[gmx-users] Young and Cheatham ions parameters for gromacs
David van der Spoel
spoel at xray.bmc.uu.se
Wed May 15 11:46:43 CEST 2019
Den 2019-05-15 kl. 08:12, skrev Harutyun Sahakyan:
> 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 ?
Before you use K+ please check
Auffinger,P., Cheatham,T.E. and Vaiana,A.C. (2007) Spontaneous formation
of KCl aggregates in biomolecular simulations: a force field issue? J.
Chem. Theory Comput., 3, 1851–1859.
> 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,
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
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