[gmx-users] polymer charmm27 parameter

[Mijiddorj B]

Dear Prof. Justin,

Thank you very much for your reply. My target polymer is the branched
polyethyleneimine. I copied a figure. I am sorry for furthermore asking. If
I understand correctly, the model compound consists of the last two heavy
atoms and first two heavy atoms along with the corresponding protons. Is it
right?
Do I need to make a model N and C terminal atoms?

Thank you for your time.

[image: image.png]

Best regards,

Mijiddorj

>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 10 Nov 2019 09:20:52 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] polymer charmm27 parameter
> Message-ID: <4ed3e913-bf3d-f79d-e997-fc03d451edcd at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 11/10/19 8:52 AM, Mijiddorj B wrote:
> > Dear GMX users,
> >
> > I would like to simulate a long polymer, which consists of the number of
> > units (monomers). I generated the charmm27 parameter for the single unit
> > using swissparam server.
> > However, I need to prepare the parameter for the long polymer chain.
> > If you have any experience, please advise me to build the topology of the
> > long polymer using the parameter of the single unit. Thanks for any
> > guidance.
>
> You need a model compound that captures all relevant degrees of freedom,
> including bonds, angles, and dihedrals between monomer units. You then
> need to parametrize those interactions so the properties of your chain
> are correct.
>
> -Justin
>
>