Jun 16, 2011

Calculating Radius of gyration and End-to-end distance using VMD

How to calculate Radius of gyration using VMD

1. Load a molecule file in VMD (polymer.xyz)
2. (Tk console)  measure rgyr [atomselect top "name H"]
(it could be "type 1" or "index 0 to 1000" instead.  'top' is the molecule ID.)
3. Answer will appear in the console

If the molecule crosses the periodic boundary, you will need to first type:
pbc join res –first 0 –last 0
pbc unwrap

It makes sure the beads in the molecules are rearranged to remove bonds stretched across the box. (This is likely to mess up the locations of non-bonded particles, but that does not matter for radius of gyration calculations.)


How to calculate End-to-end distance using VMD

1. Load a molecule file in VMD (polymer.xyz)
2. (Menu) Mouse --> Label --> Bonds
3. (Menu) Graphics --> Labels
4. (display console) Select two atoms (end atoms of a molecule), then labels and a dotted line will show the distance between two atoms (End-to-end distance)


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