[gmx-users] Gromacs with Plumed

Szilárd Páll pall.szilard at gmail.com
Thu Mar 2 15:43:47 CET 2017


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.


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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