[gmx-users] How to calculate tetrahedral order parameter in GROMACS
soham9038 at gmail.com
Wed May 8 11:07:55 CEST 2019
Thanks. I am checking.
On Wed, 8 May 2019, 2:30 pm David van der Spoel, <spoel at xray.bmc.uu.se>
> Den 2019-05-07 kl. 14:34, skrev Soham Sarkar:
> > Hello,
> > I have two systems. One containing only water and the other one
> > contains protein and water. Using g_select I made water in 1st solvation
> > shell but the use of g_hydorder I cannot understand. I read the
> > so far disscussed. For these two systems which index I need to choose,
> > water or OW? What is the use of sgang1 and sgang2? Any suggestion
> > is appreciated.
> > Thanks and regards
> > Soham
> The tool is not made for anything else than water I'm afraid. Please
> check this paper for details.
> Bjorn Steen Sæthre, Alex C. Hoffmann and David van der Spoel: Order
> parameters and algorithmic approaches for detection and demarcation of
> interfaces in hydrate-fluid and ice-fluid systems J. Chem. Theor.
> Comput. 10 pp. 5606-5616 (2014)
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
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