[gmx-users] Simulating a 282 atom molecule. How do I split it into parts?

[Jonathan Saboury]

I have this molecule I want to simulate:
http://pastebin.com/raw.php?i=7bsWKjU3

I have tried using acpype on the whole thing to obtain the needed .itp and
.gro, but it takes a couple days to finish and I get errors because I do
not have enough memory.

I was wondering if splitting this molecule into parts, much like how
proteins are split into amino acid sections, would be a feasible way to
simulate this molecule. I haven't seen any tutorials on this, so not sure.

I could split the molecule into the bowl shapes, the n-hexanes, and the
n-pentane linker. Or if that would not be the correct way, how would you do
it?

My question is how would the input sections deal with the bonds between
sections? For example, if I had a ethane and wanted to split it into two
methyl pieces, would I make the input .pdb's as CH3's? I.E.:
http://pastebin.com/raw.php?i=jhwcYbAM

And more importantly, how would I link these together in the .gro file?
(assuming it is the .gro file)

Thank you, your help is very much appreciated!

-Jonathan