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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
