[gmx-developers] gmx cluster improuvement

Boris Timofeev boristim at mail.ru
Thu Jul 26 13:05:46 CEST 2018

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.
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
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