[gmx-users] Net charge density distribution plots in GROMACS

João Henriques joao.henriques.32353 at gmail.com
Thu Sep 11 16:17:04 CEST 2014

​If you want to do something similar to what they did, why not use their
method? They're using a regular coarse-grained model, with 4 interaction
types, simulated with Metropolis Monte Carlo. They explicitly state in
their paper how they treat ion binding and overcharging, with the
respective mathematical formulation. That's exactly what you need.​ I
really can't help you more than this without actually doing the work for
you, which I'm sorry, but I won't do for obvious reasons.

CG-MC simulations are very recurrent for this type of study. Here is one
out of many, many frameworks which can be used to perform this type of


It's just an example. Google to find others, I don't want people thinking
I'm trying to advertise it, due to my involvement on the project.

Best regards,

On Thu, Sep 11, 2014 at 3:36 PM, soumadwip ghosh <soumadwipghosh at gmail.com>

> Hi,
>    Thanks for the reply. Tell me one of the 'other ways' you mentioned in
> the reply. If you kindly check the link, I want to have a  net charge
> distribution plot similar to that of figure 3.
> Thanks in advance.
> http://onlinelibrary.wiley.com/doi/10.1002/bip.22189/pdf
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