[gmx-users] HREX simulation

[Mark Abraham]

Hi,

Expanded ensemble transition matrix and REMD transition matrix are
different things. Shyno wasn't very specific, but his samples of output
include the string "Repl" which suggests the latter, whose data is not
checkpointed.

Mark

On Thu, Sep 24, 2015 at 11:19 PM Michael Shirts <mrshirts at gmail.com> wrote:

> static int do_cpt_df_hist(XDR *xd, int fflags, df_history_t *dfhist, FILE
> *list)
>    ...
>
>     case edfhTIJ:          ret = do_cpte_nmatrix(xd, cptpEDFH, i,
> fflags, nlambda, dfhist->Tij, list); break;
>     case edfhTIJEMP:       ret = do_cpte_nmatrix(xd, cptpEDFH, i,
> fflags, nlambda, dfhist->Tij_empirical, list); break;
>
> On Thu, Sep 24, 2015 at 5:06 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
> > 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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