[gmx-users] jointly-couple lipids to theromstat - MARTINI force-field

[Anirban Ghosh]

On Thu, May 3, 2012 at 5:17 PM, Weingarth, M.H. <M.H.Weingarth at uu.nl> 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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