[gmx-users] polymer charmm27 parameter

[Justin Lemkul]

On 11/11/19 10:05 AM, Mijiddorj B wrote:
> 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?

Whatever model compounds you use have to encompass all relevant internal 
degrees of freedom (bonds, angles, dihedrals).

> Do I need to make a model N and C terminal atoms?

You need termini, but N- and C-termini are protein-specific concepts, so 
no, not exactly. See e.g. 
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2009-March/040125.html

-Justin

> 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
>>
>>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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