Ismael Rodriguez Espigares

Dear Alain, The only thing that can be failing is the atomselection that selects the phosphate atoms in your simulation. Your are running membrane thickness tool with the default "name P" atomselection. Please, check that the phosphates in your simulation have as atom name "P", and that your structure (.gro) and trajectoriy (.xtc) files are loaded correctly by VMD, file paths E:/WaaL/Ecoli/centered_EcoliXTC_files/traj_files/EcoliWaal-1_PR_centered_nwt.gro and E:/WaaL/Ecoli/centered_EcoliXTC_files/traj_files/EcoliWaal-1_PR_centered_nwt.xtc...

Yes, that's it. But, the plane of the triad of atoms being parallel to the main plane of the membrane is not so important if the atoms of the triad from the same molecule are close to each other.

The Area per Lipid tool calculates both the total area per lipid and the area per lipid of each lipid species of the membrane under analysis. To this end, it uses a user-customizable selection of one key atom (e.g. sterols) or a triad of atoms (e.g. phospho- or sphingolipids). The x and y coordinates of the former set of points are projected onto a plane delimited by the simulation box, which is subsequently divided into polygons through a ** Voronoi diagram** using the qvoronoi program from the...

Question about running MEMBPLUGIN in VMD Text Mode

Please, write your questions in the "Discussion" section, and first read the wiki section. You would find there the commands for text mode. Also, you can run a computation using the GUI and the corresponding text command will be printed in the VMD terminal. Bests. Ismael.

Dear Nur Hanna Mardhiyyah , It seems that your computation has produced an empty file with no data, that is why it cannot be plotted. Please, review and repeat your computation taking special care in providing apropiate atom selections and residue names and atom names (see [LipidTilt]). If you still have problems, please post here your terminal output just after running the computation of Lipid Tilt, including the commands that are printed in there. Best, Ismael.

Dear Nur Hanna Mardhiyyah, I just realized that using "Use custom lipid resnames" does not solve your problem as it is not used by lipid interdigitation, as stated in the wiki. If you cannot change MEMBPLUGIN configuration file, then "membplugin_lipid" and "membplugin_lipids" will not include DUPS or DUPC residue names ("Use custom lipid resnames" does not change these atom selection macros). If your system only contains lipids with residue names DUPS, DUPC and CHL1 then you should use the following...

Dear Nur Hanna Mardhiyyah, Please check that DLiPS and DLiPC residue names have been added to the configuration file by: Clicking on "Configure" button in the Main window (requires writing permissions on VMD installation files inside VMD installation directory or running VMD as root or admin permissions) "Use custom lipid resnames" option on the Main window of MEMBPLUGIN. See [GUIMainwindow]. Best, Ismael. EDIT: The second solution for lipid interdigitation does not work. Please, continue reading...