| J.P. Ryckaert. Molecular Physics, 55:549--556, 1985. |
....the bond terms are substantially larger than those for angles or dihedrals [9] Although we seek to simulate the long term conformational changes of a molecule, not the rapid vibrations of the bonds, the fast bond components necessitate very short timesteps in the numerical integration. Following [10] we impose algebraic constraint equations g ff (q) 1 2 (jq i Gamma q j j 2 Gamma L ff 2 ) 0 that freeze the bond lengths, thereby removing the associated rapid vibrational modes. Thus we are concerned with efficient numerical discretization of the equations of motion (1) subject to m ....
J.P. Ryckaert. Molecular Physics, 55:549--556, 1985.
....number of rigid constraints which have to be taken into account when solving the equations of motion. The simplest form of constraint is that of a rigid bond between neighbouring atoms which, as mentioned already, is an alternative to the flexible bond model. However, other more complicated forms [38, 66] can involve more than two atoms. A particular example is the special constraints required to freeze all the degrees of freedom of hydrogen molecules in a CH 2 group [38] For a X CH 2 Y group, holding the mid point of the H H vector on the bisector of the X C Y bending angle and maintaining the ....
J.-P. Ryckaert, Molecular Physics 55 (1985) 549-556.
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