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Dear AMBER developers,
I am reading the AMBER25 manual for ion parameter suggestions and noticed that Mg2+ CM parameters with TIP3P are cited from Ref. 145 (J. Chem. Theory Comput., 2014, 10, 289–297), and found them mentioned in Ref. 144 also (J. Chem. Theory Comput., 2013, 9, 2733–2748) .
Ref. 145 mentions different set of optimized parameters for Mg2+ (Rmin/2 = 1.437 and epsilon = 0.02257962), whereas CM parameters are (Rmin/2 = 1.360 and epsilon = 0.01020237).
Can developers confirm which set is correct for RNA simulations in TIP3P and Joung-Cheatham Cl- ions?
Also, is the IOD set from Ref. 144 better for equilibrating predicted RNA models?
Thanks,
Mandar
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Received on Wed Jan 07 2026 - 04:30:02 PST
