Martínez Molecular Modeling Group

Institute of Chemistry and Center for Computing in Engineering and Science

University of Campinas

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Software
  [Software repository at GITHUB]     [Software at JuliaHub]  
  		• Packmol
    Software for constructing initial configurations for Molecular Dynamics Simulations based on packing optimization. [Home-Page]
  		• ComplexMixtures.jl
    A package to study the structure of solutions of complex solutes and solvents. [Home-Page]
  		• CellListMap.jl
    CellListMap.jl is a general, efficient and customizable implementation of cell lists, which allows the computation of general properties dependent on distances of particles within a cutoff, for example short-range potentials, forces, neighbour lists, etc. [Home-Page]
  		• TopoLink
    Software for the evaluation of structural models using chemical crosslinking mass spectrometry data. [Home-Page]
  		• PDBTools.jl
    A Julia package to manipulate PDB files. [Home-Page]
  		• LovoAlign
    Performs customizable rigid-body structural alignment using convergent algorithms based on Low-Order-Value-Optimization theory. [Home-Page]
  		• MDLovoFit
    Robust alignment method for the automatic classification of conserved and flexible substructures in MD simulations. [Home-Page]
  		• MolSimToolkit.jl
    A Julia package providing various tools to analyze molecular simulations and write custom analysis tools. [Home-Page]
  		• ProteinSecondaryStructures.jl
    A Julia package to compute protein secondary structures with STRIDE or DSSP. [Home-Page] [JuilaHub link]
  		• ChunkSplitters.jl
    A package to facilitate the parallelization of Julia code by splitting the workload into chunks. [Home-Page] [JuilaHub link]
  		• Atd-Scripts
    This is a collection of scripts to run the Anisotropic Thermal Difusion method, as described in this paper. [Home-Page]
  		• LovoFit
    Peforms linear fitting of perhaps multidimensional data with the automatic elimination of outliers. [Home-Page]
  		• Utils
    Some utility programs to analyze data. And the script coding the pathdriven method of SMD with variable directions. [Home-Page]