[gmx-users] Calculating area per lipid and monolayer thickness
mmathe01 at mail.bbk.ac.uk
Wed Mar 8 13:28:07 CET 2017
I have a system that I simulated using GROMACS v5.0.4. The system is two
monolayers of lipid on each side of a box of water. I would like to know if
there is a way to calculate area per lipid and monolayer thickness. I read
that one can use gmx energy to find box size in X and Y and you divide the
average time evolution box size( X*Y) by number of lipids.
I used commmand:
gmx energy -f md.edr -s md.tpr -o box_vector.xvg
What option should I select when prompted to get X and Y box dimensions.?
How is the box vector calculated? I have noticed that the lipids pack
closely after simulation, that means the the area per lipid will be smaller
than the initial configuration file. So does the box X and Y get smaller as
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