[gmx-users] martini: How do I know if the coarse-grained (CG) ions are added?

ZHANG Cheng 272699575 at qq.com
Sun Feb 3 01:11:37 CET 2019

I use these two lines to neutralise the system

$ gmx grompp -f minimization.mdp -r system-solvated.gro -c system-solvated.gro -p system.top -o system_genion.tpr
$ echo W | gmx genion -s system_genion.tpr -o system_genion.gro -p system.top -pname NA -nname CL -neutral -conc 0.2

(#include "martini_v2.0_ions.itp") is shown in the system.top file. However, I found out that the above two lines could still work after removing the (#include "martini_v2.0_ions.itp"). Also, I can change "NA" and "CL" to any other names without any errors.

So how the CG ions are reflected in the CG system? I think the CG ions are different from the all-atom ions, right?

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