A comparison between simulation and poisson-boltzmann fields
作者:
B. Montgomery Pettitt,
C. V. Valdeavella,
期刊:
AIP Conference Proceedings
(AIP Available online 1999)
卷期:
Volume 492,
issue 1
页码: 411-416
ISSN:0094-243X
年代: 1999
DOI:10.1063/1.1301539
出版商: AIP
数据来源: AIP
摘要:
The electrostatic potentials from molecular dynamics (MD) trajectories and Poisson-Boltzmann calculations on a tetra peptide are compared to understand the validity of the resulting free energy surface. The Tuftsin peptide with sequence, Thr-Lys-Pro-Arg, in water is used for the comparison. The results obtained from the analysis of the MD trajectories for the total electrostatic potential at points on a grid using the Ewald technique are compared with the solution to the Poisson-Boltzmann (PB) equation averaged over the same set of configurations. The latter was solved using an optimal set of dielectric constant parameters. Structural averaging of the field over the MD simulation was examined in the context of the PB results. The detailed spatial variation of the electrostatic potential on the molecular surface are not qualitatively reproducible from MD to PB. Implications of using such field calculations and the implied free energies are discussed. ©2000 American Institute of Physics.
点击下载:
PDF
(294KB)
返 回