[gmx-users] how to simulate linear rigid rod
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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