Martínez Molecular Modeling Group

Institute of Chemistry and Center for Computing in Engineering and Science

University of Campinas

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  [Software repository at GITHUB]  
  • 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]
  • MDAnalysis
    A suite of fortran codes to perform analyses of MD simulations performed mostly with NAMD or CHARMM. [Home-Page]
  • 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]