"neutral" option in gromacs.genion

[marcodigennaro]

Hello, I am trying to reproduce the tutorial from http://www.mdtutorials.com/gmx/lysozyme/index.html with GromacsWrapper.
I am stuck on the ionic addtion for charge neutrality, specifically:

gmx genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -neutral

I could not find the equivalent of "-neutral" in GromacsWrapper gromacs.genion
There is a comment here:

GromacsWrapper/gromacs/setup.py

Line 476 in 11f0daf

# neutralize (or try -neutral switch of genion???)

but it's one function in gromacs.setup, not in the gromacs.tools <class 'gromacs.tools.Genion'>

Can you advise on this? Thanks

[marcodigennaro]

You have to pass neutral=True to the command:
gromacs.genion(s='ions.tpr', o='1AKI_solv_ions.gro', p=topol, pname="NA", nname="CL", neutral=True)
and the expected behaviour is met.
Going forward, how do I pass the index of molecules to be removed?

In the example, I get:

Command line:
  gmx genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -neutral

Reading file ions.tpr, VERSION 2023.1 (single precision)
Reading file ions.tpr, VERSION 2023.1 (single precision)
Will try to add 0 NA ions and 8 CL ions.
Select a continuous group of solvent molecules
Group     0 (         System) has 35968 elements
Group     1 (        Protein) has  1960 elements
Group     2 (      Protein-H) has  1001 elements
Group     3 (        C-alpha) has   129 elements
Group     4 (       Backbone) has   387 elements
Group     5 (      MainChain) has   517 elements
Group     6 (   MainChain+Cb) has   634 elements
Group     7 (    MainChain+H) has   646 elements
Group     8 (      SideChain) has  1314 elements
Group     9 (    SideChain-H) has   484 elements
Group    10 (    Prot-Masses) has  1960 elements
Group    11 (    non-Protein) has 34008 elements
Group    12 (          Water) has 34008 elements
Group    13 (            SOL) has 34008 elements
Group    14 (      non-Water) has  1960 elements

and I have to input 13 from keyboard. How do I pass it in the python command?

[marcodigennaro]

The answer is here:

gromacs.genion(s='ions.tpr', o='1AKI_solv_ions.gro', p=topol, pname="NA", nname="CL", neutral=True, input=("13"))

pass the desired value as a tuple to the input field of gromacs.genion

I guess I just needed to do some googling at this stage on my own to get the right answers

[marcodigennaro]

where can I find the energy module? i.e. the equivalent of
gmx energy -f em.edr -o potential.xvg?

[orbeckst]

This should be available as

gromacs.energy(f="em.edr", o="potential.xvg")