Group Blog

PN vector orientation not a good measure for evaluating phospholipid force field performance, use head group order parameters instead

The article below is a "guest-author" contribution by O. H. Samuli Ollila in reaction to a recent post on this blog:

"A property commonly calculated from molecular dynamics simulations of phosphatidycholine bilayers is the angle between the membrane normal and the vector from headgroup phosphorus to nitrogen (P-N angle). Sometimes the average angle is also compared to experimental estimates.

The most extensive comparison of this kind that I have seen is in the Martini group blog, where a color coded matrix visualizes the deviation between experimental and simulation values for several key properties of lipid bilayers. The simulation values in the blog were taken from extensive study by Piggot et al. (J. Chem. Theory Comput. 8, 4593 (2012)) and experimental values from various sources.

Read more: PN vector orientation not a good measure for evaluating phospholipid force field performance, use...

Nobel Prize

Today, it was announced that the Nobel Prize in Chemistry 2013 is awarded to Martin Karplus, Michael Levitt and Arieh Warshel. It is awarded for: "Development of multiscale models for complex chemical systems".  In recent years I have been discussing the possibility of a Nobel Prize in the field of "(Bio)-Molecular Dynamics" with several colleagues, and the names of Karplus and Levitt and to a lesser extent Warshel, were very often mentioned. However, a prize like this, awarded in a relative broad research field, mostly leads to discussions of whether the right people received the prize and who should have been part of the prize winners but are not. There are dozens of people who deserve the prize in (Biomolecular) MD, and also within the range of the specific title for this Nobel prize there are probably more people who deserve it.

I think that is also an important aspect of this (or any) Nobel prize: it is awarded to specific people but it is deserved by and gives a certain recognition to the field. So if you are working on multiscale models of complex chemical systems today (Martini-model, anyone?), you have been awarded a tiny little bit of the Nobel prize today:-)

If you are interested in how the work of the laureates is placed in the history of Molecular Dynamics and what are the landmark simulations it lead to, you can find a short overview of the history of BioMolecular Dynamics in the introduction chapter of my thesis: http://dissertations.ub.rug.nl/faculties/science/2013/d.h.de.jong/

The force field jungle(2): lipids

I thought atomistic protein force fields were a jungle. They are more like a well maintained garden compared to their lipid counterparts. It seems this has three main reasons:

  1. Experimental data is unreliable and sparse. Estimates of, for example, the area per lipid vary greatly, depending on technique used and the lab where they were obtained. Furthermore, the list of properties one can measure and use to parametrize against is enormous.
  2. There a many different kinds of lipids, that all can be in different "states" depending on temperature, hydration level and other components they are mixed with.
  3. Lipids have not been the main focus of any of the "big" force fields and, arguably, of the community in general. This means that for most force fields there are no long standing, golden standard lipid parameters, that also see a steady improvement over time.

Due to these reasons many people have recently parameterized lipid forcefields, all with slightly different philosophies and/or goals. On top of that there are fewer papers comparing different lipid force fields, in comparison to the protein force fields. Therefore we'll first describe some of the available force fields based on the original papers.

Read more: The force field jungle(2): lipids

The force field jungle

Even though in our lab most work is done with or on the coarse grain Martini force field, atomistic force fields are also important in our daily work. Beit as a basis/benchmark for the Martini force field, for the use in multiscale simulations, or for some interesting projects of their own. There are several 'major' atomistic (protein) force fields around which all have many different version, each with their own strengths an weaknesses. Recently several papers were published that systematically compared a range of different force fields, trying to find out which one currently is the "King of the Jungle". What follows is a mini-review of those papers.

Read more: The force field jungle

Weblogs

Although the age of weblogs might be over its peak, they are still a usefull way of broadcasting your opinions or findings if it takes more than 140 characters. Also in science. There are plenty of general scientific weblogs, however there are only a few specific to our field of research: Molecular Dynamics or (bio)molecular modeling. These are the onces I know about and like to read:

boscoh.com/: Thorough posts both on the topic of structural bioinformatics and off topic written by Bosco K. Ho. The post are often lengthy, but they worth you time.

biophyschem.wordpress.com/blog/: Written by Durba Sengupta, a former postdoc in our lab that currently has her own lab in Pune, India. Posts are often on Martini.

rosettadesigngroup.com/blog/: Blog by the lab behind Rosetta, aiming to be a resource to the community. The blogs seems sleeping/dead since october 2012.

mem.bio.pitt.edu/blogs/keithc: posts on Matlab/python related subjects. No posts since September 2012.

As I said, it is not a long list. Did I mis out on any blog in particular (you?)? Let us know!.