Dear Prof. Axell,
i tried to simulate a composite system containing polymeric chains and a nanoparticle. the nanoparticle has a spherical shape and consists mostly of oxygen atoms. intial structure of nanoparticle was generated using Materials Studio software and imported to VMD with the .coor and .mdf file format for generating LAMMPS data file. the oxygen atoms in surface and interior part of nanoparticle should have different atom types in my data file to be used for LAMMPS. i read the online help of TopoTools plugin to do this but i were not able. could you please guid me how can i set different atom types for surface and internal oxygen atoms in the particle?
thanks in advance
Dear Prof. Axell,
i tried to simulate a composite system containing polymeric chains and a
nanoparticle. the nanoparticle has a spherical shape and consists
mostly of oxygen atoms. intial structure of nanoparticle was generated using
Materials Studio software and imported to VMD with the .coor and .mdf file
format for generating LAMMPS data file. the oxygen atoms in surface and
interior part of nanoparticle should have different atom types in my data
file to be used for LAMMPS. i read the online help of TopoTools plugin to do
this but i were not able. could you please guid me how can i set different
atom types for surface and internal oxygen atoms in the particle?
this is a question of VMD scripting. the topotools tutorial gives detailed
examples. you don't understand those, you have to learn VMD better.
VMD has many tutorials and a detailed user's guide.
axel.