Hi,
I want to analyze first hydration shell near an ionic group. For this purpose I want to calculate density of water around ionic group. I cloud find water indexes near the ionic group using gmx select. But, I don’t know how to calculate density of selected water molecules. Which tools in Gromacs are appropriated for this calculation?
Thanks
I’m not sure exactly what type of analysis you’re trying to do.
If you’re already using gmx select, and using a distance cutoff such as within x of my_ionic_group, then you already have a count of water molecules within your space and could calculate density based on the spherical cutoff zone. I don’t know what kind of meaningful information that could give you, though.
gmx rdf can provide finer spatial detail.
Dear Kevinboyd,
Thank you very much for your reply. As water molecules are in confinement in polymer matrix then their properties (like density) are different under confinement compared to bulk water. Actually, I want to study this difference. That’s why I want to calculate density of specific water molecule group.
Hello,
In my opinion, it will be a good practice to write the code for this problem. If you have any kind of molecules in your system, you can calculate the RDF/number density/mass density very easily using your own program.
hello，how do you analyze first hydration shell near an ionic group to compute diffusion coefficient？