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

João Henriques joao.henriques.32353 at gmail.com
Thu Sep 11 13:59:09 CEST 2014


First of all don't be offended, but I struggled a little bit with your
English, so I hope I got the message correctly. If my answer doesn't
correspond to your question, please let me know.

> I am using GROMACS 4.5.6 and could not find this particular tool.

That's because there isn't one. Gromacs is a MD package, you are looking in
the wrong place. To calculate charge distributions you need a titration
scheme. A constant-pH MD method would probably be able to do so, but then
there are the Mg2+ cations. Divalent (multivalent) ions are usually a
problem, specially when using a linearized Poisson Boltzmann solver to
estimate the pKa's (this is part of the internal machinery used in
constant-pH MD methods).

There are other alternative methods.

Best regards,

On Thu, Sep 11, 2014 at 1:30 PM, soumadwip ghosh <soumadwipghosh at gmail.com>

> Hello,
>       I am calculating Mg2+ concentration dependent persistence length
> calculation of RNA strands. Since, the trends of RNA chain collapse is
> different for different ionic concentration, I need to quantify if there is
> overcharging at higher concentration of divalent cation. For this, I have
> to show a charge density distribution against the distance of the RNA at
> different salt concentration. I am using GROMACS 4.5.6 and could not find
> this particular tool. Kindly help me as  its one of the reviews from the
> referee.
> Regards,
> Soumadwip
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