[gmx-users] Coordinate file for lipid bilayer

[Felipe Pineda, PhD]

To generate starting (non-equilibrated) bilayer structures for use in MD 
simulations take a look at http://www.ime.unicamp.br/~martinez/packmol/. 
Otherwise, for conventional lipids CHARMM-GUI membrane builder 
(http://www.charmm-gui.org/?doc=input/membrane).

Hope it helps!

Felipe

On 10/04/2012 07:46 AM, James Starlight wrote:
> 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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