Allows one to generate a Brownian dynamics trajectory of ions in a channel system. GCMC/BD is a web-based graphical user interface presented for grand canonical Monte Carlo (GCMC) BD simulations of channel proteins. This is a method used to maintain the desired electrochemical conditions in the boundaries (buffer regions) of the simulation system which are in (equilibrium) contact with the bulk. The webserver is designed to help users avoid most of the technical difficulties and issues encountered in setting up and simulating complex pore systems.
Center for Bioinformatics and Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, USA; Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
GCMC/BD funding source(s)
This work was supported in part by institutional funding from the University of Kansas General Research Fund allocation #2301388-003, Kansas-COBRE NIH P20 RR-17708, the National Science Foundation (NSF OCI-0503992) through TeraGrid resources provided by Purdue University, a research fellowship from the German Research Foundation, a NIH GM062342 grant, and the Intramural Research Program of the National Heart, Lung, and Blood Institute in the National Institutes of Health.