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shirtsgroup / InterMol

Conversion tool for molecular simulations
MIT License
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Figure out how/if to support bond6 in gromacs in desmond/lammps #195

Open mrshirts opened 9 years ago

mrshirts commented 9 years ago

Bond6 in gromacs does not have exclusions (I think this is correct).

type input (gromacs) output (gromacs) diff (gromacs) output (lammps) diff (lammps) Non-bonded 668731.88818198 668731.88818198 0.00000000 5.82300794 -668726.06517403

However, lammps is computing the exclusions, and desmond is giving up, but these should be supportable.

mrshirts commented 9 years ago

Should be relatively easy in Desmond, since exclusions are by atom number.

ctk3b commented 9 years ago

In the latest version of LAMMPS (10Aug15), this should be doable but may not be that simple. I think it will require tweaking this for that particular bond type http://lammps.sandia.gov/doc/pair_modify.html