Affiliation: University College London
- Force field validation for nucleic acid simulations: comparing energies and dynamics of a DNA dodecamerShantenu Jha
Centre for Computational Science, University College London, London WC1H 0AJ, United Kingdom
J Comput Chem 26:1617-27. 2005..This sets the stage for reliable large-scale simulations of nucleic acids using NAMD...
- Grid-based steered thermodynamic integration accelerates the calculation of binding free energiesPhilip W Fowler
Centre for Computational Science, Department of Chemistry, University College London, Christopher Ingold Laboratories, UK
Philos Transact A Math Phys Eng Sci 363:1999-2015. 2005..Initial results for the Src SH2 system are presented and compared to a reported experimental value. Finally, we discuss the significance of our approach...
- Comparative analysis of nucleotide translocation through protein nanopores using steered molecular dynamics and an adaptive biasing forceHugh S C Martin
Department of Chemistry, Centre for Computational Science, UCL, 20 Gordon Street, London, United Kingdom
J Comput Chem 35:692-702. 2014..We find that the ABF method produces results that are closer to experimental measurements than those from cv-SMD, whereas the net errors are smaller for the same computational cost...