molecular biophysics

J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague


These are relatively old materials to be downloaded. More recent scripts etc. coming soon. In particular, operations on GRO files will be available.


  • Radial distribution function: gr.py
  • Histogram: histogram.py
  • Extraction of positions of defined atoms along xyz trajectory: xyz_position.py
  • Calculation of the distance of a given atom from system's center along xyz trajectory: xyz_distance_from_center.py
  • Fixing an atom at a given position along an xyz trajectory: xyz_fix_atom.py
  • Fixing a given bond orientation along an xyz trajectory: xyz_fix_bond.py
  • Calculation of an angle between a plane and the z-axis along an xyz trajectory – quite useful for planes on interfaces: xyz_angle.py
  • Findinf a volume enclosed by an isosurface for a given isovalue in a Gaussian cube file: cube_vol.py
  • Calculation of a volume of the electron density defined as using a Gaussian cube file: cube_st_vol.py
  • Calculation of the shortest distance (nearest neighbors) between atoms of two given types along an xyz trajectory: xyz_nn.py

Technical documents

These are quite old and no guarantee to be still relevant.

  • How to create a residue for polarizable simulations in Amber link
  • How to prepare residues with RESP charges fitting for polarizable force fields in Amber8 link
  • How to simulate small molecules in Amber8 with your own force field link
  • How to quickly create surface maps in Gnuplot link