Simulation Protocols

How can we apply molecular dynamics simulations practically. This section gives a brief outline of a typical MD scenario. Imagine that you are interested in the response of a protein to changes in the amino add sequence, i.e., to point mutations. In this case, it is appropriate to divide the analysis into a static and a dynamic part. What we need first is a reference system, because it is advisable to base the interpretation of the calculated data on changes compared with other simulations. By taking this relative point of view, one hopes that possible errors introduced due to the assumptions and simplifications within the potential energy function may cancel out. All kinds of simulations, analyses, etc., should always be carried out for the reference and the model systems, applying the same simulation protocols. 

D. Simulation Protocol and Some Tricks for Better Simulations... 

Every molecular dynamics simulation consists of several steps. Put together, these steps are called a simulation protocol. The main steps common to most dynamic simulation protocols are the following. 

Although the formulation of GSBP is self-consistent, the validity of the approach depends on many factors especially the size of the inner region and the choice of the dielectric constant for the outer region. Therefore, for any specific application, the simulation protocol has to be carefully tested using relevant benchmarks such as pKa of key residues (see examples below in Sections 7.3.1 and 7.3.2). 

In this section, we use examples to illustrate several key issues that may significantly impact the reliability of QM/MM simulations of biological systems. In addition, we also discuss calculations that are useful for validating the simulation protocols in realistic applications. 

Although water structure and sidechain flexibilities are useful gauges for the simulation protocol, more quantitative measures are needed for reliable QM/MM simulations of enzyme systems. In this regards, we have found that reduction potential [78] and pKa [73,91] calculations are particularly useful benchmark calculations because the results are likely very sensitive to the simulation details. 

Whilst this Chapter is primarily concerned with the methods of determining the free energies of tautomeric or ionisation equilibria via computer simulation of free energy differences, many of the issues raised relate also to the determination of other molecular properties upon which behaviour of the molecule within the body may depend, such as the redox potential or the partition coefficient.6 In the next section, we shall give a brief explanation of the methods used to calculate these free energy differences -namely the use of a thermodynamic cycle in conjunction with ab initio and free energy perturbation (FEP) methods. This enables an explicit representation of the solvent environment to be used. In depth descriptions of the various simulation protocols, or the accuracy limiting factors of the simulations and methods of validation, have not been included. These are... 

This simulation protocol was employed to study the slippage processes associated with R equal to H, Me, Et and i-Pr. In all cases, the resulting energy profiles displayed two energy barriers. The first of... 

A third simulation protocol for determining Helmholtz free-energy differences can be illustrated from further manipulation of Eq. (12.19). Thus we may write... 

This approach was later extended to off-lattice models and a more detailed description of the transfer energy of the different amino acid residues [77]. Magainin, melit-tin, and several other amphipathic peptides were simulated. In these simulations, differences in the interaction of the peptides with the lipid phase were observed. For example, magainin only showed adsorption onto the lipid and no crossing of the lipid occurred, whereas melittin crossed the lipid and formed a stable transmembrane helix. These results are in full agreement with later studies reported by other research groups presented below, involving more elaborate simulation protocols and representations of the peptides and the lipid. These examples show the potential of computer simulations even when some simplifications have to be made to make the system computationally tractable. 

The subsections above have presented the details of QMSTAT and described how they fit together. In this subsection the parametrization of the intermolecular potential is described and a typical simulation protocol is given. 

This method of refinement was first applied, using the distance restraint form of Eq. [9], to the lac repressor headpiece using a model as the initial structure.9-83 It was later applied to a heptadecapeptide.84 Subsequent studies with model data showed that, with a carefully chosen simulation protocol, the method was capable of refining even poor starting structures.85 86... 

Since this early work, experience has accumulated with restrained MD and some points can be made with respect to the effects of restrained MD and simulation protocol. First, if the starting structures have already been very highly refined with respect to distances, and if the distance restraints are very numerous and accurate, then the restrained MD protocol will not make much difference. If the starting structures are less well refined or the restraints less numerous, then restrained MD will be important, as will the choice of protocol. 

In order to test the hypothesis that efficient promoter sequences will be more likely to acquire an A-DNA like conformation than other sequences, we carried out a collection of molecular dynamics simulations of the DNA double stranded dodecamers listed in Table 3. All these simulations were done with the CHARMM23 potential [93], in the presence of explicit solvent (-3500 TIP3 [99] water molecules) and 22 sodium ions (the simulation protocol is detailed in [89,100,101]). The DNA sequences were chosen to include known functional promoters (MLP, MLP2, AT, E4, 6T, CYCl, EFIA, and R28), nonfunctional promoters which could function with a mutant TBP (2C and 7G) [69,70], an inosine variant which can promote transcription (I) [102], and negative controls (GC, POLYA). This collection of sequences also includes two pairs of TATA boxes located in different contexts (MLP and MLP2, and AT and E4) in order to explore the sensitivity of the results to end effects. All the simulations started from a canonical B-DNA conformation and relaxed into a structure closer to A-DNA after 2 ns of simulation, not all the sequences achieved the same structure, as shown in Table 3, an indication that the simulation protocol is capable of identifying sequence dependent features. 

A typical MD simulation protocol consists of the following steps (1) assign the initial values to the atomic coordinates and velocities (2) integrate the equations of motion (this is the heart of the MD method) and (3) analyze the results of the simulation. These steps are discussed below in relation to zeolite modeling. 

First, it was necessary to establish a robust simulation protocol for reproducible freezing of neat water in contact with a patch of ice. The results can be summarized as follows. In previous studies of the ice/water coexistence rather short simulation times were used (up to 2 Our simulations show, however, that hundreds of nanoseconds are... 

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