Hi,
I have built a coarse grain model of clay in materials studio and assigned charges to it. I’d like to export it into a xyz file so that I can use it in lammps. Is there an easy method to accomplish this?
I’ve tried using msi2lmps to see if I can get a usable file. When I try this tool I don’t get any outputs and I’m not sure what to look for.
I am a beginner so any help would be appreciated,
Thanks,
Anam
See http://lammps.sandia.gov/doc/99/data_format.html for the details on how LAMMPS reads in structures- I don’t think xyz is a supported input format. However, VMD might have some tools to read in an MSI file and write to a lammps-style data file. I know that VMD will read in *.car files, which you should be able to generate using MS.
I’m not sure if the msi2lmp tool can be used with coarse-grained models- at least the force field files used by msi2lmp to generate data files appear to all be all atom force fields. If you’re curious that perhaps you didn’t build msi2lmp correctly, you can always try out the tests provided in the tool directory. HTH- Vanessa
Most of the molecule building tools for LAMMPS are listed at:
http://lammps.sandia.gov/prepost.html
If you are going to use coarse grained models, I suggest avoiding
software tools which limit you to a particular style of force-field or
atom_style.
Disclaimer: I wrote "moltemplate". This software is was designed with
the intent of building coarse-grained models. It is quite general and
it is distributed with a lot of coarse grained examples you can try
and modify.
In addition, check out "Topotools". It uses TCL and it is well
integrated with VMD.
Both moltemplate and topotools work with nearly all atom_styles and
force-field styles (pair, bond, angle, dihedral, improper), including
hybrid styles, and they can extract coordinate data from xyz and pdb
files. (I frequently use tools like PACKMOL to generate XYZ files
which moltemplate can read.)
You can also try creating a LAMMPS DATA file yourself manually, as
Vanessa suggested.
--- regarding Materials Studio and XYZ files ---
Force field and topology information are not stored in XYZ files, only
atom coordinates.
Personally, I agree with Vanessa. I think of Materials Studio and
"msi2lmp" as tools for building all-atom systems. I cannot comment
whether they would be suitable for building your own custom
coarse-grained models. Furthermore, my impression is that msi2lmp is
not very actively developed and maintained. People occasionally post
complaints on the mailing list about that tool.
I hope this helps.
Andrew
I’d 2nd the use of moltemplate for building coarse-grained models as I’ve used it myself and I found it worked well.
See http://lammps.sandia.gov/doc/99/data_format.html for the details
on how LAMMPS reads in structures
This is also a good suggestion, regardless. It's a good idea to read
about the format for LAMMPS data files regardless how you generate
them. You can store atom coordinates, bond topology, and even force
field parameters inside these files. And that's a good link because
it really demonstrates the file format. More comprehensive (but
somewhat harder to read) documentation is available at:
http://lammps.sandia.gov/doc/read_data.html
http://lammps.sandia.gov/doc/atom_style.html
Cheers (and thanks)
Andrew
(More details: Axel and I generally prefer storing force-field
parameters in a separate input script file containing pair_coeff,
bond_coeff, angle_coeff, … commands. For a good example of that
file format, see:
https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---part-2/in.step2e-2.
Both topotools and moltemplate can generate these commands.
Moltemplate stores them in a file named "system.in.settings".)