[gmx-users] Ever increasing versions of gromacs and problem of choosing the correct version.

[Michael Williams]

I’m new to Gromacs but I have been doing large-scale calculations for many years. I believe that most changes to Gromacs are well-documented in the release notes for each patch or version update. I would start there to see if you can find an explanation for the different results you obtained. 

I would also like to point out that a computational result that is closer to an experimental value is not always inherently “better”. Often (for example) a simpler or cruder model might have multiple inaccuracies that happen to cancel one another (especially when the overall result of a calculation is reduced to numbers representing only a few quantities). The model might then be improved (in the sense of including more real underlying physical detail or just fixing an unintended software bug), only for the previous (often accidental) error cancellation to disappear. Alternatively, you could theoretically go into the source code of any MD software and add the precise terms to give your system the exact density to match some experimental value you wanted.... but this result would be completely uninteresting unless whatever terms that were arbitrarily added to get that result either had physical meaning or very general applicability outside of your particular system. 

Good luck figuring out the problems you have been having, but I don’t think any MD software developers in the world could promise what you are asking for: a perfect turn-key simulation that requires no work or learning by the operator. Best wishes,


Mike


> On Feb 23, 2019, at 3:09 PM, atb files <atbfiles at zoho.com> wrote:
> 
> 
> 
> 
> 
>            Dear users,Does anybody know a reliable, correct, tested version of gromacs, that can be installed on high performance computing (HPC) facility.Recently, I and my colleague performed the same simulation with the same files but with different gromacs version, one is gromacs 5.0.2 and other is gromacs 2018.5. We observed the sizeable difference obtained in the density. I was using 2018.5, hoping that, since it is the latest version, it has to be better than the older version, however, 5.0.2 was giving the values close to experimental results! Now how do we beforehand know which version should be used? because we have lost 2-3 months of computational time and energy by using 2018.5. It's is good that yesterday, 2018.6 was released, however, since we have HPC which requires a lot of procedure and permissions to install new versions, I was wondering whether there is any gromacs version which I can install, which is reliable and correct and I need not to upgrade it at l
> east for 2 years.Thanks.Sent using Zoho Mail
> 
> 
> 
> 
> 
> 
> 
> 
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.