[Dynamic attractor for the Berendsen thermostat an the slow dynamics of biomacromolecules].
It was shown that the nonlinear relaxation of a model system confined to the Berendsen's thermostat is determined by an attractor regime. The latter does not correspond generally to the true thermodynamic state of the system. Therefore, the use of the Berendsen's thermostat for molecular dynamics simulations, even in the case of large protein molecules at trajectory lengths of more than 10 ns, can lead to wrong conclusions. Our results agree with the concept of slow dynamics for macroscopic systems considered within the framework of the topological approach to stochastic dynamics.
Golo
V L
VL
Lomonosov Moscow State University, Vorob'evy Gory, Moscow, 119899 Russia.
Shaĭtan
K V
KV
D001704:Biopolymers / Q000737:chemistry*; D008954:Models, Biological; D008967:Molecular Biology / Q000379:methods; D013816:Thermodynamics
D001704:Biopolymers