# Questions about some LJ parameters in charmm36 ff **URL:** \ **Category:** User discussions\ **Tags:** forcefield\ **Created:** [February 2, 2024, 6:17am UTC](https://gromacs.bioexcel.eu/t/questions-about-some-lj-parameters-in-charmm36-ff/8201 "2024-02-02T06:17:53Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![HyewonLee](https://avatars.discourse-cdn.com/v4/letter/h/6a8cbe/32.png) [@HyewonLee](https://gromacs.bioexcel.eu/u/HyewonLee)\ **Post date:** [February 2, 2024, 6:17am UTC](https://gromacs.bioexcel.eu/t/questions-about-some-lj-parameters-in-charmm36-ff/8201/1 "2024-02-02T06:17:53Z")
GROMACS version: GROMACS modification: Yes/No hello. I noticed something strange about the entries within the file “charmm36\_ljpme-jul2022.ff/ffnonbonde.itp”, available on the [MacKerell lab website](http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs) These are the ones from this contents down. (probably lines 541~597) _; from file toppar\_c36\_jul22/stream/misc/toppar\_ions\_won.str_ The units for epsilon given in Table1, which is the [reference](https://pubs.acs.org/doi/10.1021/jp309150r) for toppar\_ions\_won.str, are kJ/mol. Why are the epsilon values in this file written as if they are kcal/mol converted to kJ/mol? AG1P as an example, When the epsilon value of AG1P provided in the reference is 0.2870 kJ/mol. 0.2870\*4.184 = **1.200808**. ; type atnum mass charge ptype sigma epsilon AG1P 47 107.870000 0.000 A 0.216363662688 **1.2008080** ; Silver It’s the same as the file contents. But I think it should be 0.2870, not 1.200808. I’m not sure which one is right. Maybe I’m just not thinking straight. Thanks in advance for answers. ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [February 2, 2024, 8:17am UTC](https://gromacs.bioexcel.eu/t/questions-about-some-lj-parameters-in-charmm36-ff/8201/2 "2024-02-02T08:17:16Z")
In that reference epsilon seems to be in kcal/mol whereas all energies are in kJ/mol. ---
**Author:** ![HyewonLee](https://avatars.discourse-cdn.com/v4/letter/h/6a8cbe/32.png) [@HyewonLee](https://gromacs.bioexcel.eu/u/HyewonLee)\ **Post date:** [February 2, 2024, 10:55am UTC](https://gromacs.bioexcel.eu/t/questions-about-some-lj-parameters-in-charmm36-ff/8201/3 "2024-02-02T10:55:21Z")
I misread that, thank you. ---
**Author:** ![HyewonLee](https://avatars.discourse-cdn.com/v4/letter/h/6a8cbe/32.png) [@HyewonLee](https://gromacs.bioexcel.eu/u/HyewonLee)\ **Post date:** [February 2, 2024, 11:09am UTC](https://gromacs.bioexcel.eu/t/questions-about-some-lj-parameters-in-charmm36-ff/8201/4 "2024-02-02T11:09:21Z")
I’m really sorry, but I can’t seem to find an explanation in the reference that the units for ε are kcal mol-1, could you point me to where? I assumed it was kJ mol-1 based on what was written at the bottom of Table1. _aCompiled data are from ref 10, where the hydration model depicts the ion as a sphere with the radius r that is surrounded by the hydration shell with the thickness Δr. ΔGhyd, ΔGcalcd, and ε are in kJ mol-1 and r, Δr, and Rmin are in pm._ _bε is evaluated in eq 2 based on r and Δr._ ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [February 2, 2024, 11:24am UTC](https://gromacs.bioexcel.eu/t/questions-about-some-lj-parameters-in-charmm36-ff/8201/5 "2024-02-02T11:24:00Z")
I don’t see a unit for epsilon in table 1 (which is bad). But in the text epsilon has units kcal/mol. ---
**Author:** ![HyewonLee](https://avatars.discourse-cdn.com/v4/letter/h/6a8cbe/32.png) [@HyewonLee](https://gromacs.bioexcel.eu/u/HyewonLee)\ **Post date:** [February 2, 2024, 11:48am UTC](https://gromacs.bioexcel.eu/t/questions-about-some-lj-parameters-in-charmm36-ff/8201/6 "2024-02-02T11:48:35Z")
Isn’t the unit of epsilon in kcal mol-1 only in the force field parameter of CHARMM (cgenff)…? In gromacs, isn’t the unit of epsilon in kJ mol-1? Is charmm36\_ljpme-jul2022.ff/ffnonbonde.itp specially using kcal/mol…? The reference describes the following, it is the same as the value in Table 1. _The formula based on the hydration shell model yields ε values of 0.2007 kJ mol-1 for the sodium ion and 0.3600 kJ mol-1 for the potassium ion._ ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [February 2, 2024, 11:55am UTC](https://gromacs.bioexcel.eu/t/questions-about-some-lj-parameters-in-charmm36-ff/8201/7 "2024-02-02T11:55:55Z")
Yes, CHARMM uses kcal/mol, GROMACS kJ/mol. The paper doesn’t mention the unit, but checking once more I expect epsilon should have unit kJ/mol. Maybe @jalemkul can say more? ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [February 2, 2024, 11:59am UTC](https://gromacs.bioexcel.eu/t/questions-about-some-lj-parameters-in-charmm36-ff/8201/8 "2024-02-02T11:59:00Z")
The paper incorrectly states that ε is in kJ/mol. It is actually kcal/mol. The parameters in GROMACS are translated directly from the CHARMM toppar file provided by the author and I checked the energies (I had the same confusion some time ago when using those LJ parameters). ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [February 2, 2024, 12:04pm UTC](https://gromacs.bioexcel.eu/t/questions-about-some-lj-parameters-in-charmm36-ff/8201/9 "2024-02-02T12:04:35Z")
Thanks. I don’t think the paper states the units of epsilon that are given in table 1. So not incorrect, but lacking (and confusing). ---
**Author:** ![HyewonLee](https://avatars.discourse-cdn.com/v4/letter/h/6a8cbe/32.png) [@HyewonLee](https://gromacs.bioexcel.eu/u/HyewonLee)\ **Post date:** [February 2, 2024, 12:17pm UTC](https://gromacs.bioexcel.eu/t/questions-about-some-lj-parameters-in-charmm36-ff/8201/10 "2024-02-02T12:17:01Z")
Okay. Thank you both.