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

[abhijit Kayal]

HI,

 Copy the oplsaa.ff directory to your working directory. Then in
ffnonbonded.itp file add the following lines..
 opls_995   C      6    12.01100     0.000       A    3.40000e-01
3.61200e-01
 opls_996   C      6    12.01100     0.000       A    3.40000e-01
3.61200e-01
 opls_997   C      6    12.01100     0.000       A    3.40000e-01
3.61200e-01

Here you can modify the non bonded parameters.

Then in   atomname2type.n2t file add the following lines.
C    opls_995    0      12.011  2    C  0.142  C 0.142
C    opls_996    0      12.011  3    C  0.142  C 0.142  C 0.142
C    opls_997    0      12.011  1    C  0.142

Then use g_x2top. This will work.

Thanks
Abhijit

On Mon, Mar 23, 2015 at 8:44 AM, Alex <nedomacho at gmail.com> wrote:

> Hey Justin,
>
> Great you had a moment to look at my post.
> This is an impossible task without the coordinates input file, because
> this is now
> the realm of solid-state physics, and there really isn't a single
> "residue" that can be created once and for all. It could be really
> cumbersome to post everything, and sort of useless to everyone at this
> point, before we figure this out.
>
> Would you be OK with me emailing you the input along with the simple
> series of steps? This way you won't
> need to mess with the tutorials, I'll just show you exactly what works
> on my end and what doesn't.
>
> Thanks,
>
> Alex
>
>
>
> JL> 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. :)
> >>
>
> JL> At a conference, so time is limited.  Provide every step of what you
> did and any
> JL> problem you encountered.  Generating the topology is the hard part; if
> that was
> JL> generated successfully, there (in principle) shouldn't be issues. I
> don't do
> JL> CNT simulations and don't follow those tutorials so I don't know how
> well they
> JL> are expected to work.  The .n2t file for such species should be
> trivial to
> JL> create, and if it's derived from OPLS-AA, everything should be very
> straightforward.
>
> JL> -Justin
>
>
>
>
>
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-- 
Abhijit kayal
Research Scholar
Theoretical Chemistry
IIT Kanpur