[gmx-users] Conserved energy ("Conserved En.") in NVT simulation (Wade)

[Johnny Lu]

For V-rescale thermostat, the bussi paper seems to say the tilde H is the
integral of the auxiliary dynamics. Not sure if this is same as the
conserved energy in gromacs, which is also the integral of the auxiliary
dynamics.

I guess numerical error causes the system to lose/gain total energy in a
linear way. Rise/drop of tilde H may reflect the extra energy that the
thermostat has to put in to compensate for this numerical error. [just my
guess]

If the energy of the system is conserved without the thermostat, tilde H
should be constant... I guess.

The Bussi paper at [
marge.uochb.cas.cz/~roesel/teach/Clanky/paper5_Bussi_v_rescale.pdf] says
tilde H is the conserved quantity.