[gmx-users] how to simulate linear rigid rod

Sanku M msanku65 at yahoo.com
Sun Jan 2 01:23:48 CET 2011

  I am planning to do a simulation with a pair of rigid linear rods in SPC/E 
water . More specifically, I want to calculate the free energy of association of 
a pair of rigid rod in water, using umbrella sampling.  But, I was wondering how 
to keep a chain molecule, around 10-mer, rigid . I am not sure whether just 
constraining the bond lengths using LINCS will be good idea for stable 
simulation . But, not sure whether, the molecule will still be linear or not ?
Any suggestion will be appreciated.

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