[gmx-users] GIMLi user-contributed code for lipid mixture simulations

[Kindt, James]

Greetings Gromacs users - This note is to announce a new upload in the "user
contributions" section on the Gromacs website.  Here is the description:

GIMLi-1.0:
GROMACS Including Monte Carlo Mutation Moves for Mixtures of Lipids
(not official GROMACS!)

The purpose of this modified version of Gromacs 3.3.1 is to perform an
isomolar semi-grand canonical ensemble (constant N,Δμ,T – depending on
settings, can be also constant p,γ or A) simulation of a mixture of 2 lipid
types with different tail structures.  Why would you want to do this?  To
achieve an equilibrated lateral distribution of the lipids in your mixture
(potentially) much faster than you can by waiting for your lipids to diffuse
around your system and sample different arrangements.  This can be
particularly interesting if there are different microenvironments in your
system, determined by proximity to a membrane protein or other perturbation
to the bilayer.

For examples of how this method has been applied, please see:

P. S. Coppock, J. T. Kindt, “Atomistic simulations of mixed-lipid bilayers
in the gel and fluid phases.” Langmuir 25, 352-359 (2009).

H. Wang, J. de Joannis, Y. Jiang, J. C. Gaulding, B. Albrecht, F. Yin, K.
Khanna, and J. T. Kindt, “Bilayer edge and curvature effects on partitioning
of lipids by tail length: Atomistic simulations.” Biophysical Journal 95,
2647-2657 (2008).

J. de Joannis, Y. Jiang, F. Yin, and J. T. Kindt, “Equilibrium distributions
of DPPC and DLPC in a mixed lipid bilayer: Atomistic semi-grand canonical
ensemble simulations.” Journal of Physical Chemistry B. 110, 25875-25882
(2006).

The package contains source code, a 4 page user guide and some (limited)
installation suggestions.  If you are interested and have questions not
addressed in the user guide, don't hesitate to contact me at

jkindt[at]emory.edu

Many thanks to the Gromacs developers for making their code and their expert
advice available to groups for this sort of customization project, and to
Dr. Jason de Joannis for writing the lion's share of the Monte Carlo code.


--

James Kindt
Co-Director of Graduate Studies
Department of Chemistry
Emory University
1515 Dickey Drive
Atlanta, GA  30322
Phone (404) 712-1817
Fax   (404) 727-7412
Office: Emerson Hall, room 521
jkindt[at]emory.edu
http://www.chemistry.emory.edu/faculty/kindt/index.htm





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