Dynamical simulated annealing,

Modeling in NMR Structure Determination B. Molecular Dynamics Simulated Annealing... 

MI Sutcliffe, CM Dobson, RE Oswald. Solution structure of neuronal bungarotoxm determined by two-dimensional NMR spectroscopy Calculation of tertiary structure using systematic homologous model building, dynamical simulated annealing, and restrained molecular dynamics. Biochemistry 31 2962-2970, 1992. 

The structural modeling of PG and PLV with the anti-parallel p-sheet form is carried out by the hybrid distance geometry-dynamic simulated annealing method115 as contained in the X-PLOR 3.1 program.116 For structural calculations, the proton-proton distance restraints and the torsion angle restraints ( =—139° and v /=135°) are derived from reference data by Wiithrich et al.ni Hydrogen-bond distance restraints are used for the N and atoms (2.7-3.3 A) in the secondary structure.118 120 The reference data of intra- and intermolecular proton-proton distances are shown in Fig. 19. 

This was achieved using dynamic simulated annealing , which is a technique in molecular dynamics, and combining it with DFT theory the resulting dynamical equations being solved simultaneously rather than sequentially. 

M. Nilges, G. M. Clore, and A. M. Gronenborn, FEBS Lett., 239, 129 (1988). Determination of Three-Dimensional Structures of Proteins from Interproton Distance Data by Dynamical Simulated Annealing from a Random Array of Atoms. 

PJ.M. Folkers, G. M. Clore, P.C. Driscoll, Solution structure of recombinant hirudin and the Lys-47 glu mutant a nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing study. Biochemistry, 28 (1989) 2601. 

J. Hafner, M.C. Payne, A dynamical simulated annealing approach to the electronic structure of liquid metals. Journal of Physics, 2 (1990) 221. 

Dynamical simulated annealing (DSA)177 is a variant of restrained molecular dynamics (RMD).178 There are numerous programs available for performing molecular dynamics (MD) simulations, including GROMOS,178 AMBER,179 CHARMM,180 X-PLOR/CNS,181 and OPLS.182 In MD simulations, Newton s equations of motion are solved for all atoms under the influence of a physical force field ( physical), which for a protein has the form183... 

Lee, S.Y., Lee, J.H., Chang, H.J., Cho, J.M., Jung, J.W., and Lee, W. (1999). Solution structure of a sweet protein single-chain monellin determined by nuclear magnetic resonance and dynamical simulated annealing calculations. Biochemistry 38, 2340-2346. 

The two most eommonly nsed methods in the literatnre for stndying flexible ligands sueh as AA and AEA have been the Monte Carlo and molecnlar dynamics (MD) techniques. In their Monte Carlo study, Rabinovich and Ripatti (Rabinovich and Ripatti, 1991) foimd that polyimsaturated fatty acids whose double bonds are separated by one methylene carbon assume an extended (angle-iron) conformation when all molecnles are efficiently packed below the phase-transition temperature. MD or molecular dynamics/simulated annealing (MD/SA) studies (in vacuo) of AA (9) and of other polyimsaturated fatty acids related to AA have been published by several groups... 

An ingenious method of extending the molecular dynamics approach when incorporating quantum mechanics, is given by the scheme of Car and Parri-nello [255]. Their method combines classical MD with parameter-free quantum mechanics to result in an ab initio molecular dynamics method, sometimes also called dynamical simulated annealing. In this approach, the nuclei are treated as classical objects (the Bom-Oppenheimer approximation is still valid) but the electrons are understood from density-functional theory. As we have seen already, the interactions between the electrons and the nuclei can be described satisfactorily by pseudopotentials (see Section 2.15.2), together with plane-wave basis sets, supercells (see Section 2.18), and periodic boundary conditions. 

It is possible to use an alternative approach, regarding the minimization of the functional as an optimization problem, which can be solved by means of the simulated annealing procedure. A simulated annealing technique based on MD can be efficiently applied to minimize the KS functional the resulting technique, called dynamical simulated annealing allows the study of finite temperature properties. 

In the dynamical simulated annealing, the Rj, ot and parameters can be considered as dependent on time then the Lagrangian is introduced, i.e. ... 

Holalt TA, Engstrom A, Kraulis PJ, Lindberg G, Bennich H. Jones TA. Gronenbom AM. Clore GM. The solution conformation of the antibacterial peptide cecropin A A nuclear magnetic resonance and dynamical simulated annealing study. Biochem 1988 27 7620-7629. 

Figure 1. Low energy structure of Si4s as determined by AIMD simulations with dynamical simulated annealing. ...

A successful example in this respect is the small organolithium compound Li2C2H2. Static quantum chemical calculations show that the PES of the singlet state is characterized by a plethora of about 20 stationary points. Dynamical simulated annealing runs with AIMD result unequivocally in the surprising groxind state structure shown in Figure 2. ... 

Figure 2. Ground state structure of singlet Li2C2H2 determined in dynamical simulated annealing runs. " ...

Osguthorpe [141] employed a continuous model and molecular dynamics simulated annealing. In spite of the use of a quite detailed model (main chain united atoms and up to three united atoms per residue), its very flexible chain geometry enabled efficient sampling. The potentials were derived from the statistics of known protein stmctures. The method enabled us to obtain correct predictions of substantial fractions of the stmcture of the attempted targets, and for one of the difficult targets, the prediction resulting from this method was the most accurate. 

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