Structural and dynamic properties of the CAGQW peptide in water: A molecular dynamics simulation study using different force fields

In this paper, the structural and dynamic properties of the peptide with the sequence CAGQW have been extensively investigated using molecular dynamics simulations. Several simulations for a total simulation time of > 1.5 mus were performed using the GROMOS96 and OPLS-AA/L force fields. The effects of simulation protocols and force fields on the structural and dynamic properties of the peptide have been analyzed. Accounting for long range electrostatic interactions using the particle mesh Ewald method resulted in a tendency to slow the end-to-end contact formations. In contrast to the relatively modest effect of the simulation protocol, the force field had a larger influence on the properties of the peptide. Use of GROMOS96 resulted in a faster end-to-end contact formation kinetics than using OPLS-AA/L. The ratio of maximum lifetime values, obtained from GROMOS96 (16 ns) and OPLS-AA/L (24 ns) force fields (accounting for the difference between the experimental and calculated solvent viscosity) vs the experimental lifetime (73 ns) resulted in 4.6 and 3.0 times faster kinetics, respectively. This faster encounter kinetics can be related to the free energy profile versus end-to-end distance which indicates a stronger preference for small end-to-end distance states in the case of GROMOS96 compared to other force fields. Furthermore, the comparison with results obtained on the same peptide by Yeb and Hummer (J. Am. Chem. Soc. 2002, 124, 6563-6568) using AMBER94 and CHARMM22 force fields indicates the following order for the end-to-end contact formation kinetics: GROMOS96 > OPLS-AA/L > AMBER94 greater than or equal to CHARMM22.