Hello everyone, I have .car, .mdf file generated using Material Studio 18.1. To get the LAMMPS data file in PCFF format, I used msi2lmp tool available in LAMMPS package. But when I did minimization in LAMMPS. It is showing warning
WARNING: Inconsistent image flags (../domain.cpp:785)
Any suggestion to get LAMMPS data file correctly in PCFF format. I would be greatful if anyone could help.
Thanks,
Ankit
The coordinates in the LAMMPS data file for the initial structure produced by the builder are correct, but, as you note, they do not have image flags. LAMMPS cannot store coordinates outside the simulation box, so we can't put the unwrapped coordinates in the LAMMPS input file. We may be able to add image flags to this file, by adding this capability to the builder and all the tools that process the builder output files to produce a the LAMMPS data file, but this may take a while. In the meantime, the unwrapped coordinates are available as the "Built structures, unwrapped" output. You can download the PDB file for the structure. This file currently does not have the bonds specified, but those could be identified using e.g. OpenBabel.
Thanks Ahmed.
But statement " "Built structures, unwrapped" output. You can download the PDB file for the structure. This file currently does not have the bonds specified, but those could be identified using e.g. OpenBabel. " is little bit confusing.
Correct me if I am wrong .car .mdf file can be use as input for openbabel or generate pdb file from MS and input to OpenBabel and OpenBabel can give LAMMPS data file in PCFF format?
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