[gmx-users] Lennard Jones interactions

[Andrew Paluch]

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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