GROMACS version: 2021.3
GROMACS modification: No
I was just wondering if anyone has insight on applying position restraints for a whole lipid in MARTINI rather than a headgroup. For example, right now in the martini_v2.0_ions.itp file, there is an option for restraining the z-position of the headgroup in a bilayer simulation with #BILAYER_LIPIDHEAD_FC. One question I have is that for the following line:
[ position_restraints ]
;to fix Z postion of head group in bilayer simulation
2 1.0 0.0 0.0 BILAYER_LIPIDHEAD_FC
#endif
What does 1.0 refer to?
Secondly, if I wish to restrain the entire lipid rather than just the headgroup, would it simply be the following?
[ position_restraints ]
;to fix Z postion of head grop in bilayer simulation
1 1.0 BILAYER_LIPID_FC BILAYER_LIPID_FC BILAYER_LIPID_FC
2 1.0 BILAYER_LIPID_FC BILAYER_LIPID_FC BILAYER_LIPID_FC
…
n 1.0 BILAYER_LIPID_FC BILAYER_LIPID_FC BILAYER_LIPID_FC
where n is the total number of beads within a single lipid?
Or would I have to use gmx genrestr to generate the file?
Thank you for any suggestions!