I took a look at your input script, and realized that I
misunderstood what you were trying to do. (And it seems like you are
misunderstanding a few things about LAMMPS.) Before you continue
trying to use the "rerun" command, I suggest you try some of the other
examples that come with LAMMPS and make sure you are familiar with
what LAMMPS does and what kind of information goes in the various
files which LAMMPS reads.
1) Bond topology should be stored in a DATA file (such as
"data.hexamer_100A" in your example). Bond information is (almost)
never stored in a dump file. (The only exception to this rule is when
you are using "fix bond/break" or "fix bond/create", to form and break
bonds during a simulation. So I assumed that this was what you did
when you ran your initial simulation, before you use the "rerun"
2) "rerun" is only used to analyze trajectory file generated during a
previous simulation. I assume you have already run a simulation and
have a "dump.lammpstrj" file. (If not, then stop reading this post.)
If you notice strange energies when you use "rerun", AND you did
not notice anything out of the ordinary, when you ran the original
simulation (the one which generated the "dump.lammpstrj" file), then
you may have a problem in the way you are computing various kinds of
energy between various groups. (Have you taken a look at
In any case, what happens when you add this line to your input script?
thermo_style custom step pe epair ebond eangle edihed eimp
Do the energies printed to the terminal (and the "log.lammps" file)
I also noticed that your input script does not have any
"bond_coeff", "angle_coeff", "dihedral_coeff", "improper_coeff"
commands. Are these Coeffs located in your data file?
Alternatively, if you have doubts that there are bonds (angles,
dihedrals, etc...) in your "data.hexamer_100A" file, then you can try
looking at it with a text editor, and/or visualizing it. (I attached
a file explaining how to see the bonds in your DATA file using Axel's
topotools program and VMD. You should see lines connecting the
Comment: There are a lot of strange things in your input script.
Did you test this script before posting it? It takes some effort to
look over a script. So when you post an input script please be
careful to check that it contains lines that you are actually using.
The script you posted would cause LAMMPS to crash in at least two
fix 2 alpha_carbons backbone beta_atoms oxygens
...I would comment out the other "fix" commands as well. (Why do you
need them if you are using "rerun"? I'm not sure about some of those
"variable" commands as well.)
README_visualize.txt (2.42 KB)