Ask about LAMMPS Data Format

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1

Dear all LAMMPS Users,
i would like to ask about LAMMPS Data Format…
especially on this part:

Atoms

  1 molecule-tag atom-type q x y z nx ny nz  (nx,ny,nz are optional -
  ...                                    see "true flag" input command)
  ...                
  N molecule-tag atom-type q x y z nx ny nz  (N = # of atoms)





<b>is there someone who can explain to me about that? and if i want to make N atoms, is there
 software to generate it??</b>

**thanks..**
2

See the examples dir for many examples of data files.
See the tools dir for various tools that create data files.

Steve

3

i’ve tried to understand tools dir. but i still not understand. so, how do if I want to configure the N-Atoms???or i must type it one by one?

4

i've tried to understand tools dir. but i still not understand. so, how do if I want to configure the N-Atoms???or i must type it one by one?

sure and you need to evaluate the force manually, too.
the whole MD code is just a big deception. :wink:

but seriously, to create a data file, you have to have a
way to create initial coordinates. these can have different
sources, e.g. existing coordinate files and/or tools that
assemble or generate those. not all of those are contained
in the LAMMPS distribution. also, there are ways to run
a simulation without a data file, if the initial coordinates
can be generated by defining a lattice and a circumference
of an object.

if all of this doesn't make sense to you,
your problem is not with LAMMPS.

axel.

5

i've tried to understand tools dir. but i still not understand. so, how do
if I want to configure the N-Atoms???or i must type it one by one?

Actually, for very small molecules (5 atoms or less), this is what I still do.
Other people in our group elected to write their own scripts (a series
of for loops) to generate the data file for the biomolecules they are
simulating. (It's a bit of work. I'm sure the other tools such as
pizza.py and others may be useful, but we chose to write our own
scripts instead. We all write our own scripts which are usually
customized for each molecule. We will post the general, non-specific
ones here when they are ready.)

I think the topotools script can generate a lammps data file for you
if you have a VMD-compatible coordinate file (eg. PDB, XYZ), and a PSF
file (charmm/namd topology files). You still need to manually specify
the parameters for the force field you are using ("Pair Coeffs", "Bond
Coeffs", "Angle Coeffs", "Dihedral Coeffs", "Improper Coeffs", but
this is doable. It is far less work than typing out all the
coordinates for a big system.) I also sometimes use this script.
http://sites.google.com/site/akohlmey/software/topotools