From: Kenno Vanommeslaeghe (
Date: Tue Apr 15 2014 - 12:14:07 CDT

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

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