[gmx-users] Lennard Jones interactions

[Nilesh Dhumal]

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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