Paper Citing NAMD - Abstract
Miller, Benjamin T.; Singh, Rishi P.; Klauda, Jeffery B.; Hodoscek, Milan; Brooks, Bernard R.; Woodcock, H. Lee, I.I.I.
CHARMMing: A new, flexible web portal for CHARMM
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 48:1920-1929, SEP 2008
A new web portal for the CHARMM macromolecular modeling package, CHARMMing (CHARMM interface and graphics, http://www.charmming.org), is presented. This tool provides a user-friendly interface for the preparation, submission, monitoring, and visualization of molecular simulations (i.e., energy minimization, solvation, and dynamics). The infrastructure used to implement the web application is described. Two additional programs have been developed and integrated with CHARMMing: GENRTF, which is employed to define structural features not supported by the standard CHARMM force field, and a job broker, which is used to provide a portable method for using grid and Cluster computing with CHARMMing. The use of the program is described with three proteins: 1YJP, 1O1O, and 1UFY. Source code is provided allowing CHARMMing to be downloaded, installed, and used by supercomputing centers and research groups that have a CHARMM license. Although no software can replace a scientist's own judgment and experience, CHARMMing eases the introduction of newcomers to the molecular modeling discipline by providing a graphical method for running simulations.
