Adding Restraints

Name any one-atom, two-atom, three-atom, or four-atom selection with the Select/Select command. 

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

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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]. 

Eollowing the computational protocol of Czerminski and Elber [39,40] a number of restraints and constraints are added to (1) encourage the mean-square distances between adjacent structures to be approximately constant. 

By adding a restraint which is projected exclusively along the reaction coordinate, we can ensure that all the newly added images will be evenly spaced. This restraint is defined as a linear combination of the distances between the atoms involved in the reaction, and is given by... 

In another study with desipramine, Agras et al. (1992) studied the effect of the drug, of individual CBT, and of the combination of the two and again found CBT to be superior to drug therapy alone, with no added benefit from using the combination to effect eating disorder symptoms. There was some evidence that the combination was superior for dietary restraint thinking. 

In order to map against an internal coordinate it is necessary to be able to set that coordinate to a particular value. This can be done by constraints or restraints (see Chapter 3, Section 3.3). Constraints are only available when using second-derivative methods and are imposed by adding extra columns and rows to the matrices. Conse-... 

The conformational behavior of Aim inserted in a POPC bilayer has been investigated using the same system as described above [87]. To insert the Aim molecule, a hole was introduced by restraints and one POPC molecule was removed. The Aim was placed into the bilayer, the system was hydrated, and one sodium ion added. A second simulation was performed in which no sodium ion was added and Glu18 was protonated instead. During the simulation period of 1000 ps, the Aim molecule remained in its a-helical conformation, showing only small fluctuations in the root mean square distance (RMSD) of the Ca atoms underlining its conformational stabilization by the lipid bilayer. 

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