[gmx-users] publishing with development version of Gromacs

Erik Lindahl lindahl at cbr.su.se
Thu Aug 9 09:43:37 CEST 2007


As long as you have the exact date you checked it out from CVS it is  
possible to obtain the same version again.

However, bear in mind that CVS _does_ break periodically, and we  
don't check it like the released version. Before I do anything  
production-related with CVS I always check that I'm getting similar  
results to the released version for the system in question.



On Aug 9, 2007, at 8:15 AM, chris.neale at utoronto.ca wrote:

>> I am running protein simulations in an explicit membrane  
>> environment, and have found that the CVS development version of  
>> Gromacs works much faster than the released version. Is it okay to  
>> publish simulations performed on the development version? What  
>> kind of validation would I need if I were to do this? For  
>> instance, if I compared the first 10 ns of a simulation between  
>> the development and released versions and found that they were  
>> substantially the same, could I complete the simulations (40 more  
>> ns) with the CVS version?
> I personally never run with the cvs version because I would never  
> want to try to publish that version. However, if you are determined  
> to do this then really the only important thing is that your  
> experiments are reproducable. This means that you are going to need  
> to ensure that a future reader may obtain the _exact_ version of  
> gromacs that you used. I am not sure if this is currently possible  
> via the gromacs site... probably not. Therefore you will need to  
> provide a download of the version that you used. I am not even sure  
> that you have licence to do that. Developers?
> Some would say that you only need to personally stand behind the  
> fact that future releases of gromacs are going to reproduce any  
> results that you find. First of all, I am not sure how you would  
> know that this is true if you are not a developer and second of all  
> I don't personally believe that that condition is stringent enough.
> Another point: how enormous is your system? 40ns should be possible  
> with gromacs 3.3.1 during a couple of months of runtime for regular  
> sized membrane proteins while using a single processor and less  
> time while running in parrallel. Why bother with the hassle?
> This is, of course, just my own thoughts on the topic.
> If your run-time benifit is related to scaling then you could also  
> consider my g_desort program that is available via user  
> contributions. And then there is the single vs double precision topic.
> Chris.
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