Re: [gmx-users] Average exchange probability when extending REMD

2016-06-15 Thread Mark Abraham
Hi,

Yes, if you need that, this is the thing to do. The only place mdrun
records any of that is the .log file, and of course that is not re-read in
the next stage.You also want to avoid/manage mdrun's appending feature,
because IIRC that throws away all that end-of-log-file output when the next
run starts.

Mark

On Wed, Jun 15, 2016 at 3:47 PM OuyangYanhua <15901283...@163.com> wrote:

> Sorry, I am a little confused, what you mean is that the gromacs cannot
> automatically combine the data of the both  in the replica exchange
> statistics section. Maybe myself need write some program to combine the
> first part data and the extended data to get the average probability  of
> whole REMD?
> > 在 2016年6月15日,下午9:34,Mark Abraham  写道:
> >
> > Hi,
> >
> > That's never been implemented, unfortunately.
> >
> > Mark
> >
> > On Wed, Jun 15, 2016 at 3:25 PM OuyangYanhua <15901283...@163.com>
> wrote:
> >
> >> Hi,
> >> I extended the REMD of a protein in a explicit water and append the data
> >> to the old ones and it appended. However, at the end of the .log files,
> the
> >> replica exchange statistics section only contains the data of  extended
> >> time, it  did not combine  the former statistics and the extended
> >> statistics. why? and how to combine the both statistics.
> >>
> >> Best regards,
> >> Ouyang
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
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> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
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Re: [gmx-users] Average exchange probability when extending REMD

2016-06-15 Thread OuyangYanhua
Sorry, I am a little confused, what you mean is that the gromacs cannot 
automatically combine the data of the both  in the replica exchange statistics 
section. Maybe myself need write some program to combine the first part data 
and the extended data to get the average probability  of whole REMD?
> 在 2016年6月15日,下午9:34,Mark Abraham  写道:
> 
> Hi,
> 
> That's never been implemented, unfortunately.
> 
> Mark
> 
> On Wed, Jun 15, 2016 at 3:25 PM OuyangYanhua <15901283...@163.com> wrote:
> 
>> Hi,
>> I extended the REMD of a protein in a explicit water and append the data
>> to the old ones and it appended. However, at the end of the .log files, the
>> replica exchange statistics section only contains the data of  extended
>> time, it  did not combine  the former statistics and the extended
>> statistics. why? and how to combine the both statistics.
>> 
>> Best regards,
>> Ouyang
>> --
>> 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-requ...@gromacs.org.
>> 
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
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Re: [gmx-users] Average exchange probability when extending REMD

2016-06-15 Thread Mark Abraham
Hi,

That's never been implemented, unfortunately.

Mark

On Wed, Jun 15, 2016 at 3:25 PM OuyangYanhua <15901283...@163.com> wrote:

> Hi,
> I extended the REMD of a protein in a explicit water and append the data
> to the old ones and it appended. However, at the end of the .log files, the
> replica exchange statistics section only contains the data of  extended
> time, it  did not combine  the former statistics and the extended
> statistics. why? and how to combine the both statistics.
>
> Best regards,
> Ouyang
> --
> 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-requ...@gromacs.org.
>
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