On 6/11/18 5:20 AM, Apramita Chand wrote:
Please clarify these following doubts regarding combination rules in gromos force field: 1. The ffnonbonded.itp contains c6, c12 terms. If I choose combination rule 1 , it takes V and W as C6 and C12 as given. If combination 2 or 3 are chosen , then are the values converted to sigma and epsilon (Since for V=sigma and W=epsilon) and then used?
With combination rules 2 and 3, you have to *provide* sigma and epsilon, they're not converted.
2. If I have sigma and epsilon values for my molecule of interest, how do I add them to ffnonbonded.itp? Can I directly include sigma value under C6 and epsilon value under C12 column? And then specify combination rule as 2 or 3? If so, how should I modify the non-bonded params section? Should I compute the interactions between atoms(according to the combination rule) and include them prior to simulation??
The [nonbond_params] directive is for pair-specific LJ interactions, i.e. those that do not obey normal combination rules. You do not need to do anything here unless your pair interaction(s) require special treatment.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
