# Changing the pH of protein

**URL:** <https://gromacs.bioexcel.eu/t/changing-the-ph-of-protein/4185>\
**Category:** User discussions\
**Created:** [May 18, 2022, 1:20pm UTC](https://gromacs.bioexcel.eu/t/changing-the-ph-of-protein/4185 "2022-05-18T13:20:24Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![D429321](https://avatars.discourse-cdn.com/v4/letter/d/958977/32.png) [@D429321](https://gromacs.bioexcel.eu/u/D429321)\
**Post date:** [May 18, 2022, 1:20pm UTC](https://gromacs.bioexcel.eu/t/changing-the-ph-of-protein/4185/1 "2022-05-18T13:20:24Z")

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GROMACS version: 5.1.4  
GROMACS modification: No  
Hello respected community members. I am performing MD simulation of a protein in water. I have changed the protonation state of the titratable amino acids so as to mimick a pH of 4.0. My doubt is that now my system has a charge of 8. Do I need to add counter ions for neutralizing my system?

Thanks in advance.

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**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [May 18, 2022, 2:48pm UTC](https://gromacs.bioexcel.eu/t/changing-the-ph-of-protein/4185/2 "2022-05-18T14:48:33Z")

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Hi,  
Yes you need to neutralise the system. You can use the tool gmx genion to do that.  
/Alessandra

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**Author:** ![D429321](https://avatars.discourse-cdn.com/v4/letter/d/958977/32.png) [@D429321](https://gromacs.bioexcel.eu/u/D429321)\
**Post date:** [May 19, 2022, 7:22am UTC](https://gromacs.bioexcel.eu/t/changing-the-ph-of-protein/4185/4 "2022-05-19T07:22:05Z")

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Just a followup question. Along with the counter ions do I need to add 150 mM of NaCl to mimic the macroscopic salt concentration? Thanks in advance

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**Author:** ![D429321](https://avatars.discourse-cdn.com/v4/letter/d/958977/32.png) [@D429321](https://gromacs.bioexcel.eu/u/D429321)\
**Post date:** [May 19, 2022, 7:22am UTC](https://gromacs.bioexcel.eu/t/changing-the-ph-of-protein/4185/5 "2022-05-19T07:22:46Z")

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Thanks a lot for answering my question. I was just confused regarding this. I came across a couple of papers where ions were not added to maintain the net charge of protein in low pH. For example: In one paper authors mention that “The net charge of the system was maintained for the pH 5.0 and pH 7.9 structure of T7L after protonation and de-protonation step while the neutral pH structure was neutralized by replacing the water molecules with Cl− and Na+ counter ions based on their net charge”. DOI: 10.1186/s12900-017-0077-9). So that’s why I am confused whether to add ions or not.

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**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [May 19, 2022, 9:04am UTC](https://gromacs.bioexcel.eu/t/changing-the-ph-of-protein/4185/6 "2022-05-19T09:04:56Z")

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Hi,  
it depends which condition you aim to mimic. 150 mM NaCl is used to mimic a physiological concentration. But for example if you want to mimic see water, then you will use another concentration.  
\Alessandra