WARNING: Building an occasional neighobr list when atoms may have moved too far

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1

Dear All users

I have a small system that it is included 18 n-decane molecules, I want

to perform npt ensemble and get rdf , but i got this error, You can

download my system.data from these links:

-------------system.in-----------------------

dimension 3
neighbor 2 bin
neigh_modify delay 2

– Default styles (for solo “SPCE” water) –

units metal #### I select metal unit #######3
atom_style full

(Hybrid force fields were not necessary but are used for portability.)

pair_style lj/cut 2.5 #### 2.5 time sigma ij
bond_style harmonic
angle_style harmonic
dihedral_style multi/harmonic
pair_modify mix arithmetic

read_data “system.data”

group 1 type 2
group 2 type 1

dump 1 all atom 1000 traj_npt.lammpstrj

thermo 1000

thermo_style custom etotal ke temp pe ebond eangle edihed press vol

minimize 1.0e-5 1.0e-7 1000 10000

timestep 0.001

– run at constant pressure (Nose-Hoover)–

fix 1 all store/force
fix fxnpt all npt temp 450.0 450.0 450.0 iso 1.0 1.0 1.0

compute 1 all rdf 10 1 1
compute 2 all rdf 10 2 2
compute 3 all rdf 10 1 2

fix 2 all ave/time 100 1 100 c_1 c_2 c_3 file tmp1.rdf mode vector

– Now, finally run the simulation –

run 1000000

---- (end of examples) ----

print “All done”

2

From the manual: Section_error.html

{Building an occasional neighobr list when atoms may have moved too far}

This can cause LAMMPS to crash when the neighbor list is built.
The solution is to check for building the regular neighbor lists
more frequently.

So see if the problem persists if you do
neigh_modify check yes every 1 delay 0

If it does, then you are running bad dynamics with your
infrequent reneighboring.

Steve

3

Dear Steve

4

Dear Steve

From the manual: Section_error.html

{Building an occasional neighobr list when atoms may have moved too far}

This can cause LAMMPS to crash when the neighbor list is built.
The solution is to check for building the regular neighbor lists
more frequently.

So see if the problem persists if you do
neigh_modify check yes every 1 delay 0

Yes, I did this

I have a new problem,

As you see, My target temperature and pressure are 450 K and 1 bar
(Sorry, I have a mistake in writing,( temp and press, in my prior email))

I want to perform npt ensemble but I can not get 450 k and 1 bar, My
simulation oscillate around 13000 k and press: between -70 to 300

   fix fxnpt all npt temp 450.0 450.0 450.0 iso 1.0 1.0 1.0 drag 1

5

Ali,

I would suggest that your choice of damping factors is arbitrary and spectacularly poor. Please read the manual.

Nigel