If I understand the question, you want to know what frame a specific structure corresponds to, right? If so, you can just get the rmsd of the structure to the trajectory and search the output file for the value 0.00000. Then, use the associated frame number to calculate the time.
Pete
________________________________________
From: David Condon [dec986.gmail.com]
Sent: Friday, October 26, 2012 8:43 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Trajectory Clustering
Hi Chiara,
another useful way is to use the AMBER's 2drms feature.
I use
trajin mdall.mdcrd 1 20000 40
> 2drms out 2drms.tmp raw mass :1-4 time 4.0
>
Then you can use this awk script:
#execute by $awk -f addblanks.awk < file.in > file.out
> /^[[:blank:]]*#/ {next} # ignore comments (lines starting with #)
> NF < 3 {next} # ignore lines which don’t have at least 3 columns
> $1 != prev {printf "\n"; prev=$1} # print blank line
> {print} # print the line
>
and then go into GNUPlot and type
gnuplot>set pm3d map
> gnuplot>set pm3d corners2color c1
>
gnuplot>splot "./graph"
>
and then you can see clearly which structures have high/low RMSD to one
another.
-Dave
On Fri, Oct 26, 2012 at 8:39 AM, Gustavo Seabra <gustavo.seabra.gmail.com>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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Received on Fri Oct 26 2012 - 06:00:12 PDT
