[gmx-users] Measuring distances between residues and visualising the results

[Nikolaos Michelarakis]

Hello,

I am trying to measure the distances between certain residues over the
course of my simulation. I have created an index with these residues. So
far i have tried using gmx mdmat but since there are only five residues the
resulting map consists of 25 large boxes, of different shades, which is not
very useful. I have also tried using gmx distance but I am not sure if I am
using it correctly. When it prompts me to select the groups do I choose the
index group twice?

Any suggestions on how to better visualize the gmx_mdmat results or use gmx
distance accurately?

Thanks a lot,

Nicholas