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 <jalem...@vt.edu>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] polymer charmm27 parameter
Message-ID: <4ed3e913-bf3d-f79d-e997-fc03d451e...@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
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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