bond atoms and angles missing in step 1

Dear All
I am simulating protein in water. The starting structure is taken from protein data bank and solvated using VMD plugins. Lammps data file is created using ch2lmp tools.After energy minimization I am getting the following error
ERROR on proc 3: Bond atoms 281 283 missing on proc 3 at step 1 (neigh_bond.cpp:88)
ERROR on proc 1: Angle atoms 1675 1676 1683 missing on proc 1 at step 1 (neigh_bond.cpp:176)
I increased the pairwise cutoff, now I am before minimization I am getting “Neighbor list overflow, boost neigh_modify one”
Here follows my input file.
dimension 3
units real
boundary p p p
atom_style full

dielectric 1.0

pair_style lj/charmm/coul/long 14.0 16.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 1e-4

group solute id < 1750
group solvent id > 1750

neighbor 2.0 bin
neigh_modify every 1 delay 0

variable Tinput index in.cytc_water_heat
variable input index in.cytc_water
variable sname index cytc_water

print ======================================================================
print “500 steps CG Minimization.”
print ======================================================================
fix 3 solute spring/self 100.00
dump 1 all atom 25 {sname}_min.lammpstrj dump_modify 1 image yes scale yes dump 2 all xyz 500 min_{sname}.xyz

min_style sd
minimize 1.0e-4 1.0e-6 500 50000
min_style cg
minimize 1.0e-4 1.0e-6 500 50000

unfix 3
minimize 1.0e-4 1.0e-4 500 500000
minimize 1.0e-4 1.0e-4 500 500000
undump 1
undump 2
print .
print =====================================
print “NVE dynamics with Langevin thermostat”
print =====================================
print .

reset_timestep 0
timestep 1.00
fix shakeH all shake 1e-6 500 0 m 1.0 a 163
fix restraint solute spring/self 100.0
fix 2 all nve
velocity all create 0.0 12345678 dist uniform
thermo 1
thermo_style multi
restart 1000 {sname}_heat.restart1 {sname}_heat.restart2
dump 1 all atom 1000 ${sname}_heat.lammpstrj
dump_modify 1 image yes scale yes
variable l loop 6 #number of increments
variable i index 50 #temp increments

label loop
variable t equal v_l*$i # temperature this loop
print “temperature: $t”
fix 4 all langevin $t t 100.0 834729 run 50000 unfix 4 next l jump {Tinput} loop
unfix 2
undump 1
unfix restraint

Any suggestions would be very thankful


in.cytc_water_heat (3.84 KB)

Section error of the manual explains what both
errors mean. Since the neigh_modify one default
is 2000, you must have increased the pair cutoff
a lot, which is not a good idea, both for computation
time, and the validity of your model.