[gmx-users] MARTINI / all-atom mapping

XAvier Periole x.periole at rug.nl
Tue Aug 30 12:06:28 CEST 2011

it must be some example of mapping lipids on the website: cgmartini.nl

On Aug 30, 2011, at 3:55 AM, Michael Daily wrote:

> Hi all,
> I am trying to reverse-map some martini lipids to united atom.  In  
> order to do this, I'd prefer to have an EXACT definition of the aa- 
> to-cg mapping.  I cannot find this, only an imprecise graphic, in  
> the MARTINI paper; the martini.itp file doesn't appear to list which  
> heavy atoms are represented by each CG bead either.  For example,  
> I'm looking for something like:
> 'NC3' : ['C1', 'C2', 'C3', 'N4', 'C5', 'C6'],
>     'PO4' : ['O7', 'P8', 'O9', 'O10', 'O11','C12'],
>     'GL1' : ['C13', 'O14', 'C15', 'O16'],
>     'GL2' : ['C32', 'O33', 'C34', 'O35'],
> etc.
> For some atoms it's obvious which MARTINI groups they belong in, but  
> others on the borderline are not obvious.  For example, does C12  
> belong in PO4 or GL1?
> Anybody have a master list like this?
> Thanks,
> Mike
> -- 
> ====================================
> Michael D. Daily
> Postdoctoral research associate
> Pacific Northwest National Lab (PNNL)
> 509-375-4581
> (formerly Qiang Cui group, University of Wisconsin-Madison)
> -- 
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