Hi, I'd like to know what unit is used in the charge column of itp files. I have the same charge in two units: e/nm2 and microC/cm2, which one should I use?
Hello Andresa Messias da Silva
I hope you are doing well. Actually, there is no such fixed unit to determine surface charge density, as far as I know.
Here is a link below to convert these files into other units of interest-
http://www.endmemo.com/convert/surface%20charge%20density_s.php
Best regards
Dear Andresa Messias da Silva
GROMACS uses the elementary charge e (ca. 1.6 x 10-19 C) as standard unit of measurement for charge, therefore in the .itp files the charge column should be in fractions of e.
See here for units
https://manual.gromacs.org/documentation/2019/reference-manual/definitions.html
and here for the specifics of the topology file
https://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html
I agree with Nicola Piasentin, the .itp file define the elementary charge. It isn't atomic charge per area.
You could use the "gmx density" tool, with an extra file describing the atomic partial charges for each type of atom, with the flag -dens charge, and the corresponding axe in -d, in order to measure group charge per area.
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