GROMACS version: 2022
GROMACS modification: Yes/No
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Dear GROMACS users,
I am working on a protein system that includes iodide (I⁻) and am using the CHARMM36 force field. To define non-bonded parameters for iodide, I referred to:
Li et al., 2015 – “Systematic Parameterization of Monovalent Ions Employing the Nonbonded Model”
The reported parameters are:
• σ (sigma) = 2.567 Å
• ε (epsilon) = 0.79269938 kcal/mol
Sigma conversion (Å → nm, adjusted for CHARMM-style σ)
Sigma = Rmin/2 * 0.1 * 2^(-1/6)*2
Applying this, I got:
σ=4.5738806×10−1nm
Epsilon conversion (kcal/mol → kJ/mol)
Using the conversion factor 1 kcal/mol = 4.184 kJ/mol, I did:
ϵ=0.79269938×4.184=3.3166kJ/mol
Since CHARMM36 in GROMACS, I’m unsure whether the epsilon should be:
• 3.3166 kJ/mol (directly converted)
or
• 0.33166 kJ/mol, accounting for a potential ε/4 usage?
Could someone confirm
• What the correct ε value should be for iodide in CHARMM36 with GROMACS?
• Should I define ε = 3.3166 or ε = 0.33166 in the [ nonbond_params ] section?
Any clarification or example of similar ion parameter incorporation would be highly appreciated.
Thank you
Kumaran