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 This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).
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