"The "Hot-Solvent/Cold-Solute" Problem Revisited"Martin Lingenheil, Robert Denschlag, Rudolf Reichold, and Paul Tavan
J. Chem. Theory Comput. 4, 1293-1306 (2008)
The temperature steers the equilibrium and non-equilibrium conformational dynamics of macromolecules in solution. Therefore, corresponding molecular dynamics simulations require a strategy for temperature control which should guarantee that the experimental statistical ensemble is also sampled in silico. Several algorithms for temperature control have been proposed. All these thermostats interfere with the macromolecule's "natural" dynamics as given by the Newtonian mechanics. Furthermore, using a single thermostat for an inhomogeneous solute-solvent system can lead to stationary temperature gradients. To avoid this "hot solvent/cold solute" problem, two separate thermostats are frequently applied, one to the solute and one to the solvent. However, such a separate temperature control will perturb the dynamics of the macromolecule much more strongly than a global one and, therefore, can introduce large artifacts into its conformational dynamics. Based on the concept that an explicit solvent environment represents an ideal thermostat concerning the magnitude and time correlation of temperature fluctuations of the solute, we propose a temperature control strategy that, on the one hand, provides a homogeneous temperature distribution throughout the system together with the correct statistical ensemble for the solute molecule while, on the other hand, minimally perturbing its dynamics.
BMO authors (in alphabetic order):
Computation of structure, electrostatics, and conformational dynamics of PrPC induced by binding of Cu(II)
Photoswitchable model peptides and their conformational dynamics