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shirtsgroup / InterMol

Conversion tool for molecular simulations
MIT License
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Tilt factors ignored when converting from GROMACS to LAMMPS #357

Closed nabraham47 closed 5 years ago

nabraham47 commented 5 years ago

If tilt factors are present in the .gro file they do not show up when converting the system to LAMMPS.

mrshirts commented 5 years ago

By tilt factors, you mean the off diagonal elements (last 6 components) in the box vector in the .gro file?

Can you give an example for what the output should be for LAMMPS in this scenario (as well as what it is now?)

nabraham47 commented 5 years ago

Yes, LAMMPS refers to them as the tilt factors in their nomenclature. For example, the final line in the .gro file for one of my systems is: 2.7102121 2.5401599 2.3915862 0.0000000 0.0000000 0.0000000 0.0000000 -0.4855272 0.0000000

The .input file from InterMol has the box defined in the .lmp file as: -17.1176747 9.9844466 xlo xhi -13.8512351 11.5503637 ylo yhi -12.4969379 11.4189243 zlo zhi

What it should be is: -17.1176747 9.9844466 xlo xhi -13.8512351 11.5503637 ylo yhi -12.4969379 11.4189243 zlo zhi 0.0 -4.855272 0.0 xy xz yz

mrshirts commented 5 years ago

Got it. That should be relatively easy to fix, out of time now but hopefully can look at it tonight.