[gmx-developers] gmx cluster improuvement

[David van der Spoel]

Den 2018-08-04 kl. 22:44, skrev Boris Timofeev:
> Dear David!
> 
> Thank you very much.
> I have already made changes in gmx_cluster.cpp code, having solved both 
> problems. An  array of boxes and an array of frame numbers are formed 
> similar to the array of frames times at extraction of trajectories. To 
> my regret, commit for gromacs  repository is troubles for me so far, but 
> I hope to solve it soon.
Please start the redmine anyway and attach the code there.
Assign it to me.
> 
> Boris.
> 
> 
>     Суббота, 4 августа 2018, 16:16 +03:00 от David van der Spoel
>     <spoel at xray.bmc.uu.se>:
> 
>     Den 2018-07-26 kl. 13:05, skrev Boris Timofeev:
>      > Dear developers!
>      >
>      > In processing of results of REMD there were inconveniences which,
>     I think,
>      > it will be easy to eliminate in future versions of Gromacs.
>      >
>     This is a useful suggestions, however it is not entirely trivial to
>     choose which box one would use. Please start a redmine!
> 
> 
>      > 1. Command
>      > gmx cluster ... -cl somefile.pdb ...
>      > unlike command
>      > gmx trjconv ... -o somefile.pdb ...
>      > doesn't form record about the box sizes in the PDB file:
>      > CRYST1 boxx boxy boxz ...
>      >
>      > As a result, subsequent call
>      > gmx hbond .. -f somefile.pdb ....
>      > deals to the error:
>      >
>      > Program: gmx hbond, version 2016.2
>      > Source file: src\gromacs\gmxana\gmx_hbond.cpp (line 947)
>      > Fatal error:
>      > Your computational box has shrunk too much.
>      > gmx hbond can not handle this situation, sorry.
>      >
>      > Manual addition the record CRYST1 to pdb-file solves this problem.
>      > I suggest to add formation of the record CRYST1 to output pdb,
>      > formed by the gmx cluster command.
>      >
>      > 2. The gmx trjconv command can select parts of a trajectory by
>     means of
>      > the index file: - sub index.ndx:
>      >
>      > "Use option -sub. This assumes that the entries in the index file
>     are
>      > frame numbers and
>      > dumps each group in the index file to a separate trajectory file."
>      >
>      > It would be very convenient if the "gmx cluster" command could form,
>      > optionally, index files for the found clusters.
>      >
>      > Now this problem is solved by copying of times from gmx cluster
>      > command's log-file
>      > and transformation of times to indexes of frames manually. This
>     is very
>      > uncomfortable.
>      >
>      > Sincerely yours,
>      > Boris Timofeev
>      >
>      >
>      >
>      >
>      > --
>      > Boris Timofeev
>      >
>      >
> 
> 
>     -- 
>     David van der Spoel, Ph.D., Professor of Biology
>     Head of Department, Cell & Molecular Biology, Uppsala University.
>     Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
>     http://www.icm.uu.se
>     -- 
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> 
> 
> -- 
> Boris Timofeev
> 
> 


-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se