Molecular dynamics solvent force

To enable an atomic interpretation of the AFM experiments, we have developed a molecular dynamics technique to simulate these experiments [49], Prom such force simulations rupture models at atomic resolution were derived and checked by comparisons of the computed rupture forces with the experimental ones. In order to facilitate such checks, the simulations have been set up to resemble the AFM experiment in as many details as possible (Fig. 4, bottom) the protein-ligand complex was simulated in atomic detail starting from the crystal structure, water solvent was included within the simulation system to account for solvation effects, the protein was held in place by keeping its center of mass fixed (so that internal motions were not hindered), the cantilever was simulated by use of a harmonic spring potential and, finally, the simulated cantilever was connected to the particular atom of the ligand, to which in the AFM experiment the linker molecule was connected. [Pg.86]

Molecular mechanics methods have been used particularly for simulating surface-liquid interactions. Molecular mechanics calculations are called effective potential function calculations in the solid-state literature. Monte Carlo methods are useful for determining what orientation the solvent will take near a surface. Molecular dynamics can be used to model surface reactions and adsorption if the force held is parameterized correctly. [Pg.319]

Focuses on force field calculations for understanding the dynamic properties of proteins and nucleic acids. Provides a useful introduction to several computational techniques, including molecular mechanics minimization and molecular dynamics. Includes discussions of research involving structural changes and short time scale dynamics of these biomolecules, and the influence of solvent in these processes. [Pg.4]

Force field calculations often truncate the non bonded potential energy of a molecular system at some finite distance. Truncation (nonbonded cutoff) saves computing resources. Also, periodic boxes and boundary conditions require it. However, this approximation is too crude for some calculations. For example, a molecular dynamic simulation with an abruptly truncated potential produces anomalous and nonphysical behavior. One symptom is that the solute (for example, a protein) cools and the solvent (water) heats rapidly. The temperatures of system components then slowly converge until the system appears to be in equilibrium, but it is not. [Pg.29]

Before running a molecular dynamics simulation with solvent and a molecular mechanics method, choose the appropriate dielectric constant. You specify the type and value of the dielectric constant in the Force Field Options dialog box. The dielectric constant defines the screening effect of solvent molecules on nonbonded (electrostatic) interactions. [Pg.84]

Including solvent in a molecular dynamics simulation creates a frictional force that damps some motion of the solute. This affects in particular the motions of exposed side chain in proteins. [Pg.85]

We have presented a simple protocol to run MD simulations for systems of interest. There are, however, some tricks to improve the efficiency and accuracy of molecular dynamics simulations. Some of these techniques, which are discussed later in the book, are today considered standard practice. These methods address diverse issues ranging from efficient force field evaluation to simplified solvent representations. [Pg.52]

The rapid rise in computer speed over recent years has led to atom-based simulations of liquid crystals becoming an important new area of research. Molecular mechanics and Monte Carlo studies of isolated liquid crystal molecules are now routine. However, care must be taken to model properly the influence of a nematic mean field if information about molecular structure in a mesophase is required. The current state-of-the-art consists of studies of (in the order of) 100 molecules in the bulk, in contact with a surface, or in a bilayer in contact with a solvent. Current simulation times can extend to around 10 ns and are sufficient to observe the growth of mesophases from an isotropic liquid. The results from a number of studies look very promising, and a wealth of structural and dynamic data now exists for bulk phases, monolayers and bilayers. Continued development of force fields for liquid crystals will be particularly important in the next few years, and particular emphasis must be placed on the development of all-atom force fields that are able to reproduce liquid phase densities for small molecules. Without these it will be difficult to obtain accurate phase transition temperatures. It will also be necessary to extend atomistic models to several thousand molecules to remove major system size effects which are present in all current work. This will be greatly facilitated by modern parallel simulation methods that allow molecular dynamics simulations to be carried out in parallel on multi-processor systems [115]. [Pg.61]

This indicates that the polarity of a medium is a long-range property that goes much further than the first solvation shell and therefore involves the two adjacent bulk media properties. This result is, however, valid for compounds the solvation of which is not determined by specific interactions with the first solvent shell, but rather by long-range forces like dipole interactions. The solvation of DEPNA was determined by molecular dynamics too and similar conclusions were drawn [82]. [Pg.147]

Hybrid MPC-MD schemes may be constructed where the mesoscopic dynamics of the bath is coupled to the molecular dynamics of solute species without introducing explicit solute-bath intermolecular forces. In such a hybrid scheme, between multiparticle collision events at times x, solute particles propagate by Newton s equations of motion in the absence of solvent forces. In order to couple solute and bath particles, the solute particles are included in the multiparticle collision step [40]. The above equations describe the dynamics provided the interaction potential is replaced by Vj(rJVs) and interactions between solute and bath particles are neglected. This type of hybrid MD-MPC dynamics also satisfies the conservation laws and preserves phase space volumes. Since bath particles can penetrate solute particles, specific structural solute-bath effects cannot be treated by this rule. However, simulations may be more efficient since the solute-solvent forces do not have to be computed. [Pg.112]

Equation (4-5) can be directly utilized in statistical mechanical Monte Carlo and molecular dynamics simulations by choosing an appropriate QM model, balancing computational efficiency and accuracy, and MM force fields for biomacromolecules and the solvent water. Our group has extensively explored various QM/MM methods using different quantum models, ranging from semiempirical methods to ab initio molecular orbital and valence bond theories to density functional theory, applied to a wide range of applications in chemistry and biology. Some of these studies have been discussed before and they are not emphasized in this article. We focus on developments that have not been often discussed. [Pg.83]

Patel S, Mackerell AD, Brooks CL (2004) CHARMM fluctuating charge force field for proteins II -Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model. J Comput Chem 25(12) 1504-1514... [Pg.260]

Table 7 compares free energies of hydration125 produced by the two types of solvent models that have been presented discrete molecular and continuum. The discrete molecular involved classical force field molecular dynamics (MD) and a free energy perturbation (FEP) technique whereby the solute molecule is annihilated to dummy atoms, so that absolute AGhydration are obtained the continuum were SCRF/PCM calculations, with Claverie-Pierotti Gcavilatlon and Floris-Tomasi Gvdw. The... [Pg.54]

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