[gmx-users] Gromacs with Plumed

[Giovanni Bussi]

Hi,

thanks Szilárd for the comment.

About changing the version string, which would be the right place to do it
in the code?

About the last point, do you mean that we should try to put our code into
gromacs main trunk? This would be very nice for us (plumed developers), and
we discussed several times about this. Do you think it would be feasible?
Are there clear guidelines about what should be included, how, and where in
the code (e.g. a developer manual)?

Honestly, the current patch is very dirty (we use some global variables
here and there to avoid modifying function declarations), but with some
help we could perhaps make it clean and try to contribute it.

Thanks!

Giovanni



On Thu, Mar 2, 2017 at 3:43 PM, Szilárd Páll <pall.szilard at gmail.com> wrote:

> Hi,
>
> I'd recommend keeping a vanilla/untainted GROMACS installation
> available to users at all times. No matter how much awareness there is
> about issues or unwanted code interaction, as long as a user is not
> running an official GROMACS release, they can and should not claim
> (e.g. in a publication) that they used "GROMACS vX.Y". This is not
> just nitpicking, but a matter of scientific reproducibility.
>
> I hope that PLUMED patching also changes the version string not just
> the code so installations from "patched" source do not claim to be
> vanilla, official GROMACS. Can you or someone else aware confirm that?
>
>
> On a side-note, the uncomfortable side-effect of the patch-based
> software distribution model would of course be easy to solve if thin
> API abstractions were designed and submitted upstream in the main
> GROMACS source.
>
> Cheers,
> --
> Szilárd
>
>
> On Thu, Mar 2, 2017 at 9:09 AM, Åke Sandgren <ake.sandgren at hpc2n.umu.se>
> wrote:
> > Hi!
> >
> > Are there any known drawbacks to building Gromacs with Plumed?
> >
> > I'm mainly talking about Gromacs 2016 and later, using PLumed 2.3.0,
> > both if there are problems with any version combination i'd like to know
> > that too.
> >
> > I.e., will it cause problems for non-plumed runs, will gromacs behave
> > identical to a non-plumed build when not using plumed in the
> > plumed-build, etc.?
> >
> > Having just a single build makes my life easier :-)
> >
> > --
> > Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden
> > Internet: ake at hpc2n.umu.se   Phone: +46 90 7866134 Fax: +46 90-580 14
> > Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se
> > --
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-- 
Giovanni Bussi
Scuola Internazionale Superiore di Studi Avanzati - SISSA
via Bonomea 265, 34136 Trieste, Italy
email: bussi at sissa.it
web:   http://people.sissa.it/~bussi
          http://srnas.sissa.it