[gmx-users] Simulated annealing

[Justin A. Lemkul]

jayant james wrote:
> Hi!
> I have appended the NMR structure to a part of the protein that was not 
> resolved to the protein and now I want to perform simulated annealing of 
> the 40 amino acids (NMR structure had 33 amino acids and to link I 
> needed another 7 aa) that have been thrown into the crystal structure. I 
> am new to this simulated annealing procedure. So please help me out as 
> how to write out a typical pr.mdp file. I am thinking of increasing the 
> temp of the appended piece protein piece to about 10000K (while the rest 
> of the protein, solvent, Na+ and Cl- are at 300K) and slowly bring the 
> temperature down to 300K, say, in about 100 ps and then continue to 
> perform MD simulations.

Running a protein segment at 10000 K with solvent at 300 K will probably lead to 
some wild behavior of that protein segment, clashes with the solvent, and 
possibly an explosion of your system.  Just thinking ahead...

> 1) So would it be the wise time to apply distance constraints from the 
> protein at 300K to the appended peptide while performing simulated 
> annealing?

If you have actual NMR data, perhaps.  But attempting to simulate at 10000 K 
while simultaneously applying distance restraints might be a difficult task 
(consider a lower temperature).

> 2) If so what would be a good temperature to set it to kick in? I am 
> really confused as to how I am going to specify these 40 residues to be 
> the group that needs to be heated up.

Warm it up from some low temperature.  There is an example at:

http://www.gromacs.org/documentation/reference_4.0/online/mdp_opt.html#sa

If you want a separate temperature coupling group, make a special index group 
for it.  No idea if that will actually work, but that's how you treat components 
of your system differently, in general.

> 3) Usually I have tc-grps specified in pr.mdp as Protein and 
> Non-Protein. So how would I go about setting up the temperature groups 
> during the simulated annealing protocol?

With the special index group.  See #2.

-Justin

> Thanks
> JJ
> 
> 
>  
> On Thu, Feb 26, 2009 at 4:47 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     jayant james wrote:
> 
>         Hi!
>         I have a question with regard to a system that I am attempting
>         to model.
>         The N-terminal of chain of the protein was not resolved
>         crystallographically but was later solved by NMR.
>         Now my plan is to append the NMR structure on to chain A of the
>         protein and perform simulated annealing only for the appended
>         NMR fragment. To help it find it biologically relevent
>         orientation in the system I could also apply distance restraints
>         that I have.
>         Is this possible in Gromacs?
> 
> 
>     All except that actual construction part (modeling the two segments
>     together), yes.
> 
>     -Justin
> 
>         thanks
>         JJ
> 
> 
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> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Graduate Research Assistant
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 
> 
> 
> -- 
> Jayasundar Jayant James
> 
> www.chick.com/reading/tracts/0096/0096_01.asp 
> <http://www.chick.com/reading/tracts/0096/0096_01.asp>)
> 

-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================