[gmx-users] Analyzing With Indices Created By GMX Select

[ALEXANDER DHALIWAL]

Hi All,

I am having a problem. Using GMX Select, I have selected for some molecules
within my simulation; namely, a solute of interest and the phospholipids
surrounding it within a radius of 2 nm. This was done using the following
command:

gmx select -f md_2_25_cat.trr -s md_2_25_cat.tpr -n all_groups.ndx -on
select.ndx
...
group 5
group 7 and within 2 of resid 138
ctrl+D

This generates an index file with an independent group for every frame of
my simulation, as the molecules contained within this designation change as
time goes on. However, I am now unsure about how to use this index file in
any analyses. For instance, if I want to calculate the hydrogen bonds
between this group and the surrounding solvent, is there a way to assign a
new pairs of groups for every frame of the simulation (i.e., group SOL +
group Fr1 for Frame 1; group SOL + group Fr2 for Frame 2, etc)? Currently,
I can only compare it to a single frame group, and this isn't very helpful.
If anyone can help me with this, it would be much appreciated!

Sincerely,
Alex