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

Johnny Lu johnny.lu128 at gmail.com
Sun Oct 19 00:51:04 CEST 2014


Does this old maillist post say tilde H is conserved energy? [
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-August/083330.html
]

On Sat, Oct 18, 2014 at 12:46 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> On Sat, Oct 18, 2014 at 4:32 PM, Wade <wadelv at foxmail.com> wrote:
>
> > Dear Mark,
> >     Thank your very much for your reply. However, I still confused
> because
> > results showed that the conserved En. was time dependent (with small
> > fluctuation); but, the total energy in the ener file has small drift with
> > high fluctuations.
> >
>
> "Both these things vary" doesn't mean anything. Numbers, or it didn't
> happen ;-)
>
>
> > Further, I rechecked the code  (gmx-4.5.5) ?in these days, and I noticed
> a
> > part of code might be useful ("enerd->term[F_ECONSERVED] =
> > enerd->term[F_ETOT] +
> compute_conserved_from_auxiliary(ir,state,&MassQ);").
> > It will be actived when the leap-frog integrator is employed.
> > To assure the the conserved En. is either H or H-tilde, I changed the
> code
> > as this: "enerd->term[F_ECONSERVED] = enerd->term[F_ETOT];". Result shown
> > that the "total energy" and "conserved En." are same now in the output of
> > ener file?.
> >
>
> Great. A = A...
>
>
> > Dose it means that the conserved En. in ener file is H-tilde?
> >
>
> ...which doesn't say what B is... The question is whether there's an
> intrinsic time dependence on the value returned by
> compute_conserved_from_auxiliary. You can only do that by removing the
> *other* term.
>
>
> >
> > ?
> >
> > If yes, why does the conserved En. drifted with a constant rate in a 10
> ns
> > ?simulation for a pure water box (216 tip4p water)?
> >
> >
> Because it's characteristic of the drift of your setup or of the
> implementation of what is reported as the conserved quantity. I suggested a
> diagnostic procedure. Did you try it? If not, why not?
>
> Mark
>
> With best wishes,
> >
> >
> > Wade
> >
> >
> > (part of the code please see below, I hope I have got the key point).
> > ?
> >
> >
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> >         /* #########  BEGIN PREPARING EDR OUTPUT  ###########  */
> > /* sum up the foreign energy and dhdl terms */
> > sum_dhdl(enerd,state->lambda,ir);         /* use the directly determined
> > last velocity, not actually the averaged half steps */        if
> (bTrotter
> > && ir->eI==eiVV)         {            enerd->term[F_EKIN] = last_ekin;
> >   }        enerd->term[F_ETOT] = enerd->term[F_EPOT] +
> > enerd->term[F_EKIN];                if (bVV)        {
> > enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] +
> > saved_conserved_quantity;        }        else         {
> > enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] +
> > compute_conserved_from_auxiliary(ir,state,&MassQ);?
> >
> >
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > >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
> >
> > > Is that right? I really need your help.
> > > Any suggestion is valuable.
> > >
> > > Wade?
> > > --‍
> > --
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