[gmx-users] Lennard Jones interactions

[Andrew Paluch]

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 answers to your questions trivial.


On Jun 10, 2011, at 3:07 PM, 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?
>
> 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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