[gmx-users] Production run before starting Pulling

Justin Lemkul jalemkul at vt.edu
Mon Nov 28 14:35:55 CET 2016

On 11/28/16 5:03 AM, faride badalkhani wrote:
> Dear Gromacs users,
> I want to perform center of mass pulling simulations on a
> nanostructure-drug structure. I performed MD simulations on the
> nanostructure for 30 ns and it equilibrated well. then I docked the drun
> into the nanostructure using Auto Dock Vina software. Now I want to know if
> I should perform minimization, equilibration and production run on the
> nanostructure-drug complex again. When I run MD simulations on the


> nanostructure-drug complex obtained from docking, drug position changes
> significantly.

As should be expected.  Docking relies on lots of crude assumptions about the 
absence of water and conformational rigidity, which are of course not true in MD.

> Actually, what is the best approach for finding the starting configuration
> for pulling?

Run the simulation out and characterize the dominant binding mode(s).



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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