[gmx-users] Regarding use of g_x2top utility in Gromacs

[Alexandr Nasedkin]

Hi,

As I understood the problem, you need to distinguish between surface and 
buried carbons?

You could define two atomtypes that differ in name and use it to process 
with x2top.

Below is an example of *.n2t lines. You would need to change the charges 
and bondlengthes.

...

O    OCH    -1.05    15.9994    2    C    0.154 H 0.1    ; oxygen, -OH 
group
O    OCE    -1.05    15.9994    2    C    0.154 C 0.154    ; bridge oxygen

...

Then you need *.n2t file in your ff.

Good luck!


-Alex


On 25/11/2017 22:06, Justin Lemkul wrote:
>
>
> On 11/25/17 3:31 PM, Rakesh Pant wrote:
>> But then I how will include the C atom (which is also one of the 
>> atomtypes)?
>
> No idea, but I know people on this list have dealt with graphene oxide 
> before, so hopefully someone else chimes in.
>
> -Justin
>