Use of neutral phosphates in RNA residues

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GROMACS version: 2019
GROMACS modification: No
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Dear Gromacs users,
This has my head scratching for days with a RNA-protein-ligand complex, where the influence of counter-ions messes up the structure during equilibration and production run, with the counter-ions starting to interact with the ligands and creating artifacts in the system. And i have been using CHARMM-36 force field.
There is one school of thought where they think neutralizing the phosphate groups of the RNA backbone which in turn would negate the influence of the counter-ions in the system and would essentially would give a peaceful and correct simulations.
But then there’s some conflict with the same idea as to calculate the long range electrostatics interactions we use Ewald electrostatics which is only and only used when the system has a net-charge, if I neutralize all the phosphates of the backbone then there would be essentially no use of utilizing Ewald electrostatics to calculate long range interactions.

Thanking you in advance,
All kinds of suggestions and advices are welcome.
Regards,
Pallav

2

Hi,
Making the RNA backbone neutral will change the “identity” of RNA molecule. You will simulate another type of molecule with different biophysical properties.

My suggestion to deal with the problem are the following 1) to extensive equilibrate the position of the ions and water molecule, while the position of RNA/protein/ligand are restraint, before starting the simulation 2) if the starting structures come from an experimental structure and ions are bound to RNA, keep them in the starting structure. 3) to perform the simulation with the experimentally observed ions composition (if possible) and concentration.

Best regard
Alessandra

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