Hi Neha, You can simply add ions using genion. Its similar to what we do in AA system. You have to append #include martini_v2.0_ions.itp to your .top file.
On Fri, May 23, 2014 at 6:17 AM, Neha Gandhi <n.gandh...@gmail.com> wrote: > Hi List, > > My query is not really related to gromacs but I appreciate response from > people who might have tried using coarse grained simualtions using Martini > force field in gromacs. > > I haven't come across tutorial or mailing list where people have added > counter ions to a coarse grained protein system. Do we also coarse grained > counter-ions ? or Do I assume that some sort of potential will take care of > the effect? Or are the parameters from atomistic force fields are retained > for counter-ions? > > How do I add counter-ions in gromacs to coarse grained topology? > > Your feedback is appreciated. > > Regards, > Neha > -- > 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. > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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.
