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I am trying to recreate Fig. 5b of this paper

I have a solvated NH4+ in my system and would like to create a similar visualisation for my case.

Can this be generated using VMD? If so could someone point out what i should be looking for in the documentation? Alternatively, what other software could I use to create this? Thank y'all!

Spatial distribution of water around NH4+

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    $\begingroup$ This can be done by generating a cube file with the occupancy of water molecules around the ammonium ion. $\endgroup$
    – Hemanth Haridas
    Commented Jul 13, 2023 at 1:36
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    $\begingroup$ Its better to post link as some descriptive text rather than the raw link as described here (looks like [here](https://mattermodeling.meta.stackexchange.com/questions/423/please-use-hyperlinks-instead-of-raw-urls)) $\endgroup$
    – Tyberius ♦
    Commented Jul 13, 2023 at 13:55
  • $\begingroup$ @HemanthHaridas I have already generated a trajectory file for an ammonium ion in a water box. I'm not sure of what steps I must follow next to generate this kind of a figure using my system. $\endgroup$
    – Priyanshu Gupta
    Commented Jul 17, 2023 at 18:05
  • $\begingroup$ Thank you @Tyberius, I have edited my question as suggested. $\endgroup$
    – Priyanshu Gupta
    Commented Jul 17, 2023 at 18:07

2 Answers 2

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The figure that you have provided depicts the spatial distribution of water molecules around the NH$_4$$^+$ ion. This is generally generated by calculating the 3D probability density of water-O atoms around the NH$_4$$^+$ ion. The easiest way is to write a script that would calculate this over the trajectory.

I do not have a script that can do it, but will provide a general algorithm to do this:

For every frame in trajectory:
    Center ion to the center of the box
    Calculate 3D histogram for the water O coordinates for water molecules within a cutoff distance. 
Write this data as a Cube file.
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VIAMD software will allow you to do that. You can use the sdf function in the script editor after loading your trajectory. It would like something like that depending on your topology:

V = sdf(resname("NH4"), element('O') in resname("SOL"), 5.0);

You can then see your distribution in the density window. In Property, you will see V, by clicking on it will display in the window.

There is tutorial in the wiki of the github to tune your visualization of the SDF. VIAMD as been published here.

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    $\begingroup$ As it’s currently written, your answer is unclear. Please edit to add additional details that will help others understand how this addresses the question asked. You can find more information on how to write good answers in the help center. $\endgroup$
    – Community Bot
    Commented Dec 8, 2023 at 16:50

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