What is martini forcefield?
Martini is a coarse-grained (CG) force field developed by Marrink and coworkers at the University of Groningen, initially developed in 2004 for molecular dynamics simulation of lipids, later (2007) extended to various other molecules.
What is Charmm force field?
Website. 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.
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 coarse-grained molecular dynamics?
Coarse-grained molecular dynamics (CGMD) is the most popular technique in mesoscale modeling. Typically each bead represents three to five heavy atoms and their pendant hydrogen atoms (Marrink et al., 2007; Shinoda et al., 2007).
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 a martini model?
Introduction to Martini The model uses a four-to-one mapping, i.e. on average four heavy atoms and associated hydrogens are represented by a single interaction center. In order to keep the model simple, only four main types of interaction sites are defined: polar, non-polar, apolar, and charged.
What is Gromos force field?
GROningen MOlecular Simulation (GROMOS) is the name of a force field for molecular dynamics simulation, and a related computer software package.
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.
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 the difference between fine-grained and coarse grained?
The word ‘granular’ is used to describe something that is made up of multiple elements. If the elements are small, we call it “fine-grained,” and if the elements are large, we call it “coarse-grained.” These are terms typically used in economics, computer science and geology.
What is coarse grain?
Coarse grains generally refers to cereal grains other than wheat and rice — in the OECD countries, those used primarily for animal feed or brewing.
What can GROMACS do?
GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of calculation types, preparation and analysis tools. Several advanced techniques for free-energy calculations are supported.