How do I cite CHARMM-GUI? ¶ In general, you should cite the main CHARMM-GUI paper, as well as the references for any input generator modules and programs you used.

How do you cite CHARMM-GUI?

How do I cite CHARMM-GUI? ¶ In general, you should cite the main CHARMM-GUI paper, as well as the references for any input generator modules and programs you used.

How do you cite Amber?

When citing Amber 2018 (comprised of AmberTools18 and Amber18) in the literature, the following citation should be used: D.A. Case, I.Y. Ben-Shalom, S.R. Brozell, D.S.

What is CHARMM used for?

CHARMM is a general and flexible molecular simulation and modeling program that uses classical (empirical and semiempirical) and quantum mechanical (semiempirical or ab initio) energy functions for molecular systems of many different classes, sizes, and levels of heterogeneity and complexity.

What is the CHARMM force field?

www.academiccharmm.org. Chemistry at Harvard Macromolecular Mechanics (CHARMM) is the name of a widely used set of force fields for molecular dynamics, and the name for the molecular dynamics simulation and analysis computer software package associated with them.

How do you cite VMD?

You should cite the use of VMD using: Humphrey, W., Dalke, A. and Schulten, K., “VMD – Visual Molecular Dynamics”, J. Molec.

What is Pmemd?

Particle Mesh Ewald Molecular Dynamics (PMEMD) is the primary engine for running MD simulations with AMBER. Sander can still employed to run MD production runs on CPUs but it will be much slower. The pmemd.

What is Urey Bradley?

The second term is the Urey-Bradley term used to describe a (noncovalent) spring between the outer and atoms, active when constant , where, like the spring bond, gives the distance between the pair of atoms and. is the equilibrium distance.

Why are molecular simulations important?

Molecular modeling and simulations Molecular simulations have served to obtain values of various physical quantities (often inaccessible experimentally) to verify molecular-based theories and to gain insight into the molecular principles underlying various processes.

What is Pmemd Amber?

What is Pmemd Cuda?

The single GPU version of PMEMD is called pmemd. cuda while the multi-GPU version is called pmemd. cuda. MPI . We recommend that you build a serial (CPU) version of pmemd first.

What is CHARMM?

CHARMM is a high-performance version supporting large-scale parallelism and GPUs and is available here for a modest fee. CHARMm is the commercial version available through Biovia. If you use CHARMM in your research, please cite the following paper:

What is the toppar file for charmm36?

Toppar files for CHARMM36 all-atom carbohydrate force field. Toppar files with c32b1 release of CHARMM. Includes the CMAP extension to the CHARMM22 protein force field and various extensions of the force fields. Toppar files with c31b1 release of CHARMM.

What is the best reference book for CHARMM?

The original CHARMM reference and a brief update are: B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus: CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations, J. Comp. Chem. 4, 187-217 (1983)

Where can I find an overview of parameter optimization for CHARMM?

An overview of the parameter optimization approaches to extend the CHARMM force fields may be found in the following references or in MacKerell, Jr., A.D. “Atomistic Models and Force Fields” in Computational Biochemistry and Biophysics, O.M. Becker, A.D. MacKerell, Jr., B. Roux, and M.Watanabe, Eds., Marcel Dekker, Inc. New York, 2001, p. 7-38.