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

[Justin Lemkul]

On 3/22/15 12:50 PM, Alex wrote:
> 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. :)
>

At a conference, so time is limited.  Provide every step of what you did and any 
problem you encountered.  Generating the topology is the hard part; if that was 
generated successfully, there (in principle) shouldn't be issues.  I don't do 
CNT simulations and don't follow those tutorials so I don't know how well they 
are expected to work.  The .n2t file for such species should be trivial to 
create, and if it's derived from OPLS-AA, everything should be very straightforward.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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