Temperature molecular dynamic simulation

Fig. 9.19 Schematic illustration of an energy surface. A high-temperature molecular dynamics simulation may be ah to ooercome very high energy barriers and so explore conformational space. On minimisation, the appropriate minimum energy conformation is obtained (arrcrws).

For a conformation in a relatively deep local minimum, a room temperature molecular dynamics simulation may not overcome the barrier and search other regions of conformational space in reasonable computing time. To overcome barriers, many conformational searches use elevated temperatures (600-1200 K) at constant energy. To search conformational space adequately, run simulations of 0.5-1.0 ps each at high temperature and save the molecular structures after each simulation. Alternatively, take a snapshot of a simulation at about one picosecond intervals to store the structure. Run a geometry optimization on each structure and compare structures to determine unique low-energy conformations. 

Quenched dynamics can trap structures in local minima. To prevent this problem, you can cool the system slowly to room temperature or some appropriate lower temperature. Then run room temperature molecular dynamics simulations to search for conformations that have lower energies, closer to the starting structure. Cooling a structure slowly is called simulated annealing. 

Because the cohesive energy of the fullerene Cyo is —7.29 eV/atom and that of the graphite sheet is —7.44 eV/atom, the toroidal forms (except torus C192) are energetically stable (see Fig. 5). Finite temperature molecular-dynamics simulations show that all tori (except torus Cm2) are thermodynamically stable. 

Tu, K., Tobias, D. J. and Klein M. L. (1995). Constant pressure and temperature molecular dynamics simulation of a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine bilayer, Biophys. J., 69, 2558-2562. 

In some situations we have performed finite temperature molecular dynamics simulations [50, 51] using the aforementioned model systems. On a simplistic level, molecular dynamics can be viewed as the simulation of the finite temperature motion of a system at the atomic level. This contrasts with the conventional static quantum mechanical simulations which map out the potential energy surface at the zero temperature limit. Although static calculations are extremely important in quantifying the potential energy surface of a reaction, its application can be tedious. We have used ah initio molecular dynamics simulations at elevated temperatures (between 300 K and 800 K) to more efficiently explore the potential energy surface. 

Weakliem, P. C. and Carter, E. A. Constant temperature molecular dynamics simulations of Si(100) and Ge(100) equilibrium structure and short-time behavior. Journal of Chemical Physics 96, 3240 (1992). 

The Monte Carlo calculations were performed by means of BIOSYMs Solids Docking program and the DISCOVER molecular mechanics calculations. The procedure starts with a high temperature molecular dynamics simulation of the guest molecule in vacuo. 

One very prominent development in DFT has been the coupling of electronic structure calculations (which, when the ground state is concerned, apply to zero temperature) with finite-temperature molecular dynamics simulations. The founding paper in this field was published by Carr and Parrinello in 1985 [13]. Carr and Parrinello formulate effective equations of motion for the electrons to be solved simultaneously with the classical equations of motion for the ions. The forces on the ions are calculated from first principles by use of the Hellman-Feynman theorem. An alternative to the Carr-Parrinello method is to solve the electronic structure self-consistently at every ionic time step. Both methods are referred to as ab initio molecular dynamics (AIMD) [14]. 

Figure 31. Relative Brillouin-zone-center gap frequencies for translational in-plane modes for N2 on graphite as a function of temperature the gap frequencies A = A(T)/Ao are normalized with the corresponding ground-state gap frequency Aq, and the temperature T = T/T is normalized by the melting temperature T of the Vs solid. Circles (unfilled and filled circles refer to the a and y directions of the in-plane translations, respectively) constant temperature molecular dynamics simulations, Aq = 0.30 THz, and T = 73 K. Squares inelastic neutron scattering data [192], Aq = 0.40 THz, and T = 72 K. (Adapted from Fig. 15 of Ref. 140.)...

M. Ferrario and J. P. Ryckaert, Mol. Phys., 54, 587 (1985). Constant Pressure-Constant Temperature Molecular Dynamics Simulations for Rigid and Partially Rigid Molecular Systems. 

Ceriotti, M., Bussi, G., Parrinello, M. Langevin equation with colored noise for constant-temperature molecular dynamics simulations. Phys. Rev. Lett. 102, 020,601 (2009). doi 10. 1103/PhysRevLett.l02.020601... 

Low-temperature molecular dynamics simulations of cytochrome c oxidase were used in Ref. 84 to predict an experimentally observable Mossbauer spectral width. Predicted lineshapes were used to model Lorentzian doublets, with which published cytochrome c oxidase Mossbauer spectra were simulated. Molecular dynamics-imposed... 

Two conformations at the boundaries are required to compute a trajectory with SDEL For example, to assess protein folding, the initial unfolded conformation in the trajectory can be derived from a high-temperature molecular dynamics simulation. The final folded structure in the trajectory can be taken from the protein data bank after that native configuration has been equilibrated by MD. 

Fig. 10 Theoretically simulated thermally broadened absorption spectrum of [TrpGly Ags] at 300 K compared with the experimental photofragmentation spectrum (solid curve). The black and grey lines correspond to the statistical ensembles of spectra around the most stable isomers I [Fig. 10(b)] and II (Ags additionally bound to the N-terminus), respectively, (b) Thermal ensemble of structures at 300 K obtained from constant-temperature molecular-dynamics simulations, (c) The analysis of the leading excitations between occupied and virtual Kohn-Sham orbitals participating in the intense transition at 288 tun. (d) Electron density difference between the electronically excited state and the ground state of the dominant optically allowed transition at 288 nm. Reprinted with permission from ref. 57. Copyright 2008 by the American Physical Society.

Fig. 10(a) shows the TDDFT absorption spectra of two isomers of the [TrpGly Ags] complex at room temperature. The two isomers differ in the binding sites of the protein. The spectra have been thermally broadened by performing a constant-temperature molecular-dynamics simulation and afterwards calculating the absorption spectra for a large number of snapshot structures. Thus, a good qualitative agreement has been achieved. 

The heat capacity, Cp, of an organic crystal can be subdivided into an internal part and an external part (recall Section 6.3 and the discussion around equation 6.19). The external part is the structure-sensitive part because it depends on the lattice vibrational frequencies and hence on the cry stal structure and the packing forces within the cry stal. External contributions can be estimated by lattice dynamics simulations [7], or can be derived from variable-temperature molecular dynamics simulations (recall Section 9.5 and especially equation 9.21). 

P. Ean, D. Kominos, D. B. Kitchen, R. M. Levy, and J. Baum, Chem. Phys., 158, 295 (1991). Stabilization of a-Helical Secondary Structure During High-Temperature Molecular-Dynamics Simulations of a-Lactalbumin. 

Here we describe an alternative thermostat which exactly conserves momentum in every cell and is easily incorporated into the MFC collision step. It was originally developed by Heyes for constant-temperature molecular dynamics simulations however, the original algorithm described in [42] violates detailed balance. The thermostat consists of the following procedure which is performed independently in every collision cell as part of the coUision step ... 

---