PBMETAD UPPER_WALLS DISTANCE GYRATION | colvar vatom generic bias |
| 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 LOWER_WALLS PRINT FUNNEL_PS PATHMSD COM METAD FUNNEL UPPER_WALLS DISTANCE | generic bias colvar vatom funnel |
| 22.009 | Glycosylation in calixarenes capsule | chemistry | Metadynamics, glycosylation, supramolecular catalysis | GiovanniMaria Piccini | WHOLEMOLECULES UNITS COORDINATION BRIDGE DISTANCES LOWER_WALLS PRINT FLUSH MATHEVAL GROUP METAD FIT_TO_TEMPLATE UPPER_WALLS DISTANCE COMBINE ANGLE RMSD | adjmat generic multicolvar bias core colvar setup function |
| 21.028 | From Enhanced Sampling to Reaction Profiles | methods | collective variables, multi-state, machine learning, Deep-TDA | Enrico Trizio | COORDINATION LOWER_WALLS CENTER MATHEVAL GROUP DISTANCE ENDPLUMED DISTANCES OPES_METAD FIXEDATOM UPPER_WALLS TORSION WHOLEMOLECULES UNITS PYTORCH_MODEL PRINT FIT_TO_TEMPLATE LOAD ANGLE | pytorch generic multicolvar bias core opes colvar vatom setup function |
| 21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Adriana Pietropaolo | WHOLEMOLECULES TORSION RESTART PRINT MATHEVAL PBMETAD CONSTANT BIASVALUE | generic bias colvar setup function |
| 20.032 | Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil | materials | clustering, conformational isomers | Matteo Salvalaglio | TORSION PRINT ENDPLUMED | colvar generic |
| 19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Matteo Salvalaglio | EXTERNAL TORSION DUMPGRID PRINT COMMITTOR REWEIGHT_BIAS MATHEVAL READ CONVERT_TO_FES REWEIGHT_METAD METAD HISTOGRAM DISTANCE BIASVALUE | generic gridtools bias colvar function |
| 19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Matteo Salvalaglio | PRINT CENTER INCLUDE GROUP DISTANCE ENDPLUMED | colvar vatom generic core |
| 19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Jakub Rydzewski | UNITS MAZE_LOSS PRINT MAZE_SIMULATED_ANNEALING POSITION MAZE_OPTIMIZER_BIAS | colvar generic maze setup |
| 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 | WHOLEMOLECULES TORSION LOWER_WALLS BRIDGE DISTANCES PRINT COM MOLINFO GROUP REWEIGHT_METAD METAD ALPHABETA FUNNEL UPPER_WALLS DISTANCE COMBINE RMSD | adjmat generic multicolvar bias core colvar vatom funnel function |
| 19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Matteo Salvalaglio | RESTART DISTANCES PRINT COORDINATIONNUMBER METAD GYRATION ENDPLUMED | multicolvar generic bias symfunc colvar setup |
| 19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Michele Invernizzi | TORSION UNITS RESTART ENERGY PRINT VES_DELTA_F METAD POSITION LOAD ENDPLUMED | generic bias colvar setup ves |
| 26.007 | Metadynamics Simulations Reveal the Protonation-Dependent Conformational Landscape of GSK-3β Dual Inhibitors | chemistry | metadynamics, ligand unbinding, path CVs, funnel metadynamics | Gian Marco Elisi | COMBINE COM ENDPLUMED MOLINFO MATHEVAL UNITS FUNNEL_PS WHOLEMOLECULES RMSD ANGLE LOWER_WALLS DISTANCE METAD PATHMSD PRINT UPPER_WALLS FUNNEL | vatom colvar funnel bias function setup generic |
| 25.002 | M3_PCV-ABMD | chemistry | Adiabatic bias MD, path CVs, ligand unbinding, G protein coupled receptor | Gian Marco Elisi | ENDPLUMED UNITS ABMD PATHMSD PRINT UPPER_WALLS | bias setup generic colvar |
| 25.001 | RNA G-quadruplex folding with ST-metaD protocol | bio | RNA, G4, GQ, quadruplex, folding, metadynamics, REST2, ST-metaD | Pavlína Pokorná | COMBINE MOLINFO WHOLEMOLECULES METAD ERMSD | bias generic function colvar |
| 24.030 | NMR guided simulation of dsRBD | bio | Metainference, NMR, protein dynamics | Debadutta Patra | ALPHABETA MOLINFO WHOLEMOLECULES METAINFERENCE RDC DISTANCE STATS PRINT FLUSH GROUP ENSEMBLE | isdb colvar core multicolvar generic function |
| 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 | OPES_METAD_EXPLORE TORSION CENTER ENDPLUMED MATHEVAL ANGLE ENERGY WHOLEMOLECULES COORDINATION FIXEDATOM FIT_TO_TEMPLATE ECV_MULTITHERMAL LOWER_WALLS DISTANCE PRINT UPPER_WALLS OPES_EXPANDED GROUP | vatom colvar core opes bias generic function |
| 24.005 | Learning Markovian Dynamics with Spectral Maps | methods | spectral map, collective variables, machine learning | Jakub Rydzewski | BIASVALUE UNITS CUSTOM DISTANCE PRINT | colvar bias function setup generic |
| 24.004 | Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables | materials | metadynamics, nucleation, machine learning | Ziyue Zou | RESTART INCLUDE LOAD METAD PRINT GROUP | bias core setup generic |
| 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 MATHEVAL WHOLEMOLECULES CONSTANT LOWER_WALLS DISTANCE METAD PRINT UPPER_WALLS | bias generic function colvar |
| 23.007 | Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains | bio | metadynamics, peptoids, parallel-bias metadynamics | Jim Pfaendtner | TORSION COM PBMETAD COORDINATION WHOLEMOLECULES INCLUDE PRINT GYRATION RESTRAINT | colvar vatom generic bias |
| 23.001 | Quantum phase diagram of water | chemistry | Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella | Sigbjørn-Løland Bore | RESTART ENVIRONMENTSIMILARITY ECV_UMBRELLAS_LINE INCLUDE LOWER_WALLS PRINT UPPER_WALLS OPES_EXPANDED | opes bias setup envsim generic |
| 22.015 | Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome | bio | photodynamics, bacteriophytochrome, variationally enhanced sampling | Jakub Rydzewski | TORSION VES_LINEAR_EXPANSION PRINT OPT_AVERAGED_SGD TD_UNIFORM BF_FOURIER | colvar generic ves |
| 22.013 | Ligand dissociation from PreQ1 riboswitch | bio | ligand, RNA, metadynamics, pRAVE | Yihang Wang | COMBINE COM MOLINFO WHOLEMOLECULES COMMITTOR COORDINATIONNUMBER DISTANCE METAD PRINT RMSD | vatom colvar symfunc bias function generic |
| 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 | TORSION COM UNITS CUSTOM LOWER_WALLS DISTANCE METAD PRINT UPPER_WALLS | vatom colvar bias setup generic function |
| 21.023 | Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling | methods | enhanced sampling, collective variables, machine learning | Jakub Rydzewski | TORSION BIASVALUE ENERGY UNITS CUSTOM INCLUDE CONSTANT REWEIGHT_METAD DISTANCE METAD PRINT | colvar bias function setup generic |
| 21.020 | Reweighted Jarzynski sampling | methods | free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions | Kristof Bal | CONVERT_TO_FES UNITS VES_LINEAR_EXPANSION TD_WELLTEMPERED CONSTANT LOAD DISTANCE MOVINGRESTRAINT FLUSH REWEIGHT_BIAS UPPER_WALLS RESTRAINT BIASVALUE HISTOGRAM DUMPGRID CUSTOM BF_CHEBYSHEV COORDINATIONNUMBER REWEIGHT_METAD ANN METAD PRINT COMBINE OPES_METAD OPT_AVERAGED_SGD | ves colvar annfunc symfunc opes bias function setup gridtools generic |
| 21.014 | how to determine statistically accurate conformational ensembles | bio | metadynamics, metainference, errors, cv, SAXS, ensemble determination | Cristina Paissoni | ALPHABETA ANTIBETARMSD CENTER CONTACTMAP MOLINFO PBMETAD TORSION BIASVALUE WHOLEMOLECULES SAXS STATS METAD PRINT GYRATION ENSEMBLE | vatom isdb colvar bias secondarystructure function multicolvar generic |
| 20.028 | Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane | bio | metadynamics, KRas-4B, anionic membrane | Huixia Lu | RESTART CENTER FIT_TO_TEMPLATE DISTANCE METAD PRINT | vatom colvar bias setup generic |
| 20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Vojtech Spiwok | TORSION PRINT METAD | colvar generic bias |
| 20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Michele Invernizzi | ENDPLUMED MOLINFO UNITS ECV_UMBRELLAS_LINE LOAD RMSD TORSION ENVIRONMENTSIMILARITY UPPER_WALLS OPES_EXPANDED ECV_MULTITHERMAL_MULTIBARIC WHOLEMOLECULES CUSTOM ECV_LINEAR POSITION VOLUME ECV_MULTITHERMAL PRINT MATHEVAL ENERGY Q6 | colvar opes symfunc bias function setup envsim generic |
| 20.018 | Free energy barriers from biased molecular dynamics simulations | methods | kinetics, free energy barriers, chemical reactions, nucleation, metadynamics | Kristof Bal | CENTER CONVERT_TO_FES UNITS LOAD DISTANCE FLUSH REWEIGHT_BIAS PAIRENTROPY DENSITY LOCAL_AVERAGE CONTACT_MATRIX LOWER_WALLS UPPER_WALLS HISTOGRAM DUMPGRID VOLUME COORDINATIONNUMBER REWEIGHT_METAD METAD PRINT COMBINE SPRINT ENERGY COORDINATION Q6 | vatom volumes colvar adjmat symfunc bias function setup sprint gridtools generic |
| 20.015 | Rational design of ASCT2 inhibitors using an integrated experimental-computational approach | bio | ASCT2 transporter, small-molecules, cryo-EM, metainference | Max Bonomi | DUMPATOMS BIASVALUE MOLINFO WHOLEMOLECULES LOAD EMMIVOX PRINT GROUP | isdb core bias setup generic |
| 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 | RESTART CONVERT_TO_FES VES_LINEAR_EXPANSION TD_WELLTEMPERED LOAD BF_LEGENDRE READ REWEIGHT_BIAS LOWER_WALLS UPPER_WALLS HISTOGRAM DUMPGRID VOLUME OPT_DUMMY REWEIGHT_TEMP_PRESS PRINT COMBINE TD_MULTITHERMAL_MULTIBARIC MATHEVAL ENERGY CELL Q6 OPT_AVERAGED_SGD | ves colvar symfunc bias function setup gridtools generic |
| 19.075 | PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python | other | Python, automatic differentiation | Toni Giorgino | COMBINE TORSION CENTER ENDPLUMED ANGLE DUMPDERIVATIVES CUSTOM DISTANCE PRINT GROUP RESTRAINT | vatom colvar core bias function generic |
| 19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Giovanni Bussi | ENDPLUMED WHOLEMOLECULES COORDINATION LOWER_WALLS DISTANCE RESTRAINT | colvar generic bias |
| 19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Giovanni Bussi | TORSION COM MOLINFO MATHEVAL WHOLEMOLECULES COORDINATION INCLUDE MAXENT DISTANCE METAD SORT FLUSH PRINT | vatom colvar bias generic function |
| 19.059 | cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide | bio | bias-exchange metadynamics, cis-trans isomerization | Fabrizio Marinelli | TORSION INCLUDE RANDOM_EXCHANGES METAD PRINT | colvar generic bias |
| 19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | GiovanniMaria Piccini | COMBINE ENERGY UNITS LOWER_WALLS DISTANCE METAD PRINT UPPER_WALLS FLUSH | colvar bias function setup generic |
| 19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Gareth Tribello | ENDPLUMED UNITS CELL METAD PRINT UPPER_WALLS FCCUBIC | colvar symfunc bias setup 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 | COMBINE RESTART HISTOGRAM DUMPGRID CONVERT_TO_FES DISTANCE_FROM_CONTOUR METAD PRINT UPPER_WALLS READ REWEIGHT_BIAS | contour bias setup gridtools generic function |
| 19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | GiovanniMaria Piccini | COMBINE RESTART UPPER_WALLS UNITS DISTANCE METAD PRINT FLUSH DISTANCES | colvar bias function setup multicolvar generic |
| 26.012 | Buprenorphine Restricts the Conformational Landscape of the μ-Opioid Receptor | bio | OneOPES, GPCR, MOR, activation, euclidean path, conformational changes, allostery | Simone Aureli | CUSTOM OPES_METAD_EXPLORE COORDINATION OPES_EXPANDED ENERGY RMSD GROUP ECV_MULTITHERMAL DISTANCE CENTER PATH PRINT UPPER_WALLS VOLUME | bias generic core opes vatom colvar function mapping |
| 26.005 | Cryptic pocket discovery in Alzheimer disease risk proteins BIN1, PICALM, and CD2AP via well-tempered metadynamics | methods | cryptic pockets, Alzheimer disease, BIN1, PICALM, CD2AP, well-tempered metadynamics, endocytosis, clathrin-mediated trafficking, virtual screening | Cagrı Ozkurt | WHOLEMOLECULES ANGLE DISTANCE PRINT METAD | bias generic colvar |
| 25.025 | Enhanced Sampling of Ligand Binding Coupled to RNA Conformational Dynamics | bio | OPES, OPES Flooding , Metadynamics, RNA, Ligand binding, Free Energy, Kinetics, Funnel | Revanth Elangovan and Dhiman Ray | WHOLEMOLECULES COMMITTOR PRINT ENDPLUMED WRAPAROUND MATHEVAL DISTANCE UPPER_WALLS CUSTOM LOWER_WALLS RMSD FUNNEL OPES_METAD COORDINATION TORSION COM GROUP CENTER FUNNEL_PS METAD | bias generic funnel core opes colvar vatom function |
| 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 | CUSTOM ZDISTANCES FIXEDATOM COMMITTOR FLUSH COORDINATIONNUMBER GROUP DISTANCES DISTANCE PRINT OPES_METAD UPPER_WALLS UNITS | symfunc bias generic core opes vatom colvar setup multicolvar function |
| 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 | CUSTOM GYRATION COORDINATION TORSION WHOLEMOLECULES MOLINFO COMBINE DISTANCE ALPHARMSD PRINT OPES_METAD | generic opes colvar secondarystructure function |
| 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 | generic colvar |
| 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 | ZDISTANCES FIXEDATOM FLUSH COORDINATIONNUMBER GROUP DISTANCE PRINT OPES_METAD UPPER_WALLS UNITS | symfunc bias generic core opes vatom colvar setup 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 | FIT_TO_TEMPLATE WHOLEMOLECULES MOLINFO COMBINE ALPHARMSD POSITION ANN PRINT METAD | bias generic function colvar secondarystructure annfunc |
| 23.025 | Probing ion binding to G-quadruplexes and related events | chemistry | metadynamics, repulsive potential, nucleic acids, G-quadruplexes | Marcelo Poleto | LOWER_WALLS FIT_TO_TEMPLATE DUMPATOMS MATHEVAL WHOLEMOLECULES FLUSH COM GROUP DISTANCES UNITS RESTART DISTANCE POSITION PRINT WRAPAROUND UPPER_WALLS METAD | bias generic core vatom setup colvar multicolvar function |
| 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 OPES_METAD_EXPLORE COORDINATION FIT_TO_TEMPLATE FIXEDATOM LOWER_WALLS TORSION WHOLEMOLECULES PYTORCH_MODEL GROUP DISTANCE CENTER PATH PRINT OPES_METAD UPPER_WALLS UNITS | pytorch bias generic core opes vatom colvar setup function mapping |
| 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 | HISTOGRAM MATHEVAL WHOLEMOLECULES MOLINFO RMSD READ CONVERT_TO_FES DISTANCE REWEIGHT_METAD DUMPGRID PRINT METAD | bias generic gridtools colvar function |
| 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 | ENVIRONMENTSIMILARITY HISTOGRAM LOWER_WALLS OPES_EXPANDED ECV_UMBRELLAS_LINE RESTART PRINT UPPER_WALLS DUMPGRID | envsim bias generic opes gridtools setup |
| 22.045 | Binding mode and mechanism of enzymatic polyethylene terephthalate degradation | bio | metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation | Francesco Colizzi | LOWER_WALLS WHOLEMOLECULES COM MOVINGRESTRAINT ANGLE DISTANCE PRINT UPPER_WALLS METAD | bias colvar generic vatom |
| 22.039 | Driving and characterizing nucleation of urea and glycine polymorphs in water | bio | metadynamics, nucleation, amino acids, polymorphism | Eric Beyerle | Q6 MATHEVAL COORDINATIONNUMBER COMBINE Q4 LOAD PAIRENTROPY GROUP CENTER INCLUDE PRINT METAD | symfunc bias generic core gridtools setup vatom function |
| 21.052 | On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets | materials | Ibuprofen, unbinding, WTmetaD | Matteo Salvalaglio | TORSION COMMITTOR COORDINATIONNUMBER PRINT DISTANCE CENTER ENDPLUMED METAD | symfunc bias generic vatom colvar |
| 21.027 | EGFR activating mutations mechanism | bio | metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA | Francesco Gervasio | LOWER_WALLS MATHEVAL WHOLEMOLECULES ENERGY MOLINFO CONTACTMAP DISTANCE ALPHARMSD INCLUDE PRINT UPPER_WALLS METAD | bias generic colvar secondarystructure function |
| 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 | COORDINATION WHOLEMOLECULES MOLINFO RESTRAINT PRINT STATS | bias generic function colvar |
| 20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Matteo Salvalaglio | LOWER_WALLS MATHEVAL ENERGY PRINT UPPER_WALLS CELL VOLUME METAD | bias generic function colvar |
| 20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Glen Hocky | MATHEVAL ENERGY GROUP BIASVALUE FISST DISTANCE RESTRAINT PRINT GYRATION UNITS | fisst bias generic core colvar setup function |
| 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 Q6 BF_LEGENDRE MATHEVAL OPT_DUMMY RESTART OPT_AVERAGED_SGD VES_LINEAR_EXPANSION TD_WELLTEMPERED PRINT UPPER_WALLS VOLUME | envsim symfunc ves bias generic setup colvar function |
| 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 | LOWER_WALLS ALPHABETA WHOLEMOLECULES MOLINFO FLUSH PRINT PBMETAD GROUP BIASVALUE ANTIBETARMSD ENDPLUMED UPPER_WALLS CS2BACKBONE | bias generic isdb core secondarystructure multicolvar |
| 19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Wei Chen | COM COMBINE RESTRAINT POSITION ANN | bias function colvar vatom annfunc |
| 19.049 | Determining the sizes of solid/liquid clusters in MD trajectories of nucleation | methods | nucleation, metadynamics, clustering, Steinhardt order parameters | Gareth Tribello | Q6 CUSTOM OUTPUT_CLUSTER ONES CLUSTER_DISTRIBUTION CLUSTER_PROPERTIES COORDINATIONNUMBER MORE_THAN MATRIX_VECTOR_PRODUCT CLUSTER_NATOMS DISTANCES METAD OUTER_PRODUCT PRINT SMAC CONTACT_MATRIX DFSCLUSTERING LOCAL_Q6 | symfunc matrixtools bias clusters generic adjmat multicolvar function |
| 19.032 | Chemical reaction in solution using path collective variables based on coordination patterns | chemistry | chemical reactions, solutions, metadynamics, coordination patterns | Fabio Pietrucci | FLUSH DISTANCES RESTART PATH PRINT UPPER_WALLS METAD | bias generic setup multicolvar mapping |
| 19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Silvio Pipolo | LOWER_WALLS FUNCPATHMSD PIV PRINT UPPER_WALLS CELL METAD | bias generic colvar piv function |
| 19.030 | Coarse-Grained MetaDynamics (CG-MetaD) | bio | Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy | Vittorio Limongelli | LOWER_WALLS WHOLEMOLECULES COM DISTANCE PRINT UPPER_WALLS METAD | bias colvar generic vatom |
| 19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Mattia Bernetti | WHOLEMOLECULES ENERGY MOLINFO PRINT ALPHARMSD ENDPLUMED GYRATION METAD | bias secondarystructure generic colvar |
| 19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Carlo Camilloni | ENDPLUMED WHOLEMOLECULES MOLINFO RMSD SAXS GROUP BIASVALUE DISTANCE CENTER INCLUDE RESTRAINT PRINT STATS UPPER_WALLS | bias generic isdb core colvar vatom function |
| 19.011 | Automatic Gradient Computation for Collective Variables | other | gradient, differentiation, curvature | Toni Giorgino | ENDPLUMED | generic |
| 19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Carlo Camilloni | ALPHABETA RDC TORSION WHOLEMOLECULES MOLINFO PRINT PBMETAD METAINFERENCE GROUP DIHCOR DISTANCE CENTER ENSEMBLE RESTRAINT ENDPLUMED STATS UPPER_WALLS DHENERGY | bias generic isdb core colvar vatom multicolvar function |
| 19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Giovanni Bussi | LOWER_WALLS MOLINFO FLUSH COMBINE DISTANCES ANGLE RANDOM_EXCHANGES DISTANCE INCLUDE ERMSD PRINT UPPER_WALLS METAD | bias generic colvar multicolvar function |