Optimization molecular dynamics

There are three steps in carrying out any quantum mechanical calculation in HyperChem. First, prepare a molecule with an appropriate starting geometry. Second, choose a calculation method and its associated (Setup menu) options. Third, choose the type of calculation (single point, geometry optimization, molecular dynamics, Langevin dynamics, Monte Carlo, or vibrational analysis) with the relevant (Compute menu) options. 

Single-point, geometry optimization, molecular dynamics and vibration calculations are all available with either ab initio or semi-empirical SCFmethods. After obtaining a wavefunction via any of... 

Note You cannot use the Extended Hiickel method or any one of the SCFmethods with the Cl option being turned on for geometry optimizations, molecular dynamics simulations or vibrational calculations, in the current version of HyperChem. 

Once you have calculated an ab initio or a semi-empirical wave function via a single point calculation, geometry optimization, molecular dynamics or vibrations, you can plot the electrostatic potential surrounding the molecule, the total electronic density, the spin density, one or more molecular orbitals /i, and the electron densities of individual orbitals You can examine orbital energies and select orbitals for plotting from an orbital energy level diagram. 

Molecular modeling and computer simulation with empirical potential energy function (force field) are now routinely carried out to help understand and predict structures and dynamics of proteins and other macromolecules of biological relevance in water and membrane environments. After over 40 years of development, popular force fields such as AMBER, CHARMM, OPLS and GROMOS have been widely employed in biomolecular simulations. These force fields are used dominantly in highly optimized molecular dynamics... 

Prediction via Novel Solution Approach (Global Optimization Molecular Dynamics)... 

Yan Y J, Gillilan R E, Whitnell R M, Wilson K R and Mukamel S 1993 Optimal control of molecular dynamics -Liouville space theory J. Chem. Phys. 97 2320... 

PAW is a recent addition to the all-electron electronic structure methods whose accuracy appears to be similar to that of the general potential LAPW approach. The implementation of the molecular dynamics fonnalism enables easy stmcture optimization in this method. 

Since 5 is a function of all the intermediate coordinates, a large scale optimization problem is to be expected. For illustration purposes consider a molecular system of 100 degrees of freedom. To account for 1000 time points we need to optimize 5 as a function of 100,000 independent variables ( ). As a result, the use of a large time step is not only a computational benefit but is also a necessity for the proposed approach. The use of a small time step to obtain a trajectory with accuracy comparable to that of Molecular Dynamics is not practical for systems with more than a few degrees of freedom. Fbr small time steps, ordinary solution of classical trajectories is the method of choice. 

To compute the above expression, short molecular dynamics runs (with a small time step) are calculated and serve as exact trajectories. Using the exact trajectory as an initial guess for path optimization (with a large time step) we optimize a discrete Onsager-Machlup path. The variation of the action with respect to the optimal trajectory is computed and used in the above formula. 

D. W. Noid, B. G. Sumpter, B. Wunderlich and G. A. Pfeffer, Molecular dynamics simulations of polymers Methods for optimal Fortran programming , J. Comput. Chem., 11(2), 236-241, 1990. 

A molecular dynamics simulation nsnally starts with a molecular structure refined by geometry optimization, but wnthont atomic velocities. To completely describe the dynamics of a classical system con lain in g X atom s, yon m nsl define 6N variables. These correspond to ilX geometric coordinates (x, y, and /) and iSX variables for the velocities of each atom in the x, y, and /. directions. 

You can include geometric restraints—for interatomic distances, bond angles, and torsion angles—in any molecular dynamics calculation or geometry optim i/.ation. Here are some applications of restrain ts ... 

Tiiinpiiraiiii (3 is handled the sanii way in Langavin dynamics as it iisin molecular dynamics. High tern peraLurc runs m ay he n sed to overcome poten lial cnergy barriers. Cooling a system to a low tern -peratnre in steps may result in a different stable conformation than would be round by direct geometry optimization. 

IlyperChem provides three types ofpotential energy surface sampling algorithms. These are found m the IlyperChem Compute menu Single Point, Ceometry Optimization, and Molecular Dynamics. 

The heating phase is used to take a molecular system smoothly from lower tern peratiires, indicative of a static initial (possibly optim i/ed ) structure, to th e temperature T at which it is desired to perform the molecular dynamics simulation. The run phase then consLitn tes a sim n lation at tern peratnre T. If th e heating h as been done carefully, it may be possible to skip the equilibration phase... 

The Merck molecular force field (MMFF) is one of the more recently published force fields in the literature. It is a general-purpose method, particularly popular for organic molecules. MMFF94 was originally intended for molecular dynamics simulations, but has also seen much use for geometry optimization. It uses five valence terms, one of which is an electrostatic term, and one cross tenn. 

Model optimization is a further refinement of the secondary and tertiary structure. At a minimum, a molecular mechanics energy minimization is done. Often, molecular dynamics or simulated annealing are used. These are frequently chosen to search the region of conformational space relatively close to the starting structure. For marginal cases, this step is very important and larger simulations should be run. 

To calculate the properties of a molecule, you need to generate a well-defined structure. A calculation often requires a structure that represents a minimum on a potential energy surface. HyperChem contains several geometry optimizers to do this. You can then calculate single point properties of a molecule or use the optimized structure as a starting point for subsequent calculations, such as molecular dynamics simulations. 

There are three types of calculations in HyperChem single point, geometry optimization or minimization, and molecular dynamics. 

---