[gmx-users] HREX simulation

[Michael Shirts]

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.
>> >>> --
>> >>> 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.
>> >>>
>> >> --
>> >> 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.
>> --
>> 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.
>>
> --
> 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.