SAMPLING OF MOLECULAR-CONFORMATIONS BY MOLECULAR-DYNAMICS TECHNIQUES

In this paper we compare two different sampling methods for probing the distribution of conformations of a flexible molecule. The first method makes use of a form of umbrella sampling which effectively enhances the crossing of energy barriers. The second method, the so-called blue moon ensemble, is based on the use of an holonomic constraint which fixes the reaction coordinate. We apply these methods to the evaluation of the configurational free energy associated with the dihedral angle of one n-butane molecule in CCl4 and in gas phase. We analyse the nature and the influence, in the blue moon approach, of the compensating term which arises from constraining the reaction coordinate and setting its velocity to zero.