Out of range atoms - cannot compute PPPM

Dear all,

I ran the TIP4P water simulation with the input script downloaded from http://www.orsi.sems.qmul.ac.uk/downloads/
but the following error message was printed out

PPPM initialization …
G vector (1/distance) = 0.239192
grid = 45 45 45
stencil order = 5
estimated absolute RMS force accuracy = 0.00323434
estimated relative force accuracy = 9.74012e-06
using double precision FFTs
3d grid and FFT values/proc = 140608 91125
Setting up run …
Memory usage per processor = 119.258 Mbytes
Step Temp TempAve Press PressAve PEAve_Mo DensAve
0 447.00931 0 nan 0 0 0
ERROR on proc 0: Out of range atoms - cannot compute PPPM (…/pppm.cpp:1905)
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

Could you tell me what can cause this?
Below is the input script I downloaded.

Reference: M. Orsi, Comparative assessment of the ELBA coarse-grained

model for water, Molecular Physics, DOI:10.1080/00268976.2013.844373

units real
atom_style full
read_data data.singleTIP4P-2005
include forcefield.TIP4P-2005
pair_modify tail yes
kspace_style pppm 1.0e-5

replicate 20 20 20

variable Nrun equal 1000
variable Nf equal {Nrun}/10 variable Ne equal 10 variable Nr equal {Nf}/{Ne} variable Ndump equal {Nrun}/2
variable Nr_rdf equal 0.5*{Nrun}/{Ne}

variable watMoleMass equal 18.0153 # /(g/mol)
variable nAvog equal 6.0221415e23 # Avogadro’s number
variable watMoleculeMass equal ({watMoleMass}/{nAvog}) # /(g/molecule)
variable A3_in_cm3 equal 1e-24 # Angstrom^3 in cm^3
variable nAtoms equal atoms
variable nMolecules equal v_nAtoms/3

variable Text equal 298.0
variable Pext equal 1.0

group hydrogen type 1
group oxygen type 2

velocity all create ${Text} 1234

neighbor 2.0 bin
neigh_modify every 1 delay 0 check yes

timestep 2.0

fix constrain all shake 1.0e-4 100 0 b 1 a 1
fix integrate all npt temp {Text} {Text} 100.0 iso {Pext} {Pext} 1000.0
fix removeMomentum all momentum 1 linear 1 1 1

compute T all temp
fix TempAve all ave/time {Ne} {Nr} ${Nf} c_T

variable P equal press
fix PressAve all ave/time {Ne} {Nr} ${Nf} v_P

compute PE all pe pair kspace
variable PE_Mol equal c_PE/v_nMolecules
fix PEAve_Mol all ave/time {Ne} {Nr} ${Nf} v_PE_Mol

variable Dens equal v_nMolecules*{watMoleculeMass}/(vol*{A3_in_cm3})
fix DensAve all ave/time {Ne} {Nr} ${Nf} v_Dens file wat.dens

compute msd oxygen msd com yes
fix msd oxygen ave/time 1 1 500 c_msd[4] file wat.msd

compute rdf all rdf 1000 2 2 # oxygen-oxygen
fix rdf all ave/time {Ne} {Nr_rdf} ${Nrun} c_rdf file wat.rdf mode vector

thermo_style custom step temp f_TempAve press f_PressAve f_PEAve_Mol f_DensAve
thermo_modify flush yes
thermo ${Nf}

dump trj all atom ${Ndump} wat.lammpstrj

run ${Nrun}

#write_restart restart.wat

Any assistance will be deeply appreciated.

Best wishes. Thanks !

Step Temp TempAve Press PressAve PEAve_Mo DensAve
0 447.00931 0 nan 0 0 0

This line indicates a bad model. The pressure is NaN, which means
typically bad forces. You can’t run dynamics on bad input.

Steve

Dear Steve,

I’m very grateful for your response, but I am still in confusion.

  1. As I said before I downloaded the data and input scripts from http://www.orsi.sems.qumu.ac.uk/downloads, and there is a log file on that web which shows that the model should run well. I have noticed that the input script was written on October 19,2013. Is it because of the version of LAMMPS or some changed commands that leads to my problem?

  2. When I changed lj/cut/tip4p/long to lj/cut/tip4p/cut and deleted the command of Kspace_style , the model ran well. I don’t know why.

Once again thanks for your help.

Dear Steve,

I’m very grateful for your response, but I am still in confusion.

  1. As I said before I downloaded the data and input scripts from http://www.orsi.sems.qumu.ac.uk/downloads, and there is a log file on that web which shows that the model should run well. I have noticed that the input script was written on October 19,2013. Is it because of the version of LAMMPS or some changed commands that leads to my problem?

  2. When I changed lj/cut/tip4p/long to lj/cut/tip4p/cut and deleted the command of Kspace_style , the model ran well. I don’t know why.

These are both questions you should ask the person that uploaded those files.

Comments below.

Dear Steve,

I'm very grateful for your response, but I am still in confusion.

1) As I said before I downloaded the data and input scripts from
http://www.orsi.sems.qumu.ac.uk/downloads, and there is a log file on that
web which shows that the model should run well. I have noticed that the
input script was written on October 19,2013. Is it because of the version of
LAMMPS or some changed commands that leads to my problem?

2) When I changed lj/cut/tip4p/long to lj/cut/tip4p/cut and deleted the
command of Kspace_style , the model ran well. I don't know why.

These are both questions you should ask the person that uploaded those
files.

and to make sure there is no other problem looming, you should run
some of corresponding examples that are bundled with LAMMPS first.
there is the rhodo benchmark and the peptide example.

axel.