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@m3g Martínez Molecular Modeling Group

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    49 repositories

    • packmol

      Public
      Packmol - Initial configurations for molecular dynamics simulations
      simulationmolecular-dynamics
      Fortran
      •
      MIT License
      •51•271•1•1•Updated May 19, 2025May 19, 2025

    • CellListMap.jl

      Public
      Flexible implementation of cell lists to map the calculations of particle-pair dependent functions, such as forces, energies, neighbor lists, etc.
      molecular-dynamicsmolecular-dynamics-simulationminimum-distances
      Julia
      •
      MIT License
      •5•96•12•4•Updated May 14, 2025May 14, 2025

    • m3g.github.io

      Public
      Martínez Molecular Modeling Group
      HTML
      •0•0•0•0•Updated May 9, 2025May 9, 2025

    • Packmol.jl

      Public
      The future of Packmol
      Julia
      •
      MIT License
      •3•33•2•1•Updated May 9, 2025May 9, 2025

    • PDBTools.jl

      Public
      Read, write and manipulate atomic systems in PDB and mmCIF formats
      Julia
      •
      MIT License
      •3•12•1•0•Updated May 8, 2025May 8, 2025

    • EasyFit.jl

      Public
      Easy interface for obtaining fits for 2D data
      Julia
      •
      MIT License
      •4•43•1•0•Updated Apr 29, 2025Apr 29, 2025

    • ComplexMixtures.jl

      Public
      Package to perform minimum-distance distribution analyses of complex solute-solvent interactions
      chemistrymolecular-dynamicsmolecular-simulationmolecular-dynamics-simulationlammpsnamdgromacsambermolecular-modelingdistribution-function
      Julia
      •
      MIT License
      •3•17•1•2•Updated Apr 28, 2025Apr 28, 2025

    • PereiraMartinez2025.jl

      Public
      Supplementary information for Pereira and Martínez, 2024.
      Julia
      •
      MIT License
      •1•0•0•1•Updated Apr 25, 2025Apr 25, 2025

    • MolSimToolkit.jl

      Public
      A set of tools for analyzing molecular dynamics simulations
      Julia
      •
      MIT License
      •2•10•1•2•Updated Apr 16, 2025Apr 16, 2025

    • ShowMethodTesting.jl

      Public
      A simple package to help testing show methods for custom types.
      Julia
      •
      MIT License
      •0•0•0•0•Updated Mar 17, 2025Mar 17, 2025

    • MolSimToolkitShared.jl

      Public
      This package is a placeholder for function names that might be shared among other packages.
      Julia
      •
      MIT License
      •0•0•0•2•Updated Feb 24, 2025Feb 24, 2025

    • Piccoli_Martinez_2025.jl

      Public
      Julia
      •
      MIT License
      •1•0•0•0•Updated Jan 24, 2025Jan 24, 2025

    • JuliaNotes.jl

      Public
      A collection of examples and explanations about Julia
      Julia
      •
      MIT License
      •13•166•2•3•Updated Jan 21, 2025Jan 21, 2025

    • TestingDataRepository

      Public
      Repository that contains data files (trajectories, PDB files) that are using for testing purposes in other packages.
      MIT License
      •0•0•0•0•Updated Nov 29, 2024Nov 29, 2024

    • SPGBox.jl

      Public
      Spectral Projected Gradient Method for Box-Constrained Minimization
      Julia
      •
      MIT License
      •2•17•2•0•Updated Aug 26, 2024Aug 26, 2024

    • 2021_FortranCon

      Public
      Simulation codes shown at the FortranCon 2021
      Julia
      •
      MIT License
      •2•22•0•0•Updated Apr 12, 2024Apr 12, 2024

    • 2024_Ramos_Martinez_BGHI

      Public
      Data for Ramos, Martínez, 2024
      Tcl
      •
      MIT License
      •0•0•0•0•Updated Apr 11, 2024Apr 11, 2024

    • lovoalign

      Public
      Fortran
      •
      MIT License
      •5•10•0•0•Updated Apr 9, 2024Apr 9, 2024

    • 2023_AFP-LM_BpdA

      Public
      Julia
      •
      MIT License
      •0•0•0•0•Updated Feb 16, 2024Feb 16, 2024

    • SolventShellInteractions.jl

      Public
      Computes the interaction potential between a solute and the solvent molecules having at least one atom within a cutoff distance from the solute.
      Julia
      •
      MIT License
      •0•7•0•0•Updated Sep 12, 2023Sep 12, 2023

    • atd_scripts

      Public
      Anistropic Thermal Diffusion scripts - http://leandro.iqm.unicamp.br/atd-scripts
      Tcl
      •0•0•0•0•Updated Aug 11, 2023Aug 11, 2023

    • mdanalysis

      Public
      Fortran
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 11, 2023Aug 11, 2023

    • FundamentosDMC.jl

      Public
      Material para el curso Fundamentos de Mecánica Estadística y Simulaciones: Simulación Computacional Avanzada en Química, Bioquímica y Ciencias de Materiales. CELFI/Universidad de Buenos Aires
      Julia
      •
      MIT License
      •1•9•0•0•Updated Jul 28, 2023Jul 28, 2023

    • stride

      Public
      The original implementation of the structure identification (STRIDE) algorithm to identify protein secondary structure elements
      C
      •
      MIT License
      •3•2•0•0•Updated Jul 14, 2023Jul 14, 2023

    • MDLovoFit

      Public
      MDLovoFit is a package for the analysis of the mobility and structural fluctuation in Molecular Dynamics simulations. It allows the automatic identification of rigid and mobile regions of protein structures.
      Fortran
      •
      MIT License
      •0•1•0•0•Updated Jul 13, 2023Jul 13, 2023

    • MCKin

      Public
      Computes using a MC simulation the mean first-passage times between every pair of reaction coordinates, given a PMF
      Julia
      •0•1•0•0•Updated Jan 31, 2023Jan 31, 2023

    • jlcode_example

      Public
      Example of the use of jlcode and the JuliaMono font to write Julia code in LaTeX
      TeX
      •2•17•0•0•Updated Sep 16, 2022Sep 16, 2022

    • XEMMSB2021

      Public
      Files for XEMMSB2021
      Julia
      •0•6•0•0•Updated Aug 9, 2022Aug 9, 2022

    • CellListMapArticleCodes

      Public
      Code blocks of the CellListMap paper.
      Julia
      •
      MIT License
      •0•1•0•0•Updated Apr 20, 2022Apr 20, 2022

    • CellListMapBenchmarks.jl

      Public
      Benchmarks and examples for the CellListMap.jl package.
      Julia
      •
      MIT License
      •0•0•0•6•Updated Jan 28, 2022Jan 28, 2022
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