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 - 06:00:08 PDT
