[gmx-users] Simulated annealing

jayant james jayant.james at gmail.com
Tue Mar 10 20:57:01 CET 2009 

Hi!
So the part of my pr.mdp files that handles pressure and temperature looks
like as below and if I were to create an index file by name "N-extension" an
type it next in the tc-grps as N-extension along with the existing Protein
Non-Protein groups is this how I get to handle the simulated annealing for
the appended NMR group?
Thanks
Jayant James


; Berendsen temperature coupling is on in two groups

Tcoupl = berendsen

tc-grps = Protein Non-Protein

tau_t =       0.1      0.1

ref_t =       300      300

; Energy monitoring

energygrps =      Protein      Non-Protein

; Pressure coupling is not on

Pcoupl = parrinello-rahman

tau_p = 0.5

compressibility = 4.5e-5

ref_p = 1.0
On Sat, Mar 7, 2009 at 4:33 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ========================================
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-- 
Jayasundar Jayant James

www.chick.com/reading/tracts/0096/0096_01.asp)
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