[gmx-users] Coordinate file for lipid bilayer
Felipe Pineda, PhD
luis.pinedadecastro at lnu.se
Thu Oct 4 09:39:52 CEST 2012
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
Hope it helps!
On 10/04/2012 07:46 AM, James Starlight wrote:
> lastly, is there any other ways to obtain bilayers of desired
> dimensions started from just one lipid oriented in desired way for
> 2012/10/3, Justin Lemkul <jalemkul at vt.edu>:
>> On 10/3/12 12:38 PM, James Starlight wrote:
>>> 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
>> a sensible water layer and membrane leaflets.
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
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