Basically I want to calculate LJ interaction for OH bond. If I use eq. 4.5 in manual to calculate LJ interaction then zero.
How can I calculate LJ interaction of a bond? Nilesh On Fri, June 10, 2011 3:00 pm, Andrew Paluch wrote: > The LJ interaction is 0. But you're asking about a bond. 1-2 > interactions are typically modeled with a harmonic potential. This is most > definitely not zero. > > > On Jun 10, 2011, at 2:54 PM, Nilesh Dhumal wrote: > > >> If eplilon of hydrogen atom is zero then the lennard jones >> interaction of OH bond (at 0.22nm)is also zero. >> Is it correct? >> >> >> I used equation 4.5 to calculate LJ energy. >> >> >> Nilesh >> >> >> On Fri, June 10, 2011 2:47 pm, Justin A. Lemkul wrote: >> >>> >> >>> >>> Nilesh Dhumal wrote: >>> >>> >>>> Hello, >>>> >>>> >>>> >>>> How can I calculate Lennard Jones interaction for two selected >>>> atoms with a specific distance? >>>> >>> >>> Using energygrps might be an option if you need to monitor the >>> interaction over time. Otherwise, if the distance is fixed, just plug >>> all the parameters into the LJ equation. In theory, you could >>> calculate the interactions this way over time, as well, even if the >>> distance changes. >>> >>> -Justin >>> >>> >>> >>>> I am using Gromacs 4.0.7 version. >>>> >>>> >>>> >>>> Thanks >>>> >>>> >>>> >>>> Nilesh >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>> >>> -- >>> ======================================== >>> >>> >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> >>> >>> ======================================== >>> -- >>> gmx-users mailing list [email protected] >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to [email protected]. Can't post? >>> Read >>> http://www.gromacs.org/Support/Mailing_Lists >>> >>> >>> >>> >> >> >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/Support/ >> Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected]. Can't post? >> Read http://www.gromacs.org/Support/Mailing_Lists >> > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. Can't post? Read > http://www.gromacs.org/Support/Mailing_Lists > > > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
