[gmx-developers] gmx cluster improuvement

[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.

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
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