Creating Bonds

dear ulrike,

please always copy the mailing list on your replies.
this way people get to see how your problem gets
solved and in the future others can research the solution
in the mailing list archives. thanks.

Dear Axel,

thank you very much. I will have a look at your homepage. Maybe I will
find my logical mistake. I work the fist time with Lammps and with
MD-Methods at all.

my usual recommendation to people with no previous
experience in MD (and LAMMPS) at all, is to first practice
with a very simple example, e.g. liquid argon (which has
been _the_ standard text book example for MD) and practice
all the settings about running and analyzing an MD run with
this system, since the results are well known and well
documented. once you are comfortable, you can then move
on toward your research project. if you start with that right
away, you will be constantly confused about whether your
problems are due to not getting the formal details right or
the physics correctly.

I had created the atoms with Lammps. I could sent you the input-script.
Than I tried to use the created atom-data for the data-file. I thought,
that the atoms would be the same size. Visualization in VMD shows, that
they are the same size and have the same distance. The only problem is,
that Lammps creates them on the lattice in a cube. I would like to
create only a bead-on-a-string model.

well, the create_atoms command did what it said it did.
for your problem, you really need a different way to construct
the initial setup. have a look at the chain.f code that is bundled
with lammps in the tools directory or check out the packmol
program. the chain generator output should be directly usable,
for packmol output you'd need to generate the bond topology
and data file (which can be done with VMD as mentioned before).

tschuess,
    axel.