[gmx-users] How to calculate tetrahedral order parameter in GROMACS
David van der Spoel
spoel at xray.bmc.uu.se
Wed May 8 11:00:37 CEST 2019
Den 2019-05-07 kl. 14:34, skrev Soham Sarkar:
> 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 disscussion
> 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
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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