[gmx-users] Neutralizing the total charge of the system in vacuum

Hi all, I am performing a simulation in vacuum. The peptide has nonzero charge, so I attempted to neutralize the total charge via genion;however as it is known, it asks for a continuous group for replacing, but I have no solvent molecules for the replacement. How can I neutralize the total

Re: [gmx-users] Neutralizing the total charge of the system in vacuum

Ran Friedman, Biochemisches Inst. wrote: Hello, You can add a few ions manually or use genbox. However, it's probably better to use a vacuum force field and have your peptide uncharged for vacuum simulations. Any ions you add will have a very strong interaction with the peptide. I assume

Re: [gmx-users] Neutralizing the total charge of the system in vacuum

Hello, You can add a few ions manually or use genbox. However, it's probably better to use a vacuum force field and have your peptide uncharged for vacuum simulations. Any ions you add will have a very strong interaction with the peptide. I assume you have a good reason to simulate in vacuo