[gmx-users] creating representative structures

[Tsjerk Wassenaar]

Hi Shyno,

Is there a difference in mass-weighting? Can you try on C- alphas only?

Cheers,

Tsjerk
On Mar 16, 2016 15:55, "Shyno Mathew" <sm3334 at columbia.edu> wrote:

> 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
> --
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