Thanks, dear Justin. if I define a constraint on a bond then force constant isn't useless?
On Mon, 6 Apr 2020 at 17:12, Justin Lemkul <jalem...@vt.edu> wrote: > > > 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. > -- 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.