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

Jernej Zidar jernej.zidar at gmail.com
Thu Jan 10 13:00:36 CET 2013

So the residue numbers don't matter? They will be renumbered accordingly after I reassemble the GRO file. That's neat!


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.

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