[gmx-users] Coordinate file for lipid bilayer

[James Starlight]

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 ?

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 :) )

James

2012/10/2, Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 10/2/12 2:16 PM, James Starlight wrote:
>> Dear all!
>>
>> Recently I've forced with the same problem as was in this topic :)
>>
>> I have tieleman's lipids consisted of 128 dppc with water.
>> also I have system with the protein inserted in the same bilayer
>>
>> I wounder to know
>>
>> 1- How I could change lipid number in the pure lipid bilayer (
>> increase up to 200 lipids) with standard Gromacs tools ?
>>
>> I've tried use
>> genbox -cs dppc128_whole.gro -box 8.04542  8.04542  10.19156
>>
>> where 8.045 in x and y was higher than in the case of initial bilayer (
>> 6.045)
>> As the consequence that prodyce larger system with increased amount of
>> water in upper and lower layers but the lipid number was the same.
>>
>
> The proper approach is to set values for the box that are larger in x and y,
> but
> the same size in z.  That way, the new "solvation" occurs within the same
> plane
> as the membrane.
>
>> 2- Is there any way to increase lipid number ( to add lipids from each
>> size of the system) in the bilayer with the inserted protein ?
>>
>
> Using the same approach, with a slight modification:
>
> genbox -cp protein_in_membrane.gro -cs dppc128_whole.gro -box (x y z)
>
> Increase the values of x and y, and leave z alone.
>
> -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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