msd does not increase over time

Hello everyone,

I was trying to calculate msd of methane(UA) in polyethylene. So I inserted 10 atoms of methane using create_atoms command. I computed msd of methane group (com and average off). However, the msd tends to fluctuate over time instead of increasing. What is wrong? I don’t suppose I have done something wrong. Please have a look

The config file :

read_data “data_after_nvt.in” extra/atom/types 1

mass 8 16.043
pair_coeff 8 8 0.294 3.73
create_atoms 8 random 10 12232 NULL
velocity all create 300.0 53244 dist gaussian mom no rot no

fix 5 all nve
timestep 1.0
minimize 1.0e-18 1.0e-20 10000 100000
write_restart after_min.restart

timestep 1.0
group methane id 8
reset_timestep 0
neigh_modify delay 0 every 1
compute 1 methane msd #average yes #com yes

unfix 5
velocity all scale 300.0
fix 1 all nve
fix 2 all langevin 300.0 300.0 50.0 6243
fix 3 all vector 10 c_1[4]

variable twopoint equal c_1[4]/(4)/(stepdt+1.0e-10)
variable fitslope equal slope(f_3)/4/(10
dt)
thermo 10000
thermo_style custom step temp c_1[4] v_twopoint v_fitslope atoms
dump 1 all dcd 1000 dump.dcd
dump_modify 1 unwrap yes

run 1000000

write_restart eq.restart
write_data data_after_ch4_diffusion(trial).in

The log file output for msd:

Step Temp c_1[4] v_twopoint v_fitslope Atoms
0 300 0 0 2.5e+18 1816
10000 297.69914 0.33438037 8.3595091e-06 1.2722139e-05 1816
20000 306.01515 0.51001016 6.375127e-06 9.4823367e-06 1816
30000 305.4434 0.42816013 3.5680011e-06 7.393834e-06 1816
40000 306.55021 0.84317155 5.2698222e-06 6.6011791e-06 1816


Thanks for all the help!

Sonu Kumar

Please take a look at Fig.6 in the following article:

http://www.nature.com/articles/srep12763?WT.ec_id=SREP-20150811&spMailingID=49294578&spUserID=MzcwNDE0MDA2MjcS1&spJobID=741745829&spReportId=NzQxNzQ1ODI5S0

I think it is better to decrease the thermo value (for example 100) .

Sorry but no change :

Step Temp c_1[4] v_twopoint v_fitslope Atoms
0 300 0 0 2.5e+18 1816
100 281.7584 0.010541991 2.6354978e-05 8.1798188e-05 1816
200 295.81658 0.046753533 5.8441916e-05 0.00023945123 1816
300 294.8955 0.016421762 1.3684802e-05 0.00013510634 1816
400 308.83143 0.23796039 0.00014872524 0.00018731288 1816
500 298.92888 0.035844106 1.7922053e-05 0.00015598243 1816
600 303.98062 0.24063113 0.00010026297 0.0001343963 1816
700 296.60298 0.012021775 4.293491e-06 0.00010374255 1816
800 303.40766 0.10398573 3.2495542e-05 8.3263218e-05 1816
900 302.62013 0.30543979 8.4844386e-05 8.267191e-05 1816
1000 295.31665 0.048343411 1.2085853e-05 7.0280095e-05 1816
1100 292.26759 0.010547506 2.3971604e-06 6.0652594e-05 1816
1200 308.76132 0.0033504838 6.9801745e-07 5.2303347e-05 1816
1300 310.22956 0.044826717 8.6205225e-06 4.7397807e-05 1816
1400 306.44669 0.169028 3.0183571e-05 4.2851104e-05 1816
1500 300.72964 0.028309604 4.7182674e-06 4.2518077e-05 1816
1600 304.63449 0.036357412 5.6808456e-06 4.0147002e-05 1816

If nothing is diffusing, then the MSD will not
increase.

Steve