title: An exact expression to calculate the derivatives of position-dependent observables in molecular simulations with flexible constraints.
abstract: In this work, we introduce an algorithm to compute the derivatives of physical observables along the constrained subspace when flexible constraints are imposed on the system (i.e., constraints in which the constrained coordinates are fixed to configuration-dependent values). The presented scheme is exact, it does not contain any tunable parameter, and it only requires the calculation and inversion of a sub-block of the Hessian matrix of second derivatives of the function through which the constraints are defined. We also present a practical application to the case in which the sought observables are the Euclidean coordinates of complex molecular systems, and the function whose minimization defines the flexible constraints is the potential energy. Finally, and in order to validate the method, which, as far as we are aware, is the first of its kind in the literature, we compare it to the natural and straightforward finite-differences approach in a toy system and in three molecules of biological relevance: methanol, N-methyl-acetamide and a tri-glycine peptide.
authors.affiliation: Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, Madrid, Spain. echenique.p@gmail.com
authors.forename: Pablo
authors.initials: P
authors.lastname: Echenique
authors.forename: Claudio N
authors.initials: CN
authors.lastname: Cavasotto
authors.forename: Monica
authors.initials: M
authors.lastname: De Marco
authors.forename: Pablo
authors.initials: P
authors.lastname: Garca-Risueño
authors.forename: J L
authors.initials: JL
authors.lastname: Alonso
mesh_terms: D000081:Acetamides / Q000737:chemistry*; D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D020342:Finite Element Analysis; D005998:Glycine / Q000737:chemistry*; D000432:Methanol / Q000737:chemistry*; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D015394:Molecular Structure; D009010:Monte Carlo Method; D010455:Peptides / Q000737:chemistry; D015203:Reproducibility of Results
chemical_list: D000081:Acetamides; D010455:Peptides; D005998:Glycine; C018595:N-methylacetamide; D000432:Methanol