[gmx-users] Problem setting up SMD simulation for DNA

Justin Lemkul jalemkul at vt.edu
Wed May 17 13:34:28 CEST 2017

On 5/17/17 6:35 AM, Nicholus Bhattacharjee wrote:
> Hello user,
> I am trying to setup SMD simulation for a DNA. I am following the tutorial
> from Bevanlab where SMD was on protein performed to use as input for
> umbrella sampling.
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html
> Now for initial setup I am using the following command
> $ gmx_mpi pdb2gmx -f start.pdb -ignh -ter -o dna.gro
> I am getting new files posre.itp, topol.top & dna.gro
> According to the tutorial I should also get another file like topol_***.itp
> whi I need to modify for SMD simulation. Kindly let me know if I am doing
> anything wrong.

Don't compare apples and oranges.  You can't expect the output of the tutorial 
(for a protein complex) to be exactly the same as your system of DNA.



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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