Error: Out of range atoms - cannot compute pppm... (../pppm_tip4p.cpp:107)

Hi,

I’m working on MDS for school science fair next week and need urgent help, any help would be appreciated.

I’m getting errors in my LAMMPS simulation:

WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (…/pair.cpp:220)

WARNING: Inconsistent image flags (…/domain.cpp:759)
WARNING: Bond/angle/dihedral extent > half of periodic box length (…/domain.cpp:880)
ERROR: Out of range atoms - cannot compute PPPM (…/pppm_tip4p.cpp:107)

The issue may be related to the geometry file, containing graphene sheets and water, and bonds that seem to connect distant atoms in the graphene sheets. Is this the reason I am having these errors? I have generated a LAMMPS data file from a .xyz coordinate file through Open Babel. Topotools did not produce any bond angles and assigned the same molecule ID to the system. Is there a proper way to generate the LAMMPS data file that I am looking for, as the .xyz appears in Avogadro? Attaching source files.

CH.airebo_real (770 KB)

log.out (20.5 KB)

graphene.tip4p.LAMMPS.in (6.63 KB)

pristine_system.xyz (324 KB)

pristine.dat (993 KB)

Hi,

I'm working on MDS for school science fair next week and need urgent help,
any help would be appreciated.

apoorv,

i doubt that anybody can help you to resolve such significant and
mostly fundamental problems at multiple levels on such short notice
over e-mail.
setting up a correctly working and meaningful MD simulation take more
than building some geometries and hoping that an MD software will do
the right thing.
even if there was time, you are looking at a time span of weeks, if
not months (and some people struggle even after years) depending on
the complexity of what you want to simulate and what you want to
achieve with and learn from the simulations. your best shot is to find
a local expert that can look over your shoulder and help you with
every step (and that is likely going to be a full time commitment).

sorry,
     axel.

Thanks for the feedback, that’s alright. I was able to resolve the issue on my own and am almost finished creating and running the simulation files.

The solution was simply that the simulation box generated by Open Babel was too small. From my experience, VMD/topotools seem to be the best tools to write LAMMPS data from coordinate files, and the issue that it would not write bonds and angles was resolved by using commands to retype bonds/angles/dihedrals. Additional scripting was necessary to get the exact bonds that I wanted.