Rescaling of partial charges

GROMACS version: 2019
GROMACS modification: Yes/No
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Hello Gromacs developers and users,

I’m dealing with a highly negative charged protein-RNA-ligand complex which happens to create a lot of problems with lots of counter ions being added to the system to effectively neutralize it, and during dynamics the ions happen to go and interact with the ligand which is not what i want. Have tried using the Gromacs documentation recommended van der waal and coulombic cut-offs for PME and CHARMM36 force field with no success.

Is there any way to scale down the partial charges of charged groups in Gromacs, which can be done using CHARMM and have been performed in a few papers Why base tautomerization does not cause errors in mRNA decoding on the ribosome. Here in methods section they write, “Phosphate groups beyond 22Å from the simulation center were neutralized by scaling down the partial charges.” Although the authors of this paper have used their own simulation codes, can in anyway this method be performed in Gromacs.?

Pallav Sen,
Research Scholar,
IIT Guwahati,
Assam, India

my experience with RNA complexes is that it is critical to start the production run with the water molecules and ions good relaxed around the RNA complexes. To achieve this, at least 10ns or longer position-restrain simulation (it depends on the system) may be necessary before data production. In these pre-production phase, the position of the heavy atoms of the RNA complex are restraint, but water molecules and not-bounded ions are free to move.
I hope it helps

Yes, have tried this with longer position restrained runs of about 32 ns runs once with all of the complex and few other equilibrations with gradual reduction in position restraints(i.e. 1000,800,400…so on). With all this tactics, it hasn’t helped much either. My specific question is on charge rescaling as in mentioned in this publication. How can it be done in Gromacs?
Thanking you.

This is exactly what I have been doing and the counter ions move into the region of the ligand or so to speak in the region of low dielectric!