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

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 15 17:29:18 CEST 2010

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.


> 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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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