On 4/6/20 7:24 AM, Sina Omrani wrote:
Hi, I wanted to know how we specify a bond order in our simulation? For example, if we have a triple bond in our structure between atoms 1 and 2, is it by length and force constants or we define 1 and 2 bonds three times in the bond section of itp file? What if we use a constraint on this bond? because I get better results when I define the bond three times but haven't seen this method. is it wrong?
All interactions should be defined only once, and the parameters used should produce correct behavior. MM force fields have no concept of double or triple bonds; they only know the stiffness of the spring connecting the atoms. My guess is that if you had to add the bond three times, the force field parameters are adding together, indicating that the force constant is unsuitable for what you're trying to and needs to be refined.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 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.
