On 2011-01-02 01.23, Sanku M wrote:
Hi,
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.
Sanku
Use virtual sites. Check the manual, chapter 5.
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
[email protected] http://folding.bmc.uu.se
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