[gmx-users] Coordinate file for lipid bilayer

[James Starlight]

Justin

Previously I've expanded initial system on Z-dim before the protein
was inserted to increase both water layers.

After current processing with Genbox there is no problems in Z
actually- it look likes sandwich with two broader bread layers and
narrower cutlet :) So the lipid layer in x and y is thinker than water
( so the lipid number stay the same after resizing).

James

2012/10/2, Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 10/2/12 2:56 PM, James Starlight wrote:
>> Justin,
>>
>> I've done exactly like you provide me ( changing only x and y )
>>
>> but in that case the protein and the old lipids were slightly shifted
>> to one side of the new system. Is there any way to center the old
>> system in respect to the new solvent ?
>>
>
> Define a new box and center with editconf -c -box.
>
>> Also I've noticed that when I increase size of my system in x and y
>> dimensions both of the water layers were increased greatly than lipid
>> layer ( it's look like sandwich with two big bread pieces and smaller
>> cutlet between them :) )
>>
>
> This suggests that something is wrong with the z-dimension.  I only say that
>
> because you had a 10-nm z-length in your previous post with the Tieleman
> DPPC
> bilayer, which is far larger than the coordinate file normally has.  genbox
>
> works by tiling the solvent coordinates through the empty space in the
> solute
> configuration.  If you're expanding in 3 dimensions, you can expect weird
> things
> to happen with membrane systems.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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