I am studying translocation of dsDNA poly(AT)45 via graphene nanopore at 0.1080 V/nm electric field in 1 M KCL solution. The production run is performed in NVT ensemble using Nose-Hoover thermostat. I am trying to calculate ionic current using formula (1) given in reference link 1. This reference calculates ionic current using z-coordinates of "ions only". I have two questions:
http://pubs.acs.org/doi/abs/10.1021/nn202989w
http://pubs.rsc.org/en/Content/ArticleLanding/2015/RA/C4RA12530D#!divAbstract
Their is a tutorial provided by NAMD, you can have look on that, although you were using gromacs, I think that will be helpful to understand the ionic current. (http://www.ks.uiuc.edu/Research/nanopore/)
The RSC is the recent one and have the low eV to understand the diff in ATGC transfer across the nano pore, and the second one older. However, both of them indicating the dependence on eV to differentiate nucleotides. If I was you I will follow the RSC.
Yes, I am also planning to use the recent method. Thanks Abhishek for clearing up this ambiguity. I am already following NAMD tutorial.
welcome @Mandear, we are also doing something similar but with experimental and MD data.
Dear Abhishek , while calculating ionic current from simulations have you observed negative current? Do you feel is it fine to get negative values? because in literature I have not observed negative current values.
P.S. I am aligning my trajectory with respect to graphene before calculating current.
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