Dear LAMMPS developers/users
I am trying to create data file for a metal organic framework crystal from its unit cell structure which is in pdb and cif format. I have looked into topotools plugin and moltemplate documentations but considering the complex structure of the unit cell and periodic boundary conditions (with bonds, angles and dihedrals crossing boundaries) I could not find an appropriate way to use these tools.
I was wondering if anyone has had experience with creating data file for these complex crystals or has any ideas.
Thanks,
Hasan
If no one replies to you, you can definitely build it yourself by using some free software like Avagadro or ChemCraft. It should be an interesting exercise.
Ray
Agree on Avogadro. The workflow is to load the .cif, then build 1x1x1 “supercell”, then save the structure to some format similar do data file (Gaussian input is close enough, AFAIR). You will probably need some manual work with bonds (you don’t have this data in .cif anyway).
Regards,
Oleg
Ray Shan <rayshan819@…24…> 22 октября 2014 г. 19:25:02 написал:
Unfortunately, Hasan is correct. moltemplate does not know how to
automatically connect atoms which are nearby. Topotools can do this,
but not across periodic boundaries (if my memory is correct).
--- angular interactions ---
I don't know if data files generated with Avogadro includes a list of
"Angle", "Dihedral" and "Improper" interactions. Probably, it does.
If not, you can import the DATA file into either moltemplate (using
ltemplify.py) or topotools and then use these tools automatically
generate the 3-body angle and 4-body dihedral and improper
interactions for your system. I don't know if this comment helps you
very much.
I'm curious to know how you solve this problem.
Cheers!
Andrew
(Warning: I think there is currently a bug with the way moltemplate
uses "gaff.lt" to generate GAFF improper interactions, but if you are
manually specifying your own interactions by hand, it does not
matter.)
Thank you all for the responses. I am going to write a script to generate data file for my case. But I do not still know how to indicate in a lammps data file that a bond, angle or dihedral crosses a boundary. It might be simple but I never dealt with this problem and could find anything in the documentation or mailing list of lammps. your help is appreciated.
Hasan
Thank you all for the responses. I am going to write a script to generate
data file for my case. But I do not still know how to indicate in a lammps
data file that a bond, angle or dihedral crosses a boundary.
It is not necessary to worry about this particular issue.
When calculating the forces between atoms (including angle, dihedral,
and improper forces), LAMMPS is clever enough to automatically
determine the correct image coordinates for these atoms.
It might be
simple but I never dealt with this problem and could find anything in the
documentation or mailing list of lammps. your help is appreciated.
All you have to do is correctly identify the atom-ID of the atoms
participating in bonds, angles, dihedrals, and impropers. It does not
matter where the atoms are located spatially.
You do not need to warn LAMMPS that the atoms participating in an
interaction lie on different sides of a periodic boundary.
In fact, you don't even need to specify the angles, dihedrals, and
impropers. All you really have to do is specify a list of pairs of
atom-IDs for atoms which are bonded together. Both moltemplate and
topotools can generate the other interactions (angle, dihedral,
improper) automatically according to the atom type (and/or bond type).
Hope this helps.
Good luck.
Andrew