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
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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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<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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