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.)
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/4674.html
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)
http://www1.pacific.edu/~mmccallu/Students/page6/page6.html
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