Hello,
I am writing to inquire about the nonbonded parameters for the bsc1 and bsc0 AMBER force fields in GROMACS.
I am currently working on setting up these parameters in the mdp file for DNA. I have reviewed the recommended parameters for the AMBER force field in the previous posts, and I am seeking further clarification and guidance on the nonbonded parameters for bsc1 and bsc0 force fields specifically.
From my understanding, the following parameters are recommended for the AMBER force field:
Constraints: bonds involving H are constrained (constraints = h-bonds)
Short-range electrostatic cutoff: 1.0 nm (rcoulomb = 1.0)
Short-range van der Waals cutoff: 1.0 nm (rvdw = 1.0)
Van der Waals modifier: Potential-shift-Verlet (vdw-modifier = Potential-shift-Verlet)
Accounting for cutoff van der Waals scheme: EnerPres (DispCorr = EnerPres)
Long-range electrostatics: Particle Mesh Ewald (coulombtype = PME)
Grid spacing for FFT: 0.125 (fourierspacing = 0.125)
Certainly! Here's the revised text with corrected grammar:
Could you kindly provide insight into how I can find nonbonded parameters for the bsc1 and bsc0 force fields in a reference? I have read several references but couldn't find this information. I would be grateful if you could guide me and let me know if there is another reference for these parameters.
I would greatly appreciate any assistance or recommendations you could offer in this regard.
Thank you in advance for your time and consideration.
I look forward to your response.
Best regards,
Fatemeh ,
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Received on Wed Dec 13 2023 - 09:00:02 PST
