Paper Citing NAMD - Abstract
De Fabritiis, G.; Delgado-Buscalioni, R.; Coveney, P.V.
Energy controlled insertion of polar molecules in dense fluids
JOURNAL OF CHEMICAL PHYSICS, 121:12139-12142, DEC 22 2004
We present a method to search low energy configurations of polar molecules in the complex potential energy surfaces associated with dense fluids. The search is done in the configurational space of the translational and rotational degrees of freedom of the molecule, combining steepest-descent and Newton-Raphson steps which embed information on the average sizes of the potential energy wells obtained from prior inspection of the liquid structure. We perform a molecular dynamics simulation of a liquid water shell which demonstrates that the method enables fast and energy-controlled water molecule insertion in aqueous environments. The algorithm finds low energy configurations of incoming water molecules around three orders of magnitude faster than direct random insertion. This method represents an important step towards dynamic simulations of open systems and it may also prove useful for energy-biased ensemble average calculations of the chemical potential. (C) 2004 American Institute of Physics.
