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

[João Henriques]

​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
simulation:

https://github.com/mlund/faunus

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,
João

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

> 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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