The accuracy of molecular dynamics simulations depends on the underlying force field, defined by the form and parametrization of the interparticle potential functions and the water model. The treatment of the solvent is crucial in molecular dynamics force fields, as hydrophobic interactions and hydrogen bonding are important molecular forces. The widely used CHARMM force field was originally parametrized using a modified version of the TIP3P water model (mTIP3P), including Lennard-Jones interactions between hydrogens and oxygens. The latest version, CHARMM36, was optimized using the standard TIP3P water model (sTIP3P) for proteins, while mTIP3P is still being used for lipids. Our replica exchange molecular dynamics simulations on dynamic peptides show that the CHARMM36 force field with mTIP3P water yields less realistic folding than with sTIP3P water. Analysis of the dimensions and hydrogen bonding of the unfolded state reveals that the peptides are more solvated and extended in mTIP3P, due to a higher solvation energy of the peptide in this water model. We recommend using CHARMM36 with sTIP3P when simulating peptides, folded proteins, and natively unfolded proteins, but combinations of proteins with lipids would require a reparametrization to make their water models compatible.
|Number of pages||7|
|Journal||The Journal of Physical Chemistry. B: Materials, Surfaces, Interfaces, & Biophysical|
|Publication status||Published - 21-Apr-2016|
- MOLECULAR-DYNAMICS SIMULATIONS
- BETA-HAIRPIN FORMATION
- DISORDERED PROTEINS
- HELIX FORMATION