Mdp parameters for non-bonded interaction using the AMBER force field

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@alevilla @milosz.wieczor
I am interested in conducting DNA simulations using the bsc0 and bsc1 force fields. However, I have encountered a challenge related to the nonbonded parameters, and I find the information somewhat unclear.
In articles 1 and 2, a cutoff of 10 angstroms is mentioned.I also refer to another article 3 (which serves as a reference for amberparm99) stating that the cutoff is 9 angstroms. Given that bsc0 is developed based on the amberparm99 force field, I am unsure which cutoff value I should choose for my simulations.
Could you kindly provide clarification on this matter? Additionally, can I use these parameters (expect rcoulomb = 1.0 and rvdw = 1 that should be different) for both bsc0 and bsc1 force fields?

  • constraints = h-bonds
  • rcoulomb = 1.0
  • rvdw = 1.0
  • Potential-shift-Verlet (vdw-modifier = Potential-shift-Verlet)
  • EnerPres (DispCorr = EnerPres)
  • coulombtype = PME
  • fourierspacing = 0.125

I greatly appreciate your time and assistance in resolving these queries.
Thank you and best regards,

Ref:

  1. Galindo-Murillo, R., Robertson, J. C., Zgarbova, M., Sponer, J., Otyepka, M., Jurecka, P., & Cheatham III, T. E. (2016). Assessing the current state of amber force field modifications for DNA. Journal of chemical theory and computation , 12 (8), 4114-4127.
  2. Love, O., Galindo-Murillo, R., Zgarbová, M., Šponer, J., Jurečka, P., & Cheatham III, T. E. (2023). Assessing the Current State of Amber Force Field Modifications for DNA─ 2023 Edition. Journal of Chemical Theory and Computation .
  3. Wang, J., Cieplak, P., & Kollman, P. A. (2000). How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?. Journal of computational chemistry , 21 (12), 1049-1074