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

Justin Lemkul jalemkul at vt.edu
Thu Jan 10 12:27:05 CET 2013

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.


>    The topology file now looks like this:
> A 34345
> B 25
> SOL 10000
> A 34345
> B 25
> SOL 10000
> ...
> Thanks in advance,
> Jernej Zidar


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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