LAmmps Geometry model

Hi, Guys,

Is there any simple and platform independent software for building up geometry model for Lammps? I mean the coordinates of moleculars, bonds, angles,force field… such information, into a data file,as the part of the input file which can be read into Lammps. It seems Lammps commands inside(creat atoms, region…) could not be used to built up complicated molecular models. Thanks !

cheers,

Eric

Hi, Guys,

   Is there any simple and platform independent software for building up
geometry model for Lammps? I mean the coordinates of moleculars, bonds,
angles,force field.... such information, into a data file,as the part of the
input file which can be read into Lammps. It seems Lammps commands
inside(creat atoms, region...) could not be used to built up complicated
molecular models. Thanks !

indeed they are not meant to be used for that.

a lot of people use packmol to generate initial geometries.
most people have their own custom tools to build topologies
from that. mine is based on using VMD and Tcl scripts:
http://sites.google.com/site/akohlmey/software/topotools

i am certain others will chime in and describe their favorite methods.

axel.

http://moltemplate.org

Although it is still preliminary, I wrote a very general open-source
script for building LAMMPS data files and input scripts named
"moltemplate". It was intended to be used for building exotic
coarse-grained molecular models. It requires a shell (the classic
bourne-shell), and python (2.5 or later). It can run in mac or linux
(and windows if a shell has been installed). A rough and
"alpha"-quality version of this program is currently available for
download at the moltemplate web page.

The best way to learn how to use moltemplate is to modify the existing
examples which come bundled with it. (These are in the "examples"
subdirectory of the archive when you download it. Also look at the
examples on the main web page.)

  ---- This program has the following (serious) limitations: ----
1) There is no graphical user interface.
2) The user must manually specify the location and orientation of
every molecule. (There are some shortcuts to make crystaline,
sheet-like, helix or tube-like assemblies automatically. Hierarchical
structures are also easy to make.)
3) There is no easy way to automatically convert other common file
formats (like PDB) into moltemplate format (yet). (However you can
convert from LAMMPS data format to moltemplate format.)
4) It can not (yet) automatically solvate a molecule. (Although holes
in the solvent can be easily created.)
5) Moltemplate does not (yet) tell users if they have made a mistake.
Because moltemplate is a complicated program, mistakes are easy to
make. This can make using it difficult (Email me if you get stuck.)
6) The documentation is still incomplete.

Despite these limitations, moltemplate is -very- general may
eventually have some unique uses. I am working of fixing problems 3,
4, and (especially) 5, and 6. When I do, I will consider moltemplate
"ready" for release, and I will post a message here again. Right now,
however moltemplate is only recommended for brave souls. (Again I'm
happy to offer email support to help them, time permitting.)

I hope this ends up being useful for someone.

Cheers
Andrew

P.S.
The topotools plugin for VMD solves many of these limitations and is
very useful.
http://sites.google.com/site/akohlmey/software/topotools
I think that most users will find that topotools fits their needs well.