[gmx-users] genconf -renumber merges atom number and ID columns

[Ricardo O. S. Soares]

I thank you for the answer Justin.
Indeed, the fixed format of the .gro file is respected, therefore this is a non-problematic issue.
I'm having no problems with this spacing, It was just something I was wondering about.
Well, anyway, thanks again.

Ricardo.





>________________________________
> De: Justin A. Lemkul <jalemkul at vt.edu>
>Para: Ricardo O. S. Soares <ross_usp at yahoo.com.br>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
>Enviadas: Quinta-feira, 1 de Março de 2012 16:07
>Assunto: Re: [gmx-users] genconf -renumber merges atom number and ID columns
> 
>
>
>Ricardo O. S. Soares wrote:
>> Dear gmx users,
>> 
>> After merging two .gro files,  I set a new numbering with genconf -renumber. My results show that from the 10000th atom, the atom number and its ID are no longer separated by at least one space:
>> 
>>    75POP   C216 9998   0.705   4.657   3.200  0.0000  0.0000  0.0000
>>    75POP   H16R 9999   0.694   4.548   3.182  0.0000  0.0000  0.0000
>>    75POP   H16S10000   0.612   4.712   3.173  0.0000  0.0000  0.0000
>>    75POP   C21710001   0.731   4.684   3.350  0.0000  0.0000  0.0000
>> 
>> Is this a limitation from genconf? Is it limited to 10K atoms? I find it hard to be the case.
>> Yeah, I could write a post-processing script to add the spaces, but I'm curious about this issue.
>
>A .gro file has a fixed format:
>
>http://manual.gromacs.org/online/gro.html
>
>Is the spacing (or lack thereof) causing some problem?  As far as I can see, genconf (like other Gromacs tools) has done its job correctly.
>
>-Justin
>
>-- ========================================
>
>Justin A. Lemkul
>Ph.D. Candidate
>ICTAS Doctoral Scholar
>MILES-IGERT Trainee
>Department of Biochemistry
>Virginia Tech
>Blacksburg, VA
>jalemkul[at]vt.edu | (540) 231-9080
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>========================================
>
>
>
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