Intramolecular interaction energy of protein in vacuum from NAMD simualtions

From: dayanidhi mohanta (512cy1009_at_nitrkl.ac.in)
Date: Sat Jul 09 2016 - 08:26:13 CDT

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Dear Sir,
I want to find the intramoleculcular interaction energy of a protein in vacuum. I would like to include both the bonded and non-bonded terms in the intramolecular interactions. Is there a way to find the interaction directly from the simulations and if so, i would like to know which ensemble shall i use.

Dayanidhi Mohanta
SRF (Chemistry)
NIT Rourkela

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