I am desiring to use the special bonds command. I am only interested in
interactions of atoms with 3 bonds and 2 atoms between them such as 1 and 4
When I use this command, does it also take in to account the interactions
down the line, say 2-5 with the three bonds and two atoms between? (Which I
think it does and that’s why I want to use it, tell me if I’m wrong)
Yes. "special_bonds lj/coul 0.0 0.0 1" does that.
However, for OPLS force-fields, you want to use these settings:
special_bonds lj/coul 0.0 0.0 0.5
In terms of the actual parameters for OPLS, Does anyone have an idea of the
parameters or can someone point me in the write direction to find them?
The original parameters and force-field description are in this paper
J. Am. Chem. Soc. 1996, 118, 11225-11236
However I vaguely remember that the parameters may have been adjusted
over time, probably to fit a wider range of molecules. So, if you
want the most up-to-date force field parameters, try the BOSS manual
(near page 66)
This list has been converted to a machine-readable form, at the TINKER web-site:
Lastly, there is a molecule-builder program specifically for LAMMPS
which makes it easy to use the all-atom version of OPLS (OPLSAA).
There's an example showing how to build a long alkane chain (polymer)
using OPLSAA on this web page:
...and other examples of simple hydrocarbon molecules in the
"examples" which you can download online (click on the upper-left
Moltemplate allows you to build organic molecules relatively easily
without reading or understanding the force-field details (so please
use it with caution).
P.S. Probably the most difficult challenge of using
moltemplate.sh/oplsaa_moltemplate.py is to figure out the
atom-type-ID-number for each atom in your molecules. (For example
"@atom:80", "@atom:81" correspond to carbon bonded to different atoms,
and "@atom:85" corresponds to carbon-bound hydrogen). The sum of the
partial-charges should be zero (neutral).
If you want to use moltemplate with OPLSAA, be sure to check out the