Hello all,
I did molecular dynamic simulations of the crosslinking process of epoxy in Materials Studio. To continue the simulation in LAMMPS, I created the data file by saving the car/mdf file of the results and converted using “msi2lmp” function with PCFF. For my initial simulations, I used LAMMPS 11aug2017-MPI version. I faced no error in reading the data file (except a warning of an inconsistent image flag because of the periodic graphene in the system).
But now I have realized that in the newer version of LAMMPS, I have the following error:
“Invalid atom ID in Dihedrals section of data file”
I searched the mail list for the reasons! I found Dr. Axel Kohlmeyer response:
the old version doesn't complain, because it does not have the check
for invalid topology data.
i don't know why msi2lmp produces these files, but i suspect that
already the topology data you have as input may be incorrect.
Now here are my questions:
1- What is the origin of the problem? Does the problem come from the msi2lmp function or the way that for example Materials Studio export car/mdf file?
difficult to say in this generality.
2- Does anyone know any other way to solve this problem? Because it is really hard to create the data file manually for a class2 forcefield.
i would look at the exact data that is causing the error and try to
understand what is wrong here. it may depend on the force field
specifics.
3- If we use older versions of LAMMPS, and find no error for the simulations, then should we concern about the results?
yes. avoiding an issue without understanding it list like holding a
grenade with a pulled pin in our hand. nothing will happen initially,
but as soon as you drop it, you are in big trouble.
axel.