[gmx-users] Protein+ligand complex

Justin Lemkul jalemkul at vt.edu
Tue May 12 13:45:55 CEST 2015

On 5/12/15 7:41 AM, Kashif wrote:
> Greetings of the day,
> Can I use nvt.mdp and npt.mdp parameter file given in tutorial (
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/index.html)
>   for my 5 ns production run? As the tutorial shows 100 ps nvt and npt
> equilibration and 1000 ps (1 ns) MD Simulation run. Which parameter should
> be changed if there is any problem.

The .mdp settings (certainly within the nonbonded section) are force 
field-specific.  If you're using a different force field, you have to look up 
the appropriate values.

If you simply want to increase the number of steps, then change nsteps.

> What are the post-simulation analysis commands used for the analysis for
> protein+drug complex?

There is no recipe.  You should have a scientific question in mind based on 
physical and biological phenomena that will drive the types of analysis.



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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