Paper Citing NAMD - Abstract
Zegarra, Fabio C.; Peralta, Gian N.; Coronado, Alberto M.; Gao, Yi Qin
Free energies and forces in helix-coil transition of homopolypeptides under stretching
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 11:4019-4024, 2009
We show here that constant velocity steered molecular dynamics (SMD) simulations of alpha-helices in a vacuum present a well defined plateau in the force-extension relationship for homopolypeptides having more than (approximately) twenty residues. With the processes being far away from equilibrium, the energies strongly depend on the stretching velocity. Importantly, for a given velocity variation, the energy variation depends also on the helix sequence. Additionally, our observations show that homopolypeptides made of ten different amino acids (Ala, Cys, Gln, Ile, Leu, Met, Phe, Ser, Thr and Val) present a linear helix-coil transition.
