[gmx-users] counter ions in coarse grained simulations

Venkat Reddy venkat4bt at gmail.com
Fri May 23 12:04:51 CEST 2014

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

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

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