Contact map for membrane

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question
I have a lipid bilayer composed of three different components. Could you guide me on how to generate a contact map for these lipids using GROMACS?

2

you can use thes methods:

Use gmx mdmat -f *.xtc -s *.tpr -mean mat.xpm -frames mat1.xpm -no mat.xvg -n index.ndx (Index specific group for contact analysis)
xpm2ps -f *.xpm -o *.eps -rainbow blue

or

use vmd >>> Contact Map Plugin, Version 1.0

or

use Mdanalysis >> 4.3.2. Native contacts analysis — MDAnalysis.analysis.contacts — MDAnalysis 2.8.0 documentation

3

Could you tell me how to find the contact map for each lipid in a multi-component lipid bilayer using VMD software?

4

Hi Mosaddeghi,
Is it possible to find Contact Map using Contact Map Plugin in VMD for multi component lipid system or it is only possible in the case of protein residues ?
If it is possible then can you tell me how can I do it?