Average distance overtime

User discussions
1

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

2

You can use gmx pairdist command for this calculation.

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

1 Like
3

Maybe gmx pairdist is what you want?

4

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

5

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

6

I used gmx mindist and then did a running average on it outside of gmx. If you have the luxury to pint point exactly which pair of ions (by name and id) aggregate/interacts. Isn’t that what pairdist does for “known atoms/residues?”

I am looking for a way to select name and id of unspecified atoms/residues that has <= 5A’ interaction with a specific residue or two. If you found an answer share with us please.