Restrainers

The choice of the vector d is preponderant for the exploitation of co-occurrence matrix. For each image f several matrix can be calculated, it is imperative to restrain the analysis to significant matrix. 

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 ... 

Dock two different m o lecu Ics by restraining in term o Iccu lar (in Icratom icf distan ces. 

Restrain ts add poten lial term s to a force field calcu lalion. ravoriu g ih c value ih at you sped fy in a restrain i. Th e larger th e value of the harm on ic force con stan t. th c m ore tigh tly th e calculation restrain s th c value. 

Caution Restrain ts may sign ificantly affect the property yon are observing. When using restrain is, ch cck th eir effects on measured values. 

When using XOH signals as restrain ts, choose the distance between the nonbonded atoms. A typical distance is about 4 to 5 Angstroms. A typical force constant is 0..5 to. 5.0 kcal/A-, depending on the flexibdity ofthe rest of the molecule and the strength of the NOE signal. 

You usually rern ove restrain ts diirin g th e final ph ases of m olccti lar dynamics situ tilatious and gcom etry optimizations. 

Example If a drug molecule interacts with a receptor molecule through hydrogen bonds, then yon might restrain the distance between the donor and acceptor atoms involved in the hydrogen bonds. During a molecular dynamics simulation, these atoms would slay near an ideal value, while the rest of the molecular system fully relaxes. 

Example Molecular dynamics simulations of selected portions of proteins can demonstrate the motion of an amino acid sequence while fixing the terminal residues. These simulations can probe the motion of an alpha helix, keeping the ends restrained, as occurs n atiirally m transmembrane proteins. You can also investigate the conformations of loops with fixed endpoints. 

The UyperChem Reference manual and Genius Sianed discuss the sec neiice of steps to perform a molecular mechanics calculation. These steps in elude choosing a force field, force field option s, and possible restrain is. 

You can restrain atom s dur ing m olecu lar m ecli an ics or quart tu in mceh an ies calculation s, Cli oosiri g restrain ts, via the Restrain t Horces dialog box, applies additional h arm on ie forces which you specify, to in teratorn re distari CCS, an gles, or dihedrals that you have set up as named selections. 

Note Restraints apply to distances, angles and dihedrals between bonded ornon bonded atoms. Yon can also restrain atoms to points in space. 

You need to specify two parameters the et uilibrium value ofthe internal coordinate and the force constant for the harmonic poten tial, T h e equilibrium restraint value deperi ds on the reason you choosea restraint. If, for example, you would like a particular bond length to remain constant during a simulation, then the equ ilibritirn restrain t value would probably be Lh e initial len gth of the bond. If you wan t to force an internal coordinate to a new value, the equilibrium internal coordinate is the new value. 

Recommended values for the force constant are 7.0 kcal/mol A-for an in teratorn ic distari cc. 12,5 kcal/rn ol degree- for an angle, and 16.0 kcal/mol degree- for a dihedral angle. Use the recommended values and then, if the internal coordinate is not sufficiently restrained, try a larger force eonstant. 

See f. sin g Geometric Restrain is" on page HI for exam pies of using restrain ts. 

A restrain t (not to be confused with a Model Builder constraint) is a nser-specified one-atom tether, two-atom stretch, three-atom bend, or four-atom torsional interaction to add to the list ol molec-11 lar mechanics m teraction s computed for a molecule. These added iiueraciious are treated no differently IVoin any other stretch, bend, or torsion, except that they employ a quadratic functional form. They replace no in teraction, on ly add to the computed in teraction s. 

I lie default restraints are appropriate for molcciilar dyriam ics calculations where larger force constants would create undesirable h igh frequency motion s hut much larger force con slants may be desired for restrained geometry oplim i/ation. ... 

HyperChern docs not nse con strained oplirn izatiori bnt it is possible Lo restrain m olecular in ech an ics and i]tiarituin median ics cal-cti latiori s hy adding extra restraining forces. 

The first molecular dynamics simulations of a lipid bilayer which used an explicit representation of all the molecules was performed by van der Ploeg and Berendsen in 1982 [van dei Ploeg and Berendsen 1982]. Their simulation contained 32 decanoate molecules arranged in two layers of sixteen molecules each. Periodic boundary conditions were employed and a xmited atom force potential was used to model the interactions. The head groups were restrained using a harmonic potential of the form ... 

Solving Protein Structures Using Restrained Molecular Dynamics and Simulated Annealing... 

A particularly important application of molecular dynamics, often in conjunction with the simulated annealing method, is in the refinement of X-ray and NMR data to determine the three-dimensional structures of large biological molecules such as proteins. The aim of such refinement is to determine the conformation (or conformations) that best explain the experimental data. A modified form of molecular dynamics called restrained moleculai dynarrdcs is usually used in which additional terms, called penalty functions, are added tc the potential energy function. These extra terms have the effect of penalising conformations... 

The additional penalty function that is added to the empirical potential energy function in restrained dynamics X-ray refinement has the form ... 

Fig. 9.24 A restraining potential that does not penalise struetures in which the distance lies between the leaver and upper distances di and and uses harmonie functions outside this range (left). The harmonic potentials may also he replaeed by linear restraints further from this region (right).

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