Force Fields

What is a force field?

In the context of molecular modelling, a force field refers to the form and parameters of mathematical functions used to describe the potential energy of a system of particles

Types of force fields • All atom • united atom • coarse grained

AMBER GROMACS GROMOS

CHARMM MMFF MM2/MM3

Classical force fields:

• AMBER Stands for : Assisted Model Building with Energy Refinement

• developed by : late Peter Kollman's 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 acid parameters2. GAFF (Generalized AMBER force field): parameters for small organic molecules3. GLYCAM: for simulating carbohydrates

AmberFFC is designed to convert six AMBER force fields (FF) (Amber 91, Amber 91X, Amber 94, Amber 96, Amber 98 and Amber 99) freely available in the public domain, for use with commercial molecular modeling packages, using the Accelrys Inc.

In this different AMBER potentials models are ported for use in the GROMACS MD suite. AMBER ports for GROMACS versions 3.1.4, 3.2.1, and 3.3/3.3.1 have been tested against AMBER 8.0• AMBER-94 • AMBER-96• AMBER-GS • AMBER-99 • AMBER-99f• AMBER-99SB • AMBER-03

• 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.

• support for different force fields makes GROMACS very flexible. For example, AMBER,CHARMM can be applied to GROMACS.

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.

• GROMOS(GROningen MOlecular Simulation computer program package) is a force field for molecular dynamics simulation developed at the University of Groningen.

• The united atom force field was optimized with respect to the condensed phase properties of alkanes.

• GROMOS is also the name for the molecular dynamics simulation package associated with this force field.

• 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.

Versions of Gromos

Paper related with GROMOS05 for carbohydrates

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 .

MMFF has a wide coverage for all organic molecules for drug design.

Use of MMFF

• less accurate for protein simulations in explicit solvent .• MMFF currently cannot be run with simulations in parallel mode

Limitation

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

• http://www.charmm.org

Types of CHARMM

• CHARMm Polar H• charmm19• charmm22• charmm27

The CHARMm force field can be used for simulations with different solvent models, including explicit solvents and various types of generalized Born implicit solvent models. With a broad coverage for organic molecules and an adequate accuracy for proteins , the CHARMm force field is widely used for studying protein-ligand, protein-protein interactions.

Use of CHARMM

• Paper regarding CHARMM in pubmed:

Some other force fields

• CVFF

• OPLS

• ENZYMIX

• ECEPP/2

• QCFF/PI

• UFF

• XPROLIG