[gmx-users] replica exchange data in cpt file

[Mark Abraham]

Great.

Some of the data at the end of the .log file is easily recomputed from
the output at every exchange attempt once the .log files are
concatenated, but there will be loss of precision in re-computing the
average exchange acceptance probability, etc.

Mark

On Fri, Apr 5, 2013 at 10:37 AM, João Henriques
<joao.henriques.32353 at gmail.com> wrote:
> Thank you Mark and Francesco. I will be pleased to contribute with a fix in
> case I come up with a fairly general solution for this issue.
>
> Best regards,
> João Henriques
>
>
> On Thu, Apr 4, 2013 at 7:45 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:
>
>> Demux.pl pre-dates .cpt and -append. The only solution is to preserve your
>> .log files (e.g. with -noappend) and post-process. If you do that by
>> modifying demux.pl, please consider contributing your fix back.
>>
>> Mark
>> On Apr 4, 2013 1:42 PM, "francesco oteri" <francesco.oteri at gmail.com>
>> wrote:
>>
>> > if your -append option is activated (the default is yes),
>> > maybe Demux.pl reads the exchanging from the .log taking into account the
>> > time in the
>> > log and so you don't need to do anything.
>> > But I don't know how Demux.pl works :(
>> >
>> > Francesco
>> >
>> > 2013/4/4 João Henriques <joao.henriques.32353 at gmail.com>
>> >
>> > > That's terrible! I was just about to restart 2 hefty REMD
>> simulations...
>> > > Maybe I can move the original log files somewhere and combine them with
>> > the
>> > > restart ones afterwards by using a script. It's just an idea, because I
>> > > need to run Demux.pl on the final concatenated log file.
>> > >
>> > > Any other issues I should be aware of?
>> > >
>> > > Best regards,
>> > > João Henriques
>> > >
>> > >
>> > > On Thu, Apr 4, 2013 at 12:18 PM, francesco oteri
>> > > <francesco.oteri at gmail.com>wrote:
>> > >
>> > > > This is what I meant,
>> > > > in particular it is a problem when I want to analyze
>> > > > the data regarding the exchange probability.
>> > > >
>> > > > Francesco
>> > > >
>> > > > 2013/4/4 João Henriques <joao.henriques.32353 at gmail.com>
>> > > >
>> > > > > So let me see if I understood what Francesco said correctly.
>> > > Restarting a
>> > > > > REMD job after hitting the cluster wall-time limit resets the
>> > > information
>> > > > > stored in the log files? Can someone shed some light on this
>> subject?
>> > > > >
>> > > > > Best regards,
>> > > > > João Henriques
>> > > > > --
>> > > > > gmx-users mailing list    gmx-users at gromacs.org
>> > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > > > > * Please search the archive at
>> > > > > http://www.gromacs.org/Support/Mailing_Lists/Search before
>> posting!
>> > > > > * Please don't post (un)subscribe requests to the list. Use the
>> > > > > www interface or send it to gmx-users-request at gromacs.org.
>> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> > > > >
>> > > >
>> > > >
>> > > >
>> > > > --
>> > > > Cordiali saluti, Dr.Oteri Francesco
>> > > > --
>> > > > gmx-users mailing list    gmx-users at gromacs.org
>> > > > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > > > * Please search the archive at
>> > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> > > > * Please don't post (un)subscribe requests to the list. Use the
>> > > > www interface or send it to gmx-users-request at gromacs.org.
>> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> > > >
>> > >
>> > >
>> > >
>> > > --
>> > > João Henriques
>> > > --
>> > > gmx-users mailing list    gmx-users at gromacs.org
>> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > > * Please search the archive at
>> > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> > > * Please don't post (un)subscribe requests to the list. Use the
>> > > www interface or send it to gmx-users-request at gromacs.org.
>> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> > >
>> >
>> >
>> >
>> > --
>> > Cordiali saluti, Dr.Oteri Francesco
>> > --
>> > gmx-users mailing list    gmx-users at gromacs.org
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> > * Please don't post (un)subscribe requests to the list. Use the
>> > www interface or send it to gmx-users-request at gromacs.org.
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
> João Henriques
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists