CHARMM-GUI Lecture Series on Molecular Modeling and Simulation
نویسندگان
چکیده
منابع مشابه
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 ...
متن کاملCHARMM-GUI MDFF/xMDFF Utilizer for Molecular Dynamics Flexible Fitting Simulations in Various Environments.
X-ray crystallography and cryo-electron microscopy are two popular methods for the structure determination of biological molecules. Atomic structures are derived through the fitting and refinement of an initial model into electron density maps constructed by both experiments. Two computational approaches, MDFF and xMDFF, have been developed to facilitate this process by integrating the experime...
متن کاملCHARMM: The biomolecular simulation program
CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the stu...
متن کاملModeling and Simulation of a Molecular Single-Electron Transistor
In this paper, to understand the concept of coupling, molecule density of states that coupled to the metal electrodes will be explained then, based on this concept, a weak and strong coupling for the molecules attached to the metal electrodes will be described. Capacitance model is used to explore the connection of addition energy with the Electron affinity and the ionization energy of the mole...
متن کاملCHARMM-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...
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ژورنال
عنوان ژورنال: Biophysical Journal
سال: 2018
ISSN: 0006-3495
DOI: 10.1016/j.bpj.2017.11.1027