[gmx-users] How to use gmx h2order when using four point water model

David van der Spoel spoel at xray.bmc.uu.se
Wed Sep 11 10:55:25 CEST 2019

Den 2019-09-11 kl. 04:38, skrev Jun Zhou:
> Hi all,
> I want to obtain the water dipole orientation at the interface using gmx
> h2order. It works well when I I use 3 point water model, like SPC/E. The
> manual says that the order of water should be O H H, but for 4 point water
> model, there is a vitual atom, and this command cannot output the correct
> results. Is there any solutions for this poblem?
> Thanks,
> Jun
You can use trjconv to remove the virtual site from the trajectory, 
maybe it even works in the tool directly, without running trjconv.

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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