A unified formulation of the constant temperature molecular dynamics methods

Abstract

We report a systematic study of aqueous microsolvation of CdCl 2. The optimized structures and binding energies of the CdCl 2-(H 2 O) n clusters with n = 1-24 have been computed at the B3PW91/ 6-31G** level. The solvation patterns obtained at the DFT level are verified at the MP2/AVTZ level for n < 6. Unlike HgCl 2-(H 2 O) n case, where there are at most three Hg-O w orbital interactions, Cd also establishes four equatorial orbital interactions with water for n > 6 leading to a planar square bipyramid hexacoordination around Cd. The first solvation shell is fully attained with 12 water molecules. At the same level of theory the water binding energies are much larger than those previously found for HgCl 2 due to the stronger Cd-O w interactions arising from the smaller core of Cd. For the largest system studied, CdCl 2-(H 2 O) 24 , both penta-and hexa-coordination stable patterns around Cd are found. However, Born-Opphenheimer molecular dynamics simulations starting from these optimized geometries at 700 K reveal the greater stability of the Cd-pentacoordinated species, where a CdCl 2-(H 2 O) 3 trigonal bipyramid effective solute appears. The Cd-O(water) radial distribution function shows a bimodal distribution with two maxima at 2.4 Å and 4.2 Å, revealing the different coordination spheres, even with such a small number of solvating water molecules.

Backbone additivity in the transfer model of protein solvation

“…A full equilibration of the solvent and peptide of 1 ns was carried out using 1 fs time steps for the isothermal-isobaric ensemble (NTP) with target temperature of 300 K and pressure of 1 atm, using the Nosé-Anderson method. 58,59 The conformational ensemble of each peptide in solution was characterized using two structural parameters: the radius of gyration and distance between the peptide groups. From these two structural parameters the most probable structure was determined for each peptide backbone model and a representative structure was chosen for solvation free energy calculations.…”

Polar surface effects on the thermal conductivity of ZnO nanowires: a shell-like surface reconstruction-induced preserving mechanism

“…The two regions close to the left/right ends are maintained at high/low temperatures T L/R = (1 ± α)T via a Nóse-Hoover thermostat. 48,49 T is the average temperature, and α = 0.05 is adopted in our calculation. Thermal energy is pumped into the system through the left temperature-controlled region with thermal current J L , which will flow out of the right temperature-controlled region with current J R .…”

Replica-Permutation Method with the Suwa–Todo Algorithm beyond the Replica-Exchange Method

“…To see usefulness of the Suwa-Todo algorithm for the replica-permutation method, we per- the Gaussian constraint method [4,5] to avoid the problem of non-ergodicity in the Nosé-Hoover thermostat [6][7][8] for the non-interacting particle system. The trajectory data were stored every 10.0 fs.…”

“…The SHAKE algorithm [40] was employed to constrain bond lengths with the hydrogen atoms during our simulations. The temperature was controlled by the Nosé-Hoover thermostat [6][7][8]. The time step was taken to be 1.0 fs.…”

“…The model for the water molecules was the TIP3P rigidbody model [41]. Temperature was controlled by the Nosé-Hoover thermostat [6][7][8]. The SHAKE algorithm [40] was employed to constrain bond lengths with the hydrogen atoms of C-peptide and to fix the water molecule structures during our simulations.…”