Visualizing MARTINI simulations

It was one of “those” thursday afternoons! I had recently shifted my friday afternoon projects to thursday afternoon projects! I realised that by friday afternoon I was so tired from being a HR manager, a finance expert, a con-man, a IT expert, an architecture critic, and several other roles that I am expected to don during the week, that I have no time to be a fun scientist. So every thursday I discuss some fun projects with my collaborator who sits “just about” 1580km away. We have the entire week to make some new plots, run some new simulations, do some quirky analysis and on a thursday evening, we can sit back and relax and chat about what we did that week!  At some point, I wanted my collaborator to quickly visualise some  MARTINI simulations and see if they really matched the analysis. My quick-n-dirty suggestion was to use ngmx. She shuddered in horror and I remember seeing similar reactions from Erik in some gromacs developer meet. So I started thinking of the alternatives.

I know thanks to Martti, Clement, and Tsjerk, we have some really cool tcl scripts to visualise in CG structures in VMD. http://md.chem.rug.nl/cgmartini/index.php/tutorial/cgviz. I do use these extensively for making figures for conferences and papers – so thanks a lot Clement and Tsjerk. I also came across this really cool VMD plugin-bendix. I still think though that to explain a quick fact to a collaborator sitting in a sister institute 1580 km away, who hasnt used MARTINI before, it would be nice to have something quick-n-dirty.  One of the things that I miss most about not being in a larger group is that I dont “just pick up things” over the grapewine. So if you know of any fast visualisation methods for MARTINI simulations please do let me know!