[gmx-users] Charged systems

[Philip Loche]

Hey Sukriti,

in general all the Ewald methods only work if the system is charge neutral. If this is not the case for your system gromacs adds a so called homogenous background charge distribution. With this one can use PME, BUT for many systems this can lead to artifacts. Especially in systems with an inhomogenous dielectric constant (see: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net Charge
http://dx.doi.org/10.1021/ct400626b).

If you should add explicit counter ions depends on the observables you are interested in, because explicit ions will change the water structure close to your ions in a different way than a homogeneous background charge does.

In general I would recommend adding explicit ions maybe with a physiological salt concentration, but think of what you are interested in maybe a single ion is what you want.

Best Philip


---

Philip Loche
Stubenrauchstr. 19
12161 Berlin

Tel.: +49 30 81032987
Mobil: +49 151 40436111
Mail: philip-loche at gmx.de
> Am 18.12.2016 um 09:13 schrieb #SUKRITI GUPTA# <SUKRITI002 at e.ntu.edu.sg>:
> 
> Can anyone please help me with this.
> 
> 
> Regards
> 
> 
> Sukriti
> 
> [https://sixprd0111.outlook.com/owa/service.svc/s/GetFileAttachment?id=AAMkADNjYmY4NDc0LTVjMzUtNDNmOC1hYzdkLTU5NTZhODkwYjVhNwBGAAAAAACBUPJnHBz9Qb1jEGoiHu01BwCW%2B40K8EMKR52f2bViS6X0AAAANaBFAAC1PvQTaUN0S5CzEDGS8lwUAAIr8o3VAAABEgAQAIhFug57qj9Lg6WQKih11Lg%3D&X-OWA-CANARY=h9cz1GMp80awqK7uWU0tmwAfbhpQFtMYCkfwOWcjFqjCjKA5rnYYMRF4FV7Oec3YWfk_SWGzz4s.&retryCount=3]
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> Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI at N) | Nanyang Technological University
> N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798
> Tel: (65) 81164191 GMT+8h | Email:sukriti002 at e.ntu.edu.sg | Web:erian.ntu.edu.sg<http://www.ntu.edu.sg/home/xuzc/People.html>
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> Subject: [gmx-users] Charged systems
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> Dear all,
> 
> 
> I have a system containing one positively charged ion frozen at the centre of the box with water molecules and one negatively charged ion in bulk water. However, the overall change in my system is not neural. I am using PME electrostatics and running the simulation. I wanted to know will my result change if I have a counter-ion like Na+ to neutralize the system? I did these simulations without neutralizing the system because I read in many places that PME automatically adds a background charge to neutralize the system.
> 
> Please let me know if I should add counter ions to neutralize the system and rerun my simulations?
> 
> Thanks
> 
> Sukriti
> [https://sixprd0111.outlook.com/owa/service.svc/s/GetFileAttachment?id=AAMkADNjYmY4NDc0LTVjMzUtNDNmOC1hYzdkLTU5NTZhODkwYjVhNwBGAAAAAACBUPJnHBz9Qb1jEGoiHu01BwCW%2B40K8EMKR52f2bViS6X0AAAANaBFAAC1PvQTaUN0S5CzEDGS8lwUAAIr8o3VAAABEgAQAIhFug57qj9Lg6WQKih11Lg%3D&X-OWA-CANARY=h9cz1GMp80awqK7uWU0tmwAfbhpQFtMYCkfwOWcjFqjCjKA5rnYYMRF4FV7Oec3YWfk_SWGzz4s.&retryCount=3]
> 
> Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI at N) | Nanyang Technological University
> N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798
> Tel: (65) 81164191 GMT+8h | Email:sukriti002 at e.ntu.edu.sg | Web:erian.ntu.edu.sg<http://www.ntu.edu.sg/home/xuzc/People.html>
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