Thanks very much!
El 10/26/2012 02:47 PM, George Tzotzos escribió:
> 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
>>>>
>>>>
>>>> WARNING / LEGAL TEXT: This message is intended only for the use of the
>>>> individual or entity to which it is addressed and may contain
>>>> information which is privileged, confidential, proprietary, or exempt
>>>> from disclosure under applicable law. If you are not the intended
>>>> recipient or the person responsible for delivering the message to the
>>>> intended recipient, you are strictly prohibited from disclosing,
>>>> distributing, copying, or in any way using this message. If you have
>>>> received this communication in error, please notify the sender and
>>>> destroy and delete any copies you may have received.
>>>>
>>>> http://www.bsc.es/disclaimer
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
WARNING / LEGAL TEXT: This message is intended only for the use of the
individual or entity to which it is addressed and may contain
information which is privileged, confidential, proprietary, or exempt
from disclosure under applicable law. If you are not the intended
recipient or the person responsible for delivering the message to the
intended recipient, you are strictly prohibited from disclosing,
distributing, copying, or in any way using this message. If you have
received this communication in error, please notify the sender and
destroy and delete any copies you may have received.
http://www.bsc.es/disclaimer
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Oct 26 2012 - 09:30:03 PDT
