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

[Mark Abraham]

On Tue, Oct 14, 2014 at 4:32 PM, Wade <wadelv at foxmail.com> wrote:

> Dear Mark and ALL,
>    I am trying to calculate the conserved energy (H-tilde) in Bussi's
> stochastic velocity rescale algorithm (jcp,2007).
> In previous maillist, ‍Mark had mentioned that the conserved En. in ener
> file is the H in bussi's paper (
> http://permalink.gmane.org/gmane.science.biology.gromacs.user/63005‍‍).
> According to the eq. 15 in Bussi's paper, we just need to get the time
> integration of dK if we have had the H.
> I carefully checked the coupling.c file, and noticed a variable -
> therm_integral[i] in the fucntion vrescale_tcoupl().
> The therm_integral[i]-= Ek_new - Ek. It seems like an accumulation of the
> -dK.
> If it realy is the sum of -dK, the problem could become simple.
>

That could well be true. I did look carefully at the code earlier this
year, and decided it was correct and wrote output of sensible things.
However I don't remember whether the conserved quantity reported is H or
H-tilde, and don't have time now to go back. But IIRC because one of them
has a time dependence, you can run double-precision GROMACS in a
conservative NVE setup and observe no drift, then add this thermostat, and
from that run you will know which of H and H-tilde is reported as the
conserved quantity.

Mark

What we need to do is just like this: H-tilde=H-Tau-t* therm_integral[i].?
> Is that right? I really need your help.
> Any suggestion is valuable.
>
> Wade‍
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>