[gmx-users] Anealling

Justin A. Lemkul jalemkul at vt.edu
Tue Feb 8 01:53:12 CET 2011

TJ Mustard wrote:
>   Hi all,
> I have been having issues with my system blowing up due to bad contacts. 
> All of these contacts have been made by me when I have tried to "dock" 
> or align my protein with my ligand in pymol. I do what I can to limit 
> while still having the correct geometry and also being close enough to 
> keep waters out of the contact region. What I have found to allow md/sd 
> to run is to anneal my system under -DPOSRES for 20 ps and from 5K to 
> 300K in the first 10ps then hold at 300K till the end.
> I see no physical problem with doing this due to the restraints on my 
> ligand and protein, what I wish to know is if this will cause artifacts 
> in my system?

I see no reason why it would.  The use of annealing is very routine in system 
preparation.  Used to be that just about all simulations used it.  I think it's 
a bit less common now, but I doubt there's any reason to worry about it, as long 
as you can justify your "rough docking" approach to reviewers :)


> Thank you,
> TJ Mustard
> mustardt at onid.orst.edu


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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