GROMACS version: 2021.4
GROMACS modification: No
I have a doubt for coarse grained md simulation. I have used martinize.py script to model the protein. But from here I do not understand on what basis it modelled the protein. There are 2 chain in the protein, So, it split chain A in 5 chains, 1: 3 atoms in 1 residue,2: 278 atoms in 35 residue, 3: 6 atoms in 2 residues, 3:278 atoms in 35 residues, 5: 3 atoms in 1 residues. and for chain B, 1060 atoms in 130 residues. Suppose I want to form residue wise beads with martini. Is it possible?
Hi @Baibhabshri ,
This seems not be a GROMACS related problem. You may want to take a look at the MARTINI forum/website: http://www.cgmartini.nl. (They also provide a lot of detailed tutorials about setting up a system with MARTINI using GROMACS!)
Quick answer for the coarse graining approach in MARTINI: MARTINI merges usually 4 heavy atoms (e.g. 4 C-Atoms) to one MARTINI bead. The mapping is fixed for most standard residues like amino acids or lipids.
Hope that helped.
All the best,
Marius
But what I saw that, there were 130 residue and 1060 atoms in one chain, if that converted that in 130 beads is not it like it is residue wise bead formation?