[gmx-users] MARTINI / all-atom mapping

Michael Daily mdaily.work at gmail.com
Tue Aug 30 03:55:09 CEST 2011

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'],


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

Anybody have a master list like this?


Michael D. Daily
Postdoctoral research associate
Pacific Northwest National Lab (PNNL)
(formerly Qiang Cui group, University of Wisconsin-Madison)
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