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

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Jul 15 17:45:47 CEST 2010

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


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
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
> -- 
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-developers-request at gromacs.org.

More information about the gromacs.org_gmx-developers mailing list