Average distance overtime

Hello everyone,

I can see by eye in my simulation that overtime some ions tend to aggregate. How can I show this with a plot? Let’s say I have 10 ions and I want to see on average how close they come overtime.

Thank you in advance
Matteo

You can use gmx pairdist command for this calculation.

https://manual.gromacs.org/documentation/5.1/onlinehelp/gmx-pairdist.html

Maybe gmx pairdist is what you want?

Hi Justin,

First of all thanks for your answer. What about finding all the N(N-1) c.o.m pairwise distances (polyatomic ions), where N is the number of molecules and averaging them at each timestep. Sound reasonable?

Thank you in advance
Matteo

Same command, different selection type (COM of molecules rather than individual atoms, see option -seltype).