[gmx-users] replica exchange data in cpt file

[João Henriques]

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
> > > > > --
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> > > >
> > > >
> > > >
> > > > --
> > > > Cordiali saluti, Dr.Oteri Francesco
> > > > --
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> > >
> > >
> > >
> > > --
> > > João Henriques
> > > --
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> >
> >
> >
> > --
> > Cordiali saluti, Dr.Oteri Francesco
> > --
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-- 
João Henriques