I'm using gromacs and both all atom and coarse grained forcefields are necessary.
Regards.
Hi dear Amir
I believe Tersoff and REBO or AIREBO potentials are suitable for all kind of hydrocarbons.
There is a new FF:
Journal of Molecular Modeling
February 2014, 20:2143
A new AMBER-compatible force field parameter set for alkanes
Alexei M. Nikitin, Yury V. Milchevskiy, Alexander P. Lyubartsev
Gromos53a6 has good result for lipids, taking into account the Berger et al parameters, also:
O. Berger, O. Edholm, F. Jahnig, Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant
temperature, Biophys. J. 72 (1997) 2002–2013.
For coarse grained, we have obtained good results with Martini force field.
But, I do not know which kind of compounds are yours, or as Alexey said: in which kind of property are you interested in.
I'm intrested in phase separation properties of aliphatic and aromatic mixtures. I'm using gromacs as md software.
In this case, you need a field describing the thermodynamic properties, like AMBER-ii, TraPPE, OPLS.
However, if the phase separation is in aqueous solution, none of them does not help. Perhaps then it is better to use AMBER-i. This is previous unpublished version of AMBER-ii. In it is a more realistic interaction of alkanes with water.
William Jorgensen, the author of TIP3P and OPLS, always shows in his talks a plot, where he compares benzene dimer interaction energies of the state-of-the-art quantum chemical methods. Then he points to the fact that in the course of time, the QM energies converge to the OPLS interaction energy:-)
@Abolfazl Noorjahan
OPLS-AA does not describe the interaction of alkanes with water.
Alkanes become extremely hydrophobic.
if you have the option of using commercial software try COMPASS FF. This ab initio force field was parameterized and validated using condensed-phase properties in addition to various ab initio and empirical data for molecules in isolation.
and it works reassonable well with hydrocarbons....
- Badges
- Science topic