[gmx-users] creating representative structures

Mark Abraham mark.j.abraham at gmail.com
Tue Feb 9 08:46:42 CET 2016


On Mon, Feb 8, 2016 at 6:24 PM Shyno Mathew <sm3334 at columbia.edu> wrote:

> 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?

It'll give a structure that conforms to chemical expectations, but the
"meaning" of any plausible candidate for an "average" structure is doubtful
at best. If there is a group of microstates that share structural
similarity, it does not follow that RMSD will identify it, nor that
averaging of coordinates will produce a meaningful average. What is the RMS
average position of a set of balls being juggled?

> 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)?

I don't know, but you should try it and see. Make a trajectory of a water
molecule as PDB with a few frames and play with editing the coordinates by
hand and passing them to g_cluster until you are happy you understand how
it works.

> 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.

No idea, but again try it and see.


> Thanks in advance for your help,
> Sincerely,
> Shyno
> --
> 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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