[gmx-users] Protein - Ligand simulation

Justin Lemkul jalemkul at vt.edu
Wed Feb 12 12:09:29 CET 2014

On 2/12/14, 3:35 AM, lucaam86 wrote:
> Thank you for your reply.
> Yes, I'm not specialist and I'm introducing now in Molecular Simulation.
> I don't know Steered Molecular Dynamic, do you have tutorials or guide
> documentations for it?
> Could you explain why the tutorial suggested by Aldo is not indicated for
> me?

I didn't say that.  In fact, the tutorial is perfectly appropriate - have a look 
through it; it goes through steered MD in detail.  You don't need to do the 
umbrella sampling section, because all you're interested in is the SMD part.

The only problem is that there are a lot of other considerations that need to be 
accounted for, so you'll also need to work through the protein-ligand complex 
tutorial to understand topology organization and the basics of parametrization 
for non-standard species.


In thinking a bit more about your issue, you can probably simplify your life by 
pulling the ligand out of the protein's binding site and then creating your 
movie by playing the trajectory in reverse.  That will simplify things quite a 
bit, rather than trying to use the pull code to hit a moving target.  Pulling 
the ligand out of the active site is still not a trivial exercise and the pull 
settings used in the tutorial are probably not 100% applicable to what you're 
doing, but the logic is the same, and I provide some details about the other 
pull methods that are available.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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