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_deltaperturb*random(-1.0,1.0,{seed})
variable y atom y+v_deltaperturb*random(-1.0,1.0,{seed})
variable z atom z+v_deltaperturb*random(-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(atoms*random(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_deltamove

*random(-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 znew equal z[v_i]+v_deltamove

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}