neeru sharma wrote:
Dear Gromacs users,
I am simulating a system containing a protein with covalently attached
Mg in complex with GDP.
For nvt equilibration, I have taken protein+Mg+GDP as the single group
and Water+ions as the other. The corresponding block from the .mdp file
is below:
-- ; Temperature coupling is on
tcoupl = V-rescale
tc-grps = Protein_MG_GDP Water_and_ions
Is this coupling method correct, to treat Protein and Mg as different
quantities?
You are not treating them differently; they are in a merged group. Note,
though, that the default "Water_and_ions" group will include MG, and thus grompp
with throw a fatal error. You'll have to create a custom group for this one, as
well. Otherwise, the approach seems reasonable to me.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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