From: Aron Broom (
Date: Tue Apr 15 2014 - 13:47:48 CDT

In general, it seems from the wording of your question that maybe you are
missing a lot of basic information concerning thermodynamics, and your line
of questioning may change a lot by spending some time learning some of
those fundamentals.

In particular, computing the free energy an entire system, and then
deleting a portion of it and recalculating, is in many cases, nearly
meaningless. You've not just reorganized the system (which would be
meaningful) but actually made a different system, and are now comparing two
different things. But maybe that wasn't where you were headed. At any
rate, brushing up on the basics might allow you to formulate a less vague
or confusing question.

On Tue, Apr 15, 2014 at 1:14 PM, Kenno Vanommeslaeghe <> wrote:

> We saw your post the first time. If you didn't get a reply, then maybe you
> should think whether there's a problem with your question instead of
> posting almost the same thing again.
> On 04/15/2014 01:02 AM, manish kesherwani wrote:
>> Respected Sir,
>> I am Manish Kesherwani Phd student under Prof D.
>> Velmurugan University of Madras India. I simulated transporter channel
>> using namd from charmmgui prepared script. I observed changes in rmsd of
>> protein till 3 Ang during 15ns equilibration NVT followd by NPT. I
>> talked to Dr sunhwan charmmgui developer they told us protein can
>> fluctate due to 4 Ang low resolution structure. Then 50 ns production run
>> was carried out.
>> I am interested to calculate gas phase energy of protein for
>> calculating free energy. I observed total system potential energy is
>> negative. I extracted the protein conformation from solvated trajactory by
>> removing water and lipid and calculated the energy of protein. it shows
>> positive. I understand the protein is unstable but i am not able to take
>> any reasonable conclusion.
>> Please give some suggestion. I will be highly obiliged.
>> Thanks & Regards
>> Manish Kesherwani

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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