[gmx-users] martini: clarification on the Particle definitions (i.e. force field)

[ZHANG Cheng]

Dear martini friends,
(Sorry for still posting here as the martini forum does not get reply quickly)


I am evaluating which force field mostly suits my protein. From this link
http://www.cgmartini.nl/index.php/force-field-parameters/particle-definitions
there are 7 martini 2.x options to choose, 3 are non-polar and 4 are polar systems. Can I understand them in this way? (please do tell me any typos I have made)


Can I also suggest if a more clear hierarchy (e.g. a table or tree structure) could be shown on the website? The current representation allocates "Particle definitions", "Amino Acids" and "Pure water solvent" at different webpages, which is okay. But if there is an overall breakdown, that would be much more straightforward to follow. (a search box would also be appreciated!)


"forcefield.itp" (from martini_v2.2polIon folder) said: "It must be used with the refPOL.itp and refion.itp force field files for polarizable water and ions, respectively."  But where are "refPOL.itp" and "refion.itp" files?


1) martini_v2.0.itp
old non-polar version, not use


2) martini_v2.1.itp
old non-polar version, not use


3) martini_v2.2.itp (updated: 05-12-2012)
latest non-polar version
-ff martini22
#include "martini_v2.2.itp" in the system.top
non-polar water
non-polar amino acid
default ions


4) martini_v2.P.itp
old polar version, not use


5) martini_v2.2P.itp (updated: 05-12-2012)
default polar version
-ff martini22p
#include "martini_v2.2P.itp" in the system.top
polar water
polar amino acid
default ions





6) martini_v2.2refP.itp (updated: 06-02-2017)
refined polar version
-ff martini22p
#include "martini_v2.2refP.itp" in the system.top
polar water & must with refPOL.itp
polar amino acid
default ions




7) martini_v2.2polIon.tar.gz (updated: 06-08-2018) Contains martini_v2.2refP.itp + NaCl

refined polar version with refined ions
-ff martini22p
#include "forcefield.itp" (from martini_v2.2polIon folder) in the system.top
polar water & must with refPOL.itp
polar amino acid 
ions: ions.itp (from martini_v2.2polIon folder)






martinize.py
http://www.cgmartini.nl/images/tools/martinize/martinize-2.6/martinize.py


non-polar water
http://www.cgmartini.nl/images/applications/water/water.gro


polar water
http://www.cgmartini.nl/images/applications/water/polarize-water.gro


non-polar amino acid
http://www.cgmartini.nl/images/parameters/ITP/martini_v2.2_aminoacids.itp


polar amino acid
http://www.cgmartini.nl/images/parameters/ITP/martini_v2.2P_aminoacids.itp


default ions
http://www.cgmartini.nl/images/parameters/ITP/martini_v2.0_ions.itp


Thank you!


Yours sincerely
Cheng