So the residue numbers don't matter? They will be renumbered accordingly after I reassemble the GRO file. That's neat!
Thanks, Jernej On 10. jan. 2013, at 19:29, [email protected] wrote: > Subject: Re: [gmx-users] Reordering of a large GRO file - how > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > 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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