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

[Rakesh Pant]

Dear Alex,

But g-x2top doesn't work till we define all atom types in .n2t file.

Thanks


On 26-Nov-2017 9:34 PM, "Alexandr Nasedkin" <nasedkin at chalmers.se> wrote:

Hi,

You will need to have both ffbonded.itp and ffnonbonded.itp .

atomname2type.n2t is needed for g_x2top to make it work correctly.

Good luck.


-Alex



On 26/11/2017 10:52, Rakesh Pant wrote:

> 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
>
>
>
> <https://mailtrack.io/> Sent with Mailtrack
> <https://mailtrack.io/install?source=signature&lang=en&refer
> ral=rakesh.pant at students.iiserpune.ac.in&idSignature=22>
>
> 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
>>>
>>>
>>>
>>> <https://mailtrack.io/> Sent with Mailtrack
>>> <https://mailtrack.io/install?source=signature&lang=en&refer
>>> 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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