I have a question.
I want to measure the volume per lipid. I built a membrane with water and run the simulation for 300 ns. To measure the volume per lipid I used a .gro file from the simulation and then run the lipid-free simulation with the same mdp parameters and check the volume of the box ( I just deleted all lipid from the system and run for example 50 ns and take the average volume of the box from 20-50 ns). So at the end my Volume per lipid = (Average (50-300 ns) box volume - Average (20-50ns) box volume from the free-lipid system) / number of lipids. Is that correct? I want to check POPC parameters fo so I will compare experimental value to those from my simulation
Hi Jakub! If you are planning to use built-in routines in gromacs you shall use the one for energy (earlier versions g_energy, later versions gmx energy). As I understand, your bilayer contains the same lipid, which is POPC. So for the area per lipid you will need to extract the box sizes in xy-direction, multiply them by each other and then divide by the number of lipids in the leaflet. To obtain the volume per lipid you will need to determine the thickness of the membrane for each frame (if you plan to plot it per frame). The thickness can be determined from the calculation of electron density profiles or mass density profiles in z-direction. The distance between points of maximum of these profiles determines the bilayer thickness. If you divide it by 2, you will get a thickness of a leaflet. Then you multiply it by the area per lipid, you will get the volume per lipid. This is one of the simplest ways to do so. Some people also use Voronoi tessellation for computing the area per lipid, but since your bilayer contains only POPC, you can do it easier.
Hi Jakub! If you are planning to use built-in routines in gromacs you shall use the one for energy (earlier versions g_energy, later versions gmx energy). As I understand, your bilayer contains the same lipid, which is POPC. So for the area per lipid you will need to extract the box sizes in xy-direction, multiply them by each other and then divide by the number of lipids in the leaflet. To obtain the volume per lipid you will need to determine the thickness of the membrane for each frame (if you plan to plot it per frame). The thickness can be determined from the calculation of electron density profiles or mass density profiles in z-direction. The distance between points of maximum of these profiles determines the bilayer thickness. If you divide it by 2, you will get a thickness of a leaflet. Then you multiply it by the area per lipid, you will get the volume per lipid. This is one of the simplest ways to do so. Some people also use Voronoi tessellation for computing the area per lipid, but since your bilayer contains only POPC, you can do it easier.
Jakub Hello,
I am not using gromacs, but you can directly estimate molecular volume using two methods.
1. solvent-accessible surface area (SASA)
https://en.wikipedia.org/wiki/Accessible_surface_area
which is just rolling a solvent "sphere" around your molecules. I've used VMD with Scripp's MSMS program
http://mgltools.scripps.edu/packages/MSMS
2. Voronoi tessillation, as Inna mentioned.
https://en.wikipedia.org/wiki/Voronoi_diagram
I've used the builtin implementation in LAMMPS.
But there is an external tool for gromacs (I haven't tried it)
https://sourceforge.net/projects/aplvoro2/
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