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

[David van der Spoel]

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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