A strange phenomena simulated in an equilibrium system

Hi, all,

I am simulating an equilibrium system of high-density polymers. The simulation involves an initial relaxation in the NPT ensemble, followed by running it in the NVT ensemble. However, when I utilize the visualization software, I observe an unusual directional flow trend among the atoms. Could you please tell me how can I solve this problem or what might be causing the problem? Attached below is the code from my input file:

dimension          3
boundary           p p p
atom_style         full
atom_modify        map array  
units              lj
read_data          D11N1000l16.data

# potentials
pair_style        lj/cut 2.5 
pair_coeff        * * 1.0 1.0 2.5
bond_style        fene 
bond_coeff        1 30.0 1.5 1.0 1.0
special_bonds     fene 
angle_style       cosine 
angle_coeff       1 0.75

# define groups
group             seg type 1
group             nr type 2
fix               777 nr setforce 0.0 0.0 0.0
minimize          1e-10 1e-10 10000 10000
reset_timestep    0
neighbor          0.3 bin
neigh_modify      every 1 delay 0 check yes
unfix             777
velocity          all create 1.0 4928459  mom yes rot yes dist gaussian
fix               1 nr rigid single
fix               2 seg npt temp 1.0 1.0 10 iso 0.0 0.0 100

# Run
thermo		       100
timestep          0.01
run               1000000

unfix              2    
fix               4 seg nvt temp 1.0 1.0  10
dump            	1 all atom 500000 long.xyz
timestep          0.01
run              100000000


Could you post some snapshots of your system? It’s hard to know what’s going on from just the input script.

Sounds like the flying ice cube effect.

1 Like

As an initial observation your NPT time constants seem a bit too large for comfort. You can often start with temperature time constant at 100x the timestep and barostat time constant at 1000x. Your values are ten times larger.


The trajectory line is shown in the figure, where periodic boundary conditions are used.

The question had never been thought of before. If so, how can I solve this problem? Really appreciate the help!

Thank you for your reply.

I have changed NPT time constants before, but it doesn’t seem to work.