[gmx-users] bilayer & genbox/editconf

[K.A. Feenstra]

Chris Shaw wrote:
 > Hi all,
 >
 > Just a quick one , I hope. I am trying to simulate a set of proteins in
 > a bilayer. I have downloaded the bilayer from Peters web page. My
 > problem is some of my proteins are "too big" for the lipid/solvent and
 > poke out of the top & bottom. I have tried to use both editconf & genbox
 > to extend the box in the z direction with the box command using the
 > existing x & y coords and using a larger z value ( no -d flag). when I
 > then use genbox i get a layer of water surrounding the entire simulation
 > box or I get a few water atoms surrounding the parts of the protein
 > which "poke" out. My question is how do I increase the z coords to give
 > a uniform layer of water on the extisting simulation box.

There is a nice and reasonably straightforward way of doing this. I don't
know exactly what Peter's bilayer looks like, but I assume it will be a
box with bilayer and water which was equlibated in a simulation. That means
that this box itself will be periodic, meaning that you can stack it.
So, using that knowledge, you can use either genbox or genconf to generate
an expanded box built from stacked versions of Peter's box. Probably genbox
is most convenient, since it will build a box to a given, arbitrary, dimension
(genconf will only replicate 'whole' boxes).

So, it should go a little something like this:

genbox -cs peter-bilayer.gro -o larger-box.gro -b <x> <y> <z>

I don't know if '-b' is correct; there is in any case an option to set the
(output) box size: that is the one you want (it might be called -box or
something in stead). Further, <x> and <y> stand for the x and y box dimensions
in the input file 'peter-bilayer.gro', and <z> stands for the disired, larger,
z box dimension. Note that there is a limit to this procedure, since if <z>
is too large, you will get more than one bilayer in your new box.



-- 
Groetjes,

Anton
   ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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