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

[Alexandr Nasedkin]

Edit the content of you ffnonbonded.itp file approximately this way:

[ atomtypes ]
;name    at.num    mass        charge    ptype    sigma epsilon
C    14    12.00    1.08    A    0.44000        0.63      ;
OCE    8    15.999400    -0.70    A    0.35400        0.159705  ; C-O-C 
Bridging Oxygen;
OCH    8    15.999400    -0.51    A    0.35400        0.159705  ; C-O-H 
Oxygen;

HCO    1     1.008000    0.32    A    0.04490        0.235725  ; H-O-C 
Hydrogen;
....

You would need to search literature for respective ff parameters: all 
the above parameters are taken from another topology to give a template.


-Alex


On 26/11/2017 10:37, Rakesh Pant wrote:
> Dear Alex,
>   If I use O atoms to define the respective functional groups, then how to
> include the C atoms present in the molecule.
>
> Thanks,
> Rakesh
>
>
>
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>
> On Sun, Nov 26, 2017 at 3:08 PM, Alexandr Nasedkin <nasedkin at chalmers.se>
> wrote:
>
>> 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
>>>
>>>
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