Re: [AMBER] Trajectory Clustering

From: Ilyas Yildirim <>
Date: Fri, 26 Oct 2012 07:47:15 -0500 (CDT)

I am not sure if ptraj can do this, but you can write a simple script to
do what you want. If you know that you have definitely 10 unique
conformations for the system, you can calculate the rmsd of each
conformation with respect to time. Then, simply define a unique color for
each independent conformation (I use grace to plot rmsd data with
different colors).

Having 10 rmsd trajectory data (which represent each conformation), you
will extract the lowest rmsd values. Once you plot them using the color
notation, you will explicitly see how long each conformation is spending
in the trajectory. Hope this helps.

Good luck,

   Ilyas Yildirim, Ph.D.
   = Department of Chemistry - 2145 Sheridan Road =
   = Northwestern University - Evanston, IL 60208 =
   = Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
   = =

On Fri, 26 Oct 2012, Gustavo Seabra wrote:

> Hi Chiara,
> I don't think there is such information. What you can do is, based on the relative number of structures in each cluster, estimate the percentage of the total time spent sampling that area of space. To see the members, you can just look at the output trajectories in a program like VMD.
> Gustavo Seabra
> Professor Adjunto
> Departamento de Química Fundamental
> Universidade Federal de Pernambuco
> Recife - PE - Brasil
> +55-81-2126-7450 x5023
> On Oct 26, 2012, at 9:08 AM, Chiara Pallara wrote:
>> Hi,
>> I clustered the frames of my trajectory into 10 clusters with the
>> command cluster of ptraj module.
>> I applied the averagelinkage algorithm on the alpha carbons of my sistem
>> using this command:
>> cluster out [outfile] representative pdb average pdb averagelinkage
>> clusters 10 rms .CA
>> Now I would to know the MD times of the each cluster representative and
>> its members. Do you know where I can find this information? I did not
>> find nothig about in the output file.
>> Thanks
>> Chiara
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