[gmx-users] Question regarding coarse-graining and all-atom structure

Graham J.A. J.A.Graham at soton.ac.uk
Mon Feb 20 12:57:31 CET 2017

If you haven't had success with Martinize (I'm not sure myself if it
does lipids or not), our group's CG model generation code (https://gith
ub.com/jag1g13/pycgtool) is able to get you a CG gro file from an all-
atom one.

The drawback is that you'll have to write a mapping yourself, but it's
only 10-15 lines specifying which atoms are inside each bead.  If you
run it in mapping-only mode as "pycgtool.py -g file.gro -m file.map" it
will give you back a CG gro file.


On Sat, 2017-02-18 at 23:09 +0330, ali.khourshaei71 at student.sharif.edu
> Dear Gromacs users, 
> Is there any script I can use to coarse-grain ( based on martini
> forcefield) my lipid bilayer all-atom structure ( based on berger
> force
> field)? I know Martinize.py has been published, But it is confined to
> Protein I think. 
> Sincerely, 
> Ali

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