[gmx-users] creating representative structures

[Shyno Mathew]

Dear all,


I wrote a tcl script to do cluster analysis, using gromos method. My
results are slightly different from the g_cluster results. I see the
difference is coming from RMSD values. For example, with g_cluster, “The
RMSD ranges from 0.149614 to 0.220387 nm”


However with the tcl script, and after converting RMSD from Å to nm, the
value ranges from 0.173347 to 0.234409 nm! I am using the same selection in
both cases for RMSD calculations.


I use g_cluster the following way:

g_cluster_mpi –s ../PRO0.gro -f ../comb6.xtc -method gromos -sz
clustsize.xvg -o clusters.xpm -g cluster.log -clid clusidovertime.xvg -cl
-av out.pdb -cutoff 0.20 -dist rmsd-dist.xvg


For vmd, I use PRO0.gro, comb6.xtc and I am not considering the 0th frame,
so the RMSD values from both cases has to be identical.


thanks,

Shyno

On Mon, Feb 29, 2016 at 6:52 PM, Shyno Mathew <sm3334 at columbia.edu> wrote:

> Dear all,
>
> I was able to write a tcl script to do cluster analysis, here I am using
> the gromos method.
> However, my script is giving slightly different results! I am testing my
> script on a smaller trajectory (8 frames).
> In the gromos method, the structure with the greatest number of neighbors
> is considered as the center of the cluster.
> What if more than one structure has the highest number of neighbors. For
> example, in my calculation, both frames 4 and 6 has 6 neighbors (maximum
> neighbor count).
> When I used g_cluster, the output file shows cluster center as frame 6.
> That means if I have more than one structure that has the maximum number of
> neighbors, I can randomly choose the cluster center?
>
> thanks,
> Shyno
>
>
> On Fri, Feb 26, 2016 at 11:47 AM, Shyno Mathew <sm3334 at columbia.edu>
> wrote:
>
>> 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.
>>>
>>>
>>>
>>> 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
>>>
>>
>>
>>
>> --
>> 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
>>
>
>
>
> --
> 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
>



-- 
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