Yes I did yesterday. If somebody know the way. I also read this thread. It talks more about moltemplate rather than avagadro. If somebody has generated input file for lammps from avagadro please let me know.
Yes I did yesterday. If somebody know the way. I also read this thread. It talks more about moltemplate rather than avagadro. If somebody has generated input file for lammps from avagadro please let me know.
It is not clear where your problem lies. Your question cannot be answered in this generality. While it can be easy to build a suitable data file for some system, it can be challenging for others. There is no foolproof one-size-fits-all solution. If that would be possible, people would have implemented long ago. Both moltemplate and topotools can help with the process by automating some of the tedious tasks. However that does not relieve you from understanding your model and programming / scripting the remaining parts.
As I already mentioned, it is easy to create a data file via an intermediary file format that is understood by one of the tools capable of outputting lammps data files.
Axel
If somebody has generated
input file for lammps from avagadro please let me know.
I'm not under the impression that the Avogadro (or OpenBabel) can
output LAMMPS "data" files (or input script files) yet. However the
web page claims that it can be "extended". Anybody feeling ambitious?
(I'd love to get avogadro exporting files in moltemplate ".lt" format,
but I'm too lazy to do it.)
Yes I did yesterday. If somebody know the way. I also read this thread. It
talks more about moltemplate rather than avagadro.
LAMMPS Molecular Dynamics Simulator
That was me again. I never miss a chance to promote moltemplate!
(Unfortunately it does not have a graphical user interface, and it
currently has somewhat limited force-field support.)
Incidentally, also check out this page:
And in particular, this page:
http://montecarlo.sourceforge.net/emc/Welcome.html
Pieter gave a talk on this software (which is new).
I enjoyed his talk, and his software looked good. Check out:
I think it can make LAMMPS data files.
Pieter is so polite, he has not announced it on the mailing list yet.
I was wondering if somebody should?
I have had some good experiences with topotools. It is powerful too.
Ok I will try topo tools.
If somebody has generated
input file for lammps from avagadro please let me know.I'm not under the impression that the Avogadro (or OpenBabel) can
output LAMMPS "data" files (or input script files) yet.
Sorry. It looks like I was wrong about this:
http://open-babel.readthedocs.org/en/latest/FileFormats/The_LAMMPS_data_format.html
(it does not look like avogadro+openbabel can create LAMMPS input
scripts, but I don't think this detail is what Arun was asking about.)
Anyway, sorry Arun if I shifted the discussion away from Avogadro to
other programs.
If anyone has used Avogadro, I'm also curious to hear if it worked.
(What kind of information does it include in the data file? Does it
include pair_coeffs or other kinds of force-field data?)
If somebody has generated
input file for lammps from avagadro please let me know.I'm not under the impression that the Avogadro (or OpenBabel) can
output LAMMPS "data" files (or input script files) yet.Sorry. It looks like I was wrong about this:
The LAMMPS data format (lmpdat) — Open Babel 3.0.1 documentation
(it does not look like avogadro+openbabel can create LAMMPS input
scripts, but I don't think this detail is what Arun was asking about.)
Anyway, sorry Arun if I shifted the discussion away from Avogadro to
other programs.If anyone has used Avogadro, I'm also curious to hear if it worked.
(What kind of information does it include in the data file? Does it
include pair_coeffs or other kinds of force-field data?)
from the (limited) description it appears to be a very limited support
that would only work for very limited cases. this is not surprising,
since - like i tried to explain several times - an automated
conversion requires additional information as LAMMPS can handle such a
large variety of potentials and system setups. a simple example would
be the representation of a carbon nanotube. for a simple force field
like charmm, amber, opls, etc. you need to generate (topological)
bonds, angles, and dihedrals and assign types to atoms and those
bonded interactions, whereas with tersoff, airebo, or reaxff, those
should *not* be defined, as bonded interactions are determined
on-the-fly and the exclusions that would by default happen will make a
topology with a bond topology bogus without tweaking the exclusion
settings in special_bonds.
axel.