Shay Amram wrote:
Dear GROMACS users,
I have been trying to expand a membrane by a non-integer multiplier (for
example X1.5). This can be done using
*genbox -cs Membrane.gro -o Expanded_membrane.gro –box 1.5X 1.5Y Z***
This has worked very good with _homogenous_ membranes, and only very
short equilibrium times were required to re-equilibrate the membrane
(~10-20ns).
Now I am trying to deal the same way with _heterogeneous_ membrane
(POPG/POPE mixture, Mikko Karttunen et. al).
When trying to invoke the above command to the POPG/POPE membrane I get
a membrane with different compositions of lipids in the upper and lower
leaflets.
This happens (so I suspect) because the arrangement of lipids in each
leaflet is somewhat different so that the molecules that "get' to be
multiplied do not conserve the
same ratio of different lipids as in the original structure (which has
ratio of 1:3 POPG/POPE).
If you have an excess of POPE, you can (either manually, or by using a script)
randomly choose some POPE to be converted to (or replaced with) POPG by some
clever means. This is not a trivial task.
Is there a way to multiply the membrane by a _non-integer_ number AND
somehow conserve the ratio of different lipid species too?
The output is dependent upon the configuration of the input and the box size, so
no, there is no straightforward, automatic, way of doing so given the
constraints of your box dimensions.
Or at the very least, to have both upper and lower leaflets identical
after multiplication? (This, too, would help immensely).
If you can construct a satisfactory monolayer, you can manipulate its
coordinates (i.e. horizontal flip and translation) to create a bilayer. You
would have to do plenty of equilibration after doing so, of course.
-Justin
Thanks,
-Shay
------------------------------------------------------------------------
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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