[lammps-users] FAO Axel - Topotools

I have been using Topotools to generate my LAMMPS data file from an xyz coordinate file but am having some problems.

When it writes the LAMMPS data file, all bond types are defined as type 1, regardless of which atoms are actually bonded together. However, when it outputs the angles and dihedrals data, after I have used the guessangles/dihedrals command, the angle/dihedral type are all numbered uniquely, based on the which atoms form the angle/dihedral.

Is there anything I can do to get the bond type numbered correctly, so different atom types which are bonded together are regarded as a different type of bond.

Thanks,

Michael Doig

I have been using Topotools to generate my LAMMPS data file from an xyz
coordinate file but am having some problems.

When it writes the LAMMPS data file, all bond types are defined as type
1, regardless of which atoms are actually bonded together. However, when
it outputs the angles and dihedrals data, after I have used the
guessangles/dihedrals command, the angle/dihedral type are all numbered
uniquely, based on the which atoms form the angle/dihedral.

Is there anything I can do to get the bond type numbered correctly, so
different atom types which are bonded together are regarded as a
different type of bond.

yes. the bonding information is initially computed by VMD upon
loading the file and VMD doesn't care about bond types unless
you read a file format that has these assigned.

but if you do a: topo retypebonds
you can generate the same kind of bond type assignment that you
would get for topo guessangles and topo guessdihedrals.

cheers,
    axel.