[gmx-users] HREX simulation

[Mark Abraham]

Hi,

Some things are accumulated there, yes. But not the transition history.

Mark

On Thu, Sep 24, 2015 at 11:04 PM Michael Shirts <mrshirts at gmail.com> wrote:

> I take it back, I think it is actually accumulated.  See (in
> checkpoint.cpp):
>
> static int do_cpt_df_hist(XDR *xd, int fflags, df_history_t *dfhist, FILE
> *list)
>
>
> On Thu, Sep 24, 2015 at 4:59 PM, Michael Shirts <mrshirts at gmail.com>
> wrote:
> > Apologies: I missed the part where it was stated that the simulation
> > was restarted.  Perhaps I shouldn't have tried to steal a few min to
> > answer mailing lis questions .  . .
> >
> > Averaging would give the correct answer.
> >
> > On Thu, Sep 24, 2015 at 4:49 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
> >> Hi,
> >>
> >> It can't be an accumulated matrix. It's not written to a checkpoint, and
> >> nothing in GROMACS can read one.
> >>
> >> At some point, someone needs to roll their sleeves up, write such data
> to
> >> fields in TNG format, and stop dumping potentially useful data to a log
> >> file that'll get truncated upon restart-with-append.
> >>
> >> Mark
> >>
> >> On Thu, Sep 24, 2015 at 10:42 PM Michael Shirts <mrshirts at gmail.com>
> wrote:
> >>
> >>> > Now, to determine the acceptance rate for the whole 10ns run I should
> >>> > average these numbers as shown below?
> >>>
> >>> No, the matrix at 10ns is the accumulated matrix.  You should use the
> >>> last matrix.
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