# Free Energy Calculation: State B has non-zero total charge: -1.000000 **URL:** \ **Category:** pmx\ **Created:** [May 29, 2022, 4:36pm UTC](https://ask.bioexcel.eu/t/free-energy-calculation-state-b-has-non-zero-total-charge-1-000000/3738 "2022-05-29T16:36:39Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![sadafrani6](https://avatars.discourse-cdn.com/v4/letter/s/ee59a6/32.png) [@sadafrani6](https://ask.bioexcel.eu/u/sadafrani6)\ **Post date:** [May 29, 2022, 4:36pm UTC](https://ask.bioexcel.eu/t/free-energy-calculation-state-b-has-non-zero-total-charge-1-000000/3738/1 "2022-05-29T16:36:39Z")
Dear Bioexcel Community I need your suggestions regarding the following problem:- I am trying to calculate the free energy of mutating from Arginine to Histidine residue in a protein. I have prepared the system using pmx tools [http://pmx.mpibpc.mpg.de/janssen\_tutorial\_peptide/index.html](http://pmx.mpibpc.mpg.de/janssen_tutorial_peptide/index.html) I have neutralized the system however during the grompp I get the following error:- “State B has non-zero total charge: -1.000000” Could you please suggest to me how should I set state B to zero charge without affecting the charge of state A? Thanks in advance. Sadaf ---
**Author:** ![vgapsys](https://avatars.discourse-cdn.com/v4/letter/v/7993a0/32.png) [@vgapsys](https://ask.bioexcel.eu/u/vgapsys)\ **Post date:** [June 14, 2022, 3:11pm UTC](https://ask.bioexcel.eu/t/free-energy-calculation-state-b-has-non-zero-total-charge-1-000000/3738/2 "2022-06-14T15:11:50Z")
There are several ways to deal with this: a) simulate charged system and later correct dG for that b) retain the constant neutral charge of the simulation box. For that you could construct a single-system/double-box setup: Figure 3 in this book chapter [http://www3.mpibpc.mpg.de/groups/de\_groot/pdf/Gapsys\_MolMod\_2015.pdf](http://www3.mpibpc.mpg.de/groups/de_groot/pdf/Gapsys_MolMod_2015.pdf) Vytas