Paper Citing NAMD - Abstract
Chatterjee, S.; Gersten, B.; Thakur, S.; Burin, A.
Molecular dynamics simulations of a single stranded (ss) DNA
MOLECULAR SIMULATION, 33:573-576, 2007
The objective of this study was to develop an understanding of short-single stranded DNA (ssDNA) to aid the development of new DNA-based biosensors. The various thermodynamic macroscopic observables (temperature and energy distributions) and root mean square deviation (RMSD) of nucleic acid backbone of 12 base-sequences of ssDNA of the P53 gene between 130 and 144 codon were studied using molecular dynamics ( MD) simulations. The AMBER program was utilized to prepare the ssDNA structure of the p53 sequence and MD simulations were carried out using NAMD program. In this study, we compared the outcome of the properties of ssDNA system by different ensembles. The microcanonical ensemble (NVE) and conical ensemble (NVT) and isobaric- isothermal (NPT) ensemble were employed to characterize the equilibrium behavior of ssDNA in aqueous solution.
