[gmx-users] Query regarding energy calculation

Tushar Ranjan Moharana tusharranjanmoharana at gmail.com
Fri Feb 19 21:09:50 CET 2016

Hi everyone,
I want to calculate energy (non-bonded) between various amino acids. I have
the following queries:-

1)   If an atom belongs to two different energy groups it is showing error.
Is there any way other than using mdrun -rerun. It is fine for me if energy
between those groups which share atom/atoms will not be calculated.
2)   If a protein is simulated at two local minima (let us say lid open and
closed form of lipase) and energy is extracted (total or potential) can I
say the difference in energy is delta G. If not then what is the
significance of potential and total energy extracted by gmx energy

Thanks a lot for the help.

"A society with free knowledge is better than a society with free food"
Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB

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