Restraint forces

Tor all restraints, HyperChem uses named selections that contain two, three, or four atoms each. You use Name Selection on the Selectmenn to assign nam es to groups of selected atom s. Th en you can apply named selections as restraints for a calculation in the Restraint Forces dialog box from Restraints on the Setup menu. 

Use Restraints in the Setup menu to bring up the Restraint Forces dialog box... 

These molecular dynamics restraints are stored with the IIIX file and are relained as long as ihe Named Seleclions are slill active (structural changes not made to molecular systemli or the restraints are still rec iiested via the Restraint Forces dialog box. 

You can restrain atoms during molecular mechanics or quantum mechanics calculations. Choosing restraints, via the Restraint Forces dialog box, applies additional harmonic forces—which you specify, to interatomic distances, angles, or dihedrals that you have set up as named selections. 

Newtonian dynamics step that lead to new atomic positions r,(t + Af forces are calculated from the previous and next value for X, F,(f X i) and F,(r and used to make a time step At. For these additional steps, SHAKE corrections to the coordinates Ar,(t + At X i) and Ar,(t + At X +,) are evaluated and used to determine the restraint forces,... 

PMF) converges here the PMF is the line integral of the restraint force along... 

The problems that occur when one tries to estimate affinity in terms of component terms do not arise when perturbation methods are used with simulations in order to compute potentials of mean force or free energies for molecular transformations simulations use a simple physical force field and thereby implicitly include all component terms discussed earlier. We have used the molecular transformation approach to compute binding affinities from these first principles [14]. The basic approach had been introduced in early work, in which we studied the affinity of xenon for myoglobin [11]. The procedure was to gradually decrease the interactions between xenon atom and protein, and compute the free energy change by standard perturbation methods, cf. (10). An (issential component is to impose a restraint on the... 

In our implementation of SMD, modified versions of VMD and Sigma communicate with each other using a customized, lightweight protocol. Sigma sends atomic positions resulting from each molecular dynamics time step to VMD for display. When the user specifies restraints on parts of the displayed model, VMD sends them to Sigma, where they are converted into potential-well restraints added to the force field [21]. 

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. 

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. ... 

In a related way, ensemble molecular dynamics derives a pharmacophore using restrained molecular dynamics for a collection of molecules. A force field model is set up so that none of the atoms in each molecule sees the atoms in ainy other molecule. This enables the molecules to be overlaid in space. A restraint term is included in the potential, which forces the appropriate atoms or functional groups to be overlaid in space. 

Restraints add potential terms to a force field calculation, favoring the value that you specify in a restraint. The larger the value of the h arm on ic force con stan t, th e m ore tigh tly th e calculation restrain s the value. 

When using NOE signals as restraints, choose the distance between the nonbonded atoms. A typical distance is about 4 to 5 Angstroms. Atypical force constant is 0.5 to 5.0 kcal/A, depending on the flexibility of the rest of the molecule and the strength of the NOE signal. 

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