Tutorial-l Mailing List

From: Jeffrey Potoff (jpotoffx_at_gmail.com)
Date: Tue Apr 14 2015 - 08:48:16 CDT

In the process of adding more lipids to the topology files provided in
the NAMD residue based coarse graining tutorial, I have come across an
inconsistency between the parameter/topology files directly from the
Martini website: http://md.chem.rug.nl/cgmartini/index.php/tools2
and the files provided in the tutorial.

Specifically, the bond lengths for P5-QaL and P4-QaL are defined as 3.7
A in the GROMACS style topology/parameter files, but in the NAMD
tutorial files, these bond lengths are listed as 4.7 A. Is this simply
a typographical error, or is there a reason why these parameters were
changed to 4.7 A? There are also different bond lengths used for
QaL-NaL for charged lipids (3.7 A), and zwitterionic lipids (4.7 A), but
in the tutorial files, 4.7 A is used for everything.

Also, it looks like the parameters for the bonds are defined twice.
First as P5 QaL, the later as QaL P5, for example. Is this necessary
for using MARTINI in NAMD?

Regards,
Jeff 

-- 
Jeffrey Potoff
Professor & Director of Early Engineering Programs
Department of Chemical Engineering and Materials Science
Wayne State University			
http://potoff1.eng.wayne.edu
http://gomc.eng.wayne.edu
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