Electroneutrality in the MD Simulation

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I was working on the Lysozyme in water simulation and saw that we are neutralizing the system. Why is electroneutrality important in the MD simulations? Is it important to have an electrically neutral system every time? If not, how does one decide whether to keep the system neutral or not?


When using PME for electrostatics, a neutral system is required. Without explicit ions, a neutralizing background plasma is applied, but this can lead to significant artifacts for heterogeneous systems and should generally be avoided.

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Is this applicable to reaction field approach as well?

Reaction field is worse than PME. Reaction-field puts a neutralizing background charge in the cut-off sphere around any atom that has a charged cut-off sphere. So there is are background charges even in a net neutral system. While that does mean that you don’t make the problem worse when using a net charge in the system, you will always have worse artifacts than when using PME for any system.

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Thank you for your reply Dr. Hess.
Could you please add comments regarding:

  1. What kind of artifacts for a membrane water peptide system?
  2. Would these be similar in a coarse grain system as well- where the electrostatic interactions are short range instead of long range.

Thank you.

In general the issues with long-range electrostatics in a system with net charge are caused by regions of low dielectric being charged. Thus charged molecules have a (stronger) tendency to move into vacuum regions or the membrane interior, when present.

A coarse-grained system is not fundamentally different from an atomistic system. The question is if there is net charge. If you use RF instead of PME then charges no longer see each other beyond the cut-off distance, which causes similar issues as noted above.

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Thank you so much for your reply.