[gmx-users] publishing with development version of Gromacs

[Erik Lindahl]

Hi,

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.

Cheers,

Erik

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.
>
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before  
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php