[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:
> 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 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
> 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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