[gmx-users] Announcing a new membrane analysis tool: GridMAT-MD

Justin A. Lemkul jalemkul at vt.edu
Fri Dec 19 16:33:55 CET 2008

Hi All,

I wanted to post a quick update to my previous announcement.  If anyone is 
interested in the algorithm and validation, the paper can now be found online:


We also fixed a small bug related to desolvated systems (i.e., if solvent 
coordinates were not saved in the trajectory, and those frames were being 
analyzed).  We encourage anyone who downloaded the original version to get the 
new one if you believe this may affect you.  We created a page for bug fixes and 
revisions on our site (http://bevanlab.biochem.vt.edu/GridMAT-MD) to track 
development.  That way, I can put an end to all the shameless plugs :)

In any case, I felt I should notify those of you who have downloaded GridMAT-MD 
or were considering it.

Thanks, and enjoy.


Justin A. Lemkul wrote:
> Hi All,
> I would like to announce the availability of a new program developed 
> within our lab for membrane analysis, which we have named GridMAT-MD.  
> The program measures bilayer thickness across the membrane, projected in 
> the plane of the bilayer, as well as area per lipid.  The program *does* 
> account for the presence of membrane proteins.
> The algorithm and validation have been accepted by the Journal of 
> Computational Chemistry, and the article is now in press, although it 
> has not yet appeared in electronic format online.
> The program is written in Perl, and has been tested under all the major 
> operating systems.  Currently GridMAT-MD only supports the input of .gro 
> files, but we expect to expand upon this shortly.  Please feel free to 
> download GridMAT-MD and test it; we are offering it for free under the 
> terms and conditions of the GPL:
> http://www.bevanlab.biochem.vt.edu/GridMAT-MD
> We ask that you fill out a simple form when you download it, mostly to 
> satisfy our own curiosity to know how many people are downloading it.
> If you have any questions about usage or if you run into any problems, 
> please feel free to contact any of the developers, whose contact 
> information can be found at the GridMAT-MD site.  The tarball contains a 
> PDF users' guide which should address many questions that may arise.
> Thanks, and we hope you enjoy our little program.
> -Justin


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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