[gmx-users] counter ions in coarse grained simulations

[Venkat Reddy]

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.gandhiau at 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-request at gromacs.org.
>



-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036