Hi Axel and all, I have output a dumpfile from LAMMPS in the xyz format (dump.xyz, attached), which I wish to view using VMD. Of course, simply loading dump.xyz gives vmd no info on atom types and bonding. I know that Axel has a scripting tool to read in lammps topology files. I have attached my topology, i.e. ‘data’ file in lammps lingo, file (Polyisobutene.lammps05). When I open up the tcl prompt in vmd and attempt to read the lammps topology file, I get the following error:
% topo readlammpsdata Polyisobutene.lammps05
Info) parsing LAMMPS header.
Info) parsing LAMMPS Masses section.
-error readlammpsdata: unkown header line: 92 : BondBond Coeffs
-error readlammpsdata: cannot continue.
I am guessing that topotools was not meant to deal with type II force fields? Bond/Bond correlations are parameterized for type II FFs, but are not necessary to view trajectories.
For those trying the same stunt, i.e. viewing LAMMPS/typeII force field output, here is a workaround that worked for me: by manually editing out typeII-specific parameters (BondBond, etc.) from the lammps topology file, I was able to run the topotools command without error. Polyisobutene.lammps05 is then loaded into VMD as a new molecule and the bonding looks perfect. However, what I really want to do is to view a movie of all 200 frames in dump.xyz and I was hoping that the ‘topo readlammpsdata’ would inform vmd of the topology info relevant to dump.xyz. My understanding of the readlammpsdata script was that it would allow me to view the dump.xyz file. Have I done something wrong or misunderstood anything? Thanks,