[gmx-developers] Removal of -noaddpart option from mdrun

Thomas Piggot t.piggot at soton.ac.uk
Thu Jul 15 18:36:25 CEST 2010

This is kind of the reason I asked. For me it would be useful if I could 
easily maintain the same file naming convention in GROMACS 4 as I had 
with GROMACS 3. For GROMACS 4 up to the latest development version I 
could just use -noappend -noaddpart when the run crashed to control the 
naming to be the way I wanted.

The only way I have found to easily do this in the development version 
is to move the old files to another folder (apart from the .cpt) and 
change -deffnm to the new name when restarting (without -noappend).

Maybe the -noaddpart option could be reinstated?



chris.neale at utoronto.ca wrote:
> Further, some of us have immensely complicated management scripts and
> programs in which it is important to know the name of the expected
> output .xtc file. For example, I run my own C-based server that can run REMD
> on a distributed computing platform (calling gromacs to do the run
> segments) and my client-side scripts needs to know what the output  
> .xtc will be
> named. In this case, I always want name.xtc given -deffnm name,  
> regardless of what part number the .cpt file has stored. Also, I can't  
> allow any appending to
> any files that may exist. Backward compatibility is, in this case,
> pretty important to me. Perhaps it will be possible with some
> combinations of options and I'm just missing it, but resorting to an
> ls -ltr |tail -n 1 seems like too much of a risk for a distributed
> environment.
> Chris.
> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>> Thomas Piggot wrote:
>>> But how can I get the new files, when using -noappend, to not have   
>>> the 'part' bit in their names but just have the name as defined by   
>>> -deffnm?
>>> Maybe I am missing something obvious, sorry if this is the case.
>> Per the documentation, this isn't possible.  With -noappend, the "part"
>> number is always written.
>> Doesn't this create a problem if a run crashes?  If a file has
>> ".part000X." and it goes down, starting from a new checkpoint will use
>> a different "part" number and thus one cannot append the output?
>> That's a bit inconvenient, unless I've understood the mechanism wrong.
>> -Justin
>>> Tom
>>> Justin A. Lemkul wrote:
>>>> Justin A. Lemkul wrote:
>>>>> Thomas Piggot wrote:
>>>>>> Hi,
>>>>>> I was wondering what had happened to the -noaddpart option of   
>>>>>> mdrun in the development version (downloaded yesterday). Has   
>>>>>> this option been removed for a particular reason?
>>>>> Yes, it was removed about a month ago (6/16/2010).  The option   
>>>>> -noappend takes over.  Now mdrun looks for all necessary files   
>>>>> and will append to them, unless you tell it not to (with   
>>>>> -noappend).  If files are missing, mdrun generates an error.    
>>>>> This should be explained in the mdrun -h information.
>>>> ...rather, if some files are missing mdrun generates an error.  If  
>>>>  all files are missing, mdrun simply creates new ones with the   
>>>> desired names.
>>>> -Justin
>> -- 
>> ========================================
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> ========================================
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Dr Thomas Piggot
University of Southampton, UK.

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