[gmx-users] Lennard Jones interactions

[Justin A. Lemkul]

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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>>>
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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

========================================