[gmx-users] polymer charmm27 parameter

[Justin Lemkul]

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

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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
http://www.thelemkullab.com

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