My name is Sanjay Sriram and I am using LAMMPS to study adsorption of water on a mica surface. In order to study this behavior I am employing GCMC that runs for 200000 steps. However I am only able to run 1000 steps and I repeatedly get the lost atoms error no matter what parameter I change. Please let me know how to rectify this problem?
Impossible to say from remote based on such limited information. You obviously have not found the correct settings.
Yes, we need a minimal working example of the issue to provide meaningful help, i.e. your input script and anything else needed to run.
Sure. Im not able to attach the input file because I’m a new user. So I will just write it below
INPUT FILE
#1) Initialization
units real
dimension 3
atom_style full
boundary p p f
neighbor 2 bin
neigh_modify delay 1 every 1 check yes
pair_style lj/charmm/coul/long 11.5 25
kspace_style ewald/disp 1.0e-3
kspace_modify slab 4
bond_style harmonic
#2) Simulation Box
region box block -50 50 -50 50 -150 170 units box
create_box 14 box bond/types 2 angle/types 1 &
extra/bond/per/atom 10 extra/angle/per/atom 3 extra/special/per/atom 3
#3) Water Molecules
molecule water H2O-SPC.mol
pair_coeff 1 1 0 0 # HT
pair_coeff 2 2 0.1554 3.166 # OT
bond_coeff 1 0 1.5139 # HT HT
bond_coeff 2 450 0.9572 # HT OT
mass 1 1.008 #HT
mass 2 15.994 #OT
angle_style charmm
read_data solvwater1_autopsf.data add append
molecule water H2O-SPC.mol
#create_atoms 0 random 70 34564 NULL mol water 25367 overlap 1.33
#4) Muscovite Silica
read_data mica_unit_cell_18Nov24.data add append
pair_coeff 5 14 1.67E-06 3.302 #AlH
pair_coeff 3 14 1.67E-06 3.302 #SiH
replicate 9 6 1
#5) Separate atoms and Energy minimization
group mica type 3 4 5 6 7 8 9 10 11 12 13 14
group H2O type 1 2
delete_atoms overlap 2 H2O mica mol yes
fix 1 all nve/limit 0.1
thermo 5
info coeffs
timestep 0.1
dump mydmp all atom 100 dump.lammpstrj
minimize 1.0e-4 1.0e-6 100 1000
delete_atoms overlap 2 H2O mica mol yes
delete_atoms overlap 0.5 all all
#6) Equilibration
compute ctH2O H2O temp
compute_modify ctH2O dynamic yes
fix mynvt1 H2O nvt temp 300 300 0.1
fix_modify mynvt1 temp ctH2O
compute ctmica mica temp
fix mynvt2 mica nvt temp 300 300 0.1
fix_modify mynvt2 temp ctmica
timestep 0.001
thermo 1
run 3900
#7) Adsorption Study- Grand anonical Monte Carlo Simulation
variable tfac equal 5.0/3.0
variable xlo equal xlo+0.1
variable xhi equal xhi-0.1
variable ylo equal ylo+0.1
variable yhi equal yhi-0.1
variable zlo equal zlo+0.1
variable zhi equal zhi-0.1
region system block {xlo} {xhi} {ylo} {yhi} {zlo} {zhi}
fix fgcmc H2O gcmc 25 25 0 0 65899 300 -10 0.1 &
mol water tfac_insert ${tfac} group H2O &
full_energy pressure 10000 region system
run 10000
write_data SiOwithwater.data
write_dump all atom dump.lammpstrj