TIP-4P water model with pppm

Dear LAMMPS users,

I prepared very simple systems consisting of 4 TIP4P water molecules.

I tried to run the simulations but I got an error message “ERROR: Out of range atoms - cannot compute PPPM”

But, I checked the data files several times. And there was no problem there.

Could you check my input script?

Thank you very much.

====================================================================

Define variables

====================================================================

input data file

variable lmp_data string data.test

temperature and pressure

variable T equal 270.0

variable p equal 3/0.101325

interactions / rcut

variable rcut equal 12

number of steps / timestep

variable nstep equal “10000000”

variable dt equal 0.001

output

variable freq_thermo equal “1” # thermo output every

variable freq_frame equal “1” # frame output every

variable freq_snap equal “1” # xyz output every for safety (rerun)

====================================================================

Initialization

====================================================================

units real

boundary p p p

comm_modify vel yes cutoff 4

neigh_modify delay 0 every 1 check yes page 500000 one 50000

atom_style full

====================================================================

====================================================================

read_data ${lmp_data}

1 WH

2 WO

mass 1 1.008

mass 2 15.9994

pair_style lj/cut/tip4p/long 2 1 1 1 0.1546 12.0

pair_modify mix arithmetic

pair_coeff 1 1 0 0

pair_coeff 1 2 0 0

pair_coeff 2 2 0.1852 3.1589

bond_style harmonic

bond_coeff 1 0 0

angle_style harmonic

angle_coeff 1 0 0

kspace_style pppm/tip4p 1.0e-4

====================================================================

Constraints

====================================================================

fix shake all shake 0.0001 20 10 b 1 a 1

====================================================================

1. RELAX / NVE limit

====================================================================

fix thermostat all temp/berendsen {T} {T} 100.0

#fix barostat all press/berendsen aniso {p} {p} 1000.0

thermo ${freq_thermo}

thermo_style custom step cpuremain temp press etotal ebond

thermo_modify flush yes

dump dtrj all custom {freq_frame} {lmp_data}.lammpstrj id type x y z mol

dump dsnap all custom {freq_snap} {lmp_data}_*.lammpstrj id type x y z mol

reset_timestep 0

timestep ${dt}

run ${nstep}

unfix nvelim

undump dtrj

undump dsnap

write_restart restart.RELAX01

print “01.RELAX done”

12 atoms

8 bonds

4 angles

2 atom types

1 WH

2 WO

1 bond types

1 WH-WO

1 angle types

1 WH-WO-WH

-5.0000000 100.7137586 xlo xhi

-5.0000000 100.9912000 ylo yhi

-5.0000000 100.6824000 zlo zhi

-0.0000000 0.0000000 0.0000000 xy xz yz

Atoms

1 1 2 -1.1128000 40.3911473 33.0061704 31.9715144

2 1 1 0.5564000 40.1511599 33.9327975 31.9715144

3 1 1 0.5564000 41.3483473 33.0061704 31.9715144

4 2 2 -1.1128000 40.3911473 33.0061704 27.5520856

5 2 1 0.5564000 40.1511599 33.9327975 27.5520856

6 2 1 0.5564000 41.3483473 33.0061704 27.5520856

7 3 2 -1.1128000 40.3911473 33.0061704 37.4726856

8 3 1 0.5564000 40.1511599 33.9327975 37.4726856

9 3 1 0.5564000 41.3483473 33.0061704 37.4726856

10 4 2 -1.1128000 41.2379475 34.4728714 29.7618000

11 4 1 0.5564000 40.9979601 35.3994986 29.7618000

12 4 1 0.5564000 42.1951475 34.4728714 29.7618000

Bonds

1 1 1 2

2 1 1 3

3 1 4 5

4 1 4 6

5 1 7 8

6 1 7 9

7 1 10 11

8 1 10 12

Angles

1 1 2 1 3

2 1 5 4 6

3 1 8 7 9

4 1 11 10 12

Dear LAMMPS users,

I prepared very simple systems consisting of 4 TIP4P water molecules.

I tried to run the simulations but I got an error message “ERROR: Out of
range atoms - cannot compute PPPM”

But, I checked the data files several times. And there was no problem there.

no. the problem is with your potential parameters. specifically these:

bond_style harmonic
bond_coeff 1 0 0

angle_style harmonic
angle_coeff 1 0 0

when you are using file shake to keep atoms rigid, you don't need the
force constants, but you *do* need to provide equilibrium distance and
angle. please see
http://lammps.sandia.gov/doc/Section_howto.html#howto_8

axel.