[gmx-users] only interaction inside the molecule

[Peter Kroon]

Hi Faezeh,


have a look at the [pairs] or [pairs_nb] directives. Table 5.5 in the
manual. Note that these directives will be in your molecule itp (in the
[moleculetype] section).


Peter


On 09-11-17 10:30, Faezeh Pousaneh wrote:
> no that is not my answer Yu.
>
> for example I would like to design a molecule e.g. CO2, I would like
> oxygens connected to Carbon in each molecule, but do no interact with rest
> of system.
> I guess I should change the ffbonded.itp in the following:
>
> keep the length bond but change the interaction strength to zero, and then
> restrain the bond length in .mpd file.
> but I am not sure ?
>
>
>
> Best regards
>
>
> On Thu, Nov 9, 2017 at 10:15 AM, Du, Yu <duyu at sioc.ac.cn> wrote:
>
>> Hi,
>>
>> From your limited information, I suggest you have a look at the Tabulated
>> Potentials, www.gromacs.org/Documentation/How-tos/Tabulated_Potentials
>>
>> Best,
>> Yu
>>
>> --
>> Du, Yu
>> PhD Student,
>> Shanghai Institute of Organic Chemistry
>> 345 Ling Ling Rd., Shanghai, China.
>> Zip: 200032, Tel: (86) 021 5492 5275
>>
>>> -----Original Messages-----
>>> From: "Faezeh Pousaneh" <fpoosaneh at gmail.com>
>>> Sent Time: 2017-11-09 16:58:12 (Thursday)
>>> To: gromacs.org_gmx-users at maillist.sys.kth.se
>>> Cc:
>>> Subject: [gmx-users] only interaction inside the molecule
>>>
>>> Hi,
>>>
>>> I would like an atom of my molecule only interact (LJ) with its own
>>> molecule, not the rest of system, how can I do that?
>>>
>>> thanks for reply,
>>> Best regards
>>
>>
>> --
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