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MusCaDe is aimed at developing methods and implementing specific software for aiding multi-scale simulations. MusCaDe allows system representation at four levels: Atomistic, with explicit electrons (QM), atomistic with implicit electrons and empirical interactions (MM), coarse grained (CG) and meso-scale (MS) (low resolution models). MusCaDe uses well established theories (Density Functional Theory, DFT) and models (empiric atomistic FFs such as Amber, and Tersoff, and MARTINI coarse grained FFs), but also develops and implements original models for specific purposes ("minimalist" models for biopolymers, meso-scale models for the cytoplasm; "minimalist" connective FF for graphene).

MusCaDe realizes multi-scaling by connecting simulations of the systems at different resolutions by means of top-down and bottom-up fluxes of information. In practice this is realised by means of the following prescriptions:

  • When possible, MusCaDe uses standard models and popular and well established software packages for molecular dynamics simulations. These are
    • CPMD and QE, for DFT calculations and ab initio molecular dynamics (MD)
    • Amber, Gromacs, DL_POLY and LAMMPS for atomistic classical MD
    • Gromacs, DL_POLY and LAMMPS for CG dynamics (the latter two also for MS). Compatibility with the RedMD code for CG-biopolymers  is also provided
  • MusCaDe provides software tools for the development, parameterization and implementation of non-standard models (namely minimalist and meso-scale) into DL_POLY and LAMMPS
  • MusCaDe provides software tools to realize the flux of information among the different resolutions. These include tools for output analysis and input preparation and in general to interface different simulation or parameterization packages.
  QM MM CG MS
Statistical Analysis
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Parameterization
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Input Preparation
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
MD Simulation
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Output Analysis
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Downloads


Statistical Analysis

  • Name
    Description
    Contact
    Link
  • SecStanT 1.0.3.8
    2015-01-21

    Tool for the automatic creation of data-sets of structures from PDB files, and for the calculation of their internal variables distributions.

    652.78 Kb

MD Simulation

  • Name
    Description
    Contact
    Link
  • dl_poly 2.20
    2015-03-23

    DL_POLY 2.20 modified version that includes additional Force Fields. Please read the included doxygen documentation for more infos.

    6988.49 Kb

Parameterization