Hello everyone,
I have the following problem: The system of interest is a periodic crystal with a unit cell made of over 600 atoms (H, C, O, Cu). There is a publication which lists a bunch of 2-, 3- and 4-atom interactions (bonds, angles, dihedrsals, impropers) for that system. I have only the xyz coordinates available. So my task in now to create a lammps input which considers all the listed interactions from that publication.
I tried to do it manually but it is extremely time consuming.
The question is whether there is software which takes the available interaction coefficients and generates a file which can be read by lammps.
If there is no such software, my plan is to write a script which will iterate over all the atoms (2-, 3- and 4-fould iterations) and check whether the atom combinations fulfill the given interactions.
I would be very thankful for your help and suggestions!
Maxim Skripnik
University of Konstanz
Hello everyone,
I have the following problem: The system of interest is a periodic
crystal with a unit cell made of over 600 atoms (H, C, O, Cu). There is
a publication which lists a bunch of 2-, 3- and 4-atom interactions
(bonds, angles, dihedrsals, impropers) for that system. I have only the
xyz coordinates available. So my task in now to create a lammps input
which considers all the listed interactions from that publication.
I tried to do it manually but it is extremely time consuming.
The question is whether there is software which takes the available
interaction coefficients and generates a file which can be read by lammps.
If there is no such software, my plan is to write a script which will
iterate over all the atoms (2-, 3- and 4-fould iterations) and check
whether the atom combinations fulfill the given interactions.
the first half of your script is available in VMD:
https://sites.google.com/site/akohlmey/software/topotools
its only weakness is that VMD's bond guessing has no option to consider
bonds across periodic boundaries, so those have to added "manually", or the
unit cell coordinates have to be "unwrapped" accordingly before telling
VMD to guess the bonds.
axel.
p.s.: you don't want to loop over all 4-tupels with 600 atoms, there would
be ~130 trillion of them. 