[gmx-users] Coordinate file for lipid bilayer

[James Starlight]

Justin,


lastly, is there any other ways to obtain bilayers of desired
dimensions started from just one lipid oriented in desired way for
instance?


James

2012/10/3, Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 10/3/12 12:38 PM, James Starlight wrote:
>> 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).
>>
>
> My advice is still the same - you need box vectors that are compatible with
> both
> a sensible water layer and membrane leaflets.
>
> -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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