[gmx-users] HREX simulation

[Michael Shirts]

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.