[gmx-users] molecular composition of the system

Mark Abraham Mark.Abraham at anu.edu.au
Sat Jul 28 10:32:41 CEST 2012

On 28/07/2012 6:23 PM, James Starlight wrote:
> Dear Gromacs users!
> Sometimes I need to calculate exact numbers of different molecules of
> my system based on the initial gro file to add this information at the
> end of the topol.top file. Its not trivial task for the big
> heterogeneous systems ( e.g protein embeded into the membrane solvated
> in water and ions ). How I could make such calculations of total
> numbers of lipids, solvent and ions from initial gro file in the most
> trivial way ( mb with some external software) ?

Tools like grep, uniq, sort, wc, cut and paste do these kinds of 
operations easily. The Unix philosophy is to have small tools that do 
one thing really well, and the user combines these in scripts into 
higher level functionality. The GROMACS tool set works on the same 
ideas. Googling will give you leads on what tools exist and where one 
might use them. Man pages will tell you how.

For example, to calculate the total number of lipids, I might grep for 
the lipid residue names and use wc -l to count the number of those 
lines. If I know the number of atoms per lipid molecule, I can compute 
how many lipid molecules there are. There are other approaches depending 
on what you have available.


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