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 excluded for most molecules, since the bond/angle/dihedral
parameters implicitly account for short-range effects. The interactions of
bonded O and H atoms are accounted for by the shared electrons and the energy of
a bond (if not constrained) is indeed non-zero, but it is not a LJ term that
accounts for this energy.
-Justin
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
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========================================
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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