[gmx-users] GROMACS and CNT/graphene (probably for the 1000th time)

[Alex]

Hi All,

I'm sure you've seen this many times before, but I think it might help
those who have never done this before, are new to Gromacs, or, like
me, haven't done anything relatively advanced with it in a while.

So, here goes. My intermediate goal here was a solvated sheet of
graphene, so I followed http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube
under "Andrea Minoia's tutorial" pretty much to the word (there is a link
with the exact file content). Everything prior to solvating the system
worked without a hitch. To solvate the system, I used genbox, making
it also update the topology file (created with g_x2top). This is when
grompp started screaming about "defaults" duplicates, and, as I tried
removing the #include to cnt_oplsaa.ff/forcefield.itp from the
topology file and just put all parameters explicitly in there, there was a bunch of other problems.
Without going into detail of the latter, I don't think I know what I am doing at this
point.

Can you please help with this task in a simple & robust step-by-step way?
In fact, I'd like to write up an updated tutorial
based on our discussion, because, among other things,
Andrea's parameters are taken from oplsaa on aromatics, which can and
should be further refined. All input is greatly appreciated and I'd
especially love to hear from the Gromacs superhero Justin Lemkul. :)

Thanks!

Alex