[gmx-users] question

[jkrieger at mrc-lmb.cam.ac.uk]

Thanks. I hadn't noticed that option.

> Instead of such a complicated script, I would use 'g_select -os', which
> gives you the same output without any post-processing. Whether this
> matches
> what the original poster wanted, or whether g_rdf is more suitable,
> depends
> on what they want to count.
>
> Best regards,
> Teemu
>
> On Tue, Jan 21, 2014 at 2:04 PM, <jkrieger at mrc-lmb.cam.ac.uk> wrote:
>
>> Here is my python script as promised:
>>
>> # select filenames for reading and writing
>> fr = open('chainA_T78-waters_index.ndx','r')
>> fw = open('chainA_T78-waters_counts.xvg','w')
>>
>> line = fr.readline()
>> t = line.split('_')[-1].split()[0]
>> c = 0
>>
>> for line in fr:
>>     if line.find('[') == -1:
>>         c += len(line.split())
>>     else:
>>         fw.write(t + ' ' + str(c) + '\n')
>>         t = line.split('_')[-1].split()[0]
>>         c = 0
>>
>> fw.write(t + ' ' + str(c) + '\n')
>>
>> fr.close()
>> fw.close()
>>
>> It reads in a file from g_select that looks as follows
>> [ chain_A_T78_waters_0.000 ]
>> 45170 45172 55565 55566 55567 217685 217686 217688 217689 217690 217709
>> 217710 217711 355868 355870
>> 380249 380250 380251
>> [ chain_A_T78_waters_2.000 ]
>> 55565 55566 55567 217686 217688 217689 217690 217709 217710 217711
>> 289964
>> 355868 355870 380249 380250
>> 380251
>> [ chain_A_T78_waters_4.000 ]
>> 45170 45171 45172 55565 55566 55567 217688 217689 217690 217709 217710
>> 217711 355869 367615 380249
>> 380250 380251
>>
>> and write out a file with counts that looks like this that xmgrace can
>> read
>> 0.000 18
>> 2.000 16
>> 4.000 17
>>
>> Best wishes
>> James
>>
>> > I have no experience with g_rdf but that looks like it might work if
>> you
>> > only want the average number. Anyhow I'm writing the script to count
>> my
>> > g_select output now and I'll send it to you soon. This script should
>> allow
>> > the number to be plotted over time.
>> >
>> > Best wishes
>> > James
>> >
>> >> Dear Jkrieger
>> >>
>> >> Thanks for your attention.
>> >>
>> >> I have index file containing 2 group which are my interest.
>> >>
>> >> Unfortunately, I am beginner in scripting and I have no long time.
>> >> I should do this analysis as soon as possible. Please if you write
>> such
>> >> a
>> >> script, send me it.
>> >>
>> >> Is g_rdf -cn appropriate for my case?
>>
> --
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