[gmx-users] Gromacs for polymer and biomolecule system

Justin Lemkul jalemkul at vt.edu
Sun Mar 26 16:20:11 CEST 2017

On 3/26/17 8:46 AM, Riya Rogers wrote:
> Dear All
> I am new to Gromacs, I wanted to simulate Polymer system with biomolecule.
> Is there any tutorial?
> Also, how to include CNT with protein?
> Any suggestions ?

In general, use pdb2gmx to generate the protein topology, then generate your 
polymer or CNT topology (the method depends on what these materials are, but 
either pdb2gmx if it's a linear polymer or x2top if it's a CNT) and #include it 
within a system .top of your own creation or within the protein .top from pdb2gmx.

There are CNT tutorials online, just use Google.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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