# [gmx-users] creating representative structures

Shyno Mathew sm3334 at columbia.edu
Fri Feb 26 17:47:23 CET 2016

```Dear Prof. Mark and Prof. Stephane,

Thanks so much for your suggestions.

thanks,
Shyno

On Mon, Feb 8, 2016 at 12:23 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?
>
> 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
> Office of Graduate Student Affairs
> The Fu Foundation School Of Engineering and Applied Science
> Columbia University
>

--
Shyno Mathew
PhD Candidate
Department of Chemical Engineering