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 <[email protected]>:
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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