[gmx-users] total charge

[Lei Zhou]

Dear gmx-users,

I am doing a simulation with a small molecule (20 atoms), which
carries a net charge of -1. To calculate the solvation energy, I need
to simulate the molecule in water. To get a good estimate
of the electrostatic interaction between that molecule and water,
should I do the MD without counter ions added? If I add counter ions
to neutralize the system, will those ions affect the final result
(they will interact with the molecule) ? I am using a cutoff of 0.9
and PME for electrostatic treatment.

Thank you.

Lei Zhou
Columbia Univ., NY