[gmx-users] Reordering of a large GRO file - how

[Tsjerk Wassenaar]

Hey,

Residue numbers don't matter. You can reorder the .gro file to have all the
solvent at the end:

sed -e '/SOL/{H;d}' -e '${x;s/^\n//p;x}' file.gro

Note that this doesn't work with BSD sed, like on a Mac :p

Cheers,

Tsjerk

On Thu, Jan 10, 2013 at 1:34 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/10/13 7:00 AM, Jernej Zidar wrote:
>
>> So the residue numbers don't matter? They will be renumbered accordingly
>> after I reassemble the GRO file. That's neat!
>>
>>
> grompp won't do that.  genconf -renumber will.  If you need an index file,
> make sure to create it from a suitably numbered file after it's been
> rearranged.
>
> -Justin
>
>
>  Thanks,
>> Jernej
>>
>> On 10. jan. 2013, at 19:29, gmx-users-request at gromacs.org wrote:
>>
>>  Subject: Re: [gmx-users] Reordering of a large GRO file - how
>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>> Message-ID: <50EEA589.4030303 at vt.edu>
>>> Content-Type: text/plain; charset=UTF-8; format=flowed
>>>
>>>
>>>
>>> On 1/10/13 4:50 AM, Jernej Zidar wrote:
>>>
>>>> Hi.
>>>>    I used editconf to replicate a small lipid bilayer patch, after
>>>> editing the topology file I'm able to simulate it. I have one small
>>>> question/issue.
>>>>
>>>>    I would like to use g_membed to add a large molecule into the water
>>>> section (SOL) but editconf operates in such a way that it just
>>>> replicates the initial system, thus my SOL section is not continuous
>>>> but is scattered all over the GRO file hence the command fails.
>>>>
>>>>    Is there a smart way to "reorder" so the SOL section would be
>>>> continuous*? How does GROMPP parse the GRO file?
>>>>
>>>>
>>> Use grep and rebuild the coordinate file with cat.  grompp simply reads
>>> through
>>> the file and matches the contents of the coordinate and topology files
>>> in order
>>> to map all the necessary parameters to the corresponding atoms.
>>>
>>
>>
>>
>>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada