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@m3g Martínez Molecular Modeling Group

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    52 repositories

    • packmol

      Public
      Packmol - Initial configurations for molecular dynamics simulations
      simulationmolecular-dynamics
      Fortran
      •
      MIT License
      •50•226•2•0•Updated Oct 25, 2024Oct 25, 2024

    • 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•15•0•1•Updated Oct 22, 2024Oct 22, 2024

    • MolSimToolkit.jl

      Public
      A set of tools for analyzing molecular dynamics simulations
      Julia
      •
      MIT License
      •2•9•0•1•Updated Oct 17, 2024Oct 17, 2024

    • Packmol.jl

      Public
      The future of Packmol
      Julia
      •
      MIT License
      •1•22•1•0•Updated Oct 14, 2024Oct 14, 2024

    • m3g.github.io

      Public
      Martínez Molecular Modeling Group
      HTML
      •0•0•0•0•Updated Oct 11, 2024Oct 11, 2024

    • PDBTools.jl

      Public
      Simple structure and functions to read and write PDB files
      Julia
      •
      MIT License
      •1•11•1•4•Updated Sep 30, 2024Sep 30, 2024

    • EasyFit.jl

      Public
      Easy interface for obtaining fits for 2D data
      Julia
      •
      MIT License
      •4•37•1•0•Updated Sep 26, 2024Sep 26, 2024

    • PereiraMartinez2024.jl

      Public
      Supplementary information for Pereira and Martínez, 2024.
      Julia
      •
      MIT License
      •0•0•0•1•Updated Sep 26, 2024Sep 26, 2024

    • SPGBox.jl

      Public
      Spectral Projected Gradient Method for Box-Constrained Minimization
      Julia
      •
      MIT License
      •3•17•2•1•Updated Aug 26, 2024Aug 26, 2024

    • 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
      •4•89•10•1•Updated Aug 6, 2024Aug 6, 2024

    • JuliaNotes.jl

      Public
      A collection of examples and explanations about Julia
      Julia
      •
      MIT License
      •11•158•1•1•Updated Jun 18, 2024Jun 18, 2024

    • 2021_FortranCon

      Public
      Simulation codes shown at the FortranCon 2021
      Julia
      •
      MIT License
      •2•21•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•8•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

    • ComplexMixturesExamples

      Public
      Examples provided for the ComplexMixtures package.
      Julia
      •
      MIT License
      •0•1•0•0•Updated Feb 7, 2024Feb 7, 2024

    • BlockAverage.jl

      Public archive
      Computes the block average and error of the mean of (time-dependent) data.
      Julia
      •
      MIT License
      •0•3•0•0•Updated Jan 24, 2024Jan 24, 2024

    • PackmolInputCreator.jl

      Public archive
      Package to help creation of Packmol input files for mixtures.
      Julia
      •
      MIT License
      •0•3•0•1•Updated Dec 14, 2023Dec 14, 2023

    • MDLovoFit.jl

      Public
      Julia wrapper for the MDLovoFit package
      Julia
      •
      MIT License
      •0•2•2•5•Updated Nov 16, 2023Nov 16, 2023

    • MolecularMinimumDistances.jl

      Public
      Computes the set of minimum distances between to sets of particles, which can be grouped (like in molecules).
      Julia
      •
      MIT License
      •0•8•0•0•Updated Sep 12, 2023Sep 12, 2023

    • 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•0•0•0•Updated Jul 13, 2023Jul 13, 2023

    • AtomDistances.jl

      Public
      Simple script to illustrate how to compute distance-dependent properties using Chemfiles, PDBTools, etc.
      Julia
      •
      MIT License
      •0•0•0•0•Updated Apr 13, 2023Apr 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•0•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