> Hi all, > > > > I'm using gromacs for MD simulations on membrane proteins. As part of > the analysis I would like to calculate the average area per lipid. I've > been going about this by pulling the coordinates from the trajectory in > VMD, then importing these to Mathematica and using it to plot a voronoi > tessellation. The problem I run in to is I have to discard ~10% of the > data (when averaging over multiple frames) due to Mathematica not being > able to complete the tessellation. I believe this is occurring as a > result of PBC and Mathematica plotting concave polygons. That being > said, I have just about given up on my method.
There's no need to involve VMD to get coordinates, and nobody on here is likely to know how VMD will behave in such a case. trjconv allows you to convert a trajectory so that the coordinates have PBC-properties that are friendly for your analysis, and that plus a suitable index file to choose the atomic coordinates of relevance has to be a good start. How to then get your coordinates into a format for Mathematica for this tesselation is probably a pertinent question though. gmxdump and a perl script are probably the way forward - or even the same VMD process you were using. Mark > I was wondering if anyone out there has a script or methodology they > would be willing to share with me in order to calculate the area per > lipid with a protein present (i.e using a voronoi tessellation). I > would appreciate it tremendously! > > > > Sincerely, > > > > Stephen Dutz > > Department of Chemistry & > > Center for Macromolecular Modeling and Materials Design > > California State Polytechnic University, Pomona > > http://www.csupomona.edu/~smdutz > > > > > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
