Paper Citing NAMD - Abstract
Zhang Ning; Li Wei-Zhong; Chen Cong; Zuo Jian-Guo
Evaluation of the Application of Hydrogen Bonding Criteria to DMSO Aqueous Solution
ACTA PHYSICO-CHIMICA SINICA, 29:1891-1899, SEP 2013
Geometric and energetic criteria have been used to analyze the hydrogen bonding statistics and dynamics of aqueous solutions of dinnethylsulfoxide (DMSO) of different concentrations using molecular dynamics simulation. These two hydrogen bonding criteria both reproduced the changes of the hydrogen bonding properties of the solutions with increasing concentration. Comparison of the results obtained using the two criteria revealed that the geometric criterion cannot exclude pairs that have weak pair interaction energy. As a result, the number of hydrogen bonds determined by the geometric criterion is larger than that by the energetic criterion. The energetic criterion has less ability to distinguish pairs that have improper relative orientation compared with the geometric criterion. However, the number of deficient hydrogen bonds determined by the energetic criterion is smaller than that by the geometric one. This deficiency of the energetic criterion results in longer hydrogen bonding lifetime than that of the geometric criterion. Thus, an extended criterion involving both geometric and energetic conditions is recommended for hydrogen bonding analysis.
