[gmx-users] Young and Cheatham ions parameters for gromacs

Harutyun Sahakyan sahakyanhk at gmail.com
Wed May 15 08:12:19 CEST 2019

Dear GMX users

I would like to use Young and Cheatham ions parameters (
https://pubs.acs.org/doi/full/10.1021/jp8001614#si1) with amber99sb-ildn.
How can I convert  sigma and epsilon values and use them with gromacs? For
instance, I want to use K and Cl ions with scpe water, sigma (*R* min/2)
and epsilon (ε) presented by Cheatham are in Å and kcal/mol. However,
gromacs uses *nm *and *kJ/mol*, when I translated Å to nm and kcal to kJ
and used that values I noticed some artifacts and unusual connections
between K and Cl ions. What did I do wrong and what are the right
parameters for K and Cl in this case? I suppose conversion from Å to nm is
not correct, is sigma in gromacs *R* min/2 ?

My used parameters (nm and kJ/mol)
K     sigma 0.1593 epsilon 1.7978873936
Cl    sigma 0.2711 epsilon 0.05349244

in Young and Cheatham (Å and kcal/mol)
K     sigma  1.593 epsilon  0.4297054
Cl    sigma   2.711 epsilon  0.0127850

Thanks in advance,

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