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

Johnny Lu johnny.lu128 at gmail.com
Sat Oct 18 17:28:29 CEST 2014

Oh, integrating with rectangles under the curve causes error. I guess
larger time-steps can cause error in tilde H by this method of integration

On Sat, Oct 18, 2014 at 11:25 AM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> 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.

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