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

[XAvier Periole]

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.  
> <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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