[gmx-users] Coordinate file for lipid bilayer

[Thomas Piggot]

Hi James,

The bilayers from the CHARMM-GUI can be converted into any force field 
using a simple script. For a united-atom force field you will need to 
remove the non-polar hydrogens, rename the atoms and possibly reorder 
some of the atoms in the lipids.

As for other methods to build membranes, there are numerous different 
methods available. One of the simplest approaches is to use genconf to 
replicate a single lipid up to the desired size of membrane and perform 
and simulation to equilibrate the properties of your membrane (although 
depending upon the lipid and force field this may require simulations in 
the order of several hundreds of ns though). Another fairly simple 
method (which can also be easily used to make hexagonal membranes) is to 
self-assemble a coarse-grained membrane, map that back to an atomistic 
representation (using one of a number of available tools) and 
equilibrate. One issue using this method is that the self-assembly often 
results in uneven numbers of lipids per membrane leaflet. This, however, 
is easy to correct after the self-assembly.

Cheers

Tom

James Starlight wrote:
> 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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-- 
Dr Thomas Piggot
University of Southampton, UK.