[gmx-users] genbox + editconf

Senthil Kandasamy senthilk at engin.umich.edu
Thu Dec 19 01:09:29 CET 2002

I was not fully aware of genbox's capabilities.
However, after David's suggestion, I tried to use genbox to solvate my
system. I am still confused about some of the options in editconf and
genbox and have run into (what else?) more trouble.

I decided to try genbox on a pre-existing lipid bilayer, just as a test
case. If I do things correctly, i should get a lipid bilayer with extra
waters inserted, especially between the leaflets.Though not physically
valid,it would be an easy way to check things. 

My bilayer is approximately 10 nm x 10 nm x 10 nm (last line of gro
file). Now,  I did editconf -f bilayer.gro -c -center 0 0 0 -pbc. This
should make the molecules whole, center the molecules in the box and
center the box at the origin.

Then I did genbox -cs -box 10 10 10 -o waterbox.gro(I copied the exact
values from the gro file of the bilayer,which were close to 10 but not
exactly 10). This should create a waterbox of the same size as the
bilayer system.

Then,I did editconf -f waterbox.gro -c -center 0 0 0 -pbc -o
cent-waterbox.gro. This makes the water molecules whole, centers the
waters in the box and centers the box at the origin.

Just to check things,I overlaid both these gro files in VMD and they
overlap as they should...

Now, I should be able to solvate bilayer.gro using waterbox.gro with
genbox (If I understand genbox's capabilities correctly) . So I did
genbox -cp bilayer.gro -cs waterbox.gro -o solvated.gro

But Solvated.gro is not what it should be. I have my original bilayer
still centered at the origin. Then,there is this additional rarified
water box (the new added waters ) that is not centered at the origin. It
seems to be translated by half the box length in all three directions so
that there is only one common octant between the original bilayer and my
new added waters. Almost seems like the water box was not centered at
the origin to begin with and the origin is at one of the corners of the
box.(though it definitely was and I confirmed it by repeating these
steps multiple times.)

The box size in my solvated.gro is still 10 x 10 x 10, while the system
size is now ~15 x 15 x 15.

I am obviously doing something wrong here. Is there some option that I
am leaving out? Can some body help me out here?



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