[gmx-users] Re : adding water

Andre Farias de Moura andre at qt.dq.ufscar.br
Tue Aug 19 16:44:01 CEST 2003

dear gmx-users,

correct me if I am wrong, but it seems that it is not
necessary to remove any water molecule from the box as
long as you are using periodic boundary conditions. it
does not matter if there seems to be water molecules
above and beneath your monolayer, these molecules
belong together to the same solvent layer. so, derrick,
all you need is to add 3000 water molecules, unless
you are not going to work with periodic boundary conditions,
in which case you will need some scripting.

I hope it helps you.


      André Farias de Moura
  Laboratório de Química Teórica
Universidade Federal de São Carlos
     São Carlos - SP - Brasil

On 18 Aug 2003, Senthil Kandasamy wrote:

> dear gmx-users
> i am working with a DPPC monolayer and i want to add 3000 water
> molecules
> to it. i know that i can used the editconf and genbox commands, but how
> do
> 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
> structure.
> Hope this answer was helpful.
> Senthil
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