[gmx-users] HREX simulation

[Michael Shirts]

Ugh, sorry for missing that.  Yes, the replica exchange transition
matrix is not stored.  Some sort of unification should be possible . .
.

On Thu, Sep 24, 2015 at 5:33 PM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> 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.
>> >> >>> --
>> >> >>> 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.
>> --
>> 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.