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 <jalem...@vt.edu <mailto:jalem...@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
        <jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@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

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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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