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, [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.
--
========================================
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
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