Confusion in understanding Equilibration & Minimisation

Dear LAMMPS users,
I’m trying to simulate polymer translocation. In my Lammps script I have first defined my pair potentials then I have grouped each part as per my requirement and then I have minimized all the structural fluctuation using minimize command and lastly equilibrated my system first at low friction value and then at a bit larger friction value. To best of my knowledge, I have tried to stick to the protocols of polymer translocation. However, One thing that I don’t understand is that my simulation is running for 1e+5 iterations with each iteration of 0.01 long in lj units, for first 10050 iterations the value of “Step Temp E_pair E_mol TotEng Press” is the same; all I’m getting is some constant values for first 10050 steps and it starts fluctuating afterwards. Is this because of the fact that it takes 10050 for my system to minimize all the structural fluctuations and then it starts equilibrating? or is there something that I’m missing here?

With Regards

For figuring that out, we would have to see your input deck and your log file. Your descriptions are too vague and as a self-identified beginner, there also is a significant probability that you did not do in your input exactly what you think you did (actually, that can happen to experienced users, too, so providing a complete, runnable and - if possible - cleaned up and simplified input deck is almost always useful).

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So this is a snippet from my lammps input script.
After this I have applied electric field along x-axis. I haven’t included that part here. I believe the problem is here in this part. The physics of the problem is intact, I believe I’m messing up somewhere here.


units		    lj
dimension       3
boundary	    p p p
atom_style	    hybrid angle charge


neighbor        0.4 bin
neigh_modify    every 1 delay 0 check yes


read_data	ions2.txt


pair_style        hybrid/overlay lj/cut 1.12 coul/long 20.0 
pair_modify       shift yes 
pair_coeff        * * lj/cut 1.0 1.0 1.12246
pair_coeff        * * coul/long   

dielectric        0.3333   
kspace_style      pppm 1.0e-3   

group            membrane  id 1:1002 #graphene membrane with a pore in it.
group            leftK id 1003:1082 
group            leftCl id 1083:1162
group            ion id 1003:1162
region           field block -75.0 75.0 -1.228 49.63 0.0 50.349


#compute 	mycompute ion displace/atom
#fix 		mycompute all ave/atom 2 5 100  x y z 


fix              freeze membrane setforce 0.0 0.0 0.0
minimize         1.0e-4 1.0e-6 1000 100000
fix              1 ion nve
fix              2 ion langevin 1.2 1.2 10.0 985974 zero no
dump             1 all custom 100 e12307_2.lammpstrj id mol type x y z ix iy iz


region  side1 block  -0.01  0.01  -100.00  100     27.6    100.0      units box side out ### above the pore
region  side2 block  -0.01  0.01  -100.00  100      0.0     21.0      units box side out ### below the pore
region  side3 block  -0.01  0.01    -2.00   19   -100.0    100.0      units box side out ### left of the pore
region  side4 block  -0.01  0.01    28.00  100   -100.0    100.0      units box side out ### right of the pore

fix     p1 ion wall/region side1  lj93  1.0 1.0 1.2246
fix     p2 ion wall/region side2  lj93  1.0 1.0 1.2246
fix     p3 ion wall/region side3  lj93  1.0 1.0 1.2246
fix     p4 ion wall/region side4  lj93  1.0 1.0 1.2246

unfix            1
unfix            2
unfix            freeze

timestep	     0.001
thermo           100
run              100000 

print "Ayyyyy! Caramabaaaa" 

The issue is that you unfixed your time integration before your run statement. Remove the “unfix” lines at the bottom of your script.


I totally overlooked this. Anyway, thanks alot Michael.