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

[Rakesh Pant]

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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-- 
Rakesh Pant/राकेश पंत
Research Fellow/अनुसंधान फेलो
Indian Institute of Science Education and Research (IISER)
भारतीय विज्ञान शिक्षा एवं अनुसंधान संस्थान
Pune-411008, India/ पुणे - ४११००८, भारत
Web:http://www.iiserpune.ac.in/~arun/webarun_files/rp.htm