[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.

Thanks in advance for your help,



Shyno Mathew
PhD Candidate
Department of Chemical Engineering
Graduate Assistant
Office of Graduate Student Affairs
The Fu Foundation School Of Engineering and Applied Science
Columbia University

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