[gmx-users] regarding calculation of intra-residue energy

[Saumyak Mukherjee]

Dear all,

I have simulated myoglobin in water system. Now, I want to calculate the
self interaction energy (Coulomb) of the protein. In that case shall I
consider the interaction between the OE1 and OE2 atoms in glutamte, or
other such pairs?

Including all pairs, except the bonded pairs, the average self-energy of
the protein is coming as 8108 kT from my program. Is this value plausible?

Any comment/suggestion is appreciated.

Thanks & regards,

*Saumyak Mukherjee*

Senior Research Fellow,
Prof. Biman Bagchi's Lab,
Solid State and Structural Chemistry Unit,
Indian Institute of Science,
Bangalore - 560012,
Karnataka, India.
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