[gmx-users] Simulated annealing

[jayant james]

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.
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?
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.
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?
Thanks
JJ



On Thu, Feb 26, 2009 at 4:47 PM, Justin A. Lemkul <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 | (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)
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