[gmx-users] Limitations of simulations?

[David van der Spoel]

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!
>
> Thank you! :)
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se