Thank you very much Andrew, I appreciate it. I have a question though, is it possible to use moltemplate to generate a structure using the OPLS FF? Moltemplate does not have so much FF documentation.
Yes.
Currently, the best way to learn about how to build systems using different force fields, is to look at the examples.
There are 6 examples of molecular simulations built which use the OPLSAA force field located in this directory:
“examples/all_atom/force_field_OPLSAA”
(which is also located at github here.)
… and one example using the OPLSUA force field here:
“examples/all_atom/force_field_OPLSUA_united_atom/propane”
(which is located here)
…there are 2 examples using the LOPLSAA force field (a variant of OPLSAA for long chains) here:
https://github.com/jewettaij/moltemplate/tree/master/examples/all_atom/force_field_OPLSAA/hexadecane
https://github.com/jewettaij/moltemplate/tree/master/examples/all_atom/force_field_OPLSAA/alkane_chain_single
The best example is probably the ethelyne+benzene example which is also located here:
http://moltemplate.org/visual_examples.html#ethylene+benzene
However, to use these force fields, all of the atoms in your system will have to be given names that moltemplate understands. Moltemplate uses these names to look up force field information. Currently, the “ltemplify.py” script (I mentioned in a previous post) does not know how to infer atom type from your DATA files. You must manually rename atom type names, such as “@atom:type3” (the names assigned by “ltemplify.py”) to something like “@atom:88” (the short-hand names typically used in the “oplsaa.lt” file which can be found here).
(The list of atom type names used by OPLSAA is regrettably rather cryptic because it was converted from another file whose atom type names were thrown away and replaced by integers.)
Also, be sure to read this warning message as well:
http://moltemplate.org/force_field_recommendations.html
This also might be relevant: If the LAMMPS input script that you provided to “ltemplify.py” already contains OPLSAA force-field parameters, then “ltemplify.py” will faithfully copy the relevant “coeff” commands containing these parameters and assign them to the corresponding name, eg “@atom:type3” without knowing what they are.
hope this helps
andrew