[gmx-users] too many lincs warnings

[Meenakshi Rajput]

hello users
I had done energy minimisation of protein-ligand complex and i got negative
potential. Also the ligand was at right place after EM run but when I tried
the positional restrained run, too many lincs warnings came and md run
stopped suddenly. I am using charmm force field and mdp file settings for
position restrined run are:-
define        = -DPOSRES    ; position restrain the protein
; Run parameters
integrator    = md        ; leap-frog integrator
nsteps        = 50000        ; 2 * 50000 = 100 ps
dt        = 0.002        ; 2 fs
; Output control
nstxout        = 500        ; save coordinates every 0.2 ps
nstvout        = 500        ; save velocities every 0.2 ps
nstenergy    = 500        ; save energies every 0.2 ps
nstlog        = 500        ; update log file every 0.2 ps
; Bond parameters
continuation    = yes        ; first dynamics run
constraint_algorithm = lincs    ; holonomic constraints
constraints    = all-bonds    ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter    = 1        ; accuracy of LINCS
lincs_order    = 4        ; also related to accuracy
; Neighborsearching
cutoff-scheme   = Verlet
ns_type        = grid        ; search neighboring grid cells
nstlist        = 10        ; 10 fs
rlist        = 1.2        ; short-range neighborlist cutoff (in nm)
rcoulomb    = 1.2        ; short-range electrostatic cutoff (in nm)
rvdw        = 1.2        ; short-range van der Waals cutoff (in nm)
rvdw-switch     = 1.0
; Electrostatics
coulombtype    = PME        ; Particle Mesh Ewald for long-range
electrostatics
pme_order    = 4        ; cubic interpolation
fourierspacing    = 0.16        ; grid spacing for FFT
; Temperature coupling is on
tcoupl        = V-rescale    ; modified Berendsen thermostat
tc-grps        = Protein Non-Protein    ; two coupling groups - more
accurate
tau_t        = 0.1    0.1    ; time constant, in ps
ref_t        = 300     300    ; reference temperature, one for each group,
in K
; Pressure coupling is off
pcoupl        = no         ; no pressure coupling in NVT
; Periodic boundary conditions
pbc        = xyz        ; 3-D PBC
; Dispersion correction
DispCorr    = EnerPres    ; account for cut-off vdW scheme
; Velocity generation
gen_vel        = yes        ; assign velocities from Maxwell distribution
gen_temp    = 300        ; temperature for Maxwell distribution
gen_seed    = -1        ; generate a random seed

Please tell me if there is something wrong with mdp settings or is it some
other problem?