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(https://academic.oup.com/nar/article/42/20/12876/2902660) . 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.?
Thanking you in advance.
Regards,
Pallav Sen,
Research Scholar,
IIT Guwahati.
Technically, it's easily done, as no force field parameter is hard coded. Scientifically, you have to provide solid reasons of doing so. Keep in mind that (any) force field is designed, parameterized and validated by a lot of people with years of work. When you try to change the parameters (such as partial charges), good reasons are naturally needed.
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