[gmx-users] Finding Average Net charge as a function of distance from a polymer segment

Abhishek Gupta abhisheklovesastra at gmail.com
Mon Aug 29 11:21:44 CEST 2016

Dear Gromacs Users

I want to examine the distribution of counterions in my system at larger
length scales comparable to the size of the molecule. I have used RDF's to
find the distribution of ions till half the box size. Can I consider half
the box size as larger length scale ?
I have found in a paper that ion distribution surrounding the polymer can
be calculated without normalizing by the volume of the spherical shell via
average net charge calculation for diffuse counterions in my system.
My question is How can I find the average net charge as a function of
distance from the polymer segement for a polymer chain using GROMACS 4.0.7
My system contains a single polymer chain, counterions and mixed solvent.

I will be grateful for the solution of the above issue.

Abhishek Kumar Gupta
Research Scholar

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