[gmx-users] Merry Christmas from MemProtMD

[Mark Abraham]

Haha, that's gold! Have a good Christmas, all!

Mark

On Mon, 26 Dec 2016 07:54 Tom Newport <tom.newport at bioch.ox.ac.uk> wrote:

> *With apologies to Clement Clarke Moore*
>
>
> 1. Twas the night before Christmas, when all through the PDB,
>
> Not a protein was stirring, not even TatC,
>
> The ligands were bound in their structures with care,
>
> Hoping coarse-grained parameters soon would be there.
>
>
> 2. The tired crystal structures settled down for their naps,
>
> all snugly fitted to electron density maps.
>
> Then suddenly Santa, with all the strength he could muster,
>
> Burst into the scene with a GPU cluster.
>
>
> 3. He said with a smile: It’s simply not right;
>
> Membrane proteins should move on this most festive night.
>
> I’ll bring them to life, using MemProtMD,
>
> Run martinize, then add DPPC.
>
>
> 4. He promised them wonders, full of joy, full of fun,
>
> as he typed into bash $ gmx mdrun.
>
> The magic had started; they cheered and they jumped.
>
> And then on the screen: Error. Seg Fault. Core Dumped.
>
>
> 5. I’m sure we can fix this, he says as he winks,
>
> Now what is this error - something about lincs?
>
> He checked his coordinates, then checked all the files,
>
> That once jolly face had lost all its smiles.
>
>
> 6. He recompiled the kernel, reconfigured libcuda,
>
> As the words he was using grew steadily ruder.
>
> Through tears of frustration, he could barely persist,
>
> Even braved the wrath of the gromacs mailing list.
>
>
> 7. But before he stomped off to the pub down the road,
>
> He saw in a thread “reboot the headnode”,
>
> And quick as a flash, but quite unexplained,
>
> The jobs were all running, correctly constrained.
>
>
> 8. Santa, it seems, was jolly once more,
>
> Asked the kids to forget all those words from before.
>
> As each job completed, he chuckled with glee,
>
> Then converted to GROMOS with CG2AT
>
>
> 9. He used libraries in Python to run though trajectories,
>
> And added analyses to the simulations’ directories.
>
> Built database indexes and sent it all back,
>
> To some docker containers on a decade old mac.
>
>
> 10. The web application at last was deployed,
>
> And each membrane protein was quite overjoyed.
>
> Annotated and ready, to the web-app they came,
>
> And with metadata he could call them by name.
>
>
> 11. There’s OmpF, there’s TatC and GPCRs,
>
> Ionotropic receptors and domains we call BARs.
>
> A few aquaporins, a receptor for glycine,
>
> And LSPA, with bound globomycin.
>
>
> 12. And once he was done, folks near or far,
>
> Could find simulations with just a search bar.
>
> Then once a suitable protein was found,
>
> See all the sites where a lipid had bound.
>
>
> 13. Download the data, add in some ligands,
>
> Modify the membrane and see if it thickened.
>
> Run new simulations, see what patterns emerged,
>
> Then run it twice more and pretend it converged.
>
>
> 14. My work here is done, Santa said with a grin,
>
> I’m off to the pub to get plastered on gin.
>
> May all your experiments turn out alright;
>
> Merry Christmas to all, and to all a good night.
> --
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