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
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