[gmx-users] Merry Christmas from MemProtMD

Tom Newport tom.newport at bioch.ox.ac.uk
Sun Dec 25 21:54:00 CET 2016

*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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