[gmx-users] NVT simulations for poylsaccharides in CHARMM36

Justin Lemkul jalemkul at vt.edu
Mon Jul 17 19:47:07 CEST 2017

On 7/17/17 12:38 PM, Jivesh Madan wrote:
> Hey Justin
> I'm not quite well-versed with the nvt.mdp file and its components. I'm
> basically trying to simulate a 3 residue ( initial- AGI, middle- AGM, final
> AGF)  non protein homopolymer  in CHARMM36 which requires changes to be
> made in the nvt.mdp file accordingly. I'm attaching the .pdb, topol.top,
> files of my molecule. Please guide me on the exact changes to be made in
> the nvt file so I can proceed with my simulations in GROMACS.

The mailing list does not accept attachments.

If you're not familiar with sensible settings for running NVT, please consult 
some basic tutorial material where the different options are explained (as well 
as the manual, which provides quite extensive descriptions for everything).



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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