dear all user
I want to simulate a graphene sheet and a protein in the presence of water using MC(Monte Calro) and Tersoff and Charmm potential functions. I know how to perform a typical MC simulation from an example in lammps example files.
I got these warnings.
WARNING: No fixes defined, atoms won’t move (…/verlet.cpp:55)
WARNING: Using 12-bit tables for long-range coulomb (…/kspace.cpp:317)
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (…/pair.cpp:218)
then I used the gcmc and face to these belows and the program stopped after showing these warnings.
WARNING: Using 12-bit tables for long-range coulomb (…/kspace.cpp:317)
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (…/pair.cpp:218)
WARNING: Fix gcmc using full_energy option (…/fix_gcmc.cpp:408)
do you have any advice for me?
here is the program but without pair-coeff commands that are too long.
Monte Carlo relaxation of perturbed 2d hex lattice
set these parameters
make sure neigh skin > 2*deltamove
variable iter loop 3000 # number of Monte Carlo moves
variable deltaperturb equal 0.2 # max size of initial perturbation per dim
variable deltamove equal 0.1 # max size of MC move in one dimension
variable density equal 1.0 # reduced LJ density of atoms on lattice
variable kT equal 0.05 # effective T in Boltzmann factor
variable seed equal 582783 # RNG seed
problem setup
#units lj
units real
#atom_style atomic
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
atom_modify map array sort 0 0.0
dimension 3
#lattice hex ${density}
#region box block 0 10 0 5 -0.5 0.5
#create_box 1 box
#create_atoms 1 box
#mass 1 1.0
#pair_style lj/cut 2.5
#pair_coeff 1 1 1.0 1.0 2.5
#pair_modify shift yes
neighbor 0.3 bin
#neigh_modify delay 0 every 1 check yes
pair_style hybrid tersoff lj/charmm/coul/long 8 10
read_data structure.data
pair_coeff * * --------------------
pair_modify mix arithmetic shift yes
kspace_style pppm 1e-4
special_bonds charmm
variable e equal pe
fix gcmc3 all gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
run 0 to get energy of perfect lattice
emin = minimum energy
run 0
variable emin equal $e
disorder the system
estart = initial energy
variable x atom x+v_deltaperturbrandom(-1.0,1.0,{seed})
variable y atom y+v_deltaperturb*random(-1.0,1.0,{seed})
variable z atom z+v_deltaperturbrandom(-1.0,1.0,${seed})
set group all x v_x
set group all y v_y
set group all y v_z
#dump 1 all atom 25 dump.mc
#dump 2 all image 25 image.*.jpg type type &
zoom 1.6 adiam 1.0
#dump_modify 2 pad 5
#dump 3 all movie 25 movie.mpg type type &
zoom 1.6 adiam 1.0
#dump_modify 3 pad 5
variable elast equal $e
thermo_style custom step v_emin v_elast pe
run 0
variable estart equal $e
variable elast equal $e
loop over Monte Carlo moves
variable naccept equal 0
variable increment equal v_naccept+1
variable irandom equal floor(atomsrandom(0.0,1.0,{seed})+1)
variable rn equal random(0.0,1.0,{seed})
variable boltzfactor equal "exp(atoms(v_elast - v_e) / v_kT)"
variable xnew equal x[v_i]+v_deltamoverandom(-1.0,1.0,{seed})
variable ynew equal y[v_i]+v_deltamove*random(-1.0,1.0,{seed})
variable znew equal z[v_i]+v_deltamoverandom(-1.0,1.0,${seed})
variable xi equal x[v_i]
variable yi equal y[v_i]
variable zi equal z[v_i]
label loop
variable i equal ${irandom}
variable x0 equal {xi}
variable y0 equal {yi}
variable z0 equal ${zi}
set atom i x {xnew}
set atom i y {ynew}
set atom i z {znew}
run 1 pre no post no
if “e <= {elast}” then &
“variable elast equal e" &
"variable naccept equal {increment}” &
elif “{rn} <= {boltzfactor}” &
“variable elast equal e" &
"variable naccept equal {increment}” &
else &
“set atom i x {x0}” &
“set atom i y {y0}” &
“set atom i z {z0}”
next iter
jump SELF loop
final energy and stats
variable nb equal nbuild
variable nbuild equal ${nb}