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.
Mark
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