CHARMM-GUI: Brining Advanced Computational Techniques to Web Interface

CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues.

CHARMM-GUI, http://www.charmm-gui.org, is a web-based graphical user interface to prepare molecular simulation systems and input files to facilitate the usage of common and advanced simulation techniques. Since it is originally developed in 2006, CHARMM-GUI has been widely adopted for various purposes and now contains a number of different modules designed to setup a broad range of simulations ...

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

Proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to treat the long-range and 1-4 nonbonded in...

Advanced Radio Interface Techniques and Performance

Advanced Parallel Computing Techniques with Applications to Computational Cosmology

Advances in our ability to build parallel computers have continued unabated over the past decade. Large parallel machines have been deployed, including a 3,000 processor machine available to the academic community, as well as a 30,000 processor system at DOE. One of the planned machines (IBM’s Blue Light) for the near future includes over 65 thousand processors. At the same time, the structural...

Advanced Computational Techniques for Materials-by-design

Modeling of uncertainty propagation in multi-scale models of deformation is extremely complex considering the nonlinear coupled phenomena that need to be accounted for. The ongoing work addresses key mathematical and computational issues related to robust control of deformation processes. Our research accomplishments for this year include development of new mathematical models based on spectral...