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From: manish kesherwani (manish221288_at_gmail.com)
Date: Tue Apr 15 2014 - 00:02:12 CDT

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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