Smeared Charge System

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question

Hello Gromacs Community,

I am currently planning to conduct a simulation with a smeared charge system. Specifically, instead of using explicit ions to balance the charge in the system, I want to uniformly spread the ion charge throughout the system (smear). For example, if I need to use 2 Cl- ions for the neutrality of the system, I want to smear a charge of 2 e- throughout the system instead of using explicit Cl- ions.

Based on my knowledge, Gromacs handles long-range electrostatic interactions using PME, and PME may not be able to handle this smeared charge system. Is there any method to simulate this system in Gromacs?

Thank you in advance for your assistance!

2

Dear @joh

How do you intend to smear the charge? Because if you have a charge of -2 and you smear it across the atoms in the box by modifying all their charges, then the total will still be zero and I wouldn’t expect complains from grompp.

3

When using PME with a net charged system, GROMACS applies a background charge to neutralize the system. This is not physical and not as realistic as adding counter ions. But the effect should be similar to smearing the counter charge over the atoms in the system.

A neutralizing background charge, or smearing the counter charge may not be the solution. See, e.g., [gmx-users] What's the point of adding ions to neutralize the system? and Electroneutrality in the MD Simulation for some more information.

4

Thank you obZehn. I planned to use background charge, but your method looks better. Thank you so much!

5

Thank you, MagnusL. I just wanted to compare the difference between the system with counter ions and the system with smeared charge. If the system is homogeneous, this comparison can be fair?

6

With such a system, the comparison should be fair, as far as I can see. And the “smeared charge” approach should be equivalent (or at least very similar) to the background charge that is automatically applied when using PME with a net charged system.