Distance and angular holonomic constraints in molecular simulations

The Journal of Chemical Physics
David DubbeldamRandall Q Snurr

Abstract

Finding the energy minima of systems with constraints is a challenging problem. We develop a minimization method based on the projection operator technique to enforce distance and angle constraints in minimization and reaction-path dynamics. The application of the projection operator alone does not maintain the constraints, i.e., they are slightly violated. Therefore, we use the SHAKE-methodology to enforce the constraints after each minimization step. We have extended theta -SHAKE for bend angles and introduce phi-SHAKE and chi-SHAKE to constrain dihedral and out-of-plane angles, respectively. Two case studies are presented: (1) A mode analysis of united-atom n-butane with various internal degrees of freedom kept frozen and (2) the minimization of chromene at a fixed approach toward the catalytic site of a (salen)Mn. The obtained information on energetics can be used to explain why specific enantioselectivity is observed. Previous minimization methods work for the free molecular case, but fail when molecules are tightly confined.

References

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Citations

Apr 10, 2018·PloS One·Pouya Tavousi
Jan 17, 2020·The Journal of Chemical Physics·Maria Pechlaner, Wilfred F van Gunsteren
Dec 23, 2020·Journal of Computational Chemistry·Maria PechlanerWilfred F van Gunsteren
Nov 18, 2020·Journal of Chemical Theory and Computation·H Negrin-YuveroS Fernandez-Alberti

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Software Mentioned

mencoder
RATTLE
SHAKE
POVRAY

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