[gmx-users] genconf -renumber merges atom number and ID columns
Ricardo O. S. Soares
ross_usp at yahoo.com.br
Thu Mar 1 20:41:01 CET 2012
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.
> 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:
>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 A. Lemkul
>ICTAS Doctoral Scholar
>Department of Biochemistry
>jalemkul[at]vt.edu | (540) 231-9080
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