[lammps-users] Out of range atoms - cannot compute PPPM

Hi,
Dear All

I write a script as below, when I run it, gives an error.
This script is for interaction between one nanotube and one protein.
I read the manual but I did not notice that What should I do.

Regards,
Farrokh

dimension 3
boundary p p p
units metal
neigh_modify delay 2 every 1

lattice fcc 2.5
region A block -50 95 -50 95 -50 95

atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic

pair_style hybrid lj/charmm/coul/long 8 10 tersoff lj/cut 2
read_data proteinnanotube.data
pair_coeff 132 132 lj/charmm/coul/long 100.0 2.0
pair_coeff * * tersoff SiC.tersoff NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL C
pair_coeff 1*32 33 lj/cut 1.0 1.0

#pair_modify mix arithmetic
#kspace_modify slab 3.0

kspace_style pppm 1e-4
#kspace_modify slab 5.0
#create_box 33 A
group nanotube id > 3280
displace_atoms nanotube move 40 0 0

special_bonds charmm
fix 1 all nve
fix 2 all shake 1e-6 500 0 m 1.0
velocity all create 300.0 12345678 dist uniform

ERROR :

.
.
WARNING: Shake determinant < 0.0
WARNING: Shake determinant < 0.0
WARNING: Shake determinant < 0.0
WARNING: Shake determinant < 0.0
WARNING: Shake determinant < 0.0
Memory usage per processor = 29.6039 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -856163.9028 KinEng = 175.1087 Temp = 300.0000
PotEng = -856339.0116 E_bond = 498.4328 E_angle = 935.5953
E_dihed = 899.3600 E_impro = 0.9588 E_vdwl = -858565.5739
E_coul = 299.8871 E_long = -407.6717 Press = nan
ERROR: Out of range atoms - cannot compute PPPM

dear farrokh,

before you go on spamming the list with random iterations
of data files in the hope that sooner or later your simulation
will and probably ignoring the fact that running doesn't mean
that it is meaningful. perhaps a little word of more general
advice. the method of learning that you are trying to use is
a) highly inefficient, b) wasting time of the people that try
to give you advice and c) in the long run pretty irritating
and frustrating to everybody involved.

it looks to me that you have bitten off far too large a chunk
of work, and in that case it is always better to step back,
break the problem in pieces and address one of them at a time.
in order for people to give you the right kind of advice,
i would like to ask you a few questions:
- how much experience do you have with MD simulations at all?
- did you run simulations on each of the components of your
  multi-component system before? and were you able to validate
  those results
- is LAMMPS the only MD code that you ever used?
  if not what else? and for how long? and on what kind of system?
- what is your level of experience overall (e.g. student, post
  graduate, professor emeritus, etc.) and in what discipline?

I write a script as below, when I run it, gives an error.
This script is for interaction between one nanotube and one protein.
I read the manual but I did not notice that What should I do.

as was said on this list before about a million times, this error
message is a bit of a catchall and gets triggered when something
else has gone wrong before. there are a few things in your input
that seem very weird to me.

Regards,
Farrokh

dimension 3
boundary p p p
units metal
neigh_modify delay 2 every 1

lattice fcc 2.5
region A block -50 95 -50 95 -50 95

atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic

pair_style hybrid lj/charmm/coul/long 8 10 tersoff lj/cut 2
read_data proteinnanotube.data
pair_coeff 1*32 1*32 lj/charmm/coul/long 100.0 2.0

why do you define 32 atom types and then (re-)set them all to
the same parameter set here. on top of that, an epsilon of 100eV
and a sigma of 2.0 seems _very_ strange for a "bio" system.

pair_coeff 1*32 33 lj/cut 1.0 1.0

this one is strange as well. it would be more typical
for reduced units. or more generally speaking, how can
you expect this to work _at all_ if you don't have a
reasonable set of parameters for your system???

cheers,
    axel.