What is CHARMM force field?
Empirical force field parametrization efforts are coordinated with the program CHARMM, which was originally developed in the laboratory of Professor Martin Karplus, Department of Chemistry, Harvard University. Below gzipped tar files containing the topology and parameter files available various releases of CHARMM.
What is an additive force field?
In pairwise-additive force fields, each atom is assigned a partial charge based on the electron distribution in a molecule; typically charge assignment is carried out according to QM target data such as molecular dipole moments and electrostatic surface potentials (discussed in Section 3 in the context of force field …
What is CHARMM GUI?
CHARMM-GUI, http://www.charmm-gui.org, is a web-based graphical user interface that prepares complex biomolecular systems for molecular simulations. CHARMM-GUI creates input files for a number of programs including CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM.
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.
What is Gromacs package?
GROMACS is a molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers worldwide.
What is TIP3P water model?
The TIP3P water model as implemented in CHARMM (MacKerell) specifies a 3-site rigid water molecule with charges and Lennard-Jones parameters assigned to each of the 3 atoms. In LAMMPS the fix shake command can be used to hold the two O-H bonds and the H-O-H angle rigid.
What is MM2 force field?
The MM2* force field is a modification of MM2. MM2* includes partial charge electrostatics, explicit parametrization of conjugated systems, and extensive additional parameters.
What are molecular force fields?
The force field is a collection of equations and associated constants designed to reproduce molecular geometry and selected properties of tested structures. In molecular dynamics a molecule is described as a series of charged points (atoms) linked by springs (bonds).
What is adhesive force?
Adhesive forces are the forces that hold two materials together at their surfaces. From: Joining and Assembly of Medical Materials and Devices, 2013.
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.
What is CHARMM?
► CHARMM contains a comprehensive set of analysis and model builiding tools. ► CHARMM achieves high performance on a variety of platforms including parallel clusters and GPUs. ► CHARMM is actively maintained by a large group of developers led by Martin Karplus.
What is the CHARMM development project?
The CHARMM Development Project, which is administratively at Harvard University but involves all of the developers, is a continuing, collaborative effort to advance the CHARMM program as a state-of-the-art tool for macromolecular simulations.
What is the correct version number for CHARMM?
The current convention for version numbering began with version 26. In “cnn(a/b)m”, c is for CHARMM, nnis the version number, a(alpha) is for developmental, b(beta) is for release, and mis the revision number.
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)
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