GROMACS version:
GROMACS modification: Yes/No
Here post your question
I am conducting a molecular dynamics simulation using the CHARMM36 force field on a system containing 264 DPPC molecules and 88 cholesterol molecules, which makes up a total of 25% cholesterol. After the simulation, I obtained the output files .gro, .xtc, and .edr. From the .edr file, I extracted the Box X and Box Y dimensions using gmx energy -f npt.edr -o box.xvg. Using these dimensions, I can calculate the total area of the bilayer. To find the average area per lipid in one leaflet, I divide this total area by the sum of DPPC and cholesterol molecules in that leaflet. However, I am unsure how to calculate the average area per DPPC and per cholesterol specifically. I’m looking for guidance on how to segregate the total area to get individual areas for DPPC and cholesterol from the data files generated by GROMACS.
Hi @SAHIRE
In cases where you have more than one lipid type then the estimation of the average area per lipid is far from a trivial task. There have been a few proposed tools in the literature, e.g. MEMBplugin and g_lomepro.
Hi obZehn,
You are suggesting that the method we use for a single-component lipid bilayer, where we calculate the average area per lipid by multiplying the Box X and Box Y dimensions and then dividing by the total number of lipids in one leaflet, is not suitable for a multi-component lipid bilayer. For these more complex systems, where the bilayer includes different types of lipids, the straightforward calculation may not accurately reflect the individual areas occupied by each type of lipid. Therefore, to find the average area per lipid and specifically the area for each different lipid type within a multi-component mixture, we would need to use a specialized tool like g_lomepro, correct?
Correct!
Thank you for your assistance. I am attempting to install the MEMBplugin tool with VMD by following three steps: first, extracting the distribution archive; second, copying the membplugin1.xx subfolder—not the entire membplugin-release-1.xx distribution folder—into $VMDDIR/plugins/noarch/tcl/; and third, transferring the loadmembplugin.tcl file into the $VMDDIR/scripts/init.d/ folder. Despite completing these steps, the MEMBplugin does not appear in the VMD analysis section. I ha
ve attached a screenshot of the VMD for your reference. Could you please check and inform me if I missed any steps necessary for the installation?
It has been years since last time I used it, I can’t help you with the installation if something changed in the meantime. However, the passages you report are correct. If it does not appear there then it seems to me that you might have got some (or parts of) those passages wrong. Have you checked that the files you report are being effectively moved in the directories as supposed? Is this the same installation location of VMD or do you have more than one installed?