General Purpose Coarse-Grained Force Field

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Last Updated: Wednesday, 26 March 2014 12:54

If I would like to visit Groningen to learn how to use Martini should I be worried about the weather?

Don't worry, the weather is fine.

Is there financial support for a visit to Groningen?

Your best option is to try to get a short term fellowship from, e.g, EMBO, or from your local government. But not much is needed: we have nice couches in our offices for you to sleep, and usually plenty of food is brought into the lab every day ...

What does Martini mean?

Martini is the nickname of the city of Groningen where the force field was developed. The city of Groningen has many buildings named after the former patron Saint Martin, such as the famous Martini-tower (see picture).

The name Martini also reflects the universality of the cocktail with the same name; how a few simple ingredients (chemical building blocks) can be endlessly varied to create a complex palette of taste.

However, it is also an acronym for:

° MARrink's Toolkit INItiative

° Maybe A Realistic Theory to Investigate N-body Interactions

Ideas for other/better acronyms are welcome ....

Where do I drink the best Martinis?

There is a small craft distillery, the Quincy Street Distillery, just outside of Chicago. They make a range of spirits, including gin, and also have a small cocktail bar at the distillery. One of the home-made products is an “oude genever” style gin, called “Groninger Hoek”, which was the name of the old Dutch neighborhood in Chicago (since razed and built over). Obviously, it was meant to be a bit of a double entendre, since Groningen was the primary source of much genever imported into the US historically, and the neighborhood was so named because of the number of immigrants that came from there to settle in Chicago. And, of course, nothing tops Martinis made with Groningen-inspired Dutch-style genever!

Can I use Martini to study protein folding?

No, at the moment the secondary structure is an input parameter of the model, which implies that secondary structure elements remain fixed during the simulation. Tertiary structural changes, however, are allowed and in principle realistically described with Martini.

How should I interpret the time scale?

The Martini dynamics is faster than the all-atom dynamics because the coarse grained interactions are much smoother compared to atomistic interactions. The effective friction caused by the fine grained degrees of freedom is missing. Based on comparison of diffusion constants in the Martini model and in atomistic models, the effective time sampled using CG interactions is 3-8 fold larger. When interpreting the simulation results with the Martini model, we use a standard conversion factor of 4, which is the effective speed-up factor in the diffusion dynamics of Martini water compared to real water. The same order of acceleration of the overall dynamics is also observed for a number of other processes, including the permeation rate of water across a membrane, the sampling of the local configurational space of a lipid, and the aggregation rate of lipids into bilayers or vesicles. However, the speed-up factor might be quite different in other systems or for other processes. Particularly for protein systems no extensive testing of the actual speed up due to the caorse grained dynamics has been performed, although protein translational and rotational diffusion was found to be in good agreement with experimental data in simulations of rhodopsin. In general, however, the time scale of the Martini simulations has to be interpreted with care.

How to reintroduce atomistic detail into Martini?

For this you can use our Reverse Transformation Tool explained on the tutorial page.

Can I do multiscale simulations with Martini?

We developed a method to do hybrid simulations using virual sites, as described in [1,2], but so far it works well only for relatively simple systems (e.g. butane). We are working on it ...

[1]  A.J. Rzepiela, M. Louhivuori, C. Peter, S.J. Marrink. Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites. Phys. Chem. Chem. Phys., 13:10437-10448, 2011. abstract

[2] T.A. Wassenaar, H.I. Ingólfsson, M. Prieß, S.J. Marrink, L.V. Schäfer. Mixing Martini: electrostatic coupling in hybrid atomistic – coarse-grained biomolecular simulations. J. Phys. Chem. B, 117:3516–3530, 2013. open access

For sequential multiscaling you can use the resolution transformation as described above.

We also explored the use of the AdResS (Adaptive Resolution Simulation) scheme in combination with Martini:

[3] J. Zavadlav, M. Nuno Melo, S.J. Marrink, M. Praprotnik. Adaptive resolution simulation of an atomistic protein in MARTINI water. J. Chem. Phys., 140:054114, 2014. open access

To be continued ... !

Is Martini supported by other sofware packages apart from Gromacs?

Yes, it is implemented also in NAMD, GROMOS, and current efforts are porting it to CHARMM. A reduced version of Martini is also available through the Material Studio commercial software. Note that, for each of these software packages, the Martini implementation might differ - to an unknown extent - with that of the GROMACS implementation, so you should be careful when using Martini 'abroad'.