MacroModel Reference Manual - ISP

Chapter 4: Operation Codesarg3 Symmetry number (default = 1)arg4Control over automatic mode elimination0 Automatically skip the first 6 vibrarional modes when calculating the vibrationalcontributions.< 0 Do not automatically skip the first 6 vibrational modes. This value should be used ifthe system consists of frozen atoms plus unrestrainted atoms.arg5 Temperature (K) (default = 300.0)arg6 Volume (liters) (default = 1.0)This parameter defines the standard state (1 molar by default) for translationalentropy calculations. Use of 22.4 gives a standard state corresponding to 1 atmosphereof pressure.arg7Lower limit for frequency reportingLowest vibrational frequency considered to be a real vibrational mode (default 2.0cm –1 ). The six lowest frequencies are always skipped regardless of this setting.SDLP — SaDdLe Point searchThis is an implementation of mode-following saddle point search. For a detailed discussion ofthis topic, see Culot et al. [25]. This is the algorithm that initiated the development of the LMCSconformational search procedure. The basic idea of mode-following is to move uphill on thepotential energy surface along a ravine starting at a minimum, toward a saddle point. Themathematical definition of a ravine is the so-called minimum energy path along which onedegree of freedom is maximized while all the remaining degrees of freedom are minimized.The algorithmic implementation of mode-following is based on a coordinate transformationapplied to the FMNR (MINI command, arg1=4) algorithm.It can be shown that in a local coordinate system defined by the eigenvectors of the currentHessian during FMNR optimization, FMNR maximizes the energy along the eigenvectors withnegative eigenvalues and minimizes the energy along the eigenvectors with positive eigenvalues.Mode-following is initiated by a short move along a selected low mode of the Hessianof a minimum-energy conformation. At the new point (slightly higher than the minimumenergy point) the Hessian is reevaluated and its eigenvectors are calculated. The eigenvectorwhich is most similar to the starting low-mode eigenvector, i.e., which has the largest overlapwith it, is selected as the degree of freedom to be maximized.MacroModel 9.7 Reference Manual 61