[gmx-users] Re : adding water

Senthil Kandasamy senthilk at engin.umich.edu
Tue Aug 19 04:26:01 CEST 2003

dear gmx-users

i am working with a DPPC monolayer and i want to add 3000 water
to it. i know that i can used the editconf and genbox commands, but how
i use them to add that number of water molcules and on a particular side
of the monolayer? thanks for any help available.

 - derrick

Hi derrick, 

If I understand you correctly, you want to add a layer of water beneath
a dppc monolayer with 40 lipids. I assume that you know the dimensions
of the DPPC box in the x and y and Z directions. What are the x and y
values?  For 40 lipids, it is likely to be approximately sqrt(40*~62.5)=
5.0nm x 5.0 nm or approximately those dimensions. Now, create a water
box with the same x and y values. genbox -cs -box 5 5 z-value -o
waterin.pdb. You will have to choose the z-value appropriately to get
the necessary number of water molecules. For 3000 molecules, with
x=y=5nm, z is likely to be ~3.8 nm. This generates a water box with the
same x and y dimensions as the DPPC box. Now, all you have to do is use
editconf to recenter your dppc box and water box appropriately and merge
the pdb files. 

e.g. assume DPPC box size is 5x5x3 nm and the created water box size is
5x5x4nm. You can use 

editconf -f dppcin.pdb -o dppcout.pdb -center 0 0 0  and
editconf -f waterin.pdb -o waterout.pdb -center 0 0 -3.5 

Then, if you merge dppcout.pdb and waterout.pdb, you will get what you
are looking for. Of course, you will have to energy minimize this system
and then run a equilibration stage to get a reasonable starting

Hope this answer was helpful.


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