[gmx-users] Simulated annealing
Justin A. Lemkul
jalemkul at vt.edu
Tue Mar 10 21:00:20 CET 2009
jayant james wrote:
> 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?
Not likely, because Protein probably includes these residues. Two special
groups would (theoretically) be needed, your N-extension, then whatever is left
of your protein. Try it and see.
-Justin
> 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
> <mailto: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>
> <mailto: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/> <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>
> <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 <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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