Designing generalized statistical ensembles for numerical simulations of biopolymers.
Conformational properties of polymers, such as average dihedral angles or molecular alpha-helicity, display a rather weak dependence on the detailed arrangement of the elementary constituents (atoms). We propose a computer simulation method to explore the polymer phase space using a variant of the standard multicanonical method, in which the density of states associated to suitably chosen configurational variables is considered in place of the standard energy density of states. This configurational density of states is used in the Metropolis acceptance/rejection test when configurations are generated with the help of a hybrid Monte Carlo algorithm. The resulting configurational probability distribution is then modulated by exponential factors derived from the general principle of the maximal constrained entropy by requiring that certain average configurational quantities take preassigned (possibly temperature dependent) values. Thermal averages of other configurational quantities can be computed by using the probability distributions obtained in this way. Moments of the energy distribution require an extra canonical sampling of the system phase space at the desired temperature, in order to locally thermalize the configurational degrees of freedom. As an application of these ideas we present the study of the structural properties of two simple models: a bead-and-spring model of polyethylene with independent hindered torsions and an all-atom model of alanine and glycine oligomers with 12 amino acids in vacuum.
La Penna
Giovanni
G
Consiglio Nazionale delle Ricerche, Istituto per lo Studio delle Macromolecole (ISMac), Section of Genoa, Via De Marini 6, 16149 Genoa, Italy. lapenna@ge.ismac.cnr.it.
Morante
Silvia
S
Perico
Angelo
A
Rossi
Gian Carlo
GC
D001704:Biopolymers / Q000737:chemistry*; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D046912:Multiprotein Complexes / Q000737:chemistry
D001704:Biopolymers; D046912:Multiprotein Complexes