Example of force fields


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Example of force fields

  1. 1. Force Fields
  2. 2. What is a force field?In the context of molecularmodelling, a force field refers to theform and parameters ofmathematical functions used todescribe the potential energy of asystem of particles
  3. 3. Types of force fields • All atom • united atom • coarse grainedClassical force fields: AMBER GROMACS GROMOS CHARMM MMFF MM2/MM3
  4. 4. •• developed by : late Peter Kollmans group at the University of California, San Francisco.• AMBER is also the name for the molecular dynamics software package http://ambermd.org/family of AMBER force fields: (on basis of parameter sets)1.ff09/ff03 etc. :Peptide, protein and nucleic acidparameters2. GAFF (Generalized AMBER force field): parametersfor small organic molecules3. GLYCAM: for simulating carbohydrates
  5. 5. AmberFFC is designed to convert sixAMBER force fields (FF) (Amber 91, Amber91X, Amber 94, Amber 96, Amber 98 andAmber 99) freely available in the publicdomain, for use with commercial molecularmodeling packages, using the Accelrys Inc.
  6. 6. In this different AMBER potentials modelsare ported for use in the GROMACS MDsuite. AMBER ports for GROMACS versions3.1.4, 3.2.1, and 3.3/3.3.1 have been testedagainst AMBER 8.0• AMBER-94• AMBER-96• AMBER-GS• AMBER-99• AMBER-99f• AMBER-99SB
  7. 7. • GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics simulation package.(it is not a force field)• developed at the University of Groningen.• simulates the Newtonian equations of motion for systems with hundreds to millions of particles.• http://www.gromacs.org• rewritten in the C programming language from the Fortran77-based program GROMOS, which had been developed in the same group.
  8. 8. • support for different force fields makes GROMA For example, AMBER,CHARMM can be applied
  9. 9. Usage of Gromacs• GROMACS is open source software released under the GPL. The program is written for Unix-like operating systems; it can run on Windows machines if the Cygwin Unix layer is used• It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions.• but since GROMACS is extremely fast at calculating the Nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
  10. 10. • GROMOS(GROningen MOlecular Simulation com is a force field for molecular dynamics simulati University of Groningen.• The united atom force field was optimized with phase properties of alkanes.• GROMOS is also the name for the molecular dyn associated with this force field.
  11. 11. Versions of Gromos• GROMOS87• GROMOS96• GROMOS05• GROMOS11 There is also inclusion of the so-called "ffgmx“ force field, which is somewhat of a derivative of the GROMOS87 force field.
  12. 12. Paper related with GROMOS05 for carbohydrates
  13. 13. MMFF• MMFF is a class II force field derived from ab- initio calculations and experimental data.• It is designed to be a transferable force field for pharmaceutical compounds that accurately treats conformational energetics and nonbonded interactions . Use of MMFFMMFF has a wide coverage for all organic molecules for drug design. Limitation• less accurate for protein simulations in explicit solvent .• MMFF currently cannot be run with simulations in parallel mode
  14. 14. CHARMM• CHemistry at HARvard Macromolecular Mechanics.• The commercial version of CHARMM, called CHARMm (note the lowercase m), is available from Accelrys.• It is class I force field & has the broadest coverage for organic molecules amongst all the force fields . The CHARMm forcefield has optimized parameters for:• proteins and nucleic acids• organic molecules non-standard amino acids non-standard nucleic acid bases co-factor• metal ions
  15. 15. • http://www.charmm.org
  16. 16. Types of CHARMM• CHARMm Polar H• charmm19• charmm22• charmm27 Use of CHARMMThe CHARMm force field can be used for simulations with different solventmodels, including explicit solvents and various types of generalized Born implicitsolvent models. With a broad coverage for organic molecules and an adequate accuracy for proteins , the CHARMm force field is widely used for studyingprotein-ligand, protein-protein interactions.
  17. 17. • Paper regarding CHARMM in pubmed:
  18. 18. Some other force fields• CVFF• OPLS• ENZYMIX• ECEPP/2• QCFF/PI• UFF• XPROLIG