Dear All,
I recently asked a question about comparing the forcefields for protein
simulations and the appropriate water model to use for the same to which Justin
answered back. Thanks for the answer justin.
In addition, I found a couple of references which I think are really good for
the above topics which I would like to share with other newbies (like me) as a
future reference. This might be a good starting point for other to follow. They
are:
For the forcefields:
1: Methods Mol Biol. 2008;443:63-88.
Links
Comparison of protein force fields for molecular dynamics simulations.
Guvench O, MacKerell AD Jr.
Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD,
USA.
In the context of molecular dynamics simulations of proteins, the term "force
field" refers to the combination of a mathematical formula and associated
parameters that are used to describe the energy of the protein as a function of
its atomic coordinates. In this review, we describe the functional forms and
parameterization protocols of the widely used biomolecular force fields Amber,
CHARMM, GROMOS, and OPLS-AA. We also summarize the ability of various readily
available noncommercial molecular dynamics packages to perform simulations
using these force fields, as well as to use modern methods for the generation
of constant-temperature, constant-pressure ensembles and to treat long-range
interactions. Finally, we finish with a discussion of the ability of these
force fields to support the modeling of proteins in conjunction with nucleic
acids, lipids, carbohydrates, and/or small molecules.
For the water models.
2: 1: J Chem Phys. 2005 Apr 1;122(13):134508.
Solvation free energies of amino acid side chain analogs for common molecular
mechanics water models.
Shirts MR, Pande VS.
Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA.
Quantitative free energy computation involves both using a model that is
sufficiently faithful to the experimental system under study (accuracy) and
establishing statistically meaningful measures of the uncertainties resulting
from finite sampling (precision). In order to examine the accuracy of a range
of common water models used for protein simulation for their solute/solvent
properties, we calculate the free energy of hydration of 15 amino acid side
chain analogs derived from the OPLS-AA parameter set with the TIP3P, TIP4P,
SPC, SPC/E, TIP3P-MOD, and TIP4P-Ew water models. We achieve a high degree of
statistical precision in our simulations, obtaining uncertainties for the free
energy of hydration of 0.02-0.06 kcal/mol, equivalent to that obtained in
experimental hydration free energy measurements of the same molecules. We find
that TIP3P-MOD, a model designed to give improved free energy of hydration for
methane, gives uniformly the closest match to
experiment; we also find that the ability to accurately model pure water
properties does not necessarily predict ability to predict solute/solvent
behavior. We also evaluate the free energies of a number of novel modifications
of TIP3P designed as a proof of concept that it is possible to obtain much
better solute/solvent free energetic behavior without substantially negatively
affecting pure water properties. We decrease the average error to zero while
reducing the root mean square error below that of any of the published water
models, with measured liquid water properties remaining almost constant with
respect to our perturbations. This demonstrates there is still both room for
improvement within current fixed-charge biomolecular force fields and
significant parameter flexibility to make these improvements. Recent research
in computational efficiency of free energy methods allows us to perform
simulations on a local cluster that previously required
large scale distributed computing, performing four times as much computational
work in approximately a tenth of the computer time as a similar study a year
ago.
Thanks
Rama
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