[gmx-users] how to simulate linear rigid rod

David van der Spoel spoel at xray.bmc.uu.se
Sun Jan 2 11:43:37 CET 2011

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.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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