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+

  • 1
    $\begingroup$ This can be done by generating a cube file with the occupancy of water molecules around the ammonium ion. $\endgroup$ Jul 13 at 1:36
  • 2
    $\begingroup$ 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
    Jul 13 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. $\endgroup$ Jul 17 at 18:05
  • $\begingroup$ Thank you @Tyberius, I have edited my question as suggested. $\endgroup$ Jul 17 at 18:07

1 Answer 1


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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