# [gmx-users] creating representative structures

Shyno Mathew sm3334 at columbia.edu
Mon Feb 8 18:23:52 CET 2016

```Dear all,

I have few questions regarding creating representative structures. For
simplicity, let’s say I have a trajectory of 5 frames:

1.       g_rmsf: After reading previous posts, here is what I understood.
The average structures calculated using g_rmsf (by specifying –ox) is
literally the average of x, y, z co-ordinates of each atom over all the 5
frames in my case. Energy minimizing this averaged structure might give a
meaningful structure?

2.       g_cluster: Here I am using the gromos method. I read the reference
paper (Daura et al.). Using gromos method and by just specifying –cl (not
–av) I get the middle structures for each cluster. Let’s say I get 2
clusters using rmsd 0.16. Now the representative structures of these two
clusters (obtained in the out.pdb) should exactly correspond to two frames
in my original trajectory (the one with 5 frames)?

3.       My final question is regarding how exactly g_cluster works, here
is what I understand from Daura et al.

If I use g_cluster with gromos method, the code will look for neighbors of
each frame within specified cutoff.

Assume the first time the code finds the following:

frame 0 has two neighbors: frames 2,3  within cutoff

frame 1 has three neighbors: frames 2, 3, 4 within cutoff

frame 2 has four neighbors: frames 0, 1, 3, 4 within cutoff

frame 3 has three neighbors: frames 0,1, 2 within cutoff

frame 4 has two neighbors: frames 1,2 within cutoff

Since frame 2 has the highest number of neighbors, it's considered the
center cluster and this frame along with neighbors are removed. The same
calculation is performed on the remaining frames if I had more frames.

Sincerely,

Shyno

--
Shyno Mathew
PhD Candidate
Department of Chemical Engineering