[gmx-users] Limitations of simulations?

Justin Lemkul jalemkul at vt.edu
Wed Jul 24 13:10:54 CEST 2013

On 7/24/13 6:44 AM, David van der Spoel wrote:
> On 2013-07-24 01:57, Jonathan Saboury wrote:
>> I just finished this tutorial and found it very informative:
>> http://cinjweb.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf
>> However, This was based on a complex from a pdb.
>> I was wondering if it was possible to just simulate the protein without
>> complex and put the ligand as a solute and actually have it complex with
>> the protein. Obviously, if it could do this it would take a much longer
>> time than just simulating a complex, but if given enough time, could it
>> complex?
> Yes, there are some examples. A paper was published by Shaw and co-worker in J.
> Amer. Chem. Soc. a year or two ago.
>> I have no formal experience with simulations and currently have no one
>> around me with enough knowledge on these topic to mentor me, so any help is
>> very much appreciated!

For the rest of us mere mortals who don't have access to specialized hardware 
that allows for 10- or 20-microsecond simulations, the brute force approach is 
rather futile.  Techniques like steered MD and Hamiltonian replica exchange MD 
are probably more feasible.  Unbiased simulations of sufficient length, using 
"standard" supercomputing hardware, would probably take years.



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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