Re: [AMBER] Trajectory Clustering

From: George Tzotzos <gtzotzos.me.com>
Date: Fri, 26 Oct 2012 14:47:16 +0200

Chiara

Have you had a look at the test-out.txt file? See attached example. I think, it provides the information you wanted, unless I misread your message.

Regards

George






On Oct 26, 2012, at 2:43 PM, David Condon wrote:

> 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 - 06:00:11 PDT
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