1. Force Fields

2. 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

3. Types of force fields
• All atom
• united atom
• coarse grained
Classical force fields:
AMBER GROMACS GROMOS
CHARMM MMFF MM2/MM3

4. •
• 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
parameters
2. GAFF (Generalized AMBER force field): parameters
for small organic molecules
3. GLYCAM: for simulating carbohydrates

5. 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.

6. 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

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. • support for different force fields makes GROMA
For example, AMBER,CHARMM can be applied

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. • 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. 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. Paper related with GROMOS05 for carbohydrates

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 MMFF
MMFF 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. 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. • http://www.charmm.org

16. Types of CHARMM
• CHARMm Polar H
• charmm19
• charmm22
• charmm27
Use of CHARMM
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.

17. • Paper regarding CHARMM in pubmed:

18. Some other force fields
• CVFF
• OPLS
• ENZYMIX
• ECEPP/2
• QCFF/PI
• UFF
• XPROLIG