[gmx-users] Coordinate file for lipid bilayer

Justin Lemkul jalemkul at vt.edu
Wed Oct 3 13:15:40 CEST 2012

On 10/3/12 1:59 AM, James Starlight wrote:
> Justin,
> I've told about lower lipid density at the left and right edges of the
> new system ( see new pic bellow with marked regions).
> http://imageshack.us/photo/my-images/10/dppc.png/
> I've started with system consisted of 118 lipids and 6000 water in dims 6x6x10
> I've created new box with the desired sizes for my system as well as
> centered it in it. Finally I've resized it via
> genbox -cp prot_in_lipids_old.gro -cs dppc128_whole.gro -box 8.04542
> 8.04542  10.19156
> As the result I've obtain syste of 128 lipids and 13000 water with dims 8x8x10
> I have the same system with the popc lipids with the same dims where
> there are 200 lipids
> Why only 10 lipids were added after resizing ? How I could increase
> this number of added lipids ( expesially in regions with lower lipid
> density- see pic) ?

genbox decides whether or not to put molecules in the box if they can be added 
intact; anything sticking out of the box is removed.  Since water molecules are 
small, this is easy to do.  Since a lipid molecule is large, it is not so easy. 
  The hydrocarbon tails are very flexible and thus may have configurations 
leading them to stick out of the box, so genbox won't add them.  You will likely 
have to gradually increase the box dimensions in x and y to allow for more 
lipids to be added, striking a balance between the (much larger) number of water 
molecules and number of lipids added.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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