[gmx-users] Coordinate file for lipid bilayer

[James Starlight]

Justin,

Might the modifications of the vdwradii.dat be suitable for such
system expanding or (on other hand) reduction (as in the below picture
are shown). In the lattter case I defined new box dimensions (smaller
than initial box dims) and would like to remove all side water-lipids
layer which are beyond new pbc dimensions)?

http://imageshack.us/content_round.php?page=done&l=img138/5497/reduction.png

James

2012/10/3, Justin Lemkul <jalemkul at vt.edu>:
>
>
> 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
>
> --
> ========================================
>
> 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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