As we know that density analysis is one of the worthwhile analysis to validate the our bilayer membrane model. I am using the gmx density of gromacs software to calculate the lipids headgroup density. For that I need to create the ndx file for the lipids groups, but all atoms of head group are not able to select during .ndx file preparation.
An index group for the lipid headgroups can be created by entering the atom name and their number, but all atoms are not assigned in the index file. So I am not able to understand why are all atoms not selected or some specific atoms I have to select to create index file. Instead of it I would like to ask one more thing that how I have to assign an atom number as given in below command line.
Command line:
gmx make_ndx -f md_0_1.tpr -o density_groups.ndx
...
> 12 & a C1 | a C2 | a C3 | a N4 | ... | a O11
> name 22 Headgroups
Open up your coordinate file, label the atoms, and see what makes sense to designate as a headgroup atom. The atom names are force field- and lipid-specific so you can't just copy from my tutorial, which is what it appears you've done above.
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