Dear Lammps Users,
I am trying to equilibrate a simulation of a quarternary system at room conditions. The system has 5054 atoms. I have reduced the timestep from 0.1 to 0.001, 0.0001 but the temperature still suddenly increases from the desired temperature of 300K to about 20,000K. Initially, I ran lammps with NVT and it crashed. I also tried with NPT and it crashed too. I have checked the forum for this and many explanations include things like bad starting structure, but my structure doesn’t have any overlap when I checked the trajectory files. Will anyone be kind enough to help me with more information on this and what could be wrong with my system? The input and output are below
Input
LJ system with NVT ensemble
variable name string NAME # Molecule id
variable simtemp equal 300 # Simulated Temperature [K]
variable runnumber string 01 # Output File Name
variable prunnumber string pre # Input File Name
Setup Parameters
units real
dimension 3
boundary p p p
atom_style full
neighbor 2.0 bin
neigh_modify every 1 delay 0 check yes page 1000000
kspace_style pppm 10.00 1.0e-4
pair_style lj/charmm/coul/long 10.00 10.10
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
improper_style cvff
atom_modify sort 0 0.0
Read initial File (from towhee)
read_data ${name}.data.lj.lammps
Set NVT Ensemble
fix 1 all nvt temp {simtemp} {simtemp} 100.0
timestep 0.01
thermo_style custom step temp pe etotal press vol density
thermo 100
Number of Steps
run 10000
Output:
LAMMPS (31 Mar 2017)
Reading data file …
orthogonal box = (0 0 0) to (136.492 136.492 136.492)
1 by 2 by 13 MPI processor grid
reading atoms …
5054 atoms
scanning bonds …
4 = max bonds/atom
scanning angles …
6 = max angles/atom
scanning dihedrals …
29 = max dihedrals/atom
scanning impropers …
1 = max impropers/atom
reading bonds …
5094 bonds
reading angles …
9652 angles
reading dihedrals …
15353 dihedrals
reading impropers …
150 impropers
Finding 1-2 1-3 1-4 neighbors …
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
11 = max # of 1-3 neighbors
25 = max # of 1-4 neighbors
26 = max # of special neighbors
PPPM initialization …
WARNING: Using 12-bit tables for long-range coulomb (…/kspace.cpp:321)
G vector (1/distance) = 0.0208563
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.152714
estimated relative force accuracy = 0.000459892
using double precision FFTs
3d grid and FFT values/proc = 252 2
Neighbor list info …
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 1000000
master list distance cutoff = 12.1
ghost atom cutoff = 12.1
binsize = 6.05, bins = 23 23 23
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Setting up Verlet run …
Unit style : real
Current step : 0
Time step : 0.01
Per MPI rank memory allocation (min/avg/max) = 23.73 | 24.03 | 24.71 Mbytes
Step Temp PotEng TotEng Press Volume Density
0 0 3689.8292 3689.8292 -225.22945 2542868.7 0.017500513
100 21.222107 3371.7753 3691.4233 -207.95153 2542868.7 0.017500513
200 67.568239 2678.2396 3695.9547 -167.44168 2542868.7 0.017500513
300 105.24375 2119.4717 3704.6565 -127.15881 2542868.7 0.017500513
400 118.18293 1931.1047 3711.1799 -102.50564 2542868.7 0.017500513
500 120.52841 1888.3346 3703.7375 -91.683563 2542868.7 0.017500513
600 134.88693 1681.1706 3712.8419 -84.762618 2542868.7 0.017500513
700 162.53654 1259.5326 3707.6634 -79.875571 2542868.7 0.017500513
800 179.96757 992.93081 3703.6083 -84.108201 2542868.7 0.017500513
900 165.45898 1208.6334 3700.782 -101.47157 2542868.7 0.017500513
1000 125.39855 1821.5937 3710.3509 -120.88218 2542868.7 0.017500513
1100 90.482497 2349.3985 3712.2489 -121.36373 2542868.7 0.017500513
1200 85.478187 2421.7085 3709.1838 -89.630138 2542868.7 0.017500513
1300 105.20471 2114.0944 3698.6911 -33.823747 2542868.7 0.017500513
1400 122.38581 1861.9185 3705.2976 22.355566 2542868.7 0.017500513
1500 118.29593 1924.9802 3706.7574 57.955553 2542868.7 0.017500513
1600 102.44666 2175.418 3718.473 69.579695 2542868.7 0.017500513
1700 99.919901 2215.6145 3720.6114 66.44368 2542868.7 0.017500513
1800 120.93504 1902.7437 3724.2713 56.123276 2542868.7 0.017500513
1900 147.32577 1498.3758 3717.4014 36.261336 2542868.7 0.017500513
2000 151.79805 1432.4247 3718.8121 3.536272 2542868.7 0.017500513
2100 128.67457 1783.9789 3722.0795 -33.610054 2542868.7 0.017500513
2200 101.20762 2217.3335 3741.726 -53.975073 2542868.7 0.017500513
2300 96.778462 2291.1893 3748.8697 -40.508329 2542868.7 0.017500513
2400 117.70275 1972.3302 3745.1729 3.7068705 2542868.7 0.017500513
2500 140.22214 1623.6656 3735.6962 55.667183 2542868.7 0.017500513
2600 142.07065 1601.3032 3741.176 90.509896 2542868.7 0.017500513
2700 126.95791 1826.8819 3739.1262 98.071803 2542868.7 0.017500513
2800 118.69872 1949.6021 3737.4462 84.306055 2542868.7 0.017500513
2900 132.67953 1742.3035 3740.727 57.757458 2542868.7 0.017500513
3000 157.43757 1388.5388 3759.8688 19.883319 2542868.7 0.017500513
3100 166.82295 1254.9636 3767.6565 -30.906055 2542868.7 0.017500513
3200 148.66778 1530.3172 3769.5562 -86.557647 2542868.7 0.017500513
3300 118.1772 2001.6326 3781.6216 -126.58188 2542868.7 0.017500513
3400 101.81793 2238.2464 3771.8314 -130.9985 2542868.7 0.017500513
3500 109.81434 2104.364 3758.3912 -95.917317 2542868.7 0.017500513
3600 127.05051 1847.7906 3761.4295 -38.536601 2542868.7 0.017500513
3700 131.50654 1774.025 3754.7809 14.950467 2542868.7 0.017500513
3800 119.31192 1946.6509 3743.731 47.902019 2542868.7 0.017500513
3900 108.63384 2107.3483 3743.5949 59.345711 2542868.7 0.017500513
4000 118.22576 1965.2651 3745.9855 55.174671 2542868.7 0.017500513
4100 144.83255 1585.897 3767.3696 37.660261 2542868.7 0.017500513
4200 165.20493 1282.2023 3770.5244 4.5036624 2542868.7 0.017500513
4300 160.93193 1354.073 3778.0351 -39.511775 2542868.7 0.017500513
4400 138.42008 1670.6386 3755.5264 -77.311977 2542868.7 0.017500513
4500 121.59073 1927.6169 3759.0206 -85.94671 2542868.7 0.017500513
4600 125.69101 1869.9329 3763.0951 -55.698018 2542868.7 0.017500513
4700 141.79354 1655.1058 3790.8048 2.3160124 2542868.7 0.017500513
4800 148.83911 1566.8597 3808.6794 63.165723 2542868.7 0.017500513
4900 138.56611 1712.7963 3799.8837 106.15292 2542868.7 0.017500513
5000 124.77221 1935.5735 3814.8967 125.00581 2542868.7 0.017500513
5100 127.21432 1897.4957 3813.602 121.38098 2542868.7 0.017500513
5200 150.40629 1558.5616 3823.9861 96.846877 2542868.7 0.017500513
5300 3728.4023 4265.1133 60422.433 947.2913 2542868.7 0.017500513
5400 1793.022 33441.347 60447.905 -214.8213 2542868.7 0.017500513
5500 652.77658 50599.356 60431.499 -901.74469 2542868.7 0.017500513
5600 2098.2558 28820.518 60424.517 -37.392318 2542868.7 0.017500513
5700 3675.3845 4938.9536 60297.717 900.42515 2542868.7 0.017500513
5800 5910.3472 26478.462 115500.31 953.99627 2542868.7 0.017500513
5900 1993.369 85029.001 115053.19 -1205.5226 2542868.7 0.017500513
6000 2859.2515 95541.742 138607.88 -1136.5546 2542868.7 0.017500513
6100 5564.8839 54405.714 138224.18 419.4443 2542868.7 0.017500513
6200 7084.1543 30771.117 137472.88 1375.8039 2542868.7 0.017500513
6300 23798.452 52083.992 410537.07 5472.6931 2542868.7 0.017500513
6400 14060.467 202995.91 414775.13 19.677439 2542868.7 0.017500513
ERROR on proc 15: Bond atoms 4813 4921 missing on proc 15 at step 6450 (…/ntopo_bond_all.cpp:63)