Hi there!
I am running a system of L-serine substrate, using CHARMM force field. During the process of NPT and getting the final results, I have faced the following error:
“ERROR on proc 0: Bond atoms 5282 5291 missing on proc 0 at step 2515 (src/ntopo_bond_all.cpp:61)
Last command: run 2000000”
Could anyone please help me to resolve this issue?
In case it is needed, I have attached my error script here.
Nlocal: 2100.00 ave 2247 max 1987 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Nghost: 6318.25 ave 6521 max 6203 min
Histogram: 1 1 1 0 0 0 0 0 0 1
Neighs: 308664.0 ave 355784 max 277249 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 1234654
Ave neighs/atom = 146.98262
Ave special neighs/atom = 8.8571429
Neighbor list builds = 917
Dangerous builds = 23
fix 1 all npt temp 300.0 300.0 100.0 iso 2.0 2.0 1000.0
#Exports …
timestep 1
thermo 1000
thermo_style custom step cpu temp pe ke etotal ecoul epair density
dump 1 all atom 1000 dump.txt
run 2000000
PPPM initialization …
using 12-bit tables for long-range coulomb (src/kspace.cpp:340)
G vector (1/distance) = 0.25589473
grid = 32 32 15
stencil order = 5
estimated absolute RMS force accuracy = 0.033822043
estimated relative force accuracy = 0.00010185408
using double precision FFTW3
3d grid and FFT values/proc = 8820 4096
Setting up Verlet run …
Unit style : real
Current step : 2468
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 16.76 | 17.04 | 17.16 Mbytes
Step CPU Temp PotEng KinEng TotEng E_coul E_pair Density
2468 0 200 -468802.56 5007.1647 -463795.4 -576685.27 -668312.3 0.71883945
ERROR on proc 0: Bond atoms 5282 5291 missing on proc 0 at step 2515 (src/ntopo_bond_all.cpp:61)
Last command: run 2000000
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.