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
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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