[gmx-users] Coordinate file for lipid bilayer

[James Starlight]

Dear Felipe,

thanks for advise. Does the Packmol software suitable for generation
coordinates of the bergers ( for gromos 56 ff) lipids ? As I know
CHARMM-GUI membrane builder is suitable for only CHARMM force field
lipids.

James

2012/10/4 Felipe Pineda, PhD <luis.pinedadecastro at lnu.se>:
> 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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