Downloads

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

Scripts

• 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