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 <[email protected]>:
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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