[gmx-users] Bilayer area questions again!

Rama Gullapalli quantrum75 at yahoo.com
Thu Sep 15 19:03:39 CEST 2005

Dear Dallas and David,
Thank you for your replies. I pretty much understand
what you are saying that the periodic boundary
conditions will take care of molecules in the box and
how the system size doesnt matter.

I went back and did something to work out some doubts
of mine.

I took ONE bilayer from the end of my equilibriation
run, used editconf to make 2 run structures with TWO
different box dimensions,

1) 5.6 by 5.7 by 8.5, 

2) 6.6 by 6.7 by 8.5

The i ran a simulation on both of the boxes for 100
picoseconds each (NPT run).

Now, the box length vectors over the course of this
simulation remained pretty much the same and are
stable, hovering around within +/- 0.1 nm of the
original box dimensions.I know this is a short
simulation, but the same thing has happened to me over
the course of even 10 nanoseconds of simulation
earlier too.

Now my question is, is it not wrong to APRIORI assign
the box size to give a value within the required area
per lipid and thus, compute the result? (eg the first
run gives an area per lipid of 0.50 ^2 nm versus the
second box which is roughly 0.68 ^ 2 nm and thus, the
correct area)

When i ran the equilibriation for the bilayer earlier
over 10 nanoseconds using NPT coupling, the box size
remained quite the same at the end of the
equilibriation, that is 5.8 by 5.7 by 8.5 (+/- 0.1
nm), when i actually expected the box dimensions to
increase to roughly 6.6 by 6.7 by 8.5 and give me the
correct area per lipid post equilibriation.

Thanks for your time, but this is one issue which i
need to clarify quite badly to know im on the right
track. Also, the other properties of the bilayer, like
temperature, density of the bilayer seem to be ok.


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