OUTPUT

Hi Laamp Users,

When the following input is given,

dimension 3
units real
atom_style full
bond_style harmonic
angle_style charmm
boundary p p p
read_data ligand.data
pair_style lj/cut 20
pair_coeff * * 1.0 1.0
bond_coeff * 100.0 1.2
variable tempset equal 100.0 # K
velocity all create {tempset} 53244 dist gaussian mom yes rot yes minimize 1.0e-12 1.0e-12 10000 1000000 variable timestepc equal 1.0 timestep {timestepc}
neigh_modify delay 0 every 1 check yes page 500000 one 50000
thermo_style custom step pe ke etotal temp press density
thermo 400
thermo_modify norm no
dump 2 all atom 400 dump.lammpstrj
run 8000

The following information is delivered at the command prompt

WARNING: OMP_NUM_THREADS environment is not set. (…/comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
Reading data file …
orthogonal box = (-0.5 -0.5 -0.5) to (0.5 0.5 0.5)
1 by 1 by 1 MPI processor grid
reading atoms …
256 atoms
scanning bonds …
9 = max bonds/atom
reading bonds …
384 bonds
Finding 1-2 1-3 1-4 neighbors …
Special bond factors lj: 0 0 0
Special bond factors coul: 0 0 0
10 = max # of 1-2 neighbors
49 = max # of 1-3 neighbors
272 = max # of 1-4 neighbors
48 = max # of special neighbors
WARNING: Resetting reneighboring criteria during minimization (…/min.cpp:168)
Neighbor list info …
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 22
ghost atom cutoff = 22
binsize = 11, bins = 1 1 1
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (…/doma
in.cpp:925)
Setting up cg style minimization …
Unit style : real

There is no progress after “real”

How to fix it?

Thanks,

Subashini.K

Hi Laamp Users,

When the following input is given,

dimension 3
units real
atom_style full
bond_style harmonic
angle_style charmm
boundary p p p
read_data ligand.data
pair_style lj/cut 20
pair_coeff * * 1.0 1.0
bond_coeff * 100.0 1.2
variable tempset equal 100.0 # K
velocity all create \{tempset\} 53244 dist gaussian mom yes rot yes minimize 1\.0e\-12 1\.0e\-12 10000 1000000 variable timestepc equal 1\.0 timestep {timestepc}
neigh_modify delay 0 every 1 check yes page 500000 one 50000
thermo_style custom step pe ke etotal temp press density
thermo 400
thermo_modify norm no
dump 2 all atom 400 dump.lammpstrj
run 8000

The following information is delivered at the command prompt

WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:90)
  using 1 OpenMP thread(s) per MPI task
Reading data file ...
  orthogonal box = (-0.5 -0.5 -0.5) to (0.5 0.5 0.5)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  256 atoms
  scanning bonds ...
  9 = max bonds/atom
  reading bonds ...
  384 bonds
Finding 1-2 1-3 1-4 neighbors ...
Special bond factors lj: 0 0 0
Special bond factors coul: 0 0 0
  10 = max # of 1-2 neighbors
  49 = max # of 1-3 neighbors
  272 = max # of 1-4 neighbors
  48 = max # of special neighbors
WARNING: Resetting reneighboring criteria during minimization
(../min.cpp:168)
Neighbor list info ...
  1 neighbor list requests
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 22
  ghost atom cutoff = 22
  binsize = 11, bins = 1 1 1
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms
(../doma
in.cpp:925)
Setting up cg style minimization ...
  Unit style : real

There is no progress after "real"

How to fix it?

see the thermo command.
http://lammps.sandia.gov/doc/thermo.html

but you should pay attention to this warning, too:

WARNING: Proc sub-domain size < neighbor skin, could lead to lost
atoms (../domain.cpp:925)

looking at the rest of the output, there seems to be something very
wrong with your data file. your box is 1x1x1 angstrom despite having
256 atoms in it. i don't suppose you are interested in studying
nuclear fusion, right? :wink:

axel.