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First program for a class in molecular modelling (done in june 2016). Its an implementation of simple Molecular Dynamics for atoms with a possibility to choose from different algorithms (Verlet, VelocityVerlet, Leepfrog) and potentials (Lenard-Jones, SoftWall, min-barrier-bin).

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hansiu/modelo2-simpleMD

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modelo2-simpleMD

First program for a class in molecular modelling (done in june 2016). Its an implementation of simple Molecular Dynamics for atoms with a possibility to choose from different algorithms (Verlet, VelocityVerlet, Leepfrog) and potentials (Lenard-Jones, SoftWall, min-barrier-bin).

How to use:

  • Prepare the config.ini file (example in the example folder sym2) either by hand or using the MakeConfig function from configmaker.py
  • Go for the main script: python main.py
  • When it finishes it prints "END" - then in the folder in which the script was executed the following files should show:
    • traj.pdb is a pdb file with a trajectory that you can view i.e. in Chimera
    • energie.png is a graph of energies
    • stat.txt is a text file with energy statistics for a graph.

Note: if you are using Lenard-Jones's potential with some other potential, then please place the Lenard-Jones last on the list in the config.ini file. Otherwise the energies may be wrong - Lenard Jones potential calculates the energies in the other way than all the other potentials.

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First program for a class in molecular modelling (done in june 2016). Its an implementation of simple Molecular Dynamics for atoms with a possibility to choose from different algorithms (Verlet, VelocityVerlet, Leepfrog) and potentials (Lenard-Jones, SoftWall, min-barrier-bin).

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