[gmx-users] Coordinate file for lipid bilayer

[James Starlight]

Justin,

thanks for advises.

Finally how I could effectively reduce size of my system (in x and y )
to the defined pbc box size ( see picture to the previous comment) ?

I've noticed that increasing of x and y to the 12 nm I obtain ideal
shape of the bilayer without miss-matches of the left and right sizes.
But when I try to decrease dimensions of that system from 12 to 8 nm

genbox -cs xz.gro -box 8.04542 8.04542 10.19156

I've obtained the system with the broadered water layers again ( as in
the picture which I've shown).

James

2012/10/3, Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 10/3/12 8:59 AM, James Starlight wrote:
>> 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
>>
>
> I don't know if that will have much of an effect or not.  The values in
> vdwradii.dat are used to determine if there is atomic overlap with
> coordinates
> being added (solvent) to the solute configuration.
>
> -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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