[gmx-users] creating representative structures
sm3334 at columbia.edu
Mon Feb 8 18:23:52 CET 2016
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
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,
Department of Chemical Engineering
Office of Graduate Student Affairs
The Fu Foundation School Of Engineering and Applied Science
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