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

[Justin Lemkul]

On 3/23/15 7:38 PM, Alex wrote:
> Okay, I am learning here. Here's what I did:
>
> 1. Copied the entire oplsaa folder in the local directory.
>
> 2. Added the following to ffnonbonded.itp:
>   opls_995   CJ      6    12.01100     0.000       A    3.40000e-01  3.61200e-01
>   opls_996   CJ      6    12.01100     0.000       A    3.40000e-01  3.61200e-01
>   opls_997   CJ      6    12.01100     0.000       A    3.40000e-01  3.61200e-01
>
> 3. Added the following to ffbonded.itp
> under dihedral types:
>    CJ     CJ     CJ     CJ      3     17.30770   0.00000 -17.30770   0.00000   0.00000   0.00000 ; From opt. Brenner
> under angle types:
>    CJ     CJ     CJ      2   120.000    776.923   ; G96 angle, param from opt. Brenner
> under bond types:
>    CJ    CJ      1    0.14200   420420.0   ; from opt. Brenner 698.129 N/m
>
> 4. Added the following to atomname2type.n2t:
> CJ   opls_995    0      12.011  2    C  0.142  C 0.142
> CJ   opls_996    0      12.011  3    C  0.142  C 0.142  C 0.142
> CJ   opls_997    0      12.011  1    C  0.142
>
> After all of this g_x2top with -noparam does almost everything right (the angle type
> needs to be manually changed to 2, although it is explicitly 2 above).
> But whatever, I can run the in vacuo dynamic simulation, and the sheet
> behaves beautifully and respects my PBC (the box has precise in-plane
> dimensions).
>
> I have solvated my sheet with quite a bit of SPC water (~32K molecules), about to test some
> energy minimization followed by a dynamic simulation.
>
> Does the above sound reasonable?
>

Yep.

-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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