Hi Hemant,
You can load your trajectory into vmd, and you can measure the
interaction energy via GUI:
Extension/Analysis/NAMD Energy
If your selection for water molecules is based on the location inside
the nanotube, then don't forget to click
Update selections every frames.
HTH,
Balazs
> Sorry for not mentioning my question very clearly.
> I want interaction energy of water molecules inside nanotube.since
> my nanotube is in water box so water inside tube will have contribution
> from both nanotube and water outside nanotube.
> It is widely quoted in literature water loses energy when it goes
> inside nanotube,I want to quantify energy loss.
>
> With regrads,
> Hemant Kumar
> Graduate Student
> CCMT,Department of Physics
> IISC,Bangalore
> URL www.physics.iisc.ernet.in/~hemant
>
> On Tue, 11 May 2010, Bill Ross wrote:
>
>>> Thanks sir,for you quick reply
>>> Due to rigidness,bond and angle energy will remain
>>> constant but I want to look change in VDW and coulombic energy.
>>> In particular,when water enters inside nanotube how
>>> its interaction energy changes.
>>
>> So you don't want the *internal* energy of a water (since vdw and
>> electrostatic will also be constant) - it sounds like you want the
>> energy of *interaction* between some number of waters in free solution
>> to compare with the interaction energy of the same number of waters
>> in the nanotube. Another possibility is that you want the energy of
>> a number of waters in free solution with the rest of the waters, to
>> compare with the energy of the same number of waters with the nanotube
>> itself.
>>
>> Bill
>>
>>
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Received on Wed May 12 2010 - 00:00:03 PDT
