Use more steps of equilibration.  The distance between ions was still changing slightly when only 1000 steps were used.
@@ -6,9 +6,6 @@ Restrained minimization
ntmin = 1,
maxcyc = 1000,
ncyc = 500,
- ntr = 1,
- restraint_wt = 1.0,
- restraintmask = ':1-2',
ntb = 1,
ntf = 1,
ntc = 1,
