GROMACS version:2021.7
GROMACS modification: Yes/No
i am working of different lipid groups created using charmm-gui but where to find the head group atom information of the lipid, for POPG, DSM,PSM,POPI,SAPI,SSM,SOPE,SOPS?
What do you mean specifically? You can just visualize the box and check the names with a software like VMD.
i have used spingomylein lipid in my membrane system, now i need to calculate the acyl chain order parameter but the sn-1 and sn-2 chain numbering of that DSM lipid which im giving is wrong , can you help me out in this!
Generally speaking the automatic grouping of GROMACS works mainly on the basic topology of the systems, e.g., splitting it in Water, Protein, C-alpha, etc. If you want specific groups to calculate some quantities then you have to define them by hand yourself. For the order parameter you have to select the carbons of the tails you are interested into and put them in separate groups, generating and index file that contains only these groups, e.g.
[ carbon_1 ]
; all the first carbons of the lipid types you are interested into
[ carbon_2 ]
; all the second carbons ...
;...
;...
[ carbon_N]
;...
It is a bit tedious to build but a good exercise to understand gmx make_ndx and gmx order. You can find here a tutorial that does order parameter calculation for lipids (go towards the end of it).
Thank you for your help!! It worked out
Subashree