An exact expression to calculate the derivatives of position-dependent observables in molecular simulations with flexible constraints

Details An exact expression to calculate the derivatives of position-dependent observables in molecular simulations with flexible constraints An exact expression to calculate the derivatives of position-dependent observables in molecular simulations with flexible constraints

2010-06-24

arxiv.org/abs/1006.4847v3

PLoS one 6 (2011) e24563

Physics

Computational Physics

13 pages, 8 figures, published version

Scientific paper

10.1371/journal.pone.0024563

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 hard 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 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 three molecules of biological relevance: methanol, N-methyl-acetamide and a tri-glycine peptide

Affiliated with

Also associated with

No associations

Rating

An exact expression to calculate the derivatives of position-dependent observables in molecular simulations with flexible constraints does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.

If you have personal experience with An exact expression to calculate the derivatives of position-dependent observables in molecular simulations with flexible constraints, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and An exact expression to calculate the derivatives of position-dependent observables in molecular simulations with flexible constraints will most certainly appreciate the feedback.

Rate now

Comments { 0 }

Profile ID: LFWR-SCP-O-676508