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

[Justin Lemkul]

On 3/22/15 10:33 PM, Alex wrote:
> Hi,
>
>
> Thanks for your suggestion. Just before we try this: the point of what I am
> doing is _not_ making CNT/graphene simply "run" in solvent, I know it can be
> done. I specifically want to reparameterize the bond, angle, and the dihedral
> constants with something that I know to be at least somewhat representative of
> graphene and isn't something from oplsaa, which comes from an entirely different
> paradigm. The Andrea Minoia's tutorial actually allows that level of flexibility.
>
>
> What I understand from your suggestion is that nb parameters will be set, while
> all bonded parameters will be inherited from oplsaa. I am not interested in
> that. Can it be extended toward actually specifying the bond, angle, and
> dihedral energy constants, as well as their types?
>
>
> For instance, I am comfortable with the bond type 1, angle type 2 (G96) and
> dihedral type #3 (Ryckaert-Bellemans), and I have exact constant values so that
> the experimental phonon spectrum of graphene is reproduced relatively closely.
> It may not matter much in a biomolecular simulation, but this level of
> flexibility should be available.
>
>
> Any thoughts?

For this, the cleanest approach is to create a custom force field, and its 
contents should be rather simple - bonded and nonbonded parameters for some C 
type (for the CNT) and whatever solvent type(s) you need.  It's actually a very 
bare-bones force field.  The proposal before about using values from OPLS-AA is 
a good guide; these are the things you need to define.  In reality, this could 
all be in one file:

[ defaults ]
...whatever...

[ atomtypes ]
...whatever...

[ nonbond_params ]
(if needed)

[ bondtypes ], [ angletypes ], [ dihedraltypes ], ...

Then create the .n2t file for creating the CNT.  That part is the easiest of all 
of it since everything is (should be) equally spaced. :)

-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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