Hello, yes the virtual sites are connected to one chlorine each and the two atoms mentioned in the error are one of the LP and an oxygen that is O1 of the ligand, which is 10 bonds away from the chlorine (parent of the LP with number 4141). This is my mdp for the production that is the failed step (minimization and equilibration ended fine):
integrator = md
dt = 0.002
nsteps = 500000
nstxout-compressed = 50000
nstxout = 0
nstvout = 0
nstfout = 0
nstcalcenergy = 100
nstenergy = 1000
nstlog = 1000
;
cutoff-scheme = Verlet
nstlist = 10
vdwtype = Cut-off
vdw-modifier = Force-switch
rvdw_switch = 1.0
rvdw = 1.2
rlist = 1.2
rcoulomb = 1.2
coulombtype = PME
;
tcoupl = v-rescale
tc_grps = SOLU SOLV
tau_t = 1.0 1.0
ref_t = 310 310
;
pcoupl = C-rescale
pcoupltype = isotropic
tau_p = 5.0
ref_p = 1.0
compressibility = 4.5e-5
refcoord_scaling = com
;
constraints = h-bonds
constraint_algorithm = LINCS
lincs-order = 6
lincs-iter = 2
;
nstcomm = 100
comm_mode = linear