I'm trying to determine the impact of charge on an aspartic acid in my protein. I've setup a simulation in which the aspartic acid is neutral and one in which it's negatively charged. My conundrum is that if I use PME I must have counter-ions to accurately compute long-range electrostatics - however, neutralizing both systems would ultimately negate my exploration of charge. I've always run simulations with PME and I'm wondering if not including it in this case would be appropriate. Is there a work around that I'm missing?
Last edited by ca4930; 07/19/21 09:12 PM.