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

[Rakesh Pant]

Dear,  Alex
Does it mean, we do not need to define all the atomtypes in the .nt2 file.
It is enough to define all types in bonded and non-bonded itp.

Thanks,
Rakesh



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On Sun, Nov 26, 2017 at 3:27 PM, Alexandr Nasedkin <nasedkin at chalmers.se>
wrote:

> 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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>> ral=rakesh.pant at students.iiserpune.ac.in&idSignature=22>
>>
>> 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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>>
>>
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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