The separation of groups for temperature control is originally
necessary to avoid (or correct for) temperature gradient in the
system, which occurs when systems parts have different frequencies of
motions. Typically the water molecules and a protein would be
separated to avoid the freezing of the protein and the heating up of
the solvent.
It would not make much difference to couple the dppc and dppg lipid
groups separately or together. To form a separate group you need a
sufficient amount of particle to avoid large (and therefore more
difficult to control) fluctuations. Ions are generally coupled to the
solvent they are embedded into.
Anirban suggestion is fine.
On May 3, 2012, at 1:56 PM, Anirban Ghosh wrote:
On Thu, May 3, 2012 at 5:17 PM, Weingarth, M.H.
<[email protected]> wrote:
Hello,
I am a bit confused by a comment which I find in all MARTINI example
md.mdp scripts concerning the tc-groups :
It is stated there to couple groups separately:
<< MARTINI -Normal temperature and pressure coupling schemes can be
used. It
; is recommended to couple individual groups in your system
seperately>>
I am simulating a mixed dppc:dppg membrane (see below my
parameters). Even these two different lipids-types should be coupled
separately? (and how about Na+ (Qd particles) and water - also
separately?)
I would greatly appreciate any comment on this issue.
Thanks a lot
Markus
my parameter:
; Temperature coupling:
tcoupl = berendsen
; Groups to couple separately:
tc-grps = DPPC DPPG W NAA Protein
Generally in membrane protein simulations different coupling groups
are used to increase the accuracy of the calculations (more
realistic). In your system you can make make three groups: Protein,
Lipids(DPPC+DPPG) and Sol+Ions(Na+Qd)
-Anirban
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