[gmx-users] only interaction inside the molecule

[Du, Yu]

Hi Faezeh, 

I got you point. I believe the link and the PDB file in that webpage I mentioned previously can help you. You need an index.ndx file that defines the specific oxygens in your system and the rest of the system.

The charge, the vdw sigma and epsilon (or c6 and c12) in the top file of your CO2 is global parameters, which means that if you change them the interaction in a single molecule will also be changed.

Best, 
Yu

> -----Original Messages-----
> From: "Faezeh Pousaneh" <fpoosaneh at gmail.com>
> Sent Time: 2017-11-09 17:30:02 (Thursday)
> To: gmx-users <gmx-users at gromacs.org>
> Cc: 
> Subject: Re: [gmx-users] only interaction inside the molecule
> 
> 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