[gmx-users] Lennard-Jones Interactions in Gromacs

Hi In a supporting Information of a paper is written: "The description of the LF radical force fields is complete, as soon as also the parameters of the Lennard-Jones potentials are given. For these parameters we adopt the values specified in the CHARMM22 force field for the basic atom types"

Re: [gmx-users] Lennard Jones interactions

Nilesh Dhumal wrote: 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? This type of measurement doesn't make any sense. Bonded interactions up to 3 bonds away are exclu

Re: [gmx-users] Lennard Jones interactions

First you need to understand how you are modeling both your intramolecular and intermolecular interactions. If this is unclear to you, then you should probable read up on some basic material before moving forward. If you understand how you are modeling your system, you should find the answe

Re: [gmx-users] Lennard Jones interactions

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 > i

Re: [gmx-users] Lennard Jones interactions

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

Re: [gmx-users] Lennard Jones interactions

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

Re: [gmx-users] Lennard Jones interactions

You can calculate that by hand on a calculator in a few seconds. There is no need to use Gromacs. On Jun 10, 2011, at 2:27 PM, Nilesh Dhumal wrote: Hello, How can I calculate Lennard Jones interaction for two selected atoms with a specific distance? I am using Gromacs 4.0.7 version. Tha

Re: [gmx-users] Lennard Jones interactions

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 e

[gmx-users] Lennard Jones interactions

Hello, How can I calculate Lennard Jones interaction for two selected atoms with a specific distance? I am using Gromacs 4.0.7 version. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http: