CHARMM potential, vibrational energy

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 Vibrational analysis has been extended via addition of the MOLVIB module (K. Kuczera and J. Wiorkiewicz-Kuczera, unpublished), which allows for the determination of potential energy distributions and the analysis of lattice modes in combination with the CRYSTAL facility.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. 

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