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

Justin Lemkul jalemkul at vt.edu
Thu Jan 10 13:34:29 CET 2013

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.


> 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


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