[gmx-users] Query regarding energy calculation

[Tushar Ranjan Moharana]

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
(g_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