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

Alexandr Nasedkin nasedkin at chalmers.se
Sun Nov 26 10:29:45 CET 2017


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 
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!


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

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