Vibration Fixing field problems

Minimization and vibrational analysis are useful for the determination of force field parameters, system preparation, and the study of many problems of biological interest. A new optimizer based on a truncated Newton method (TNPACK) that is effective for large molecules has been added to CHARMM. All minimizers, excluding TNPACK, support the use of holonomic constraints on selected bonds and angles (SHAKE). Vibrational analysis has been extended via addition of the MOLVIB module (K. Kuczera and J. Wiorkiewicz-Kuczera, unpublished), which allows for the determination of potential energy distributions and the analysis of lattice modes in combination with the CRYSTAL facility. Minimizations may also be performed in the presence of a variety of structural constraints. This allows for atomic positions, internal coordinates, interatomic distances, etc. to be fixed or constrained to specified values. Such constraint methods may be used in molecular dynamics simulations. 

Historically, determination of the bond contribution has not been a problem for MC simulations. That i.s in part because in MC, unlike MD, bonds do not vibrate unless their flexibility is explicitly built in as part of an allowable move. No correction is required to keep bond lengths fixed. In such a case, there is no ambiguity about the fact that the bond lengths are a X-dependent parameter of the force field. The most commonly used MC simulation package for free energy calculations has properly addressed this issue since it was developed. 

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